Multiple sequence alignment - TraesCS2B01G378600

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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 TraesCS2B01G378600 chr2B 100.000 3362 0 0 1 3362 541631096 541634457 0.000000e+00 6209.0
1 TraesCS2B01G378600 chr2B 94.327 758 29 7 2616 3360 666104861 666105617 0.000000e+00 1149.0
2 TraesCS2B01G378600 chr2B 82.319 1380 178 41 1007 2360 541906875 541908214 0.000000e+00 1136.0
3 TraesCS2B01G378600 chr2B 90.854 492 29 6 2615 3090 491291757 491292248 0.000000e+00 645.0
4 TraesCS2B01G378600 chr2B 97.297 333 8 1 3031 3362 491292226 491292558 6.300000e-157 564.0
5 TraesCS2B01G378600 chr2D 93.521 2346 82 36 207 2504 460364149 460366472 0.000000e+00 3426.0
6 TraesCS2B01G378600 chr2D 84.000 1175 152 22 1201 2360 460709511 460710664 0.000000e+00 1096.0
7 TraesCS2B01G378600 chr2D 95.489 133 6 0 68 200 591540697 591540829 2.630000e-51 213.0
8 TraesCS2B01G378600 chr2D 72.117 789 169 39 1356 2123 621948011 621947253 1.230000e-44 191.0
9 TraesCS2B01G378600 chr2D 97.101 69 2 0 2 70 460364085 460364153 2.120000e-22 117.0
10 TraesCS2B01G378600 chr2A 92.528 2369 100 41 239 2551 603374283 603376630 0.000000e+00 3323.0
11 TraesCS2B01G378600 chr2A 81.295 1374 184 45 1019 2360 603545955 603547287 0.000000e+00 1046.0
12 TraesCS2B01G378600 chr2A 92.434 489 24 5 2615 3090 572842482 572842970 0.000000e+00 686.0
13 TraesCS2B01G378600 chr2A 96.997 333 9 1 3031 3362 572842948 572843280 2.930000e-155 558.0
14 TraesCS2B01G378600 chr2A 96.154 130 5 0 71 200 570148702 570148831 2.630000e-51 213.0
15 TraesCS2B01G378600 chr2A 97.959 49 1 0 22 70 603374198 603374246 5.980000e-13 86.1
16 TraesCS2B01G378600 chr5B 94.993 759 25 6 2616 3362 345809044 345809801 0.000000e+00 1179.0
17 TraesCS2B01G378600 chr5B 94.350 761 30 6 2615 3362 474615382 474614622 0.000000e+00 1155.0
18 TraesCS2B01G378600 chr5B 95.455 132 6 0 69 200 599327067 599326936 9.450000e-51 211.0
19 TraesCS2B01G378600 chr3A 92.288 765 27 8 2615 3362 108909199 108909948 0.000000e+00 1057.0
20 TraesCS2B01G378600 chr3A 96.923 130 4 0 71 200 40287028 40287157 5.650000e-53 219.0
21 TraesCS2B01G378600 chr7A 92.073 492 23 6 2615 3090 606191245 606191736 0.000000e+00 678.0
22 TraesCS2B01G378600 chr7A 97.297 333 8 1 3031 3362 606191714 606192046 6.300000e-157 564.0
23 TraesCS2B01G378600 chrUn 90.854 492 29 7 2615 3090 122644785 122645276 0.000000e+00 645.0
24 TraesCS2B01G378600 chrUn 95.536 336 12 2 3028 3362 122645251 122645584 4.940000e-148 534.0
25 TraesCS2B01G378600 chr6B 82.277 773 62 35 2620 3362 690881527 690880800 1.730000e-167 599.0
26 TraesCS2B01G378600 chr4B 93.000 200 13 1 3164 3362 97891385 97891186 1.180000e-74 291.0
27 TraesCS2B01G378600 chr4B 92.857 196 13 1 3167 3362 535057653 535057847 1.970000e-72 283.0
28 TraesCS2B01G378600 chr7B 97.710 131 3 0 70 200 592741158 592741288 3.380000e-55 226.0
29 TraesCS2B01G378600 chr3B 97.692 130 3 0 71 200 20827652 20827781 1.210000e-54 224.0
30 TraesCS2B01G378600 chr3B 97.692 130 3 0 71 200 296060915 296061044 1.210000e-54 224.0
31 TraesCS2B01G378600 chr3B 96.183 131 5 0 70 200 718686122 718685992 7.310000e-52 215.0
32 TraesCS2B01G378600 chr6D 96.947 131 4 0 70 200 446643657 446643787 1.570000e-53 220.0


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 TraesCS2B01G378600 chr2B 541631096 541634457 3361 False 6209.00 6209 100.0000 1 3362 1 chr2B.!!$F1 3361
1 TraesCS2B01G378600 chr2B 666104861 666105617 756 False 1149.00 1149 94.3270 2616 3360 1 chr2B.!!$F3 744
2 TraesCS2B01G378600 chr2B 541906875 541908214 1339 False 1136.00 1136 82.3190 1007 2360 1 chr2B.!!$F2 1353
3 TraesCS2B01G378600 chr2B 491291757 491292558 801 False 604.50 645 94.0755 2615 3362 2 chr2B.!!$F4 747
4 TraesCS2B01G378600 chr2D 460364085 460366472 2387 False 1771.50 3426 95.3110 2 2504 2 chr2D.!!$F3 2502
5 TraesCS2B01G378600 chr2D 460709511 460710664 1153 False 1096.00 1096 84.0000 1201 2360 1 chr2D.!!$F1 1159
6 TraesCS2B01G378600 chr2A 603374198 603376630 2432 False 1704.55 3323 95.2435 22 2551 2 chr2A.!!$F4 2529
7 TraesCS2B01G378600 chr2A 603545955 603547287 1332 False 1046.00 1046 81.2950 1019 2360 1 chr2A.!!$F2 1341
8 TraesCS2B01G378600 chr2A 572842482 572843280 798 False 622.00 686 94.7155 2615 3362 2 chr2A.!!$F3 747
9 TraesCS2B01G378600 chr5B 345809044 345809801 757 False 1179.00 1179 94.9930 2616 3362 1 chr5B.!!$F1 746
10 TraesCS2B01G378600 chr5B 474614622 474615382 760 True 1155.00 1155 94.3500 2615 3362 1 chr5B.!!$R1 747
11 TraesCS2B01G378600 chr3A 108909199 108909948 749 False 1057.00 1057 92.2880 2615 3362 1 chr3A.!!$F2 747
12 TraesCS2B01G378600 chr7A 606191245 606192046 801 False 621.00 678 94.6850 2615 3362 2 chr7A.!!$F1 747
