Multiple sequence alignment - TraesCS6B01G025800

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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 TraesCS6B01G025800 chr6B 100.000 2619 0 0 1 2619 15745075 15742457 0.000000e+00 4837
1 TraesCS6B01G025800 chr6B 80.000 1200 222 11 968 2162 52568273 52567087 0.000000e+00 870
2 TraesCS6B01G025800 chr6B 79.545 1188 229 10 979 2162 16428985 16430162 0.000000e+00 835
3 TraesCS6B01G025800 chr6B 78.925 1172 231 12 997 2163 15751004 15749844 0.000000e+00 782
4 TraesCS6B01G025800 chr6B 78.383 1175 235 12 981 2148 52981067 52979905 0.000000e+00 745
5 TraesCS6B01G025800 chr6B 77.138 1181 247 16 977 2148 16433123 16434289 0.000000e+00 664
6 TraesCS6B01G025800 chr6B 76.663 887 196 10 1282 2163 14318227 14319107 6.130000e-132 481
7 TraesCS6B01G025800 chr6B 100.000 199 0 0 2963 3161 15742113 15741915 4.980000e-98 368
8 TraesCS6B01G025800 chr6D 92.698 2424 126 17 214 2619 8657052 8654662 0.000000e+00 3448
9 TraesCS6B01G025800 chr6D 79.779 1266 237 13 890 2148 8552907 8551654 0.000000e+00 902
10 TraesCS6B01G025800 chr6D 76.586 1529 305 40 977 2484 8894035 8895531 0.000000e+00 791
11 TraesCS6B01G025800 chr6D 97.970 197 3 1 2963 3159 8654274 8654079 1.090000e-89 340
12 TraesCS6B01G025800 chr6D 76.801 569 126 5 1574 2139 8915626 8916191 6.580000e-82 315
13 TraesCS6B01G025800 chr6A 92.272 1488 70 20 857 2343 9338837 9340280 0.000000e+00 2069
14 TraesCS6B01G025800 chr6A 75.499 1053 236 21 1122 2163 15694728 15695769 2.190000e-136 496
15 TraesCS6B01G025800 chr6A 75.552 589 139 5 1562 2148 9474636 9475221 5.160000e-73 285
16 TraesCS6B01G025800 chr6A 92.857 70 5 0 3001 3070 9480077 9480146 5.580000e-18 102
17 TraesCS6B01G025800 chr3D 79.146 1194 224 21 966 2148 33330527 33329348 0.000000e+00 802
18 TraesCS6B01G025800 chr1B 76.559 1203 263 15 977 2169 48062370 48061177 2.660000e-180 641
19 TraesCS6B01G025800 chr5B 91.837 196 14 2 2964 3159 37063577 37063770 4.020000e-69 272
20 TraesCS6B01G025800 chr5B 92.727 110 7 1 3050 3159 15814355 15814247 1.170000e-34 158
21 TraesCS6B01G025800 chr2B 91.892 111 7 2 3050 3159 529499653 529499762 1.520000e-33 154


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 TraesCS6B01G025800 chr6B 15741915 15745075 3160 True 2602.5 4837 100.0000 1 3161 2 chr6B.!!$R4 3160
1 TraesCS6B01G025800 chr6B 52567087 52568273 1186 True 870.0 870 80.0000 968 2162 1 chr6B.!!$R2 1194
2 TraesCS6B01G025800 chr6B 15749844 15751004 1160 True 782.0 782 78.9250 997 2163 1 chr6B.!!$R1 1166
3 TraesCS6B01G025800 chr6B 16428985 16434289 5304 False 749.5 835 78.3415 977 2162 2 chr6B.!!$F2 1185
4 TraesCS6B01G025800 chr6B 52979905 52981067 1162 True 745.0 745 78.3830 981 2148 1 chr6B.!!$R3 1167
5 TraesCS6B01G025800 chr6B 14318227 14319107 880 False 481.0 481 76.6630 1282 2163 1 chr6B.!!$F1 881
6 TraesCS6B01G025800 chr6D 8654079 8657052 2973 True 1894.0 3448 95.3340 214 3159 2 chr6D.!!$R2 2945
7 TraesCS6B01G025800 chr6D 8551654 8552907 1253 True 902.0 902 79.7790 890 2148 1 chr6D.!!$R1 1258
8 TraesCS6B01G025800 chr6D 8894035 8895531 1496 False 791.0 791 76.5860 977 2484 1 chr6D.!!$F1 1507
9 TraesCS6B01G025800 chr6D 8915626 8916191 565 False 315.0 315 76.8010 1574 2139 1 chr6D.!!$F2 565
10 TraesCS6B01G025800 chr6A 9338837 9340280 1443 False 2069.0 2069 92.2720 857 2343 1 chr6A.!!$F1 1486
11 TraesCS6B01G025800 chr6A 15694728 15695769 1041 False 496.0 496 75.4990 1122 2163 1 chr6A.!!$F4 1041
12 TraesCS6B01G025800 chr6A 9474636 9475221 585 False 285.0 285 75.5520 1562 2148 1 chr6A.!!$F2 586
13 TraesCS6B01G025800 chr3D 33329348 33330527 1179 True 802.0 802 79.1460 966 2148 1 chr3D.!!$R1 1182
14 TraesCS6B01G025800 chr1B 48061177 48062370 1193 True 641.0 641 76.5590 977 2169 1 chr1B.!!$R1 1192

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
55 56 0.027194 CGCCGAGCAACATGATGAAG 59.973 55.0 7.22 0.0 0.00 3.02 F
114 115 0.178873 AAGTCTCCTACCCCAAGCCA 60.179 55.0 0.00 0.0 0.00 4.75 F
115 116 0.178873 AGTCTCCTACCCCAAGCCAA 60.179 55.0 0.00 0.0 0.00 4.52 F
1466 1499 0.382515 CAGTACTACCTGCCTCTCGC 59.617 60.0 0.00 0.0 38.31 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1724 0.394352 GTGCCTGAACATCCCGGATT 60.394 55.000 0.73 0.00 0.00 3.01 R
1738 1771 0.817634 TTGGCGGTGACCTTCTGTTG 60.818 55.000 0.00 0.00 0.00 3.33 R
2060 2093 1.557832 TGTAAGGGCACATGTACCTCC 59.442 52.381 18.55 13.55 32.29 4.30 R
