Multiple sequence alignment - TraesCS4B01G194900

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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 TraesCS4B01G194900 chr4B 100.000 4485 0 0 1 4485 418751041 418755525 0.000000e+00 8283.0
1 TraesCS4B01G194900 chr4D 92.864 3924 177 37 193 4063 339225498 339229371 0.000000e+00 5600.0
2 TraesCS4B01G194900 chr4D 90.753 292 15 2 4123 4404 339229391 339229680 3.270000e-101 379.0
3 TraesCS4B01G194900 chr4D 83.974 156 8 5 62 200 339099702 339099857 2.810000e-27 134.0
4 TraesCS4B01G194900 chr4D 95.833 48 2 0 4437 4484 339229678 339229725 1.340000e-10 78.7
5 TraesCS4B01G194900 chr4A 95.784 2941 101 12 944 3872 132703443 132700514 0.000000e+00 4723.0
6 TraesCS4B01G194900 chr4A 90.657 578 29 11 3923 4478 132700308 132699734 0.000000e+00 745.0
7 TraesCS4B01G194900 chr4A 88.079 302 17 7 610 910 132703731 132703448 1.550000e-89 340.0
8 TraesCS4B01G194900 chr2D 88.843 242 27 0 1240 1481 35686249 35686008 9.430000e-77 298.0
9 TraesCS4B01G194900 chr2D 91.026 78 7 0 1768 1845 35685686 35685609 6.140000e-19 106.0
10 TraesCS4B01G194900 chr2B 88.843 242 27 0 1240 1481 58846549 58846308 9.430000e-77 298.0
11 TraesCS4B01G194900 chr2B 86.207 145 20 0 3040 3184 58844341 58844197 1.670000e-34 158.0
12 TraesCS4B01G194900 chr2B 91.026 78 7 0 1768 1845 58846006 58845929 6.140000e-19 106.0
13 TraesCS4B01G194900 chr2A 87.805 246 30 0 1236 1481 38915287 38915042 5.680000e-74 289.0
14 TraesCS4B01G194900 chr2A 91.026 78 7 0 1768 1845 38914725 38914648 6.140000e-19 106.0
15 TraesCS4B01G194900 chr2A 94.737 38 2 0 1 38 122026364 122026401 4.850000e-05 60.2
16 TraesCS4B01G194900 chr7D 84.034 238 36 2 1242 1478 495138746 495138982 1.260000e-55 228.0
17 TraesCS4B01G194900 chr5D 80.889 225 35 8 1258 1478 249523633 249523853 2.150000e-38 171.0
18 TraesCS4B01G194900 chr5A 80.889 225 35 8 1258 1478 332215310 332215530 2.150000e-38 171.0
19 TraesCS4B01G194900 chr5B 80.444 225 36 8 1258 1478 282264904 282265124 9.980000e-37 165.0
20 TraesCS4B01G194900 chr7A 91.837 49 4 0 1 49 712670086 712670134 8.050000e-08 69.4


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 TraesCS4B01G194900 chr4B 418751041 418755525 4484 False 8283.000000 8283 100.000000 1 4485 1 chr4B.!!$F1 4484
1 TraesCS4B01G194900 chr4D 339225498 339229725 4227 False 2019.233333 5600 93.150000 193 4484 3 chr4D.!!$F2 4291
2 TraesCS4B01G194900 chr4A 132699734 132703731 3997 True 1936.000000 4723 91.506667 610 4478 3 chr4A.!!$R1 3868
3 TraesCS4B01G194900 chr2D 35685609 35686249 640 True 202.000000 298 89.934500 1240 1845 2 chr2D.!!$R1 605

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
31 32 0.179161 ACAGACGCAGACGCTCATAC 60.179 55.0 0.00 0.0 45.53 2.39 F
34 35 0.179161 GACGCAGACGCTCATACACT 60.179 55.0 0.00 0.0 45.53 3.55 F
36 37 0.179163 CGCAGACGCTCATACACTCA 60.179 55.0 0.00 0.0 35.30 3.41 F
551 553 0.248215 CATCGGCAAAATCCAGACGC 60.248 55.0 0.00 0.0 35.90 5.19 F
565 567 0.392595 AGACGCCCGGAATCTTTTCC 60.393 55.0 0.73 0.0 46.85 3.13 F
1912 1968 0.535102 AGAGGTGGCGTTTTGGTGAG 60.535 55.0 0.00 0.0 0.00 3.51 F
2234 2290 1.101635 CATCCACTGCATCCTGGCTG 61.102 60.0 0.00 0.0 38.52 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 1536 0.039035 AGGCTAAAACCGGCATGGAA 59.961 50.000 0.00 0.00 42.00 3.53 R
1898 1954 0.453793 CACAACTCACCAAAACGCCA 59.546 50.000 0.00 0.00 0.00 5.69 R
1912 1968 4.771590 TCAAGGAATCATCAAGCACAAC 57.228 40.909 0.00 0.00 0.00 3.32 R
2072 2128 0.385473 CCAACCAATTCACACGTCGC 60.385 55.000 0.00 0.00 0.00 5.19 R
2262 2318 0.846427 AGAGGCCCCATCACAAAGGA 60.846 55.000 0.00 0.00 0.00 3.36 R
3464 3580 1.622312 TCAATCAGAGCTCTGTGCACT 59.378 47.619 36.32 18.29 45.94 4.40 R
4028 4302 1.002544 AGCAGGAGAGCCACAAACTAC 59.997 52.381 0.00 0.00 36.29 2.73 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
21 22 4.466567 TTTGAACACATTACAGACGCAG 57.533 40.909 0.00 0.00 0.00 5.18
22 23 3.378911 TGAACACATTACAGACGCAGA 57.621 42.857 0.00 0.00 0.00 4.26
23 24 3.057019 TGAACACATTACAGACGCAGAC 58.943 45.455 0.00 0.00 0.00 3.51
25 26 0.366871 CACATTACAGACGCAGACGC 59.633 55.000 0.00 0.00 45.53 5.19
26 27 0.243907 ACATTACAGACGCAGACGCT 59.756 50.000 0.00 0.00 45.53 5.07
27 28 0.917259 CATTACAGACGCAGACGCTC 59.083 55.000 0.00 0.00 45.53 5.03
28 29 0.526211 ATTACAGACGCAGACGCTCA 59.474 50.000 0.00 0.00 45.53 4.26
29 30 0.526211 TTACAGACGCAGACGCTCAT 59.474 50.000 0.00 0.00 45.53 2.90