13 TraesCS2B01G378600 chrUn 122644785 122645584 799 False 589.50 645 93.1950 2615 3362 2 chrUn.!!$F1 747
14 TraesCS2B01G378600 chr6B 690880800 690881527 727 True 599.00 599 82.2770 2620 3362 1 chr6B.!!$R1 742

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
186 187 0.035820 TTGGGACTATGCGGGTTGTC 60.036 55.0 0.0 0.0 0.00 3.18 F
963 1012 0.106519 AAGCAGGAGCCACACTGTTT 60.107 50.0 0.0 0.0 43.56 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1751 1.143838 CCACGATCGGGAATGAGCA 59.856 57.895 21.38 0.0 0.0 4.26 R
2954 3063 0.039617 CTGCGGCCGTGATTTGAAAA 60.040 50.000 28.70 0.0 0.0 2.29 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
65 66 2.182904 CATGAACATCACATGGTGCG 57.817 50.000 0.00 0.00 40.66 5.34
66 67 1.469703 CATGAACATCACATGGTGCGT 59.530 47.619 0.00 0.00 40.66 5.24
67 68 1.155889 TGAACATCACATGGTGCGTC 58.844 50.000 0.00 0.00 32.98 5.19
68 69 0.095245 GAACATCACATGGTGCGTCG 59.905 55.000 0.00 0.00 32.98 5.12
69 70 1.298157 AACATCACATGGTGCGTCGG 61.298 55.000 0.00 0.00 32.98 4.79
70 71 1.741401 CATCACATGGTGCGTCGGT 60.741 57.895 0.00 0.00 32.98 4.69
71 72 1.447838 ATCACATGGTGCGTCGGTC 60.448 57.895 0.00 0.00 32.98 4.79
72 73 2.166130 ATCACATGGTGCGTCGGTCA 62.166 55.000 0.00 0.00 32.98 4.02
73 74 2.048222 ACATGGTGCGTCGGTCAG 60.048 61.111 0.00 0.00 0.00 3.51
74 75 2.815211 CATGGTGCGTCGGTCAGG 60.815 66.667 0.00 0.00 0.00 3.86
75 76 4.760047 ATGGTGCGTCGGTCAGGC 62.760 66.667 0.00 0.00 36.35 4.85
81 82 3.114616 CGTCGGTCAGGCTGCAAG 61.115 66.667 10.34 3.05 0.00 4.01
82 83 2.031163 GTCGGTCAGGCTGCAAGT 59.969 61.111 10.34 0.00 35.30 3.16
83 84 2.031012 TCGGTCAGGCTGCAAGTG 59.969 61.111 10.34 0.00 35.30 3.16
84 85 3.052082 CGGTCAGGCTGCAAGTGG 61.052 66.667 10.34 0.00 35.30 4.00
85 86 2.674380 GGTCAGGCTGCAAGTGGG 60.674 66.667 10.34 0.00 35.30 4.61
86 87 2.431683 GTCAGGCTGCAAGTGGGA 59.568 61.111 10.34 0.00 35.30 4.37
87 88 1.001641 GTCAGGCTGCAAGTGGGAT 60.002 57.895 10.34 0.00 35.30 3.85
88 89 1.001764 TCAGGCTGCAAGTGGGATG 60.002 57.895 10.34 0.00 35.30 3.51
89 90 1.001764 CAGGCTGCAAGTGGGATGA 60.002 57.895 0.00 0.00 35.30 2.92
90 91 1.030488 CAGGCTGCAAGTGGGATGAG 61.030 60.000 0.00 0.00 35.30 2.90
91 92 1.203441 AGGCTGCAAGTGGGATGAGA 61.203 55.000 0.50 0.00 35.30 3.27
92 93 1.028868 GGCTGCAAGTGGGATGAGAC 61.029 60.000 0.50 0.00 35.30 3.36
93 94 1.364626 GCTGCAAGTGGGATGAGACG 61.365 60.000 0.00 0.00 35.30 4.18
94 95 1.364626 CTGCAAGTGGGATGAGACGC 61.365 60.000 0.00 0.00 0.00 5.19
95 96 2.456119 GCAAGTGGGATGAGACGCG 61.456 63.158 3.53 3.53 0.00 6.01
96 97 1.811266 CAAGTGGGATGAGACGCGG 60.811 63.158 12.47 0.00 0.00 6.46
97 98 3.019003 AAGTGGGATGAGACGCGGG 62.019 63.158 12.47 0.00 0.00 6.13
98 99 3.458163 GTGGGATGAGACGCGGGA 61.458 66.667 12.47 0.00 0.00 5.14
99 100 3.147595 TGGGATGAGACGCGGGAG 61.148 66.667 12.47 0.00 0.00 4.30
100 101 3.148279 GGGATGAGACGCGGGAGT 61.148 66.667 12.47 0.00 0.00 3.85
101 102 2.413765 GGATGAGACGCGGGAGTC 59.586 66.667 12.47 0.00 41.23 3.36
102 103 2.413765 GATGAGACGCGGGAGTCC 59.586 66.667 12.47 0.00 41.83 3.85
103 104 3.140225 GATGAGACGCGGGAGTCCC 62.140 68.421 19.37 19.37 41.83 4.46
104 105 3.957435 ATGAGACGCGGGAGTCCCA 62.957 63.158 28.08 6.82 45.83 4.37
105 106 4.131088 GAGACGCGGGAGTCCCAC 62.131 72.222 28.08 17.85 45.83 4.61
106 107 4.988716 AGACGCGGGAGTCCCACA 62.989 66.667 28.08 0.00 45.83 4.17
107 108 3.771160 GACGCGGGAGTCCCACAT 61.771 66.667 28.08 6.79 45.83 3.21
108 109 2.363276 ACGCGGGAGTCCCACATA 60.363 61.111 28.08 0.00 45.83 2.29
109 110 1.952102 GACGCGGGAGTCCCACATAA 61.952 60.000 28.08 0.00 45.83 1.90
110 111 1.335132 ACGCGGGAGTCCCACATAAT 61.335 55.000 28.08 3.84 45.83 1.28
111 112 0.880278 CGCGGGAGTCCCACATAATG 60.880 60.000 28.08 10.69 45.83 1.90
112 113 0.180406 GCGGGAGTCCCACATAATGT 59.820 55.000 28.08 0.00 45.83 2.71
113 114 1.810412 GCGGGAGTCCCACATAATGTC 60.810 57.143 28.08 2.87 45.83 3.06
114 115 1.538204 CGGGAGTCCCACATAATGTCG 60.538 57.143 28.08 5.89 45.83 4.35
115 116 1.583054 GGAGTCCCACATAATGTCGC 58.417 55.000 0.00 0.00 0.00 5.19
116 117 1.134521 GGAGTCCCACATAATGTCGCA 60.135 52.381 0.00 0.00 0.00 5.10
117 118 2.485479 GGAGTCCCACATAATGTCGCAT 60.485 50.000 0.00 0.00 0.00 4.73
118 119 2.802816 GAGTCCCACATAATGTCGCATC 59.197 50.000 0.00 0.00 0.00 3.91
119 120 2.170397 AGTCCCACATAATGTCGCATCA 59.830 45.455 0.00 0.00 0.00 3.07
120 121 2.942376 GTCCCACATAATGTCGCATCAA 59.058 45.455 0.00 0.00 0.00 2.57
121 122 2.942376 TCCCACATAATGTCGCATCAAC 59.058 45.455 0.00 0.00 0.00 3.18
122 123 2.033299 CCCACATAATGTCGCATCAACC 59.967 50.000 0.00 0.00 0.00 3.77
123 124 2.033299 CCACATAATGTCGCATCAACCC 59.967 50.000 0.00 0.00 0.00 4.11
124 125 2.682352 CACATAATGTCGCATCAACCCA 59.318 45.455 0.00 0.00 0.00 4.51