2292 2342 3.764885 AACAAACAAGCAGTGACAGTC 57.235 42.857 0.00 0.00 0.00 3.51 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 3.212450 GGTTGACGAAGGAGGTCAC 57.788 57.895 0.00 0.00 43.59 3.67
19 20 0.666577 GGTTGACGAAGGAGGTCACG 60.667 60.000 0.00 0.00 43.59 4.35
20 21 0.031721 GTTGACGAAGGAGGTCACGT 59.968 55.000 0.00 0.00 43.59 4.49
21 22 4.863984 GACGAAGGAGGTCACGTC 57.136 61.111 0.00 0.00 45.51 4.34
22 23 1.154263 GACGAAGGAGGTCACGTCG 60.154 63.158 0.00 0.00 43.60 5.12
23 24 2.178521 CGAAGGAGGTCACGTCGG 59.821 66.667 0.00 0.00 36.45 4.79
24 25 2.330372 CGAAGGAGGTCACGTCGGA 61.330 63.158 0.00 0.00 36.45 4.55
25 26 1.507174 GAAGGAGGTCACGTCGGAG 59.493 63.158 0.00 0.00 0.00 4.63
26 27 1.935327 GAAGGAGGTCACGTCGGAGG 61.935 65.000 0.00 0.00 0.00 4.30
27 28 2.360852 GGAGGTCACGTCGGAGGA 60.361 66.667 4.48 0.00 0.00 3.71
28 29 2.408241 GGAGGTCACGTCGGAGGAG 61.408 68.421 4.48 0.00 0.00 3.69
29 30 2.361357 AGGTCACGTCGGAGGAGG 60.361 66.667 4.48 0.00 0.00 4.30
30 31 2.360852 GGTCACGTCGGAGGAGGA 60.361 66.667 4.48 0.00 0.00 3.71
31 32 2.408241 GGTCACGTCGGAGGAGGAG 61.408 68.421 4.48 0.00 0.00 3.69
32 33 2.750637 TCACGTCGGAGGAGGAGC 60.751 66.667 4.48 0.00 0.00 4.70
33 34 3.827898 CACGTCGGAGGAGGAGCC 61.828 72.222 4.48 0.00 0.00 4.70
49 50 3.853330 CCGACGCCGAGCAACATG 61.853 66.667 0.00 0.00 38.22 3.21
50 51 2.809174 CGACGCCGAGCAACATGA 60.809 61.111 0.00 0.00 38.22 3.07
51 52 2.167219 CGACGCCGAGCAACATGAT 61.167 57.895 0.00 0.00 38.22 2.45
52 53 1.349627 GACGCCGAGCAACATGATG 59.650 57.895 0.00 0.00 0.00 3.07
53 54 1.079197 ACGCCGAGCAACATGATGA 60.079 52.632 7.22 0.00 0.00 2.92
54 55 0.673333 ACGCCGAGCAACATGATGAA 60.673 50.000 7.22 0.00 0.00 2.57
55 56 0.027194 CGCCGAGCAACATGATGAAG 59.973 55.000 7.22 0.00 0.00 3.02
56 57 1.372582 GCCGAGCAACATGATGAAGA 58.627 50.000 7.22 0.00 0.00 2.87
57 58 1.329906 GCCGAGCAACATGATGAAGAG 59.670 52.381 7.22 0.00 0.00 2.85
58 59 1.938577 CCGAGCAACATGATGAAGAGG 59.061 52.381 7.22 0.48 0.00 3.69
59 60 2.625737 CGAGCAACATGATGAAGAGGT 58.374 47.619 7.22 0.00 0.00 3.85
60 61 2.350804 CGAGCAACATGATGAAGAGGTG 59.649 50.000 7.22 0.00 0.00 4.00
61 62 3.341823 GAGCAACATGATGAAGAGGTGT 58.658 45.455 7.22 0.00 0.00 4.16
62 63 3.079578 AGCAACATGATGAAGAGGTGTG 58.920 45.455 7.22 0.00 0.00 3.82
63 64 3.076621 GCAACATGATGAAGAGGTGTGA 58.923 45.455 7.22 0.00 0.00 3.58
64 65 3.126514 GCAACATGATGAAGAGGTGTGAG 59.873 47.826 7.22 0.00 0.00 3.51
65 66 3.623906 ACATGATGAAGAGGTGTGAGG 57.376 47.619 0.00 0.00 0.00 3.86
66 67 2.909006 ACATGATGAAGAGGTGTGAGGT 59.091 45.455 0.00 0.00 0.00 3.85
67 68 3.268330 CATGATGAAGAGGTGTGAGGTG 58.732 50.000 0.00 0.00 0.00 4.00
68 69 2.608623 TGATGAAGAGGTGTGAGGTGA 58.391 47.619 0.00 0.00 0.00 4.02
69 70 3.176411 TGATGAAGAGGTGTGAGGTGAT 58.824 45.455 0.00 0.00 0.00 3.06
70 71 3.055602 TGATGAAGAGGTGTGAGGTGATG 60.056 47.826 0.00 0.00 0.00 3.07
71 72 1.625315 TGAAGAGGTGTGAGGTGATGG 59.375 52.381 0.00 0.00 0.00 3.51
72 73 1.902508 GAAGAGGTGTGAGGTGATGGA 59.097 52.381 0.00 0.00 0.00 3.41
73 74 2.260639 AGAGGTGTGAGGTGATGGAT 57.739 50.000 0.00 0.00 0.00 3.41
74 75 2.555664 AGAGGTGTGAGGTGATGGATT 58.444 47.619 0.00 0.00 0.00 3.01
75 76 2.915604 AGAGGTGTGAGGTGATGGATTT 59.084 45.455 0.00 0.00 0.00 2.17
76 77 4.104086 AGAGGTGTGAGGTGATGGATTTA 58.896 43.478 0.00 0.00 0.00 1.40
77 78 4.536090 AGAGGTGTGAGGTGATGGATTTAA 59.464 41.667 0.00 0.00 0.00 1.52
78 79 4.589908 AGGTGTGAGGTGATGGATTTAAC 58.410 43.478 0.00 0.00 0.00 2.01
79 80 3.694566 GGTGTGAGGTGATGGATTTAACC 59.305 47.826 0.00 0.00 0.00 2.85
80 81 4.331968 GTGTGAGGTGATGGATTTAACCA 58.668 43.478 0.00 0.00 44.41 3.67
89 90 4.771114 ATGGATTTAACCATCCGAGTGA 57.229 40.909 0.00 0.00 46.24 3.41
90 91 3.869065 TGGATTTAACCATCCGAGTGAC 58.131 45.455 2.46 0.00 45.39 3.67
91 92 2.864343 GGATTTAACCATCCGAGTGACG 59.136 50.000 0.00 0.00 42.18 4.35
92 93 1.717194 TTTAACCATCCGAGTGACGC 58.283 50.000 0.00 0.00 41.07 5.19
93 94 0.457166 TTAACCATCCGAGTGACGCG 60.457 55.000 3.53 3.53 41.07 6.01
94 95 1.307355 TAACCATCCGAGTGACGCGA 61.307 55.000 15.93 0.00 41.07 5.87
95 96 2.149803 AACCATCCGAGTGACGCGAA 62.150 55.000 15.93 0.00 41.07 4.70
96 97 1.445410 CCATCCGAGTGACGCGAAA 60.445 57.895 15.93 0.00 41.07 3.46
97 98 1.413767 CCATCCGAGTGACGCGAAAG 61.414 60.000 15.93 0.00 41.07 2.62
98 99 0.732880 CATCCGAGTGACGCGAAAGT 60.733 55.000 15.93 2.29 41.07 2.66