30 31 1.375551 TACAGACGCAGACGCTCATA 58.624 50.000 0.00 0.00 45.53 2.15
31 32 0.179161 ACAGACGCAGACGCTCATAC 60.179 55.000 0.00 0.00 45.53 2.39
32 33 0.179163 CAGACGCAGACGCTCATACA 60.179 55.000 0.00 0.00 45.53 2.29
33 34 0.179161 AGACGCAGACGCTCATACAC 60.179 55.000 0.00 0.00 45.53 2.90
34 35 0.179161 GACGCAGACGCTCATACACT 60.179 55.000 0.00 0.00 45.53 3.55
35 36 0.179161 ACGCAGACGCTCATACACTC 60.179 55.000 0.00 0.00 45.53 3.51
36 37 0.179163 CGCAGACGCTCATACACTCA 60.179 55.000 0.00 0.00 35.30 3.41
37 38 1.272781 GCAGACGCTCATACACTCAC 58.727 55.000 0.00 0.00 34.30 3.51
38 39 1.914634 CAGACGCTCATACACTCACC 58.085 55.000 0.00 0.00 0.00 4.02
39 40 1.474478 CAGACGCTCATACACTCACCT 59.526 52.381 0.00 0.00 0.00 4.00
40 41 1.746220 AGACGCTCATACACTCACCTC 59.254 52.381 0.00 0.00 0.00 3.85
41 42 1.746220 GACGCTCATACACTCACCTCT 59.254 52.381 0.00 0.00 0.00 3.69
42 43 2.943690 GACGCTCATACACTCACCTCTA 59.056 50.000 0.00 0.00 0.00 2.43
43 44 3.556999 ACGCTCATACACTCACCTCTAT 58.443 45.455 0.00 0.00 0.00 1.98
44 45 3.316588 ACGCTCATACACTCACCTCTATG 59.683 47.826 0.00 0.00 0.00 2.23
45 46 3.565902 CGCTCATACACTCACCTCTATGA 59.434 47.826 0.00 0.00 0.00 2.15
53 54 3.889196 CTCACCTCTATGAGCGTAGAC 57.111 52.381 0.00 0.00 39.77 2.59
54 55 2.210961 TCACCTCTATGAGCGTAGACG 58.789 52.381 0.00 0.00 43.27 4.18
55 56 1.941294 CACCTCTATGAGCGTAGACGT 59.059 52.381 3.73 0.00 42.22 4.34
56 57 3.129109 CACCTCTATGAGCGTAGACGTA 58.871 50.000 3.73 0.00 42.22 3.57
57 58 3.184783 CACCTCTATGAGCGTAGACGTAG 59.815 52.174 3.73 0.00 42.22 3.51
58 59 2.737783 CCTCTATGAGCGTAGACGTAGG 59.262 54.545 3.73 0.00 42.22 3.18
59 60 2.141517 TCTATGAGCGTAGACGTAGGC 58.858 52.381 3.73 0.00 42.22 3.93
62 63 4.631773 AGCGTAGACGTAGGCTGA 57.368 55.556 4.80 0.00 46.30 4.26
63 64 3.097461 AGCGTAGACGTAGGCTGAT 57.903 52.632 4.80 0.00 46.30 2.90
64 65 2.251409 AGCGTAGACGTAGGCTGATA 57.749 50.000 4.80 0.00 46.30 2.15
65 66 1.872313 AGCGTAGACGTAGGCTGATAC 59.128 52.381 4.80 0.00 46.30 2.24
66 67 1.872313 GCGTAGACGTAGGCTGATACT 59.128 52.381 0.00 0.00 42.22 2.12
67 68 2.096318 GCGTAGACGTAGGCTGATACTC 60.096 54.545 0.00 0.00 42.22 2.59
68 69 2.479656 CGTAGACGTAGGCTGATACTCC 59.520 54.545 0.00 0.00 34.11 3.85
69 70 2.730934 AGACGTAGGCTGATACTCCA 57.269 50.000 0.00 0.00 0.00 3.86
70 71 2.299521 AGACGTAGGCTGATACTCCAC 58.700 52.381 0.00 0.00 0.00 4.02
71 72 2.092321 AGACGTAGGCTGATACTCCACT 60.092 50.000 0.00 0.00 0.00 4.00
72 73 2.688958 GACGTAGGCTGATACTCCACTT 59.311 50.000 0.00 0.00 0.00 3.16
73 74 2.688958 ACGTAGGCTGATACTCCACTTC 59.311 50.000 0.00 0.00 0.00 3.01
74 75 2.952978 CGTAGGCTGATACTCCACTTCT 59.047 50.000 0.00 0.00 0.00 2.85
75 76 4.135306 CGTAGGCTGATACTCCACTTCTA 58.865 47.826 0.00 0.00 0.00 2.10
76 77 4.214545 CGTAGGCTGATACTCCACTTCTAG 59.785 50.000 0.00 0.00 0.00 2.43
77 78 4.258457 AGGCTGATACTCCACTTCTAGT 57.742 45.455 0.00 0.00 0.00 2.57
78 79 3.957497 AGGCTGATACTCCACTTCTAGTG 59.043 47.826 0.00 0.00 45.53 2.74
79 80 3.702045 GGCTGATACTCCACTTCTAGTGT 59.298 47.826 6.13 0.00 44.50 3.55
80 81 4.160626 GGCTGATACTCCACTTCTAGTGTT 59.839 45.833 6.13 0.00 44.50 3.32
81 82 5.360144 GGCTGATACTCCACTTCTAGTGTTA 59.640 44.000 6.13 0.00 44.50 2.41
82 83 6.460399 GGCTGATACTCCACTTCTAGTGTTAG 60.460 46.154 6.13 5.72 44.50 2.34
83 84 6.319152 GCTGATACTCCACTTCTAGTGTTAGA 59.681 42.308 6.13 0.00 44.50 2.10
84 85 7.468084 GCTGATACTCCACTTCTAGTGTTAGAG 60.468 44.444 6.13 7.72 44.50 2.43
85 86 7.631007 TGATACTCCACTTCTAGTGTTAGAGA 58.369 38.462 14.39 2.25 44.50 3.10
86 87 7.771361 TGATACTCCACTTCTAGTGTTAGAGAG 59.229 40.741 14.39 11.15 44.50 3.20
87 88 5.883180 ACTCCACTTCTAGTGTTAGAGAGT 58.117 41.667 14.39 11.62 44.50 3.24
88 89 7.018487 ACTCCACTTCTAGTGTTAGAGAGTA 57.982 40.000 14.39 0.00 44.50 2.59
89 90 6.880529 ACTCCACTTCTAGTGTTAGAGAGTAC 59.119 42.308 14.39 0.00 44.50 2.73
90 91 6.179040 TCCACTTCTAGTGTTAGAGAGTACC 58.821 44.000 6.13 0.00 44.50 3.34
91 92 5.944599 CCACTTCTAGTGTTAGAGAGTACCA 59.055 44.000 6.13 0.00 44.50 3.25
92 93 6.603997 CCACTTCTAGTGTTAGAGAGTACCAT 59.396 42.308 6.13 0.00 44.50 3.55
93 94 7.201750 CCACTTCTAGTGTTAGAGAGTACCATC 60.202 44.444 6.13 0.00 44.50 3.51
94 95 7.337184 CACTTCTAGTGTTAGAGAGTACCATCA 59.663 40.741 0.00 0.00 41.19 3.07
95 96 7.337436 ACTTCTAGTGTTAGAGAGTACCATCAC 59.663 40.741 0.00 0.00 37.24 3.06
96 97 6.959904 TCTAGTGTTAGAGAGTACCATCACT 58.040 40.000 0.00 0.00 38.26 3.41
97 98 7.049133 TCTAGTGTTAGAGAGTACCATCACTC 58.951 42.308 0.00 0.00 44.44 3.51