125 126 2.682856 ACATAATGTCGCATCAACCCAC 59.317 45.455 0.00 0.00 0.00 4.61
126 127 2.481289 TAATGTCGCATCAACCCACA 57.519 45.000 0.00 0.00 0.00 4.17
127 128 1.838112 AATGTCGCATCAACCCACAT 58.162 45.000 0.00 0.00 0.00 3.21
128 129 2.708216 ATGTCGCATCAACCCACATA 57.292 45.000 0.00 0.00 0.00 2.29
129 130 2.481289 TGTCGCATCAACCCACATAA 57.519 45.000 0.00 0.00 0.00 1.90
130 131 2.997980 TGTCGCATCAACCCACATAAT 58.002 42.857 0.00 0.00 0.00 1.28
131 132 3.351740 TGTCGCATCAACCCACATAATT 58.648 40.909 0.00 0.00 0.00 1.40
132 133 4.518249 TGTCGCATCAACCCACATAATTA 58.482 39.130 0.00 0.00 0.00 1.40
133 134 5.129634 TGTCGCATCAACCCACATAATTAT 58.870 37.500 0.00 0.00 0.00 1.28
134 135 5.008514 TGTCGCATCAACCCACATAATTATG 59.991 40.000 21.42 21.42 39.55 1.90
153 154 8.682936 AATTATGTGGGATTAAGTGAGATGTC 57.317 34.615 0.00 0.00 0.00 3.06
154 155 4.487714 TGTGGGATTAAGTGAGATGTCC 57.512 45.455 0.00 0.00 0.00 4.02
155 156 3.843619 TGTGGGATTAAGTGAGATGTCCA 59.156 43.478 0.00 0.00 0.00 4.02
156 157 4.192317 GTGGGATTAAGTGAGATGTCCAC 58.808 47.826 0.00 0.00 35.94 4.02
157 158 3.843619 TGGGATTAAGTGAGATGTCCACA 59.156 43.478 0.00 0.00 37.01 4.17
158 159 4.474651 TGGGATTAAGTGAGATGTCCACAT 59.525 41.667 0.00 0.00 39.70 3.21
159 160 5.665360 TGGGATTAAGTGAGATGTCCACATA 59.335 40.000 0.00 0.00 36.57 2.29
160 161 6.157820 TGGGATTAAGTGAGATGTCCACATAA 59.842 38.462 0.00 0.00 36.57 1.90
161 162 7.054124 GGGATTAAGTGAGATGTCCACATAAA 58.946 38.462 0.00 0.00 36.57 1.40
162 163 7.556275 GGGATTAAGTGAGATGTCCACATAAAA 59.444 37.037 0.00 0.00 36.57 1.52
163 164 8.956426 GGATTAAGTGAGATGTCCACATAAAAA 58.044 33.333 0.00 0.00 36.57 1.94
170 171 9.520204 GTGAGATGTCCACATAAAAATAATTGG 57.480 33.333 0.00 0.00 36.57 3.16
171 172 8.694540 TGAGATGTCCACATAAAAATAATTGGG 58.305 33.333 0.00 0.00 36.57 4.12
172 173 8.837099 AGATGTCCACATAAAAATAATTGGGA 57.163 30.769 0.00 0.00 36.57 4.37
173 174 8.695456 AGATGTCCACATAAAAATAATTGGGAC 58.305 33.333 0.00 0.00 41.94 4.46
174 175 8.608185 ATGTCCACATAAAAATAATTGGGACT 57.392 30.769 0.00 0.00 42.06 3.85
175 176 9.707957 ATGTCCACATAAAAATAATTGGGACTA 57.292 29.630 0.00 0.00 42.06 2.59
176 177 9.707957 TGTCCACATAAAAATAATTGGGACTAT 57.292 29.630 0.00 0.00 42.06 2.12
177 178 9.965824 GTCCACATAAAAATAATTGGGACTATG 57.034 33.333 0.00 0.00 39.27 2.23
178 179 8.637986 TCCACATAAAAATAATTGGGACTATGC 58.362 33.333 0.00 0.00 0.00 3.14
179 180 7.594758 CCACATAAAAATAATTGGGACTATGCG 59.405 37.037 0.00 0.00 0.00 4.73
180 181 7.594758 CACATAAAAATAATTGGGACTATGCGG 59.405 37.037 0.00 0.00 0.00 5.69
181 182 5.529581 AAAAATAATTGGGACTATGCGGG 57.470 39.130 0.00 0.00 0.00 6.13
182 183 3.876309 AATAATTGGGACTATGCGGGT 57.124 42.857 0.00 0.00 0.00 5.28
183 184 3.876309 ATAATTGGGACTATGCGGGTT 57.124 42.857 0.00 0.00 0.00 4.11
184 185 1.762708 AATTGGGACTATGCGGGTTG 58.237 50.000 0.00 0.00 0.00 3.77
185 186 0.623723 ATTGGGACTATGCGGGTTGT 59.376 50.000 0.00 0.00 0.00 3.32
186 187 0.035820 TTGGGACTATGCGGGTTGTC 60.036 55.000 0.00 0.00 0.00 3.18
187 188 1.195442 TGGGACTATGCGGGTTGTCA 61.195 55.000 0.00 0.00 0.00 3.58
188 189 0.180406 GGGACTATGCGGGTTGTCAT 59.820 55.000 0.00 0.00 0.00 3.06
189 190 1.414919 GGGACTATGCGGGTTGTCATA 59.585 52.381 0.00 0.00 0.00 2.15
190 191 2.038557 GGGACTATGCGGGTTGTCATAT 59.961 50.000 0.00 0.00 0.00 1.78
191 192 3.259876 GGGACTATGCGGGTTGTCATATA 59.740 47.826 0.00 0.00 0.00 0.86
192 193 4.243270 GGACTATGCGGGTTGTCATATAC 58.757 47.826 0.00 0.00 0.00 1.47
193 194 4.243270 GACTATGCGGGTTGTCATATACC 58.757 47.826 0.00 0.00 0.00 2.73
202 203 3.744426 GGTTGTCATATACCCACATACGC 59.256 47.826 0.00 0.00 0.00 4.42
203 204 4.373527 GTTGTCATATACCCACATACGCA 58.626 43.478 0.00 0.00 0.00 5.24
204 205 4.251543 TGTCATATACCCACATACGCAG 57.748 45.455 0.00 0.00 0.00 5.18
227 228 1.526887 GGAGTTGATGATGCCGGGA 59.473 57.895 2.18 0.00 0.00 5.14
234 235 2.587322 GATGATGCCGGGACCGTCAA 62.587 60.000 4.32 0.00 37.81 3.18
327 348 1.207089 CGAGAATGGAGTAGCCCACAA 59.793 52.381 0.00 0.00 39.34 3.33
328 349 2.354704 CGAGAATGGAGTAGCCCACAAA 60.355 50.000 0.00 0.00 39.34 2.83
341 362 1.958579 CCCACAAATCCATGCGATCAT 59.041 47.619 0.00 0.00 0.00 2.45
377 398 1.518903 GCGCTTAGGGCCATGATTCC 61.519 60.000 10.30 0.00 37.74 3.01
384 405 1.852309 AGGGCCATGATTCCATGTACA 59.148 47.619 6.18 0.00 46.68 2.90
391 415 5.764686 GCCATGATTCCATGTACACTATGAA 59.235 40.000 0.00 0.00 46.68 2.57
396 420 7.272244 TGATTCCATGTACACTATGAACGAAT 58.728 34.615 0.00 0.00 0.00 3.34
454 478 1.446966 GAGCGTGGACTCAAGAGGC 60.447 63.158 1.73 0.00 36.65 4.70
524 548 4.507756 CGATCGATCAAGAAATAGCCACAA 59.492 41.667 24.40 0.00 0.00 3.33
606 634 6.401047 CGTGAGCTCTTCGAATCATTTGTAAA 60.401 38.462 20.96 0.00 0.00 2.01
648 676 4.133820 CGGATATACTGGCATCCAACAAA 58.866 43.478 5.04 0.00 40.75 2.83