99 100 0.456312 ATCCGAGTGACGCGAAAGTC 60.456 55.000 15.93 11.78 41.07 3.01
100 101 1.081376 CCGAGTGACGCGAAAGTCT 60.081 57.895 15.93 3.23 41.47 3.24
101 102 1.066114 CCGAGTGACGCGAAAGTCTC 61.066 60.000 15.93 11.73 41.47 3.36
102 103 1.066114 CGAGTGACGCGAAAGTCTCC 61.066 60.000 15.93 0.00 41.47 3.71
103 104 0.241481 GAGTGACGCGAAAGTCTCCT 59.759 55.000 15.93 0.00 41.47 3.69
104 105 1.467734 GAGTGACGCGAAAGTCTCCTA 59.532 52.381 15.93 0.00 41.47 2.94
105 106 1.199558 AGTGACGCGAAAGTCTCCTAC 59.800 52.381 15.93 0.00 41.47 3.18
106 107 0.524862 TGACGCGAAAGTCTCCTACC 59.475 55.000 15.93 0.00 41.47 3.18
107 108 0.179142 GACGCGAAAGTCTCCTACCC 60.179 60.000 15.93 0.00 38.09 3.69
108 109 1.141234 CGCGAAAGTCTCCTACCCC 59.859 63.158 0.00 0.00 0.00 4.95
109 110 1.601419 CGCGAAAGTCTCCTACCCCA 61.601 60.000 0.00 0.00 0.00 4.96
110 111 0.611714 GCGAAAGTCTCCTACCCCAA 59.388 55.000 0.00 0.00 0.00 4.12
111 112 1.405661 GCGAAAGTCTCCTACCCCAAG 60.406 57.143 0.00 0.00 0.00 3.61
112 113 1.405661 CGAAAGTCTCCTACCCCAAGC 60.406 57.143 0.00 0.00 0.00 4.01
113 114 0.992695 AAAGTCTCCTACCCCAAGCC 59.007 55.000 0.00 0.00 0.00 4.35
114 115 0.178873 AAGTCTCCTACCCCAAGCCA 60.179 55.000 0.00 0.00 0.00 4.75
115 116 0.178873 AGTCTCCTACCCCAAGCCAA 60.179 55.000 0.00 0.00 0.00 4.52
116 117 0.696501 GTCTCCTACCCCAAGCCAAA 59.303 55.000 0.00 0.00 0.00 3.28
117 118 1.285078 GTCTCCTACCCCAAGCCAAAT 59.715 52.381 0.00 0.00 0.00 2.32
118 119 1.564348 TCTCCTACCCCAAGCCAAATC 59.436 52.381 0.00 0.00 0.00 2.17
119 120 1.566231 CTCCTACCCCAAGCCAAATCT 59.434 52.381 0.00 0.00 0.00 2.40
120 121 1.564348 TCCTACCCCAAGCCAAATCTC 59.436 52.381 0.00 0.00 0.00 2.75
121 122 1.410224 CCTACCCCAAGCCAAATCTCC 60.410 57.143 0.00 0.00 0.00 3.71
122 123 1.284785 CTACCCCAAGCCAAATCTCCA 59.715 52.381 0.00 0.00 0.00 3.86
123 124 0.712380 ACCCCAAGCCAAATCTCCAT 59.288 50.000 0.00 0.00 0.00 3.41
124 125 1.117150 CCCCAAGCCAAATCTCCATG 58.883 55.000 0.00 0.00 0.00 3.66
125 126 1.342275 CCCCAAGCCAAATCTCCATGA 60.342 52.381 0.00 0.00 0.00 3.07
126 127 2.029623 CCCAAGCCAAATCTCCATGAG 58.970 52.381 0.00 0.00 0.00 2.90
127 128 1.407979 CCAAGCCAAATCTCCATGAGC 59.592 52.381 0.00 0.00 0.00 4.26
128 129 2.097036 CAAGCCAAATCTCCATGAGCA 58.903 47.619 0.00 0.00 0.00 4.26
129 130 1.760192 AGCCAAATCTCCATGAGCAC 58.240 50.000 0.00 0.00 0.00 4.40
130 131 0.743097 GCCAAATCTCCATGAGCACC 59.257 55.000 0.00 0.00 0.00 5.01
131 132 1.956636 GCCAAATCTCCATGAGCACCA 60.957 52.381 0.00 0.00 0.00 4.17
132 133 2.662866 CCAAATCTCCATGAGCACCAT 58.337 47.619 0.00 0.00 35.44 3.55
133 134 3.028850 CCAAATCTCCATGAGCACCATT 58.971 45.455 0.00 0.00 31.94 3.16
134 135 3.181479 CCAAATCTCCATGAGCACCATTG 60.181 47.826 0.00 0.00 31.94 2.82
135 136 3.657398 AATCTCCATGAGCACCATTGA 57.343 42.857 0.00 0.00 31.94 2.57
136 137 2.408271 TCTCCATGAGCACCATTGAC 57.592 50.000 0.00 0.00 31.94 3.18
137 138 1.012086 CTCCATGAGCACCATTGACG 58.988 55.000 0.00 0.00 31.94 4.35
138 139 1.026182 TCCATGAGCACCATTGACGC 61.026 55.000 0.00 0.00 31.94 5.19
139 140 1.307355 CCATGAGCACCATTGACGCA 61.307 55.000 0.00 0.00 31.94 5.24
140 141 0.736636 CATGAGCACCATTGACGCAT 59.263 50.000 0.00 0.00 31.94 4.73
141 142 0.736636 ATGAGCACCATTGACGCATG 59.263 50.000 0.00 0.00 29.34 4.06
142 143 1.226491 GAGCACCATTGACGCATGC 60.226 57.895 7.91 7.91 36.52 4.06
143 144 2.577644 GCACCATTGACGCATGCG 60.578 61.111 36.79 36.79 46.03 4.73
144 145 2.100797 CACCATTGACGCATGCGG 59.899 61.111 39.95 24.80 44.69 5.69
160 161 3.443045 GGCGTAACTCCGACGGGA 61.443 66.667 15.25 0.00 40.66 5.14
168 169 2.681591 TCCGACGGGAGGAGTCAT 59.318 61.111 15.25 0.00 37.43 3.06
169 170 1.000019 TCCGACGGGAGGAGTCATT 60.000 57.895 15.25 0.00 37.43 2.57
170 171 1.141881 CCGACGGGAGGAGTCATTG 59.858 63.158 5.81 0.00 38.46 2.82
171 172 1.141881 CGACGGGAGGAGTCATTGG 59.858 63.158 0.00 0.00 38.46 3.16
172 173 1.522569 GACGGGAGGAGTCATTGGG 59.477 63.158 0.00 0.00 38.42 4.12
173 174 1.972660 GACGGGAGGAGTCATTGGGG 61.973 65.000 0.00 0.00 38.42 4.96
174 175 2.746375 CGGGAGGAGTCATTGGGGG 61.746 68.421 0.00 0.00 0.00 5.40
175 176 1.619669 GGGAGGAGTCATTGGGGGT 60.620 63.158 0.00 0.00 0.00 4.95
176 177 1.609783 GGAGGAGTCATTGGGGGTG 59.390 63.158 0.00 0.00 0.00 4.61
177 178 1.077429 GAGGAGTCATTGGGGGTGC 60.077 63.158 0.00 0.00 0.00 5.01
178 179 1.852157 AGGAGTCATTGGGGGTGCA 60.852 57.895 0.00 0.00 0.00 4.57
179 180 1.379044 GGAGTCATTGGGGGTGCAG 60.379 63.158 0.00 0.00 0.00 4.41