98 99 5.571285 AGTGTTAGAGAGTACCATCACTCA 58.429 41.667 6.08 0.00 46.15 3.41
99 100 6.010850 AGTGTTAGAGAGTACCATCACTCAA 58.989 40.000 6.08 0.00 46.15 3.02
100 101 6.665680 AGTGTTAGAGAGTACCATCACTCAAT 59.334 38.462 6.08 0.00 46.15 2.57
101 102 7.834681 AGTGTTAGAGAGTACCATCACTCAATA 59.165 37.037 6.08 0.00 46.15 1.90
102 103 8.634444 GTGTTAGAGAGTACCATCACTCAATAT 58.366 37.037 6.08 0.00 46.15 1.28
103 104 9.862149 TGTTAGAGAGTACCATCACTCAATATA 57.138 33.333 6.08 0.00 46.15 0.86
107 108 9.593565 AGAGAGTACCATCACTCAATATAATGA 57.406 33.333 6.08 0.00 46.15 2.57
110 111 9.988815 GAGTACCATCACTCAATATAATGAAGT 57.011 33.333 0.00 0.00 43.70 3.01
114 115 8.713971 ACCATCACTCAATATAATGAAGTACCA 58.286 33.333 0.00 0.00 0.00 3.25
115 116 9.730705 CCATCACTCAATATAATGAAGTACCAT 57.269 33.333 0.00 0.00 0.00 3.55
118 119 9.764363 TCACTCAATATAATGAAGTACCATGAC 57.236 33.333 0.00 0.00 0.00 3.06
119 120 8.993121 CACTCAATATAATGAAGTACCATGACC 58.007 37.037 0.00 0.00 0.00 4.02
120 121 8.713971 ACTCAATATAATGAAGTACCATGACCA 58.286 33.333 0.00 0.00 0.00 4.02
121 122 9.559732 CTCAATATAATGAAGTACCATGACCAA 57.440 33.333 0.00 0.00 0.00 3.67
122 123 9.913310 TCAATATAATGAAGTACCATGACCAAA 57.087 29.630 0.00 0.00 0.00 3.28
125 126 5.982890 AATGAAGTACCATGACCAAAAGG 57.017 39.130 0.00 0.00 0.00 3.11
126 127 4.447138 TGAAGTACCATGACCAAAAGGT 57.553 40.909 0.00 0.00 38.14 3.50
127 128 4.798882 TGAAGTACCATGACCAAAAGGTT 58.201 39.130 0.00 0.00 35.62 3.50
128 129 5.942961 TGAAGTACCATGACCAAAAGGTTA 58.057 37.500 0.00 0.00 35.62 2.85
129 130 6.366340 TGAAGTACCATGACCAAAAGGTTAA 58.634 36.000 0.00 0.00 35.62 2.01
130 131 7.007723 TGAAGTACCATGACCAAAAGGTTAAT 58.992 34.615 0.00 0.00 35.62 1.40
131 132 8.164733 TGAAGTACCATGACCAAAAGGTTAATA 58.835 33.333 0.00 0.00 35.62 0.98
132 133 9.185680 GAAGTACCATGACCAAAAGGTTAATAT 57.814 33.333 0.00 0.00 35.62 1.28
133 134 9.541884 AAGTACCATGACCAAAAGGTTAATATT 57.458 29.630 0.00 0.00 35.62 1.28
134 135 8.966868 AGTACCATGACCAAAAGGTTAATATTG 58.033 33.333 0.00 0.00 35.62 1.90
135 136 7.790782 ACCATGACCAAAAGGTTAATATTGT 57.209 32.000 0.00 0.00 0.00 2.71
136 137 7.836842 ACCATGACCAAAAGGTTAATATTGTC 58.163 34.615 0.00 0.00 0.00 3.18
137 138 7.673926 ACCATGACCAAAAGGTTAATATTGTCT 59.326 33.333 0.00 0.00 0.00 3.41
138 139 8.190784 CCATGACCAAAAGGTTAATATTGTCTC 58.809 37.037 0.00 0.00 0.00 3.36
139 140 8.960591 CATGACCAAAAGGTTAATATTGTCTCT 58.039 33.333 0.00 0.00 0.00 3.10
140 141 8.335532 TGACCAAAAGGTTAATATTGTCTCTG 57.664 34.615 0.00 0.00 0.00 3.35
141 142 7.942341 TGACCAAAAGGTTAATATTGTCTCTGT 59.058 33.333 0.00 0.00 0.00 3.41
142 143 8.110860 ACCAAAAGGTTAATATTGTCTCTGTG 57.889 34.615 0.00 0.00 0.00 3.66
143 144 7.724061 ACCAAAAGGTTAATATTGTCTCTGTGT 59.276 33.333 0.00 0.00 0.00 3.72
144 145 9.226606 CCAAAAGGTTAATATTGTCTCTGTGTA 57.773 33.333 0.00 0.00 0.00 2.90
158 159 7.761409 TGTCTCTGTGTATATTTTTCAATGGC 58.239 34.615 0.00 0.00 0.00 4.40
159 160 7.148086 TGTCTCTGTGTATATTTTTCAATGGCC 60.148 37.037 0.00 0.00 0.00 5.36
160 161 6.889177 TCTCTGTGTATATTTTTCAATGGCCA 59.111 34.615 8.56 8.56 0.00 5.36
161 162 7.560991 TCTCTGTGTATATTTTTCAATGGCCAT 59.439 33.333 14.09 14.09 0.00 4.40
162 163 8.759481 TCTGTGTATATTTTTCAATGGCCATA 57.241 30.769 21.15 0.00 0.00 2.74
163 164 9.194972 TCTGTGTATATTTTTCAATGGCCATAA 57.805 29.630 21.15 9.75 0.00 1.90
164 165 9.985730 CTGTGTATATTTTTCAATGGCCATAAT 57.014 29.630 21.15 16.65 0.00 1.28
165 166 9.761504 TGTGTATATTTTTCAATGGCCATAATG 57.238 29.630 21.15 15.21 0.00 1.90
166 167 9.206870 GTGTATATTTTTCAATGGCCATAATGG 57.793 33.333 21.15 9.43 41.55 3.16
183 184 7.886338 CCATAATGGCCTCTAATTTCCTAAAC 58.114 38.462 3.32 0.00 0.00 2.01
184 185 7.039714 CCATAATGGCCTCTAATTTCCTAAACC 60.040 40.741 3.32 0.00 0.00 3.27
185 186 4.245251 TGGCCTCTAATTTCCTAAACCC 57.755 45.455 3.32 0.00 0.00 4.11
186 187 3.856206 TGGCCTCTAATTTCCTAAACCCT 59.144 43.478 3.32 0.00 0.00 4.34
187 188 5.041015 TGGCCTCTAATTTCCTAAACCCTA 58.959 41.667 3.32 0.00 0.00 3.53
188 189 5.132144 TGGCCTCTAATTTCCTAAACCCTAG 59.868 44.000 3.32 0.00 0.00 3.02
189 190 5.368816 GGCCTCTAATTTCCTAAACCCTAGA 59.631 44.000 0.00 0.00 0.00 2.43
190 191 6.044520 GGCCTCTAATTTCCTAAACCCTAGAT 59.955 42.308 0.00 0.00 0.00 1.98
191 192 7.421499 GGCCTCTAATTTCCTAAACCCTAGATT 60.421 40.741 0.00 0.00 0.00 2.40
200 201 4.868734 CCTAAACCCTAGATTCACGTGAAC 59.131 45.833 31.87 23.57 36.80 3.18
203 204 2.897969 ACCCTAGATTCACGTGAACTGT 59.102 45.455 31.87 20.72 36.80 3.55