739 768 5.104444 TCCTCAGGTAGAACTGTAGGAGTAG 60.104 48.000 10.11 0.00 38.60 2.57
759 794 2.295349 AGAGGTTTCAGCAGCAACAATG 59.705 45.455 0.00 0.00 0.00 2.82
777 820 1.314534 TGCCAGTACCATGCATGCAC 61.315 55.000 25.37 19.19 0.00 4.57
778 821 1.314534 GCCAGTACCATGCATGCACA 61.315 55.000 25.37 5.73 0.00 4.57
779 822 1.395635 CCAGTACCATGCATGCACAT 58.604 50.000 25.37 13.89 0.00 3.21
780 823 1.335810 CCAGTACCATGCATGCACATC 59.664 52.381 25.37 11.85 0.00 3.06
781 824 2.018515 CAGTACCATGCATGCACATCA 58.981 47.619 25.37 6.13 0.00 3.07
854 901 0.393448 TTTATATACCCCTGCGCGCA 59.607 50.000 34.12 34.12 0.00 6.09
855 902 0.393448 TTATATACCCCTGCGCGCAA 59.607 50.000 35.50 20.72 0.00 4.85
863 910 4.439472 CTGCGCGCAACCCGTAAC 62.439 66.667 35.50 0.00 39.71 2.50
906 953 2.876645 CAGTCGCGCTCCGTCTTC 60.877 66.667 5.56 0.00 38.35 2.87
907 954 3.362797 AGTCGCGCTCCGTCTTCA 61.363 61.111 5.56 0.00 38.35 3.02
908 955 3.173240 GTCGCGCTCCGTCTTCAC 61.173 66.667 5.56 0.00 38.35 3.18
909 956 3.362797 TCGCGCTCCGTCTTCACT 61.363 61.111 5.56 0.00 38.35 3.41
910 957 2.876645 CGCGCTCCGTCTTCACTC 60.877 66.667 5.56 0.00 0.00 3.51
911 958 2.569134 GCGCTCCGTCTTCACTCT 59.431 61.111 0.00 0.00 0.00 3.24
912 959 1.080434 GCGCTCCGTCTTCACTCTT 60.080 57.895 0.00 0.00 0.00 2.85
963 1012 0.106519 AAGCAGGAGCCACACTGTTT 60.107 50.000 0.00 0.00 43.56 2.83
984 1033 3.628646 ATTCCTGCTGCCGACACCC 62.629 63.158 0.00 0.00 0.00 4.61
1158 1219 1.003355 CATCGGGATTGGGATCGGG 60.003 63.158 0.00 0.00 32.84 5.14
1293 1360 2.553904 CCAGAGGTTCAAGCAGACCATT 60.554 50.000 0.00 0.00 0.00 3.16
1734 1801 2.285602 CGTCAACAACAACCAGTTCTCG 60.286 50.000 0.00 0.00 38.74 4.04
2231 2298 3.423154 CGCCGGCTTCTTCCACAC 61.423 66.667 26.68 0.00 0.00 3.82
2290 2366 1.131303 CCACCACCCCAAGGACTACA 61.131 60.000 0.00 0.00 36.73 2.74
2291 2367 0.036306 CACCACCCCAAGGACTACAC 59.964 60.000 0.00 0.00 36.73 2.90
2292 2368 0.104620 ACCACCCCAAGGACTACACT 60.105 55.000 0.00 0.00 36.73 3.55
2372 2454 3.066190 CCCGTGAGTCCGTGGCTA 61.066 66.667 0.00 0.00 0.00 3.93
2407 2506 2.792674 CGTACACGTGCTGAAGAAGAAA 59.207 45.455 17.22 0.00 34.11 2.52
2410 2509 2.158957 ACACGTGCTGAAGAAGAAAGGA 60.159 45.455 17.22 0.00 0.00 3.36
2416 2515 3.755378 TGCTGAAGAAGAAAGGAGAATGC 59.245 43.478 0.00 0.00 0.00 3.56
2423 2522 0.449388 GAAAGGAGAATGCGCTGTGG 59.551 55.000 9.73 0.00 0.00 4.17
2480 2579 5.982516 GCTGGTTTGTGTTGATATTGTTTGA 59.017 36.000 0.00 0.00 0.00 2.69
2541 2640 0.970640 TACTACCAGCAAGGCGTGAA 59.029 50.000 4.11 0.00 43.14 3.18
2551 2650 5.050091 CCAGCAAGGCGTGAATAATAAGTAG 60.050 44.000 4.11 0.00 0.00 2.57
2552 2651 5.050091 CAGCAAGGCGTGAATAATAAGTAGG 60.050 44.000 4.11 0.00 0.00 3.18
2553 2652 5.054477 GCAAGGCGTGAATAATAAGTAGGA 58.946 41.667 4.11 0.00 0.00 2.94
2554 2653 5.177696 GCAAGGCGTGAATAATAAGTAGGAG 59.822 44.000 4.11 0.00 0.00 3.69
2555 2654 5.470047 AGGCGTGAATAATAAGTAGGAGG 57.530 43.478 0.00 0.00 0.00 4.30
2556 2655 3.995048 GGCGTGAATAATAAGTAGGAGGC 59.005 47.826 0.00 0.00 0.00 4.70
2557 2656 4.262506 GGCGTGAATAATAAGTAGGAGGCT 60.263 45.833 0.00 0.00 0.00 4.58
2558 2657 4.686554 GCGTGAATAATAAGTAGGAGGCTG 59.313 45.833 0.00 0.00 0.00 4.85
2559 2658 5.230942 CGTGAATAATAAGTAGGAGGCTGG 58.769 45.833 0.00 0.00 0.00 4.85
2560 2659 5.552178 GTGAATAATAAGTAGGAGGCTGGG 58.448 45.833 0.00 0.00 0.00 4.45
2561 2660 4.041691 TGAATAATAAGTAGGAGGCTGGGC 59.958 45.833 0.00 0.00 0.00 5.36
2562 2661 1.893315 AATAAGTAGGAGGCTGGGCA 58.107 50.000 0.00 0.00 0.00 5.36
2563 2662 1.428869 ATAAGTAGGAGGCTGGGCAG 58.571 55.000 0.00 0.00 0.00 4.85
2564 2663 0.042731 TAAGTAGGAGGCTGGGCAGT 59.957 55.000 0.00 0.00 0.00 4.40
2565 2664 1.557269 AAGTAGGAGGCTGGGCAGTG 61.557 60.000 0.00 0.00 0.00 3.66
2566 2665 2.688666 TAGGAGGCTGGGCAGTGG 60.689 66.667 0.00 0.00 0.00 4.00
2575 2674 4.115199 GGGCAGTGGGCACTAGGG 62.115 72.222 0.00 0.00 44.81 3.53
2577 2676 3.330720 GCAGTGGGCACTAGGGGT 61.331 66.667 0.00 0.00 43.97 4.95
2579 2678 2.207189 AGTGGGCACTAGGGGTGT 59.793 61.111 0.00 0.00 46.86 4.16
2580 2679 2.224159 AGTGGGCACTAGGGGTGTG 61.224 63.158 0.00 0.00 46.86 3.82
2581 2680 2.122144 TGGGCACTAGGGGTGTGT 60.122 61.111 0.00 0.00 46.86 3.72
2582 2681 1.772567 TGGGCACTAGGGGTGTGTT 60.773 57.895 0.00 0.00 46.86 3.32
2583 2682 1.357272 TGGGCACTAGGGGTGTGTTT 61.357 55.000 0.00 0.00 46.86 2.83
2584 2683 0.893727 GGGCACTAGGGGTGTGTTTG 60.894 60.000 0.00 0.00 46.86 2.93
2585 2684 0.893727 GGCACTAGGGGTGTGTTTGG 60.894 60.000 0.00 0.00 46.86 3.28
2586 2685 0.179001 GCACTAGGGGTGTGTTTGGT 60.179 55.000 0.00 0.00 46.86 3.67
2587 2686 1.072648 GCACTAGGGGTGTGTTTGGTA 59.927 52.381 0.00 0.00 46.86 3.25
2588 2687 2.874457 GCACTAGGGGTGTGTTTGGTAG 60.874 54.545 0.00 0.00 46.86 3.18
2589 2688 1.350019 ACTAGGGGTGTGTTTGGTAGC 59.650 52.381 0.00 0.00 0.00 3.58