180 181 1.685224 GAGTCATTGGGGGTGCAGA 59.315 57.895 0.00 0.00 0.00 4.26
181 182 0.393537 GAGTCATTGGGGGTGCAGAG 60.394 60.000 0.00 0.00 0.00 3.35
182 183 1.379044 GTCATTGGGGGTGCAGAGG 60.379 63.158 0.00 0.00 0.00 3.69
183 184 1.852157 TCATTGGGGGTGCAGAGGT 60.852 57.895 0.00 0.00 0.00 3.85
184 185 1.679977 CATTGGGGGTGCAGAGGTG 60.680 63.158 0.00 0.00 0.00 4.00
185 186 2.162906 ATTGGGGGTGCAGAGGTGT 61.163 57.895 0.00 0.00 0.00 4.16
186 187 2.142292 ATTGGGGGTGCAGAGGTGTC 62.142 60.000 0.00 0.00 0.00 3.67
187 188 4.035102 GGGGGTGCAGAGGTGTCC 62.035 72.222 0.00 0.00 0.00 4.02
188 189 4.394712 GGGGTGCAGAGGTGTCCG 62.395 72.222 0.00 0.00 0.00 4.79
189 190 3.311110 GGGTGCAGAGGTGTCCGA 61.311 66.667 0.00 0.00 0.00 4.55
190 191 2.048127 GGTGCAGAGGTGTCCGAC 60.048 66.667 0.00 0.00 0.00 4.79
191 192 2.430921 GTGCAGAGGTGTCCGACG 60.431 66.667 0.00 0.00 0.00 5.12
192 193 3.680786 TGCAGAGGTGTCCGACGG 61.681 66.667 7.84 7.84 0.00 4.79
193 194 3.681835 GCAGAGGTGTCCGACGGT 61.682 66.667 14.79 0.00 0.00 4.83
194 195 3.048602 CAGAGGTGTCCGACGGTT 58.951 61.111 14.79 0.00 0.00 4.44
195 196 1.080705 CAGAGGTGTCCGACGGTTC 60.081 63.158 14.79 9.17 0.00 3.62
196 197 2.260743 GAGGTGTCCGACGGTTCC 59.739 66.667 14.79 14.12 0.00 3.62
197 198 2.522436 AGGTGTCCGACGGTTCCA 60.522 61.111 14.79 6.67 0.00 3.53
198 199 1.885163 GAGGTGTCCGACGGTTCCAT 61.885 60.000 14.79 0.00 0.00 3.41
199 200 1.004200 GGTGTCCGACGGTTCCATT 60.004 57.895 14.79 0.00 0.00 3.16
200 201 1.017701 GGTGTCCGACGGTTCCATTC 61.018 60.000 14.79 3.35 0.00 2.67
201 202 1.017701 GTGTCCGACGGTTCCATTCC 61.018 60.000 14.79 0.00 0.00 3.01
202 203 1.449070 GTCCGACGGTTCCATTCCC 60.449 63.158 14.79 0.00 0.00 3.97
207 208 3.723922 CGGTTCCATTCCCGGGGT 61.724 66.667 23.50 7.14 40.54 4.95
208 209 2.044352 GGTTCCATTCCCGGGGTG 60.044 66.667 23.50 19.61 0.00 4.61
209 210 2.044352 GTTCCATTCCCGGGGTGG 60.044 66.667 29.70 29.70 37.55 4.61
210 211 4.055227 TTCCATTCCCGGGGTGGC 62.055 66.667 30.36 0.00 35.87 5.01
250 251 1.362406 GAAAGCGGAAGGAGAAGGCG 61.362 60.000 0.00 0.00 0.00 5.52
267 268 0.804989 GCGTTGTGAATGGGGAAGAG 59.195 55.000 0.00 0.00 0.00 2.85
269 270 2.504367 CGTTGTGAATGGGGAAGAGTT 58.496 47.619 0.00 0.00 0.00 3.01
271 272 3.058224 CGTTGTGAATGGGGAAGAGTTTC 60.058 47.826 0.00 0.00 0.00 2.78
272 273 3.874383 TGTGAATGGGGAAGAGTTTCA 57.126 42.857 0.00 0.00 34.90 2.69
287 288 2.866762 AGTTTCACTGAGAACTTGTCGC 59.133 45.455 0.00 0.00 35.56 5.19
290 291 0.597637 CACTGAGAACTTGTCGCGGT 60.598 55.000 6.13 0.00 45.59 5.68
326 327 9.788960 GTGAGAGAGTTGTTAAGTTTTTGAAAT 57.211 29.630 0.00 0.00 0.00 2.17
362 363 8.349983 CAAAATTTCGAGGAATTAACCGGATAT 58.650 33.333 9.46 0.00 34.73 1.63
369 370 6.585322 CGAGGAATTAACCGGATATGAGTTAC 59.415 42.308 9.46 0.00 34.73 2.50
410 411 9.657728 TTTTAAGGAGTTAACCCTTTTAATGGA 57.342 29.630 24.45 9.54 40.94 3.41
436 437 3.873952 GCTAGAGATGCCTTAACTTGTGG 59.126 47.826 0.00 0.00 0.00 4.17
440 441 4.079253 GAGATGCCTTAACTTGTGGGAAA 58.921 43.478 0.00 0.00 0.00 3.13
469 470 1.390123 CTGATACACAACGTTGCTCCG 59.610 52.381 27.61 15.74 0.00 4.63
492 493 4.675510 ACATTGCTTCACTCAACAAACTG 58.324 39.130 0.00 0.00 0.00 3.16
504 505 6.432783 CACTCAACAAACTGGTTTATATCCCA 59.567 38.462 0.00 0.00 0.00 4.37
527 528 3.241322 GCGCTCACATTTGTATTTGCATC 59.759 43.478 0.00 0.00 0.00 3.91
528 529 4.413969 CGCTCACATTTGTATTTGCATCA 58.586 39.130 0.00 0.00 0.00 3.07
529 530 4.858140 CGCTCACATTTGTATTTGCATCAA 59.142 37.500 0.00 0.00 0.00 2.57
530 531 5.004061 CGCTCACATTTGTATTTGCATCAAG 59.996 40.000 0.00 0.00 0.00 3.02
531 532 5.865552 GCTCACATTTGTATTTGCATCAAGT 59.134 36.000 0.00 0.00 0.00 3.16
532 533 7.028962 GCTCACATTTGTATTTGCATCAAGTA 58.971 34.615 0.00 0.00 0.00 2.24
533 534 7.008628 GCTCACATTTGTATTTGCATCAAGTAC 59.991 37.037 0.00 5.59 37.17 2.73
534 535 8.109705 TCACATTTGTATTTGCATCAAGTACT 57.890 30.769 11.59 0.00 37.42 2.73
535 536 8.022550 TCACATTTGTATTTGCATCAAGTACTG 58.977 33.333 0.00 6.26 37.42 2.74
536 537 7.809331 CACATTTGTATTTGCATCAAGTACTGT 59.191 33.333 0.00 6.72 37.42 3.55
585 586 1.144936 GGCCACTCAATCTCCCTCG 59.855 63.158 0.00 0.00 0.00 4.63
586 587 1.144936 GCCACTCAATCTCCCTCGG 59.855 63.158 0.00 0.00 0.00 4.63
587 588 1.826024 CCACTCAATCTCCCTCGGG 59.174 63.158 0.00 0.00 0.00 5.14
639 640 7.722795 TTATGTTCTTGAAATCACAACGAGA 57.277 32.000 0.00 0.00 0.00 4.04
650 651 9.663904 TGAAATCACAACGAGAAAGAAAAATAG 57.336 29.630 0.00 0.00 0.00 1.73