232 233 1.590525 GGCGGCAATGCATCACATG 60.591 57.895 7.79 0.00 39.60 3.21
236 237 0.248743 GGCAATGCATCACATGTCCG 60.249 55.000 7.79 0.00 39.60 4.79
247 248 1.001815 CACATGTCCGGTTTGTGTTCC 60.002 52.381 19.29 0.00 36.77 3.62
250 251 2.181521 GTCCGGTTTGTGTTCCGCA 61.182 57.895 0.00 0.00 44.63 5.69
255 256 0.869880 GGTTTGTGTTCCGCAACAGC 60.870 55.000 0.00 0.00 43.42 4.40
284 285 1.380246 TGGATTGCCACAGATGCCC 60.380 57.895 0.00 0.00 39.92 5.36
289 290 0.680618 TTGCCACAGATGCCCAAAAG 59.319 50.000 0.00 0.00 0.00 2.27
290 291 1.079612 GCCACAGATGCCCAAAAGC 60.080 57.895 0.00 0.00 0.00 3.51
307 308 3.994729 GCATGCAGCGTATCAAACA 57.005 47.368 14.21 0.00 0.00 2.83
313 314 1.804151 GCAGCGTATCAAACACCTTCA 59.196 47.619 0.00 0.00 0.00 3.02
314 315 2.225491 GCAGCGTATCAAACACCTTCAA 59.775 45.455 0.00 0.00 0.00 2.69
319 320 5.178809 AGCGTATCAAACACCTTCAACTTAC 59.821 40.000 0.00 0.00 0.00 2.34
331 332 1.270550 TCAACTTACGACCTTCCCGTC 59.729 52.381 0.00 0.00 40.95 4.79
434 435 6.441924 TCCCAAACATTTAGATTTTGCCCATA 59.558 34.615 0.00 0.00 0.00 2.74
474 475 1.340308 TGGCAGTTGACATGAGGATGG 60.340 52.381 0.00 0.00 33.39 3.51
483 484 4.264253 TGACATGAGGATGGCAAGTTTAG 58.736 43.478 0.00 0.00 45.22 1.85
492 493 7.615365 TGAGGATGGCAAGTTTAGTTGATAATT 59.385 33.333 0.00 0.00 0.00 1.40
493 494 9.120538 GAGGATGGCAAGTTTAGTTGATAATTA 57.879 33.333 0.00 0.00 0.00 1.40
551 553 0.248215 CATCGGCAAAATCCAGACGC 60.248 55.000 0.00 0.00 35.90 5.19
556 558 1.376683 CAAAATCCAGACGCCCGGA 60.377 57.895 0.73 0.00 35.27 5.14
561 563 1.338136 ATCCAGACGCCCGGAATCTT 61.338 55.000 0.73 0.00 34.22 2.40
565 567 0.392595 AGACGCCCGGAATCTTTTCC 60.393 55.000 0.73 0.00 46.85 3.13
706 709 3.900892 CCATCCCGGTCCGAGTCG 61.901 72.222 14.39 5.29 0.00 4.18
741 744 3.458118 CCAACTCCATAGTCCATACCCAA 59.542 47.826 0.00 0.00 33.75 4.12
930 943 1.519455 GGACGCACAAGATCCTCGG 60.519 63.158 0.00 0.00 0.00 4.63
933 946 2.184322 GCACAAGATCCTCGGCGA 59.816 61.111 10.14 10.14 0.00 5.54
1196 1212 2.257691 TCCGTCTTCGAGGAGGATAG 57.742 55.000 17.66 2.72 39.71 2.08
1203 1219 1.232909 TCGAGGAGGATAGAAGGGGT 58.767 55.000 0.00 0.00 0.00 4.95
1467 1483 4.821589 GCGCTCTTCGTCCTGGGG 62.822 72.222 0.00 0.00 41.07 4.96
1580 1598 4.761975 TCTTGTCCTGTAACGACTGTTTT 58.238 39.130 0.00 0.00 39.54 2.43
1750 1769 2.380304 GATGCTAAGAAAGGCGGCGC 62.380 60.000 26.17 26.17 0.00 6.53
1761 1780 4.683334 GCGGCGCCTTGTGTGAAC 62.683 66.667 26.68 0.00 0.00 3.18
1764 1783 2.713154 GCGCCTTGTGTGAACGTT 59.287 55.556 0.00 0.00 0.00 3.99
1869 1925 1.301677 GCTCTTTGCTTCTCGGTGGG 61.302 60.000 0.00 0.00 38.95 4.61
1898 1954 4.820716 GCATGCATAATTCTTCAGAGAGGT 59.179 41.667 14.21 0.00 32.44 3.85
1912 1968 0.535102 AGAGGTGGCGTTTTGGTGAG 60.535 55.000 0.00 0.00 0.00 3.51
2072 2128 3.670055 CACAAAGCTGCTTGATTTTACCG 59.330 43.478 16.73 0.00 31.16 4.02
2201 2257 6.314784 CGATTTGTTCCAACCTAATGAGAAC 58.685 40.000 0.00 0.00 37.83 3.01
2234 2290 1.101635 CATCCACTGCATCCTGGCTG 61.102 60.000 0.00 0.00 38.52 4.85
2262 2318 1.352622 TGGGGTTCTTGCAGGTCTGT 61.353 55.000 0.00 0.00 0.00 3.41
2328 2384 4.130118 CCCATATGTGGTAAGAGCTTCAC 58.870 47.826 7.81 0.00 44.48 3.18
2572 2650 3.481112 AACGTTCGAAATACAATGGCC 57.519 42.857 0.00 0.00 0.00 5.36
2577 2655 4.601019 GTTCGAAATACAATGGCCTGATG 58.399 43.478 3.32 2.54 0.00 3.07
2634 2712 7.696453 CGGGTTTGCTGTTTTAAGTAGAATATG 59.304 37.037 0.00 0.00 0.00 1.78
2648 2726 7.701539 AGTAGAATATGCATGTGGAAAACAA 57.298 32.000 10.16 0.00 43.61 2.83
2652 2730 8.851541 AGAATATGCATGTGGAAAACAAAAAT 57.148 26.923 10.16 0.00 43.61 1.82
2657 2735 7.712264 TGCATGTGGAAAACAAAAATCTAAG 57.288 32.000 0.00 0.00 43.61 2.18
2689 2767 8.087750 TCGATGTTCTTAAAGAAAATGGCAAAT 58.912 29.630 0.00 0.00 32.48 2.32
2747 2839 1.727467 GCACATCCCGCCAACATAC 59.273 57.895 0.00 0.00 0.00 2.39
2748 2840 2.013807 CACATCCCGCCAACATACG 58.986 57.895 0.00 0.00 0.00 3.06
2786 2878 9.660180 GTTACATTTATTTCTGACTTCTCCTCT 57.340 33.333 0.00 0.00 0.00 3.69
2847 2948 6.873605 TGACATGTGTGGTACTTATTCAAGAG 59.126 38.462 1.15 0.00 35.60 2.85
2855 2956 7.618117 TGTGGTACTTATTCAAGAGAGGTATCA 59.382 37.037 0.00 0.00 35.60 2.15
2856 2957 7.921745 GTGGTACTTATTCAAGAGAGGTATCAC 59.078 40.741 0.00 0.00 34.33 3.06
2913 3014 2.959707 AGAAGAGTAATCCTAGCGGTGG 59.040 50.000 0.00 0.00 0.00 4.61
3023 3131 7.593273 GTCCTAGTCTGATTTCTTATCGACATG 59.407 40.741 0.00 0.00 0.00 3.21
3124 3232 1.832883 TACACCATGACATTGGCACC 58.167 50.000 0.00 0.00 40.68 5.01
3202 3310 2.593978 CACCATCCCCTGCTCCTG 59.406 66.667 0.00 0.00 0.00 3.86