2590 2689 0.694196 TAGGGGTGTGTTTGGTAGCC 59.306 55.000 0.00 0.00 0.00 3.93
2591 2690 1.065997 AGGGGTGTGTTTGGTAGCCT 61.066 55.000 0.00 0.00 32.73 4.58
2592 2691 0.893727 GGGGTGTGTTTGGTAGCCTG 60.894 60.000 0.00 0.00 32.73 4.85
2593 2692 1.524008 GGGTGTGTTTGGTAGCCTGC 61.524 60.000 0.00 0.00 0.00 4.85
2594 2693 1.574428 GTGTGTTTGGTAGCCTGCG 59.426 57.895 0.00 0.00 0.00 5.18
2595 2694 2.258013 TGTGTTTGGTAGCCTGCGC 61.258 57.895 0.00 0.00 0.00 6.09
2596 2695 3.047280 TGTTTGGTAGCCTGCGCG 61.047 61.111 0.00 0.00 41.18 6.86
2597 2696 3.799755 GTTTGGTAGCCTGCGCGG 61.800 66.667 9.96 9.96 41.18 6.46
2598 2697 4.010224 TTTGGTAGCCTGCGCGGA 62.010 61.111 20.25 3.19 41.18 5.54
2599 2698 3.950794 TTTGGTAGCCTGCGCGGAG 62.951 63.158 21.89 21.89 41.18 4.63
2601 2700 4.143333 GGTAGCCTGCGCGGAGAA 62.143 66.667 30.34 11.20 41.18 2.87
2602 2701 2.107141 GTAGCCTGCGCGGAGAAT 59.893 61.111 30.34 18.61 41.18 2.40
2603 2702 2.106938 TAGCCTGCGCGGAGAATG 59.893 61.111 30.34 13.70 41.18 2.67
2606 2705 2.898840 CCTGCGCGGAGAATGCAT 60.899 61.111 30.34 0.00 38.07 3.96
2607 2706 2.630317 CTGCGCGGAGAATGCATC 59.370 61.111 24.56 0.00 38.07 3.91
2608 2707 2.890109 CTGCGCGGAGAATGCATCC 61.890 63.158 24.56 0.00 38.07 3.51
2609 2708 3.654020 GCGCGGAGAATGCATCCC 61.654 66.667 8.83 0.85 32.86 3.85
2610 2709 2.109799 CGCGGAGAATGCATCCCT 59.890 61.111 0.00 0.00 32.86 4.20
2611 2710 1.367471 CGCGGAGAATGCATCCCTA 59.633 57.895 0.00 0.00 32.86 3.53
2612 2711 0.946221 CGCGGAGAATGCATCCCTAC 60.946 60.000 0.00 0.00 32.86 3.18
2613 2712 0.394565 GCGGAGAATGCATCCCTACT 59.605 55.000 0.00 0.00 32.86 2.57
2955 3064 3.459063 GCCGGTCTACCTCGCCTT 61.459 66.667 1.90 0.00 0.00 4.35
2972 3091 0.039617 CTTTTCAAATCACGGCCGCA 60.040 50.000 28.58 13.44 0.00 5.69
2976 3095 2.751436 AAATCACGGCCGCAGCAT 60.751 55.556 28.58 9.15 42.56 3.79
3060 3222 2.592993 CCTTCCTGCCTCGTTCCCA 61.593 63.158 0.00 0.00 0.00 4.37
3091 3254 0.991920 CACCCTTCCTTCCTGCCTTA 59.008 55.000 0.00 0.00 0.00 2.69
3111 3293 2.352032 GCTCACAGGGAGTAGCCGT 61.352 63.158 0.44 0.00 45.88 5.68
3114 3296 0.830444 TCACAGGGAGTAGCCGTTGT 60.830 55.000 0.00 0.00 36.07 3.32
3118 3300 1.549170 CAGGGAGTAGCCGTTGTTACT 59.451 52.381 0.00 0.00 40.72 2.24
3258 3470 2.035066 AGTGCTTGTCATGCTGGAAAAC 59.965 45.455 11.58 1.31 0.00 2.43
3263 3476 3.557577 TGTCATGCTGGAAAACAATCG 57.442 42.857 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.117794 CGATTTCATTACTAACCGGCGA 58.882 45.455 9.30 0.00 0.00 5.54
64 65 3.114616 CTTGCAGCCTGACCGACG 61.115 66.667 0.00 0.00 0.00 5.12
65 66 2.031163 ACTTGCAGCCTGACCGAC 59.969 61.111 0.00 0.00 0.00 4.79
66 67 2.031012 CACTTGCAGCCTGACCGA 59.969 61.111 0.00 0.00 0.00 4.69
67 68 3.052082 CCACTTGCAGCCTGACCG 61.052 66.667 0.00 0.00 0.00 4.79
68 69 2.490270 ATCCCACTTGCAGCCTGACC 62.490 60.000 0.00 0.00 0.00 4.02
69 70 1.001641 ATCCCACTTGCAGCCTGAC 60.002 57.895 0.00 0.00 0.00 3.51
70 71 1.001764 CATCCCACTTGCAGCCTGA 60.002 57.895 0.00 0.00 0.00 3.86
71 72 1.001764 TCATCCCACTTGCAGCCTG 60.002 57.895 0.00 0.00 0.00 4.85
72 73 1.203441 TCTCATCCCACTTGCAGCCT 61.203 55.000 0.00 0.00 0.00 4.58
73 74 1.028868 GTCTCATCCCACTTGCAGCC 61.029 60.000 0.00 0.00 0.00 4.85
74 75 1.364626 CGTCTCATCCCACTTGCAGC 61.365 60.000 0.00 0.00 0.00 5.25
75 76 1.364626 GCGTCTCATCCCACTTGCAG 61.365 60.000 0.00 0.00 0.00 4.41
76 77 1.375908 GCGTCTCATCCCACTTGCA 60.376 57.895 0.00 0.00 0.00 4.08
77 78 2.456119 CGCGTCTCATCCCACTTGC 61.456 63.158 0.00 0.00 0.00 4.01
78 79 1.811266 CCGCGTCTCATCCCACTTG 60.811 63.158 4.92 0.00 0.00 3.16
79 80 2.579201 CCGCGTCTCATCCCACTT 59.421 61.111 4.92 0.00 0.00 3.16
80 81 3.461773 CCCGCGTCTCATCCCACT 61.462 66.667 4.92 0.00 0.00 4.00
81 82 3.432051 CTCCCGCGTCTCATCCCAC 62.432 68.421 4.92 0.00 0.00 4.61
82 83 3.147595 CTCCCGCGTCTCATCCCA 61.148 66.667 4.92 0.00 0.00 4.37
83 84 3.140225 GACTCCCGCGTCTCATCCC 62.140 68.421 4.92 0.00 0.00 3.85
84 85 2.413765 GACTCCCGCGTCTCATCC 59.586 66.667 4.92 0.00 0.00 3.51
85 86 2.413765 GGACTCCCGCGTCTCATC 59.586 66.667 4.92 0.00 34.38 2.92
86 87 3.148279 GGGACTCCCGCGTCTCAT 61.148 66.667 4.92 0.00 34.50 2.90
95 96 1.810412 GCGACATTATGTGGGACTCCC 60.810 57.143 7.25 7.25 45.71 4.30
96 97 1.134521 TGCGACATTATGTGGGACTCC 60.135 52.381 1.24 0.00 0.00 3.85
97 98 2.309528 TGCGACATTATGTGGGACTC 57.690 50.000 1.24 0.00 0.00 3.36
98 99 2.170397 TGATGCGACATTATGTGGGACT 59.830 45.455 1.24 0.00 28.46 3.85
99 100 2.560504 TGATGCGACATTATGTGGGAC 58.439 47.619 1.24 0.00 28.46 4.46
100 101 2.942376 GTTGATGCGACATTATGTGGGA 59.058 45.455 1.24 2.79 30.49 4.37
101 102 2.033299 GGTTGATGCGACATTATGTGGG 59.967 50.000 1.24 0.00 0.00 4.61
102 103 2.033299 GGGTTGATGCGACATTATGTGG 59.967 50.000 1.24 2.21 0.00 4.17