679 682 5.966742 ACACTTCTATTTTTGGGAGAAGC 57.033 39.130 10.09 0.00 39.45 3.86
802 806 5.279306 GGACCTTATTTTTCTTGGGTGGTTC 60.279 44.000 0.00 0.00 0.00 3.62
804 808 5.903010 ACCTTATTTTTCTTGGGTGGTTCTT 59.097 36.000 0.00 0.00 0.00 2.52
805 809 6.041637 ACCTTATTTTTCTTGGGTGGTTCTTC 59.958 38.462 0.00 0.00 0.00 2.87
820 824 5.010617 GTGGTTCTTCTTTTAGGGCATTTGA 59.989 40.000 0.00 0.00 0.00 2.69
839 843 9.357652 GCATTTGAGCTGATCTAAATTGTTTTA 57.642 29.630 0.00 0.00 0.00 1.52
877 881 3.244387 GGAGCTGATCTAAATGGGTCTCC 60.244 52.174 0.00 0.00 0.00 3.71
895 912 0.911769 CCATAGTCCAACTCAGCCCA 59.088 55.000 0.00 0.00 0.00 5.36
896 913 1.134280 CCATAGTCCAACTCAGCCCAG 60.134 57.143 0.00 0.00 0.00 4.45
897 914 0.543749 ATAGTCCAACTCAGCCCAGC 59.456 55.000 0.00 0.00 0.00 4.85
898 915 1.553690 TAGTCCAACTCAGCCCAGCC 61.554 60.000 0.00 0.00 0.00 4.85
899 916 3.650950 TCCAACTCAGCCCAGCCC 61.651 66.667 0.00 0.00 0.00 5.19
951 971 1.966451 CGCAAACCCTCACCACTCC 60.966 63.158 0.00 0.00 0.00 3.85
953 973 2.069165 GCAAACCCTCACCACTCCCT 62.069 60.000 0.00 0.00 0.00 4.20
1466 1499 0.382515 CAGTACTACCTGCCTCTCGC 59.617 60.000 0.00 0.00 38.31 5.03
1638 1671 1.078567 CCTGCTCACCTCCAGCTTC 60.079 63.158 0.00 0.00 37.79 3.86
1642 1675 1.599606 GCTCACCTCCAGCTTCGAGA 61.600 60.000 8.84 0.00 33.75 4.04
1685 1718 4.937781 CGAAGGCCTCGGTATACG 57.062 61.111 5.23 0.00 44.20 3.06
1738 1771 4.160635 CCGTCGCATTTGTCGGCC 62.161 66.667 0.00 0.00 36.68 6.13
1765 1798 1.283613 AGGTCACCGCCAAATTGGATA 59.716 47.619 17.47 0.00 40.96 2.59
1797 1830 1.875963 GTTTGGGTGGTCAGATGCG 59.124 57.895 0.00 0.00 0.00 4.73
1888 1921 2.239907 TCAGAGTTCCTGATCTCCGAGA 59.760 50.000 0.00 0.00 46.38 4.04
2060 2093 4.560035 GGTGAATGAGAATGTTTTCATGCG 59.440 41.667 0.22 0.00 40.66 4.73
2292 2342 7.304735 GCTGTCTGATATAGTATGTCTGTCAG 58.695 42.308 23.02 23.02 37.94 3.51
2294 2344 8.384607 TGTCTGATATAGTATGTCTGTCAGAC 57.615 38.462 23.67 23.67 46.56 3.51
2296 2346 8.503196 GTCTGATATAGTATGTCTGTCAGACTG 58.497 40.741 28.67 1.11 46.31 3.51
2298 2348 8.384607 TGATATAGTATGTCTGTCAGACTGTC 57.615 38.462 28.67 19.04 46.31 3.51
2462 2727 8.993121 CACACATATTGAAAGTAAGAGAGTGTT 58.007 33.333 0.00 0.00 33.57 3.32
2563 2860 3.428725 GCCACGGAGATGATATGAGCTAG 60.429 52.174 0.00 0.00 0.00 3.42
2597 2894 8.046107 TCAAATGAACTCACAAAAATTCCCTTT 58.954 29.630 0.00 0.00 0.00 3.11
2605 2903 8.100164 ACTCACAAAAATTCCCTTTGAAGAAAA 58.900 29.630 7.85 0.00 37.25 2.29
3018 3360 4.729868 AGTTTGTTGGTTCCTTGCTCTAT 58.270 39.130 0.00 0.00 0.00 1.98
3073 3629 5.098211 GCAGTATCTTTGTTTGAAGATGCC 58.902 41.667 9.69 2.14 44.71 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.169271 ACGTGACCTCCTTCGTCA 57.831 55.556 0.00 0.00 37.91 4.35
4 5 1.154263 CGACGTGACCTCCTTCGTC 60.154 63.158 0.00 6.50 45.70 4.20
5 6 2.623915 CCGACGTGACCTCCTTCGT 61.624 63.158 0.00 0.00 39.21 3.85
8 9 1.977544 CCTCCGACGTGACCTCCTT 60.978 63.158 0.00 0.00 0.00 3.36
9 10 2.361357 CCTCCGACGTGACCTCCT 60.361 66.667 0.00 0.00 0.00 3.69
10 11 2.360852 TCCTCCGACGTGACCTCC 60.361 66.667 0.00 0.00 0.00 4.30
11 12 2.408241 CCTCCTCCGACGTGACCTC 61.408 68.421 0.00 0.00 0.00 3.85
12 13 2.361357 CCTCCTCCGACGTGACCT 60.361 66.667 0.00 0.00 0.00 3.85
13 14 2.360852 TCCTCCTCCGACGTGACC 60.361 66.667 0.00 0.00 0.00 4.02
14 15 3.053849 GCTCCTCCTCCGACGTGAC 62.054 68.421 0.00 0.00 0.00 3.67
15 16 2.750637 GCTCCTCCTCCGACGTGA 60.751 66.667 0.00 0.00 0.00 4.35
16 17 3.827898 GGCTCCTCCTCCGACGTG 61.828 72.222 0.00 0.00 0.00 4.49
32 33 3.853330 CATGTTGCTCGGCGTCGG 61.853 66.667 10.62 0.65 36.95 4.79
33 34 2.167219 ATCATGTTGCTCGGCGTCG 61.167 57.895 1.15 1.15 37.82 5.12
34 35 1.083806 TCATCATGTTGCTCGGCGTC 61.084 55.000 6.85 0.30 0.00 5.19
35 36 0.673333 TTCATCATGTTGCTCGGCGT 60.673 50.000 6.85 0.00 0.00 5.68
36 37 0.027194 CTTCATCATGTTGCTCGGCG 59.973 55.000 0.00 0.00 0.00 6.46
37 38 1.329906 CTCTTCATCATGTTGCTCGGC 59.670 52.381 0.00 0.00 0.00 5.54
38 39 1.938577 CCTCTTCATCATGTTGCTCGG 59.061 52.381 0.00 0.00 0.00 4.63
39 40 2.350804 CACCTCTTCATCATGTTGCTCG 59.649 50.000 0.00 0.00 0.00 5.03
40 41 3.126514 CACACCTCTTCATCATGTTGCTC 59.873 47.826 0.00 0.00 0.00 4.26
41 42 3.079578 CACACCTCTTCATCATGTTGCT 58.920 45.455 0.00 0.00 0.00 3.91
42 43 3.076621 TCACACCTCTTCATCATGTTGC 58.923 45.455 0.00 0.00 0.00 4.17
43 44 3.688185 CCTCACACCTCTTCATCATGTTG 59.312 47.826 0.00 0.00 0.00 3.33