3220 3328 2.487372 CCTGAGCTCTTGCCTTTTTCTC 59.513 50.000 16.19 0.00 40.80 2.87
3229 3337 2.229792 TGCCTTTTTCTCGAACATGCT 58.770 42.857 0.00 0.00 0.00 3.79
3298 3414 2.488153 GTTTGGATGTAACCTGCAGACC 59.512 50.000 17.39 7.20 0.00 3.85
3464 3580 6.436261 CAAAGTGAGTCAGAAACGAGTACTA 58.564 40.000 0.00 0.00 0.00 1.82
3556 3674 7.364149 TGTGACTTAAGAGTTAAACACCCTA 57.636 36.000 10.09 0.00 35.88 3.53
3596 3714 3.054434 TCGGATTGGTGAGTCCATGAATT 60.054 43.478 0.00 0.00 46.60 2.17
3597 3715 3.696051 CGGATTGGTGAGTCCATGAATTT 59.304 43.478 0.00 0.00 46.60 1.82
3598 3716 4.881273 CGGATTGGTGAGTCCATGAATTTA 59.119 41.667 0.00 0.00 46.60 1.40
3599 3717 5.532406 CGGATTGGTGAGTCCATGAATTTAT 59.468 40.000 0.00 0.00 46.60 1.40
3600 3718 6.039717 CGGATTGGTGAGTCCATGAATTTATT 59.960 38.462 0.00 0.00 46.60 1.40
3601 3719 7.416664 CGGATTGGTGAGTCCATGAATTTATTT 60.417 37.037 0.00 0.00 46.60 1.40
3602 3720 8.260114 GGATTGGTGAGTCCATGAATTTATTTT 58.740 33.333 0.00 0.00 46.60 1.82
3672 3790 4.589216 TGTAAAAGAGCAATTGCAGCTT 57.411 36.364 30.89 27.12 43.58 3.74
3714 3832 0.249911 GCTTGCTGGTATAGTCCCCG 60.250 60.000 0.00 0.00 0.00 5.73
3805 3924 4.651045 AGAGGTGGCAGTTCAAATTTTCTT 59.349 37.500 0.00 0.00 0.00 2.52
3883 4002 1.372087 GGCTCCGATGCTTTGGACAG 61.372 60.000 4.42 0.00 31.64 3.51
3958 4232 4.455877 AGAAAGATCGATTGTTTCCCACAC 59.544 41.667 21.60 5.79 33.98 3.82
3973 4247 2.094675 CCACACTTGGGAAGCCTATTG 58.905 52.381 0.00 0.00 39.57 1.90
4043 4317 5.948992 AATCTTTGTAGTTTGTGGCTCTC 57.051 39.130 0.00 0.00 0.00 3.20
4053 4327 3.767806 TGGCTCTCCTGCTGCTCG 61.768 66.667 0.00 0.00 0.00 5.03
4064 4338 1.216710 GCTGCTCGTTGCTACTCCT 59.783 57.895 0.00 0.00 43.37 3.69
4074 4348 1.267121 TGCTACTCCTTCTGTCCCAC 58.733 55.000 0.00 0.00 0.00 4.61
4145 4419 3.550437 ATAGGAGTGCATGTGTTCCTC 57.450 47.619 14.61 0.78 40.43 3.71
4146 4420 1.356124 AGGAGTGCATGTGTTCCTCT 58.644 50.000 7.84 0.00 35.11 3.69
4152 4426 4.147321 AGTGCATGTGTTCCTCTTTCAAT 58.853 39.130 0.00 0.00 0.00 2.57
4153 4427 4.022589 AGTGCATGTGTTCCTCTTTCAATG 60.023 41.667 0.00 0.00 0.00 2.82
4171 4445 2.781681 TGGAAAGACGGGATTTCTCC 57.218 50.000 8.52 0.00 41.26 3.71
4257 4541 2.009774 GTTCCTACATTCTGCACGCAT 58.990 47.619 0.00 0.00 0.00 4.73
4272 4556 5.312895 TGCACGCATGGGAATATACTTATT 58.687 37.500 17.76 0.00 0.00 1.40
4273 4557 5.181056 TGCACGCATGGGAATATACTTATTG 59.819 40.000 17.76 0.59 0.00 1.90
4290 4574 5.358160 ACTTATTGTACCACCGTAGTAGACC 59.642 44.000 0.00 0.00 0.00 3.85
4484 4780 1.379176 CAGCCTCCTCTCCTCGTCA 60.379 63.158 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.025229 GTCTGCGTCTGTAATGTGTTCAAA 60.025 41.667 0.00 0.00 0.00 2.69
1 2 3.493129 GTCTGCGTCTGTAATGTGTTCAA 59.507 43.478 0.00 0.00 0.00 2.69
2 3 3.057019 GTCTGCGTCTGTAATGTGTTCA 58.943 45.455 0.00 0.00 0.00 3.18
3 4 2.090658 CGTCTGCGTCTGTAATGTGTTC 59.909 50.000 0.00 0.00 0.00 3.18
4 5 2.058798 CGTCTGCGTCTGTAATGTGTT 58.941 47.619 0.00 0.00 0.00 3.32
5 6 1.698165 CGTCTGCGTCTGTAATGTGT 58.302 50.000 0.00 0.00 0.00 3.72
6 7 0.366871 GCGTCTGCGTCTGTAATGTG 59.633 55.000 0.00 0.00 40.81 3.21
7 8 2.738147 GCGTCTGCGTCTGTAATGT 58.262 52.632 0.00 0.00 40.81 2.71
18 19 1.272781 GTGAGTGTATGAGCGTCTGC 58.727 55.000 0.00 0.00 43.24 4.26
19 20 1.474478 AGGTGAGTGTATGAGCGTCTG 59.526 52.381 0.00 0.00 0.00 3.51
20 21 1.746220 GAGGTGAGTGTATGAGCGTCT 59.254 52.381 0.00 0.00 0.00 4.18
21 22 1.746220 AGAGGTGAGTGTATGAGCGTC 59.254 52.381 0.00 0.00 0.00 5.19
22 23 1.840737 AGAGGTGAGTGTATGAGCGT 58.159 50.000 0.00 0.00 0.00 5.07
23 24 3.565902 TCATAGAGGTGAGTGTATGAGCG 59.434 47.826 0.00 0.00 29.97 5.03
24 25 5.119931 CTCATAGAGGTGAGTGTATGAGC 57.880 47.826 5.41 0.00 41.37 4.26
25 26 4.320129 CGCTCATAGAGGTGAGTGTATGAG 60.320 50.000 11.71 11.71 46.43 2.90
26 27 3.565902 CGCTCATAGAGGTGAGTGTATGA 59.434 47.826 8.80 0.00 46.50 2.15
27 28 3.894920 CGCTCATAGAGGTGAGTGTATG 58.105 50.000 8.80 0.00 46.50 2.39
32 33 3.207778 GTCTACGCTCATAGAGGTGAGT 58.792 50.000 5.87 0.00 45.80 3.41
33 34 2.222213 CGTCTACGCTCATAGAGGTGAG 59.778 54.545 0.00 0.00 46.59 3.51
34 35 2.210961 CGTCTACGCTCATAGAGGTGA 58.789 52.381 0.00 0.00 34.03 4.02
35 36 1.941294 ACGTCTACGCTCATAGAGGTG 59.059 52.381 11.67 0.67 44.56 4.00
36 37 2.328819 ACGTCTACGCTCATAGAGGT 57.671 50.000 1.74 8.30 42.59 3.85
37 38 2.737783 CCTACGTCTACGCTCATAGAGG 59.262 54.545 1.74 7.34 44.43 3.69
38 39 2.158058 GCCTACGTCTACGCTCATAGAG 59.842 54.545 1.74 0.00 44.43 2.43