103 104 2.682352 TGGGTTGATGCGACATTATGTG 59.318 45.455 1.24 0.00 0.00 3.21
104 105 2.682856 GTGGGTTGATGCGACATTATGT 59.317 45.455 0.00 0.00 0.00 2.29
105 106 2.682352 TGTGGGTTGATGCGACATTATG 59.318 45.455 0.00 0.00 0.00 1.90
106 107 2.997980 TGTGGGTTGATGCGACATTAT 58.002 42.857 0.00 0.00 0.00 1.28
107 108 2.481289 TGTGGGTTGATGCGACATTA 57.519 45.000 0.00 0.00 0.00 1.90
108 109 1.838112 ATGTGGGTTGATGCGACATT 58.162 45.000 0.00 0.00 0.00 2.71
109 110 2.708216 TATGTGGGTTGATGCGACAT 57.292 45.000 0.00 0.00 0.00 3.06
110 111 2.481289 TTATGTGGGTTGATGCGACA 57.519 45.000 0.00 0.00 0.00 4.35
111 112 5.008613 ACATAATTATGTGGGTTGATGCGAC 59.991 40.000 26.51 0.00 44.66 5.19
112 113 5.129634 ACATAATTATGTGGGTTGATGCGA 58.870 37.500 26.51 0.00 44.66 5.10
113 114 5.437289 ACATAATTATGTGGGTTGATGCG 57.563 39.130 26.51 0.39 44.66 4.73
127 128 9.778741 GACATCTCACTTAATCCCACATAATTA 57.221 33.333 0.00 0.00 0.00 1.40
128 129 7.721399 GGACATCTCACTTAATCCCACATAATT 59.279 37.037 0.00 0.00 0.00 1.40
129 130 7.147320 TGGACATCTCACTTAATCCCACATAAT 60.147 37.037 0.00 0.00 0.00 1.28
130 131 6.157820 TGGACATCTCACTTAATCCCACATAA 59.842 38.462 0.00 0.00 0.00 1.90
131 132 5.665360 TGGACATCTCACTTAATCCCACATA 59.335 40.000 0.00 0.00 0.00 2.29
132 133 4.474651 TGGACATCTCACTTAATCCCACAT 59.525 41.667 0.00 0.00 0.00 3.21
133 134 3.843619 TGGACATCTCACTTAATCCCACA 59.156 43.478 0.00 0.00 0.00 4.17
134 135 4.192317 GTGGACATCTCACTTAATCCCAC 58.808 47.826 0.00 0.00 35.41 4.61
135 136 3.843619 TGTGGACATCTCACTTAATCCCA 59.156 43.478 0.00 0.00 36.21 4.37
136 137 4.487714 TGTGGACATCTCACTTAATCCC 57.512 45.455 0.00 0.00 36.21 3.85
137 138 8.506168 TTTTATGTGGACATCTCACTTAATCC 57.494 34.615 0.00 0.00 35.86 3.01
144 145 9.520204 CCAATTATTTTTATGTGGACATCTCAC 57.480 33.333 0.00 0.00 37.76 3.51
145 146 8.694540 CCCAATTATTTTTATGTGGACATCTCA 58.305 33.333 0.00 0.00 37.76 3.27
146 147 8.912988 TCCCAATTATTTTTATGTGGACATCTC 58.087 33.333 0.00 0.00 37.76 2.75
147 148 8.695456 GTCCCAATTATTTTTATGTGGACATCT 58.305 33.333 0.00 0.00 39.56 2.90
148 149 8.695456 AGTCCCAATTATTTTTATGTGGACATC 58.305 33.333 0.00 0.00 41.66 3.06
149 150 8.608185 AGTCCCAATTATTTTTATGTGGACAT 57.392 30.769 0.00 0.00 41.66 3.06
150 151 9.707957 ATAGTCCCAATTATTTTTATGTGGACA 57.292 29.630 0.00 0.00 41.66 4.02
151 152 9.965824 CATAGTCCCAATTATTTTTATGTGGAC 57.034 33.333 0.00 0.00 39.97 4.02
152 153 8.637986 GCATAGTCCCAATTATTTTTATGTGGA 58.362 33.333 0.00 0.00 0.00 4.02
153 154 7.594758 CGCATAGTCCCAATTATTTTTATGTGG 59.405 37.037 0.00 0.00 0.00 4.17
154 155 7.594758 CCGCATAGTCCCAATTATTTTTATGTG 59.405 37.037 0.00 0.00 0.00 3.21
155 156 7.255801 CCCGCATAGTCCCAATTATTTTTATGT 60.256 37.037 0.00 0.00 0.00 2.29
156 157 7.090173 CCCGCATAGTCCCAATTATTTTTATG 58.910 38.462 0.00 0.00 0.00 1.90
157 158 6.780522 ACCCGCATAGTCCCAATTATTTTTAT 59.219 34.615 0.00 0.00 0.00 1.40
158 159 6.130569 ACCCGCATAGTCCCAATTATTTTTA 58.869 36.000 0.00 0.00 0.00 1.52
159 160 4.959839 ACCCGCATAGTCCCAATTATTTTT 59.040 37.500 0.00 0.00 0.00 1.94
160 161 4.542697 ACCCGCATAGTCCCAATTATTTT 58.457 39.130 0.00 0.00 0.00 1.82
161 162 4.178956 ACCCGCATAGTCCCAATTATTT 57.821 40.909 0.00 0.00 0.00 1.40
162 163 3.876309 ACCCGCATAGTCCCAATTATT 57.124 42.857 0.00 0.00 0.00 1.40
163 164 3.117663 ACAACCCGCATAGTCCCAATTAT 60.118 43.478 0.00 0.00 0.00 1.28
164 165 2.240160 ACAACCCGCATAGTCCCAATTA 59.760 45.455 0.00 0.00 0.00 1.40
165 166 1.005450 ACAACCCGCATAGTCCCAATT 59.995 47.619 0.00 0.00 0.00 2.32
166 167 0.623723 ACAACCCGCATAGTCCCAAT 59.376 50.000 0.00 0.00 0.00 3.16
167 168 0.035820 GACAACCCGCATAGTCCCAA 60.036 55.000 0.00 0.00 0.00 4.12
168 169 1.195442 TGACAACCCGCATAGTCCCA 61.195 55.000 0.00 0.00 0.00 4.37
169 170 0.180406 ATGACAACCCGCATAGTCCC 59.820 55.000 0.00 0.00 0.00 4.46
170 171 2.902705 TATGACAACCCGCATAGTCC 57.097 50.000 0.00 0.00 0.00 3.85
171 172 4.243270 GGTATATGACAACCCGCATAGTC 58.757 47.826 0.00 0.00 31.20 2.59
172 173 3.007614 GGGTATATGACAACCCGCATAGT 59.992 47.826 0.00 0.00 45.73 2.12
173 174 3.596214 GGGTATATGACAACCCGCATAG 58.404 50.000 0.00 0.00 45.73 2.23
174 175 3.688694 GGGTATATGACAACCCGCATA 57.311 47.619 0.00 0.00 45.73 3.14
175 176 2.561478 GGGTATATGACAACCCGCAT 57.439 50.000 0.00 0.00 45.73 4.73
180 181 3.744426 GCGTATGTGGGTATATGACAACC 59.256 47.826 0.00 0.00 34.85 3.77
181 182 4.373527 TGCGTATGTGGGTATATGACAAC 58.626 43.478 0.00 0.00 0.00 3.32
182 183 4.627058 CTGCGTATGTGGGTATATGACAA 58.373 43.478 0.00 0.00 0.00 3.18
183 184 3.554129 GCTGCGTATGTGGGTATATGACA 60.554 47.826 0.00 0.00 0.00 3.58
184 185 2.993899 GCTGCGTATGTGGGTATATGAC 59.006 50.000 0.00 0.00 0.00 3.06
185 186 2.352323 CGCTGCGTATGTGGGTATATGA 60.352 50.000 14.93 0.00 0.00 2.15
186 187 1.992667 CGCTGCGTATGTGGGTATATG 59.007 52.381 14.93 0.00 0.00 1.78