44 45 3.328931 ACCTCACACCTCTTCATCATGTT 59.671 43.478 0.00 0.00 0.00 2.71
45 46 2.909006 ACCTCACACCTCTTCATCATGT 59.091 45.455 0.00 0.00 0.00 3.21
46 47 3.055602 TCACCTCACACCTCTTCATCATG 60.056 47.826 0.00 0.00 0.00 3.07
47 48 3.176411 TCACCTCACACCTCTTCATCAT 58.824 45.455 0.00 0.00 0.00 2.45
48 49 2.608623 TCACCTCACACCTCTTCATCA 58.391 47.619 0.00 0.00 0.00 3.07
49 50 3.529533 CATCACCTCACACCTCTTCATC 58.470 50.000 0.00 0.00 0.00 2.92
50 51 2.238144 CCATCACCTCACACCTCTTCAT 59.762 50.000 0.00 0.00 0.00 2.57
51 52 1.625315 CCATCACCTCACACCTCTTCA 59.375 52.381 0.00 0.00 0.00 3.02
52 53 1.902508 TCCATCACCTCACACCTCTTC 59.097 52.381 0.00 0.00 0.00 2.87
53 54 2.030027 TCCATCACCTCACACCTCTT 57.970 50.000 0.00 0.00 0.00 2.85
54 55 2.260639 ATCCATCACCTCACACCTCT 57.739 50.000 0.00 0.00 0.00 3.69
55 56 3.356529 AAATCCATCACCTCACACCTC 57.643 47.619 0.00 0.00 0.00 3.85
56 57 4.567747 GGTTAAATCCATCACCTCACACCT 60.568 45.833 0.00 0.00 0.00 4.00
57 58 3.694566 GGTTAAATCCATCACCTCACACC 59.305 47.826 0.00 0.00 0.00 4.16
58 59 4.331968 TGGTTAAATCCATCACCTCACAC 58.668 43.478 0.00 0.00 31.96 3.82
59 60 4.649267 TGGTTAAATCCATCACCTCACA 57.351 40.909 0.00 0.00 31.96 3.58
69 70 3.677700 CGTCACTCGGATGGTTAAATCCA 60.678 47.826 6.92 0.00 45.64 3.41
70 71 2.864343 CGTCACTCGGATGGTTAAATCC 59.136 50.000 0.00 0.00 42.46 3.01
71 72 2.284417 GCGTCACTCGGATGGTTAAATC 59.716 50.000 0.00 0.00 40.26 2.17
72 73 2.277084 GCGTCACTCGGATGGTTAAAT 58.723 47.619 0.00 0.00 40.26 1.40
73 74 1.717194 GCGTCACTCGGATGGTTAAA 58.283 50.000 0.00 0.00 40.26 1.52
74 75 0.457166 CGCGTCACTCGGATGGTTAA 60.457 55.000 0.00 0.00 40.26 2.01
75 76 1.138036 CGCGTCACTCGGATGGTTA 59.862 57.895 0.00 0.00 40.26 2.85
76 77 2.126071 CGCGTCACTCGGATGGTT 60.126 61.111 0.00 0.00 40.26 3.67
77 78 2.149803 TTTCGCGTCACTCGGATGGT 62.150 55.000 5.77 0.00 40.26 3.55
78 79 1.413767 CTTTCGCGTCACTCGGATGG 61.414 60.000 5.77 0.00 40.26 3.51
79 80 0.732880 ACTTTCGCGTCACTCGGATG 60.733 55.000 5.77 0.00 40.26 3.51
80 81 0.456312 GACTTTCGCGTCACTCGGAT 60.456 55.000 5.77 0.00 40.26 4.18
81 82 1.081641 GACTTTCGCGTCACTCGGA 60.082 57.895 5.77 0.00 40.26 4.55
82 83 1.066114 GAGACTTTCGCGTCACTCGG 61.066 60.000 5.77 0.00 40.26 4.63
83 84 1.066114 GGAGACTTTCGCGTCACTCG 61.066 60.000 5.77 0.00 43.12 4.18
84 85 0.241481 AGGAGACTTTCGCGTCACTC 59.759 55.000 5.77 9.20 37.44 3.51
85 86 1.199558 GTAGGAGACTTTCGCGTCACT 59.800 52.381 5.77 1.59 43.67 3.41
86 87 1.615502 GTAGGAGACTTTCGCGTCAC 58.384 55.000 5.77 0.00 43.67 3.67
87 88 0.524862 GGTAGGAGACTTTCGCGTCA 59.475 55.000 5.77 0.00 43.67 4.35
88 89 0.179142 GGGTAGGAGACTTTCGCGTC 60.179 60.000 5.77 0.00 43.67 5.19
89 90 1.602327 GGGGTAGGAGACTTTCGCGT 61.602 60.000 5.77 0.00 43.67 6.01
90 91 1.141234 GGGGTAGGAGACTTTCGCG 59.859 63.158 0.00 0.00 43.67 5.87
91 92 0.611714 TTGGGGTAGGAGACTTTCGC 59.388 55.000 0.00 0.00 43.67 4.70
92 93 1.405661 GCTTGGGGTAGGAGACTTTCG 60.406 57.143 0.00 0.00 43.67 3.46
93 94 1.065345 GGCTTGGGGTAGGAGACTTTC 60.065 57.143 0.00 0.00 43.67 2.62
94 95 0.992695 GGCTTGGGGTAGGAGACTTT 59.007 55.000 0.00 0.00 43.67 2.66
95 96 0.178873 TGGCTTGGGGTAGGAGACTT 60.179 55.000 0.00 0.00 43.67 3.01
97 98 0.696501 TTTGGCTTGGGGTAGGAGAC 59.303 55.000 0.00 0.00 0.00 3.36
98 99 1.564348 GATTTGGCTTGGGGTAGGAGA 59.436 52.381 0.00 0.00 0.00 3.71
99 100 1.566231 AGATTTGGCTTGGGGTAGGAG 59.434 52.381 0.00 0.00 0.00 3.69
100 101 1.564348 GAGATTTGGCTTGGGGTAGGA 59.436 52.381 0.00 0.00 0.00 2.94
101 102 1.410224 GGAGATTTGGCTTGGGGTAGG 60.410 57.143 0.00 0.00 0.00 3.18
102 103 1.284785 TGGAGATTTGGCTTGGGGTAG 59.715 52.381 0.00 0.00 0.00 3.18
103 104 1.377690 TGGAGATTTGGCTTGGGGTA 58.622 50.000 0.00 0.00 0.00 3.69
104 105 0.712380 ATGGAGATTTGGCTTGGGGT 59.288 50.000 0.00 0.00 0.00 4.95
105 106 1.117150 CATGGAGATTTGGCTTGGGG 58.883 55.000 0.00 0.00 0.00 4.96
106 107 2.029623 CTCATGGAGATTTGGCTTGGG 58.970 52.381 0.00 0.00 0.00 4.12
107 108 1.407979 GCTCATGGAGATTTGGCTTGG 59.592 52.381 0.00 0.00 0.00 3.61
108 109 2.097036 TGCTCATGGAGATTTGGCTTG 58.903 47.619 0.00 0.00 0.00 4.01
109 110 2.097825 GTGCTCATGGAGATTTGGCTT 58.902 47.619 0.00 0.00 0.00 4.35
110 111 1.684248 GGTGCTCATGGAGATTTGGCT 60.684 52.381 0.00 0.00 0.00 4.75
111 112 0.743097 GGTGCTCATGGAGATTTGGC 59.257 55.000 0.00 0.00 0.00 4.52
112 113 2.133281 TGGTGCTCATGGAGATTTGG 57.867 50.000 0.00 0.00 0.00 3.28