39 40 2.141517 GCCTACGTCTACGCTCATAGA 58.858 52.381 1.74 0.00 44.43 1.98
40 41 2.096169 CAGCCTACGTCTACGCTCATAG 60.096 54.545 1.74 0.00 44.43 2.23
41 42 1.871676 CAGCCTACGTCTACGCTCATA 59.128 52.381 1.74 0.00 44.43 2.15
42 43 0.663688 CAGCCTACGTCTACGCTCAT 59.336 55.000 1.74 0.00 44.43 2.90
43 44 0.392060 TCAGCCTACGTCTACGCTCA 60.392 55.000 1.74 0.00 44.43 4.26
44 45 0.945813 ATCAGCCTACGTCTACGCTC 59.054 55.000 1.74 0.00 44.43 5.03
45 46 1.872313 GTATCAGCCTACGTCTACGCT 59.128 52.381 1.74 0.00 44.43 5.07
46 47 1.872313 AGTATCAGCCTACGTCTACGC 59.128 52.381 1.74 0.00 44.43 4.42
47 48 2.479656 GGAGTATCAGCCTACGTCTACG 59.520 54.545 0.00 0.04 40.98 3.51
48 49 3.250521 GTGGAGTATCAGCCTACGTCTAC 59.749 52.174 0.00 0.00 36.25 2.59
49 50 3.136077 AGTGGAGTATCAGCCTACGTCTA 59.864 47.826 0.00 0.00 36.25 2.59
50 51 2.092321 AGTGGAGTATCAGCCTACGTCT 60.092 50.000 0.00 0.00 36.25 4.18
51 52 2.299521 AGTGGAGTATCAGCCTACGTC 58.700 52.381 0.00 0.00 36.25 4.34
52 53 2.438800 AGTGGAGTATCAGCCTACGT 57.561 50.000 0.00 0.00 36.25 3.57
53 54 2.952978 AGAAGTGGAGTATCAGCCTACG 59.047 50.000 0.00 0.00 36.25 3.51
54 55 5.009210 CACTAGAAGTGGAGTATCAGCCTAC 59.991 48.000 0.00 0.00 42.35 3.18
55 56 5.133941 CACTAGAAGTGGAGTATCAGCCTA 58.866 45.833 0.00 0.00 42.35 3.93
56 57 3.957497 CACTAGAAGTGGAGTATCAGCCT 59.043 47.826 0.00 0.00 42.35 4.58
57 58 4.314740 CACTAGAAGTGGAGTATCAGCC 57.685 50.000 0.00 0.00 42.35 4.85
69 70 7.337436 GTGATGGTACTCTCTAACACTAGAAGT 59.663 40.741 0.00 0.00 33.66 3.01
70 71 7.554835 AGTGATGGTACTCTCTAACACTAGAAG 59.445 40.741 0.00 0.00 35.95 2.85
71 72 7.403671 AGTGATGGTACTCTCTAACACTAGAA 58.596 38.462 0.00 0.00 35.95 2.10
72 73 6.959904 AGTGATGGTACTCTCTAACACTAGA 58.040 40.000 0.00 0.00 35.95 2.43
73 74 6.824196 TGAGTGATGGTACTCTCTAACACTAG 59.176 42.308 0.00 0.00 45.70 2.57
74 75 6.718294 TGAGTGATGGTACTCTCTAACACTA 58.282 40.000 0.00 0.00 45.70 2.74
75 76 5.571285 TGAGTGATGGTACTCTCTAACACT 58.429 41.667 0.00 0.00 45.70 3.55
76 77 5.899120 TGAGTGATGGTACTCTCTAACAC 57.101 43.478 7.35 0.00 45.70 3.32
77 78 8.768501 ATATTGAGTGATGGTACTCTCTAACA 57.231 34.615 7.35 0.00 45.70 2.41
81 82 9.593565 TCATTATATTGAGTGATGGTACTCTCT 57.406 33.333 7.35 0.00 45.70 3.10
84 85 9.988815 ACTTCATTATATTGAGTGATGGTACTC 57.011 33.333 0.00 0.00 45.71 2.59
88 89 8.713971 TGGTACTTCATTATATTGAGTGATGGT 58.286 33.333 0.00 0.00 0.00 3.55
89 90 9.730705 ATGGTACTTCATTATATTGAGTGATGG 57.269 33.333 0.00 0.00 0.00 3.51
92 93 9.764363 GTCATGGTACTTCATTATATTGAGTGA 57.236 33.333 0.00 0.00 0.00 3.41
93 94 8.993121 GGTCATGGTACTTCATTATATTGAGTG 58.007 37.037 0.00 0.00 0.00 3.51
94 95 8.713971 TGGTCATGGTACTTCATTATATTGAGT 58.286 33.333 0.00 2.63 0.00 3.41
95 96 9.559732 TTGGTCATGGTACTTCATTATATTGAG 57.440 33.333 0.00 0.00 0.00 3.02
96 97 9.913310 TTTGGTCATGGTACTTCATTATATTGA 57.087 29.630 0.00 0.00 0.00 2.57
99 100 9.354673 CCTTTTGGTCATGGTACTTCATTATAT 57.645 33.333 0.00 0.00 34.07 0.86
100 101 8.746052 CCTTTTGGTCATGGTACTTCATTATA 57.254 34.615 0.00 0.00 34.07 0.98
101 102 7.645058 CCTTTTGGTCATGGTACTTCATTAT 57.355 36.000 0.00 0.00 34.07 1.28
103 104 5.982890 CCTTTTGGTCATGGTACTTCATT 57.017 39.130 0.00 0.00 34.07 2.57
132 133 8.243426 GCCATTGAAAAATATACACAGAGACAA 58.757 33.333 0.00 0.00 0.00 3.18
133 134 7.148086 GGCCATTGAAAAATATACACAGAGACA 60.148 37.037 0.00 0.00 0.00 3.41
134 135 7.148086 TGGCCATTGAAAAATATACACAGAGAC 60.148 37.037 0.00 0.00 0.00 3.36
135 136 6.889177 TGGCCATTGAAAAATATACACAGAGA 59.111 34.615 0.00 0.00 0.00 3.10
136 137 7.099266 TGGCCATTGAAAAATATACACAGAG 57.901 36.000 0.00 0.00 0.00 3.35
137 138 7.658525 ATGGCCATTGAAAAATATACACAGA 57.341 32.000 14.09 0.00 0.00 3.41
138 139 9.985730 ATTATGGCCATTGAAAAATATACACAG 57.014 29.630 26.37 0.00 0.00 3.66
139 140 9.761504 CATTATGGCCATTGAAAAATATACACA 57.238 29.630 26.37 0.00 0.00 3.72
140 141 9.206870 CCATTATGGCCATTGAAAAATATACAC 57.793 33.333 26.37 0.00 0.00 2.90
158 159 7.039714 GGTTTAGGAAATTAGAGGCCATTATGG 60.040 40.741 5.01 6.92 41.55 2.74
159 160 7.039714 GGGTTTAGGAAATTAGAGGCCATTATG 60.040 40.741 5.01 0.00 0.00 1.90
160 161 7.010771 GGGTTTAGGAAATTAGAGGCCATTAT 58.989 38.462 5.01 0.00 0.00 1.28
161 162 6.161526 AGGGTTTAGGAAATTAGAGGCCATTA 59.838 38.462 5.01 0.00 0.00 1.90
162 163 5.043356 AGGGTTTAGGAAATTAGAGGCCATT 60.043 40.000 5.01 0.00 0.00 3.16
163 164 4.482398 AGGGTTTAGGAAATTAGAGGCCAT 59.518 41.667 5.01 0.00 0.00 4.40
164 165 3.856206 AGGGTTTAGGAAATTAGAGGCCA 59.144 43.478 5.01 0.00 0.00 5.36