187 188 1.616865 ACGCTGCGTATGTGGGTATAT 59.383 47.619 27.89 0.00 38.73 0.86
188 189 1.001048 GACGCTGCGTATGTGGGTATA 60.001 52.381 29.03 0.00 41.37 1.47
189 190 0.249322 GACGCTGCGTATGTGGGTAT 60.249 55.000 29.03 0.00 41.37 2.73
190 191 1.140161 GACGCTGCGTATGTGGGTA 59.860 57.895 29.03 0.00 41.37 3.69
191 192 2.125673 GACGCTGCGTATGTGGGT 60.126 61.111 29.03 1.75 41.37 4.51
192 193 3.254654 CGACGCTGCGTATGTGGG 61.255 66.667 29.03 9.30 41.37 4.61
193 194 3.254654 CCGACGCTGCGTATGTGG 61.255 66.667 29.03 21.78 41.37 4.17
194 195 2.202557 TCCGACGCTGCGTATGTG 60.203 61.111 29.03 17.09 41.37 3.21
195 196 2.102357 CTCCGACGCTGCGTATGT 59.898 61.111 29.03 4.86 41.37 2.29
196 197 1.516386 AACTCCGACGCTGCGTATG 60.516 57.895 29.03 22.08 41.37 2.39
197 198 1.516386 CAACTCCGACGCTGCGTAT 60.516 57.895 29.03 6.21 41.37 3.06
198 199 1.929806 ATCAACTCCGACGCTGCGTA 61.930 55.000 29.03 12.03 41.37 4.42
199 200 3.282745 ATCAACTCCGACGCTGCGT 62.283 57.895 29.37 29.37 45.10 5.24
200 201 2.507102 ATCAACTCCGACGCTGCG 60.507 61.111 21.91 21.91 0.00 5.18
201 202 0.807667 ATCATCAACTCCGACGCTGC 60.808 55.000 0.00 0.00 0.00 5.25
202 203 0.926155 CATCATCAACTCCGACGCTG 59.074 55.000 0.00 0.00 0.00 5.18
203 204 0.807667 GCATCATCAACTCCGACGCT 60.808 55.000 0.00 0.00 0.00 5.07
204 205 1.638467 GCATCATCAACTCCGACGC 59.362 57.895 0.00 0.00 0.00 5.19
227 228 5.842907 TCGATCTATTCATCATTTGACGGT 58.157 37.500 0.00 0.00 32.84 4.83
234 235 4.081476 TGCCCGATCGATCTATTCATCATT 60.081 41.667 22.43 0.00 0.00 2.57
267 277 4.035208 GCGTGTCTCCTTTGAAAGAAAGAA 59.965 41.667 6.49 0.00 0.00 2.52
269 279 3.312421 TGCGTGTCTCCTTTGAAAGAAAG 59.688 43.478 6.49 3.91 0.00 2.62
327 348 3.748083 AGCTGTAATGATCGCATGGATT 58.252 40.909 0.00 0.00 34.82 3.01
328 349 3.007723 AGAGCTGTAATGATCGCATGGAT 59.992 43.478 0.00 0.00 38.35 3.41
341 362 2.617308 AGCGCGTAGAATAGAGCTGTAA 59.383 45.455 8.43 0.00 41.71 2.41
377 398 7.891782 ACGTAAATTCGTTCATAGTGTACATG 58.108 34.615 0.00 0.00 41.37 3.21
380 401 6.527722 TGGACGTAAATTCGTTCATAGTGTAC 59.472 38.462 0.00 0.00 43.17 2.90
417 441 6.906678 CACGCTCATCGATCATATTTCAAAAA 59.093 34.615 0.00 0.00 41.67 1.94
418 442 6.421405 CACGCTCATCGATCATATTTCAAAA 58.579 36.000 0.00 0.00 41.67 2.44
421 445 3.989817 CCACGCTCATCGATCATATTTCA 59.010 43.478 0.00 0.00 41.67 2.69
422 446 4.090642 GTCCACGCTCATCGATCATATTTC 59.909 45.833 0.00 0.00 41.67 2.17
423 447 3.990469 GTCCACGCTCATCGATCATATTT 59.010 43.478 0.00 0.00 41.67 1.40
481 505 0.968901 AGACATCGCACCTTCCGGTA 60.969 55.000 0.00 0.00 43.24 4.02
648 676 2.684881 CTGGAACTTGCTGTCTTGTTGT 59.315 45.455 0.00 0.00 0.00 3.32
739 768 2.669364 CATTGTTGCTGCTGAAACCTC 58.331 47.619 11.61 0.00 30.61 3.85
759 794 1.314534 TGTGCATGCATGGTACTGGC 61.315 55.000 25.64 12.10 0.00 4.85
777 820 0.454600 GAACTGGCCATGTGCTGATG 59.545 55.000 5.51 0.00 40.92 3.07
778 821 0.682209 GGAACTGGCCATGTGCTGAT 60.682 55.000 5.51 0.00 40.92 2.90
779 822 1.303561 GGAACTGGCCATGTGCTGA 60.304 57.895 5.51 0.00 40.92 4.26
780 823 2.345760 GGGAACTGGCCATGTGCTG 61.346 63.158 5.51 0.00 40.92 4.41
781 824 2.036256 GGGAACTGGCCATGTGCT 59.964 61.111 5.51 0.00 40.92 4.40
854 901 0.538746 CTGGCCTTTGGTTACGGGTT 60.539 55.000 3.32 0.00 0.00 4.11
855 902 1.074248 CTGGCCTTTGGTTACGGGT 59.926 57.895 3.32 0.00 0.00 5.28
858 905 2.340328 GCCCTGGCCTTTGGTTACG 61.340 63.158 3.32 0.00 34.56 3.18
859 906 3.694746 GCCCTGGCCTTTGGTTAC 58.305 61.111 3.32 0.00 34.56 2.50
906 953 1.621301 CTCGCGCCAAGTGAAGAGTG 61.621 60.000 0.00 0.00 39.12 3.51
907 954 1.373497 CTCGCGCCAAGTGAAGAGT 60.373 57.895 0.00 0.00 39.12 3.24
908 955 2.097038 CCTCGCGCCAAGTGAAGAG 61.097 63.158 0.00 0.00 39.12 2.85
909 956 2.048222 CCTCGCGCCAAGTGAAGA 60.048 61.111 0.00 0.00 39.12 2.87
910 957 3.121030 CCCTCGCGCCAAGTGAAG 61.121 66.667 0.00 0.00 39.12 3.02
911 958 4.697756 CCCCTCGCGCCAAGTGAA 62.698 66.667 0.00 0.00 39.12 3.18
963 1012 2.268920 GTCGGCAGCAGGAATGGA 59.731 61.111 0.00 0.00 0.00 3.41
984 1033 1.202348 GCCATTCTTTTTCTCACCGGG 59.798 52.381 6.32 0.00 0.00 5.73
994 1043 2.973082 GCGGCCTGCCATTCTTTT 59.027 55.556 9.17 0.00 37.76 2.27
1229 1296 1.863880 CGCTCGTTCTCGAAGTCGG 60.864 63.158 0.11 0.00 45.61 4.79
1684 1751 1.143838 CCACGATCGGGAATGAGCA 59.856 57.895 21.38 0.00 0.00 4.26
1734 1801 2.115291 GTTGCTCGGGATCTTGCCC 61.115 63.158 0.00 0.00 45.10 5.36
2080 2147 2.636412 CGGAGAGCGTGAGGTTGGA 61.636 63.158 0.00 0.00 45.11 3.53
2231 2298 1.218316 GGGCAGTAGGTCTTGGTCG 59.782 63.158 0.00 0.00 0.00 4.79
2290 2366 2.042843 CTCCTCCCTACCGGCAGT 60.043 66.667 0.00 0.00 0.00 4.40
2291 2367 2.840102 CCTCCTCCCTACCGGCAG 60.840 72.222 0.00 0.00 0.00 4.85
2313 2395 4.124351 TTGTACTCCTCCGCCGCG 62.124 66.667 5.59 5.59 0.00 6.46
2399 2498 2.746362 CAGCGCATTCTCCTTTCTTCTT 59.254 45.455 11.47 0.00 0.00 2.52