113 114 3.697542 TCAATGGTGCTCATGGAGATTTG 59.302 43.478 0.00 0.00 35.99 2.32
114 115 3.698040 GTCAATGGTGCTCATGGAGATTT 59.302 43.478 0.00 0.00 36.53 2.17
115 116 3.285484 GTCAATGGTGCTCATGGAGATT 58.715 45.455 0.00 0.00 36.53 2.40
116 117 2.744166 CGTCAATGGTGCTCATGGAGAT 60.744 50.000 0.00 0.00 36.53 2.75
117 118 1.405933 CGTCAATGGTGCTCATGGAGA 60.406 52.381 0.00 0.00 36.53 3.71
118 119 1.012086 CGTCAATGGTGCTCATGGAG 58.988 55.000 0.00 0.00 36.53 3.86
119 120 1.026182 GCGTCAATGGTGCTCATGGA 61.026 55.000 0.00 0.00 35.99 3.41
120 121 1.307355 TGCGTCAATGGTGCTCATGG 61.307 55.000 0.00 0.00 35.99 3.66
121 122 0.736636 ATGCGTCAATGGTGCTCATG 59.263 50.000 0.00 0.00 35.99 3.07
122 123 0.736636 CATGCGTCAATGGTGCTCAT 59.263 50.000 0.06 0.00 37.79 2.90
123 124 1.925415 GCATGCGTCAATGGTGCTCA 61.925 55.000 0.00 0.00 33.25 4.26
124 125 1.226491 GCATGCGTCAATGGTGCTC 60.226 57.895 0.00 0.00 33.25 4.26
125 126 2.879907 GCATGCGTCAATGGTGCT 59.120 55.556 0.00 0.00 33.25 4.40
126 127 2.577644 CGCATGCGTCAATGGTGC 60.578 61.111 31.33 0.00 34.35 5.01
127 128 2.100797 CCGCATGCGTCAATGGTG 59.899 61.111 35.55 16.09 37.81 4.17
128 129 3.814268 GCCGCATGCGTCAATGGT 61.814 61.111 35.55 0.00 37.81 3.55
137 138 3.925238 CGGAGTTACGCCGCATGC 61.925 66.667 15.24 7.91 40.20 4.06
138 139 2.202690 TCGGAGTTACGCCGCATG 60.203 61.111 22.06 0.00 45.89 4.06
139 140 2.202703 GTCGGAGTTACGCCGCAT 60.203 61.111 22.06 0.00 45.89 4.73
140 141 4.764336 CGTCGGAGTTACGCCGCA 62.764 66.667 22.06 8.88 45.89 5.69
143 144 3.443045 TCCCGTCGGAGTTACGCC 61.443 66.667 14.39 0.00 39.00 5.68
151 152 1.000019 AATGACTCCTCCCGTCGGA 60.000 57.895 14.39 0.00 36.45 4.55
152 153 1.141881 CAATGACTCCTCCCGTCGG 59.858 63.158 3.60 3.60 34.17 4.79
153 154 1.141881 CCAATGACTCCTCCCGTCG 59.858 63.158 0.00 0.00 34.17 5.12
154 155 1.522569 CCCAATGACTCCTCCCGTC 59.477 63.158 0.00 0.00 0.00 4.79
155 156 1.995626 CCCCAATGACTCCTCCCGT 60.996 63.158 0.00 0.00 0.00 5.28
156 157 2.746375 CCCCCAATGACTCCTCCCG 61.746 68.421 0.00 0.00 0.00 5.14
157 158 1.619669 ACCCCCAATGACTCCTCCC 60.620 63.158 0.00 0.00 0.00 4.30
158 159 1.609783 CACCCCCAATGACTCCTCC 59.390 63.158 0.00 0.00 0.00 4.30
159 160 1.077429 GCACCCCCAATGACTCCTC 60.077 63.158 0.00 0.00 0.00 3.71
160 161 1.852157 TGCACCCCCAATGACTCCT 60.852 57.895 0.00 0.00 0.00 3.69
161 162 1.379044 CTGCACCCCCAATGACTCC 60.379 63.158 0.00 0.00 0.00 3.85
162 163 0.393537 CTCTGCACCCCCAATGACTC 60.394 60.000 0.00 0.00 0.00 3.36
163 164 1.687612 CTCTGCACCCCCAATGACT 59.312 57.895 0.00 0.00 0.00 3.41
164 165 1.379044 CCTCTGCACCCCCAATGAC 60.379 63.158 0.00 0.00 0.00 3.06
165 166 1.852157 ACCTCTGCACCCCCAATGA 60.852 57.895 0.00 0.00 0.00 2.57
166 167 1.679977 CACCTCTGCACCCCCAATG 60.680 63.158 0.00 0.00 0.00 2.82
167 168 2.142292 GACACCTCTGCACCCCCAAT 62.142 60.000 0.00 0.00 0.00 3.16
168 169 2.776526 ACACCTCTGCACCCCCAA 60.777 61.111 0.00 0.00 0.00 4.12
169 170 3.249189 GACACCTCTGCACCCCCA 61.249 66.667 0.00 0.00 0.00 4.96
170 171 4.035102 GGACACCTCTGCACCCCC 62.035 72.222 0.00 0.00 0.00 5.40
171 172 4.394712 CGGACACCTCTGCACCCC 62.395 72.222 0.00 0.00 0.00 4.95
172 173 3.311110 TCGGACACCTCTGCACCC 61.311 66.667 0.00 0.00 0.00 4.61
173 174 2.048127 GTCGGACACCTCTGCACC 60.048 66.667 2.62 0.00 0.00 5.01
174 175 2.430921 CGTCGGACACCTCTGCAC 60.431 66.667 9.10 0.00 0.00 4.57
175 176 3.680786 CCGTCGGACACCTCTGCA 61.681 66.667 4.91 0.00 0.00 4.41
176 177 3.222354 AACCGTCGGACACCTCTGC 62.222 63.158 20.51 0.00 0.00 4.26
177 178 1.080705 GAACCGTCGGACACCTCTG 60.081 63.158 20.51 0.00 0.00 3.35
178 179 2.273912 GGAACCGTCGGACACCTCT 61.274 63.158 20.51 0.00 0.00 3.69
179 180 1.885163 ATGGAACCGTCGGACACCTC 61.885 60.000 20.51 5.96 0.00 3.85
180 181 1.477685 AATGGAACCGTCGGACACCT 61.478 55.000 20.51 5.51 0.00 4.00
181 182 1.004200 AATGGAACCGTCGGACACC 60.004 57.895 20.51 17.17 0.00 4.16
182 183 1.017701 GGAATGGAACCGTCGGACAC 61.018 60.000 20.51 7.58 0.00 3.67
183 184 1.294138 GGAATGGAACCGTCGGACA 59.706 57.895 20.51 13.99 0.00 4.02
184 185 1.449070 GGGAATGGAACCGTCGGAC 60.449 63.158 20.51 11.30 0.00 4.79
185 186 2.983791 GGGAATGGAACCGTCGGA 59.016 61.111 20.51 0.00 0.00 4.55
186 187 2.510691 CGGGAATGGAACCGTCGG 60.511 66.667 10.48 10.48 44.85 4.79
191 192 2.044352 CACCCCGGGAATGGAACC 60.044 66.667 26.32 0.00 0.00 3.62
192 193 2.044352 CCACCCCGGGAATGGAAC 60.044 66.667 30.69 0.00 35.33 3.62
193 194 4.055227 GCCACCCCGGGAATGGAA 62.055 66.667 35.75 0.00 35.33 3.53