165 166 4.521536 AGGGTTTAGGAAATTAGAGGCC 57.478 45.455 0.00 0.00 0.00 5.19
166 167 6.496144 TCTAGGGTTTAGGAAATTAGAGGC 57.504 41.667 0.00 0.00 0.00 4.70
167 168 8.714906 TGAATCTAGGGTTTAGGAAATTAGAGG 58.285 37.037 0.00 0.00 0.00 3.69
168 169 9.549078 GTGAATCTAGGGTTTAGGAAATTAGAG 57.451 37.037 0.00 0.00 0.00 2.43
169 170 8.202137 CGTGAATCTAGGGTTTAGGAAATTAGA 58.798 37.037 0.00 0.00 0.00 2.10
170 171 7.985752 ACGTGAATCTAGGGTTTAGGAAATTAG 59.014 37.037 0.00 0.00 0.00 1.73
171 172 7.767198 CACGTGAATCTAGGGTTTAGGAAATTA 59.233 37.037 10.90 0.00 0.00 1.40
172 173 6.598064 CACGTGAATCTAGGGTTTAGGAAATT 59.402 38.462 10.90 0.00 0.00 1.82
173 174 6.070424 TCACGTGAATCTAGGGTTTAGGAAAT 60.070 38.462 17.62 0.00 0.00 2.17
174 175 5.246656 TCACGTGAATCTAGGGTTTAGGAAA 59.753 40.000 17.62 0.00 0.00 3.13
175 176 4.773674 TCACGTGAATCTAGGGTTTAGGAA 59.226 41.667 17.62 0.00 0.00 3.36
176 177 4.346730 TCACGTGAATCTAGGGTTTAGGA 58.653 43.478 17.62 0.00 0.00 2.94
177 178 4.730949 TCACGTGAATCTAGGGTTTAGG 57.269 45.455 17.62 0.00 0.00 2.69
178 179 5.577164 CAGTTCACGTGAATCTAGGGTTTAG 59.423 44.000 31.81 12.96 36.33 1.85
179 180 5.011329 ACAGTTCACGTGAATCTAGGGTTTA 59.989 40.000 31.81 4.08 36.33 2.01
180 181 4.202326 ACAGTTCACGTGAATCTAGGGTTT 60.202 41.667 31.81 8.21 36.33 3.27
181 182 3.323979 ACAGTTCACGTGAATCTAGGGTT 59.676 43.478 31.81 9.67 36.33 4.11
182 183 2.897969 ACAGTTCACGTGAATCTAGGGT 59.102 45.455 31.81 19.88 36.33 4.34
183 184 3.056821 TGACAGTTCACGTGAATCTAGGG 60.057 47.826 31.81 19.36 36.33 3.53
184 185 4.174411 TGACAGTTCACGTGAATCTAGG 57.826 45.455 31.81 20.69 36.33 3.02
185 186 6.712241 AATTGACAGTTCACGTGAATCTAG 57.288 37.500 31.81 22.47 36.33 2.43
186 187 7.351981 CAAAATTGACAGTTCACGTGAATCTA 58.648 34.615 31.81 21.83 36.33 1.98
187 188 6.201517 CAAAATTGACAGTTCACGTGAATCT 58.798 36.000 31.81 25.28 36.33 2.40
188 189 5.399301 CCAAAATTGACAGTTCACGTGAATC 59.601 40.000 31.81 24.70 36.33 2.52
189 190 5.163561 ACCAAAATTGACAGTTCACGTGAAT 60.164 36.000 31.81 17.85 36.33 2.57
190 191 4.156922 ACCAAAATTGACAGTTCACGTGAA 59.843 37.500 26.53 26.53 0.00 3.18
191 192 3.692101 ACCAAAATTGACAGTTCACGTGA 59.308 39.130 15.76 15.76 0.00 4.35
200 201 0.667184 GCCGCCACCAAAATTGACAG 60.667 55.000 0.00 0.00 0.00 3.51
203 204 0.683973 ATTGCCGCCACCAAAATTGA 59.316 45.000 0.00 0.00 0.00 2.57
236 237 0.869880 GCTGTTGCGGAACACAAACC 60.870 55.000 19.24 1.59 37.15 3.27
250 251 0.478072 TCCATGTCCAACCAGCTGTT 59.522 50.000 13.81 4.33 37.80 3.16
255 256 0.819582 GGCAATCCATGTCCAACCAG 59.180 55.000 0.00 0.00 0.00 4.00
280 281 2.344500 GCTGCATGCTTTTGGGCA 59.656 55.556 20.33 0.00 46.63 5.36
284 285 2.547913 TGATACGCTGCATGCTTTTG 57.452 45.000 20.33 8.64 40.11 2.44
289 290 1.538276 GTGTTTGATACGCTGCATGC 58.462 50.000 11.82 11.82 34.37 4.06
290 291 1.739466 AGGTGTTTGATACGCTGCATG 59.261 47.619 0.00 0.00 37.42 4.06
291 292 2.113860 AGGTGTTTGATACGCTGCAT 57.886 45.000 0.00 0.00 37.42 3.96
298 299 6.347160 GGTCGTAAGTTGAAGGTGTTTGATAC 60.347 42.308 0.00 0.00 39.48 2.24
307 308 2.038164 GGGAAGGTCGTAAGTTGAAGGT 59.962 50.000 0.00 0.00 39.48 3.50
357 358 9.052365 ACTTCCTCTTTCCAATATAAGAGACTT 57.948 33.333 12.62 0.00 46.58 3.01
399 400 3.732048 AATGTTTGGGACTTATCGGGT 57.268 42.857 0.00 0.00 0.00 5.28
400 401 5.433526 TCTAAATGTTTGGGACTTATCGGG 58.566 41.667 0.00 0.00 0.00 5.14
401 402 7.568199 AATCTAAATGTTTGGGACTTATCGG 57.432 36.000 0.00 0.00 0.00 4.18
402 403 9.289303 CAAAATCTAAATGTTTGGGACTTATCG 57.711 33.333 0.00 0.00 0.00 2.92
403 404 9.087424 GCAAAATCTAAATGTTTGGGACTTATC 57.913 33.333 0.00 0.00 33.72 1.75
404 405 8.040727 GGCAAAATCTAAATGTTTGGGACTTAT 58.959 33.333 0.00 0.00 33.72 1.73
455 456 1.386533 CCATCCTCATGTCAACTGCC 58.613 55.000 0.00 0.00 0.00 4.85
466 467 4.365514 TCAACTAAACTTGCCATCCTCA 57.634 40.909 0.00 0.00 0.00 3.86
533 535 1.376609 GGCGTCTGGATTTTGCCGAT 61.377 55.000 0.00 0.00 35.77 4.18
535 537 2.485122 GGCGTCTGGATTTTGCCG 59.515 61.111 0.00 0.00 35.77 5.69
546 548 0.392595 GGAAAAGATTCCGGGCGTCT 60.393 55.000 0.00 0.00 45.44 4.18
547 549 2.095750 GGAAAAGATTCCGGGCGTC 58.904 57.895 0.00 0.00 45.44 5.19
741 744 1.956170 GTCGGCATCGCGATGGAAT 60.956 57.895 40.84 12.47 39.16 3.01
1196 1212 2.764547 CTCCCCCGAGACCCCTTC 60.765 72.222 0.00 0.00 38.52 3.46
1518 1534 0.179137 GCTAAAACCGGCATGGAAGC 60.179 55.000 0.00 0.00 42.00 3.86
1520 1536 0.039035 AGGCTAAAACCGGCATGGAA 59.961 50.000 0.00 0.00 42.00 3.53
1679 1697 2.010145 ACATGCACTCATCGTACCAC 57.990 50.000 0.00 0.00 0.00 4.16