2401 2500 2.079925 ACAGCGCATTCTCCTTTCTTC 58.920 47.619 11.47 0.00 0.00 2.87
2402 2501 1.808945 CACAGCGCATTCTCCTTTCTT 59.191 47.619 11.47 0.00 0.00 2.52
2404 2503 0.449388 CCACAGCGCATTCTCCTTTC 59.551 55.000 11.47 0.00 0.00 2.62
2407 2506 2.270205 CCCACAGCGCATTCTCCT 59.730 61.111 11.47 0.00 0.00 3.69
2410 2509 1.078848 GAGACCCACAGCGCATTCT 60.079 57.895 11.47 0.71 0.00 2.40
2541 2640 3.584848 CTGCCCAGCCTCCTACTTATTAT 59.415 47.826 0.00 0.00 0.00 1.28
2555 2654 3.984193 CTAGTGCCCACTGCCCAGC 62.984 68.421 11.02 0.00 42.52 4.85
2556 2655 2.270205 CTAGTGCCCACTGCCCAG 59.730 66.667 11.02 0.00 42.52 4.45
2557 2656 3.329889 CCTAGTGCCCACTGCCCA 61.330 66.667 11.02 0.00 42.52 5.36
2558 2657 4.115199 CCCTAGTGCCCACTGCCC 62.115 72.222 11.02 0.00 42.52 5.36
2559 2658 4.115199 CCCCTAGTGCCCACTGCC 62.115 72.222 11.02 0.00 42.52 4.85
2560 2659 3.330720 ACCCCTAGTGCCCACTGC 61.331 66.667 11.02 0.00 42.52 4.40
2561 2660 2.671070 CACCCCTAGTGCCCACTG 59.329 66.667 11.02 1.86 42.52 3.66
2569 2668 1.350019 GCTACCAAACACACCCCTAGT 59.650 52.381 0.00 0.00 0.00 2.57
2570 2669 1.339727 GGCTACCAAACACACCCCTAG 60.340 57.143 0.00 0.00 0.00 3.02
2571 2670 0.694196 GGCTACCAAACACACCCCTA 59.306 55.000 0.00 0.00 0.00 3.53
2572 2671 1.065997 AGGCTACCAAACACACCCCT 61.066 55.000 0.00 0.00 0.00 4.79
2573 2672 0.893727 CAGGCTACCAAACACACCCC 60.894 60.000 0.00 0.00 0.00 4.95
2574 2673 1.524008 GCAGGCTACCAAACACACCC 61.524 60.000 0.00 0.00 0.00 4.61
2575 2674 1.852067 CGCAGGCTACCAAACACACC 61.852 60.000 0.00 0.00 0.00 4.16
2576 2675 1.574428 CGCAGGCTACCAAACACAC 59.426 57.895 0.00 0.00 0.00 3.82
2577 2676 2.258013 GCGCAGGCTACCAAACACA 61.258 57.895 0.30 0.00 35.83 3.72
2578 2677 2.561373 GCGCAGGCTACCAAACAC 59.439 61.111 0.30 0.00 35.83 3.32
2579 2678 3.047280 CGCGCAGGCTACCAAACA 61.047 61.111 8.75 0.00 36.88 2.83
2580 2679 3.799755 CCGCGCAGGCTACCAAAC 61.800 66.667 8.75 0.00 36.88 2.93
2581 2680 3.950794 CTCCGCGCAGGCTACCAAA 62.951 63.158 8.75 0.00 40.77 3.28
2582 2681 4.451150 CTCCGCGCAGGCTACCAA 62.451 66.667 8.75 0.00 40.77 3.67
2584 2683 3.447025 ATTCTCCGCGCAGGCTACC 62.447 63.158 8.75 0.00 40.77 3.18
2585 2684 2.107141 ATTCTCCGCGCAGGCTAC 59.893 61.111 8.75 0.00 40.77 3.58
2586 2685 2.106938 CATTCTCCGCGCAGGCTA 59.893 61.111 8.75 0.00 40.77 3.93
2589 2688 2.890109 GATGCATTCTCCGCGCAGG 61.890 63.158 8.75 10.32 39.39 4.85
2590 2689 2.630317 GATGCATTCTCCGCGCAG 59.370 61.111 8.75 0.00 39.39 5.18
2591 2690 2.896854 GGATGCATTCTCCGCGCA 60.897 61.111 8.75 0.00 40.50 6.09
2592 2691 2.715532 TAGGGATGCATTCTCCGCGC 62.716 60.000 4.63 0.00 33.29 6.86
2593 2692 0.946221 GTAGGGATGCATTCTCCGCG 60.946 60.000 4.63 0.00 33.29 6.46
2594 2693 0.394565 AGTAGGGATGCATTCTCCGC 59.605 55.000 4.63 0.00 33.29 5.54
2595 2694 2.918712 AAGTAGGGATGCATTCTCCG 57.081 50.000 4.63 0.00 33.29 4.63
2596 2695 4.583871 CCATAAGTAGGGATGCATTCTCC 58.416 47.826 4.63 0.00 0.00 3.71
2597 2696 8.969031 GAGCCCATAAGTAGGGATGCATTCTC 62.969 50.000 4.63 0.00 46.98 2.87
2598 2697 7.273917 GAGCCCATAAGTAGGGATGCATTCT 62.274 48.000 4.63 6.83 46.98 2.40
2599 2698 5.105117 GAGCCCATAAGTAGGGATGCATTC 61.105 50.000 0.00 0.00 46.98 2.67
2600 2699 3.245052 GAGCCCATAAGTAGGGATGCATT 60.245 47.826 0.00 0.00 46.98 3.56
2601 2700 2.307098 GAGCCCATAAGTAGGGATGCAT 59.693 50.000 0.00 0.00 46.98 3.96
2602 2701 1.699634 GAGCCCATAAGTAGGGATGCA 59.300 52.381 1.67 0.00 46.98 3.96
2603 2702 1.981495 AGAGCCCATAAGTAGGGATGC 59.019 52.381 1.67 0.00 46.98 3.91
2604 2703 3.906846 AGAAGAGCCCATAAGTAGGGATG 59.093 47.826 1.67 0.00 46.98 3.51
2608 2707 2.370189 CCCAGAAGAGCCCATAAGTAGG 59.630 54.545 0.00 0.00 0.00 3.18
2609 2708 2.224402 GCCCAGAAGAGCCCATAAGTAG 60.224 54.545 0.00 0.00 0.00 2.57
2610 2709 1.768870 GCCCAGAAGAGCCCATAAGTA 59.231 52.381 0.00 0.00 0.00 2.24
2611 2710 0.548510 GCCCAGAAGAGCCCATAAGT 59.451 55.000 0.00 0.00 0.00 2.24
2612 2711 0.548031 TGCCCAGAAGAGCCCATAAG 59.452 55.000 0.00 0.00 0.00 1.73
2613 2712 1.225373 ATGCCCAGAAGAGCCCATAA 58.775 50.000 0.00 0.00 0.00 1.90
2954 3063 0.039617 CTGCGGCCGTGATTTGAAAA 60.040 50.000 28.70 0.00 0.00 2.29
2955 3064 1.578926 CTGCGGCCGTGATTTGAAA 59.421 52.632 28.70 0.42 0.00 2.69
2972 3091 2.107750 CGGCGAGATCCACATGCT 59.892 61.111 0.00 0.00 0.00 3.79
3060 3222 3.642741 AAGGGTGAGGAGGGCGGAT 62.643 63.158 0.00 0.00 0.00 4.18
3091 3254 4.042251 GCTACTCCCTGTGAGCCT 57.958 61.111 0.00 0.00 45.61 4.58
3111 3293 4.523083 AGCAGTTTCTGGTCAAGTAACAA 58.477 39.130 0.15 0.00 37.71 2.83
3258 3470 5.794687 TTGATACTTAGCACAACCGATTG 57.205 39.130 0.00 0.00 41.98 2.67
3263 3476 7.651704 ACAAACAAATTGATACTTAGCACAACC 59.348 33.333 0.00 0.00 41.85 3.77


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

AutoCloner maintained by Alex Coulton.