1750 1769 3.554524 CTGCAATAACGTTCACACAAGG 58.445 45.455 2.82 0.00 0.00 3.61
1761 1780 1.869767 GCTGATCCTCCTGCAATAACG 59.130 52.381 0.00 0.00 0.00 3.18
1764 1783 1.141657 GTGGCTGATCCTCCTGCAATA 59.858 52.381 0.00 0.00 35.26 1.90
1869 1925 6.500910 TCTGAAGAATTATGCATGCATGAAC 58.499 36.000 37.43 26.61 37.82 3.18
1898 1954 0.453793 CACAACTCACCAAAACGCCA 59.546 50.000 0.00 0.00 0.00 5.69
1912 1968 4.771590 TCAAGGAATCATCAAGCACAAC 57.228 40.909 0.00 0.00 0.00 3.32
2072 2128 0.385473 CCAACCAATTCACACGTCGC 60.385 55.000 0.00 0.00 0.00 5.19
2122 2178 1.571460 CTCCTCGCAAACTGCACAC 59.429 57.895 0.00 0.00 45.36 3.82
2234 2290 1.405933 GCAAGAACCCCAATCATTGCC 60.406 52.381 0.00 0.00 37.62 4.52
2262 2318 0.846427 AGAGGCCCCATCACAAAGGA 60.846 55.000 0.00 0.00 0.00 3.36
2554 2632 2.675844 TCAGGCCATTGTATTTCGAACG 59.324 45.455 5.01 0.00 0.00 3.95
2609 2687 7.488150 GCATATTCTACTTAAAACAGCAAACCC 59.512 37.037 0.00 0.00 0.00 4.11
2610 2688 8.026607 TGCATATTCTACTTAAAACAGCAAACC 58.973 33.333 0.00 0.00 0.00 3.27
2634 2712 6.202570 TGCTTAGATTTTTGTTTTCCACATGC 59.797 34.615 0.00 0.00 34.43 4.06
2760 2852 9.660180 AGAGGAGAAGTCAGAAATAAATGTAAC 57.340 33.333 0.00 0.00 0.00 2.50
2847 2948 2.159014 TGGGCATAACACGTGATACCTC 60.159 50.000 25.01 10.16 0.00 3.85
2855 2956 2.941210 CCACTTGGGCATAACACGT 58.059 52.632 0.00 0.00 0.00 4.49
2941 3042 2.191128 AAACTGAAGCAGCTACTGGG 57.809 50.000 0.00 0.00 34.37 4.45
2981 3089 9.817809 CAGACTAGGACTGTTAAGCAATTATAA 57.182 33.333 9.93 0.00 0.00 0.98
2982 3090 9.197306 TCAGACTAGGACTGTTAAGCAATTATA 57.803 33.333 15.36 0.00 36.81 0.98
2983 3091 8.079211 TCAGACTAGGACTGTTAAGCAATTAT 57.921 34.615 15.36 0.00 36.81 1.28
2984 3092 7.476540 TCAGACTAGGACTGTTAAGCAATTA 57.523 36.000 15.36 0.00 36.81 1.40
3017 3125 2.987413 TAGTTTGCAAAGCCATGTCG 57.013 45.000 13.26 0.00 0.00 4.35
3023 3131 5.127031 TCCATTCCTATTAGTTTGCAAAGCC 59.873 40.000 13.26 1.40 0.00 4.35
3058 3166 3.855255 TCAAGTGTTGTCAATCCTCCA 57.145 42.857 0.00 0.00 0.00 3.86
3124 3232 5.506815 CGGGAAAAGATGATGAATGACATGG 60.507 44.000 0.00 0.00 39.56 3.66
3202 3310 2.417719 TCGAGAAAAAGGCAAGAGCTC 58.582 47.619 5.27 5.27 41.70 4.09
3220 3328 4.266029 GCCACATATTTTGAAGCATGTTCG 59.734 41.667 0.00 0.00 29.31 3.95
3229 3337 7.012704 GCTCTAGAGAATGCCACATATTTTGAA 59.987 37.037 24.24 0.00 0.00 2.69
3316 3432 4.320275 GGTTCTTTGTAGTACTTGCCAAGC 60.320 45.833 3.88 0.00 0.00 4.01
3464 3580 1.622312 TCAATCAGAGCTCTGTGCACT 59.378 47.619 36.32 18.29 45.94 4.40
3599 3717 9.388346 GTACATTCGTGTTTCATGATGTAAAAA 57.612 29.630 0.00 0.00 31.86 1.94
3600 3718 7.742525 CGTACATTCGTGTTTCATGATGTAAAA 59.257 33.333 0.00 0.00 31.86 1.52
3601 3719 7.095565 ACGTACATTCGTGTTTCATGATGTAAA 60.096 33.333 0.00 0.00 42.56 2.01
3602 3720 6.366604 ACGTACATTCGTGTTTCATGATGTAA 59.633 34.615 0.00 0.00 42.56 2.41
3645 3763 6.338214 TGCAATTGCTCTTTTACAATGGTA 57.662 33.333 29.37 1.93 42.66 3.25
3805 3924 7.279090 GGCTAAGTTTCTTGCCTTTTTACAAAA 59.721 33.333 12.23 0.00 41.92 2.44
3825 3944 3.955471 TCAGTCATTGGAAAGGGCTAAG 58.045 45.455 0.00 0.00 42.69 2.18
3883 4002 6.998968 TTACTGTTCTGTACTAGTAGCTCC 57.001 41.667 1.87 0.00 0.00 4.70
3958 4232 4.019174 ACAATGACAATAGGCTTCCCAAG 58.981 43.478 0.00 0.00 0.00 3.61
3973 4247 8.025445 AGAGCATAAGAAAACAATGACAATGAC 58.975 33.333 0.00 0.00 0.00 3.06
4028 4302 1.002544 AGCAGGAGAGCCACAAACTAC 59.997 52.381 0.00 0.00 36.29 2.73
4053 4327 1.623811 TGGGACAGAAGGAGTAGCAAC 59.376 52.381 0.00 0.00 0.00 4.17
4108 4382 5.491982 CTCCTATTTTGGAGCACTGTTACT 58.508 41.667 0.00 0.00 45.84 2.24
4146 4420 5.076873 AGAAATCCCGTCTTTCCATTGAAA 58.923 37.500 0.00 0.00 38.14 2.69
4152 4426 1.280998 GGGAGAAATCCCGTCTTTCCA 59.719 52.381 0.00 0.00 40.59 3.53
4153 4427 2.039818 GGGAGAAATCCCGTCTTTCC 57.960 55.000 0.00 0.00 40.59 3.13
4171 4445 2.235650 AGTCAGGTCAGACATCACATGG 59.764 50.000 2.17 0.00 40.98 3.66
4240 4524 0.659427 CCATGCGTGCAGAATGTAGG 59.341 55.000 0.00 0.00 39.61 3.18
4245 4529 2.346766 TATTCCCATGCGTGCAGAAT 57.653 45.000 19.96 19.96 33.79 2.40
4257 4541 6.327104 ACGGTGGTACAATAAGTATATTCCCA 59.673 38.462 0.00 0.00 44.16 4.37
4272 4556 1.277842 TCGGTCTACTACGGTGGTACA 59.722 52.381 0.00 0.00 0.00 2.90
4273 4557 1.936547 CTCGGTCTACTACGGTGGTAC 59.063 57.143 0.00 0.00 0.00 3.34
4290 4574 5.050295 ACGCCTTTCTTTCTTTCTTTACTCG 60.050 40.000 0.00 0.00 0.00 4.18
4424 4720 1.740025 GCCGTGAATTCTTCCTTCCTG 59.260 52.381 7.05 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.