224 225 4.152625 CTTCCGCTTTCGCTGCCG 62.153 66.667 0.00 0.00 0.00 5.69
228 229 0.390472 CTTCTCCTTCCGCTTTCGCT 60.390 55.000 0.00 0.00 0.00 4.93
231 232 1.362406 CGCCTTCTCCTTCCGCTTTC 61.362 60.000 0.00 0.00 0.00 2.62
250 251 3.888930 TGAAACTCTTCCCCATTCACAAC 59.111 43.478 0.00 0.00 0.00 3.32
267 268 2.347661 CGCGACAAGTTCTCAGTGAAAC 60.348 50.000 0.00 2.48 36.30 2.78
269 270 1.487482 CGCGACAAGTTCTCAGTGAA 58.513 50.000 0.00 0.00 0.00 3.18
271 272 0.597637 ACCGCGACAAGTTCTCAGTG 60.598 55.000 8.23 0.00 0.00 3.66
272 273 0.318784 GACCGCGACAAGTTCTCAGT 60.319 55.000 8.23 0.00 0.00 3.41
287 288 3.258622 ACTCTCTCACTTTTAAGGGACCG 59.741 47.826 0.00 0.00 32.43 4.79
290 291 5.888982 ACAACTCTCTCACTTTTAAGGGA 57.111 39.130 0.00 0.00 35.74 4.20
344 345 5.135508 ACTCATATCCGGTTAATTCCTCG 57.864 43.478 0.00 0.00 0.00 4.63
388 389 7.180229 CCAATCCATTAAAAGGGTTAACTCCTT 59.820 37.037 17.71 17.71 45.73 3.36
398 399 5.694995 TCTCTAGCCAATCCATTAAAAGGG 58.305 41.667 0.00 0.00 0.00 3.95
445 446 3.728845 AGCAACGTTGTGTATCAGTTCT 58.271 40.909 27.78 10.55 0.00 3.01
446 447 3.120649 GGAGCAACGTTGTGTATCAGTTC 60.121 47.826 27.78 8.45 0.00 3.01
448 449 2.413837 GGAGCAACGTTGTGTATCAGT 58.586 47.619 27.78 4.52 0.00 3.41
450 451 1.000052 TCGGAGCAACGTTGTGTATCA 60.000 47.619 27.78 6.97 34.94 2.15
460 461 0.179215 GAAGCAATGTCGGAGCAACG 60.179 55.000 0.00 0.00 0.00 4.10
469 470 4.736793 CAGTTTGTTGAGTGAAGCAATGTC 59.263 41.667 0.00 0.00 0.00 3.06
492 493 2.143925 GTGAGCGCTGGGATATAAACC 58.856 52.381 18.48 0.00 0.00 3.27
504 505 2.228582 TGCAAATACAAATGTGAGCGCT 59.771 40.909 11.27 11.27 0.00 5.92
527 528 6.958255 TGTGATCACATTGAAACAGTACTTG 58.042 36.000 24.56 0.00 36.21 3.16
564 565 0.622665 AGGGAGATTGAGTGGCCAAG 59.377 55.000 7.24 0.00 0.00 3.61
585 586 1.498865 CCTAATCACATGTCGCGCCC 61.499 60.000 0.00 0.00 0.00 6.13
586 587 1.498865 CCCTAATCACATGTCGCGCC 61.499 60.000 0.00 0.00 0.00 6.53
587 588 1.934463 CCCTAATCACATGTCGCGC 59.066 57.895 0.00 0.00 0.00 6.86
592 593 2.877097 TGTGTGCCCTAATCACATGT 57.123 45.000 0.00 0.00 44.96 3.21
661 664 6.322201 GGATGATGCTTCTCCCAAAAATAGAA 59.678 38.462 0.88 0.00 0.00 2.10
663 666 5.595542 TGGATGATGCTTCTCCCAAAAATAG 59.404 40.000 9.80 0.00 0.00 1.73
678 681 5.860716 GTCTCAAAAGAACTTTGGATGATGC 59.139 40.000 5.06 0.00 44.00 3.91
679 682 6.860023 GTGTCTCAAAAGAACTTTGGATGATG 59.140 38.462 5.06 0.00 44.00 3.07
779 783 5.538813 AGAACCACCCAAGAAAAATAAGGTC 59.461 40.000 0.00 0.00 0.00 3.85
791 795 3.826729 CCCTAAAAGAAGAACCACCCAAG 59.173 47.826 0.00 0.00 0.00 3.61
802 806 4.460382 TCAGCTCAAATGCCCTAAAAGAAG 59.540 41.667 0.00 0.00 0.00 2.85
804 808 4.032960 TCAGCTCAAATGCCCTAAAAGA 57.967 40.909 0.00 0.00 0.00 2.52
805 809 4.643784 AGATCAGCTCAAATGCCCTAAAAG 59.356 41.667 0.00 0.00 0.00 2.27
839 843 8.270744 AGATCAGCTCCAGTTGATAGTAAAAAT 58.729 33.333 5.96 0.00 44.27 1.82
841 845 7.187824 AGATCAGCTCCAGTTGATAGTAAAA 57.812 36.000 5.96 0.00 44.27 1.52
842 846 6.798427 AGATCAGCTCCAGTTGATAGTAAA 57.202 37.500 5.96 0.00 44.27 2.01
843 847 7.898014 TTAGATCAGCTCCAGTTGATAGTAA 57.102 36.000 5.96 5.21 44.27 2.24
844 848 7.898014 TTTAGATCAGCTCCAGTTGATAGTA 57.102 36.000 5.96 0.00 44.27 1.82
845 849 6.798427 TTTAGATCAGCTCCAGTTGATAGT 57.202 37.500 5.96 0.75 44.27 2.12
846 850 6.649973 CCATTTAGATCAGCTCCAGTTGATAG 59.350 42.308 5.96 0.00 44.27 2.08
855 859 3.244387 GGAGACCCATTTAGATCAGCTCC 60.244 52.174 0.00 0.00 33.45 4.70
877 881 1.745141 GCTGGGCTGAGTTGGACTATG 60.745 57.143 0.00 0.00 0.00 2.23
906 923 2.046892 CGTCTGGTCCAGCCTTGG 60.047 66.667 14.64 0.00 46.49 3.61
912 929 2.357517 GTGTGGCGTCTGGTCCAG 60.358 66.667 13.21 13.21 32.15 3.86
951 971 3.827898 GGTGCGAGACGGAGGAGG 61.828 72.222 0.00 0.00 0.00 4.30
953 973 1.945354 GAATGGTGCGAGACGGAGGA 61.945 60.000 0.00 0.00 0.00 3.71
1638 1671 1.664017 CATCGCCTGGATGCTCTCG 60.664 63.158 0.00 0.00 45.57 4.04
1691 1724 0.394352 GTGCCTGAACATCCCGGATT 60.394 55.000 0.73 0.00 0.00 3.01
1738 1771 0.817634 TTGGCGGTGACCTTCTGTTG 60.818 55.000 0.00 0.00 0.00 3.33
1765 1798 3.377172 CACCCAAACGTCTTCTTCAAGTT 59.623 43.478 0.00 0.00 0.00 2.66
1797 1830 2.045926 ACAGCAATGCCGACCTCC 60.046 61.111 0.00 0.00 0.00 4.30
1888 1921 2.454459 AATGCCGGTTCCAACCCCAT 62.454 55.000 1.90 3.66 46.53 4.00
2060 2093 1.557832 TGTAAGGGCACATGTACCTCC 59.442 52.381 18.55 13.55 32.29 4.30
2251 2290 5.003804 CAGACAGCCAACATTTAGTTAGGT 58.996 41.667 0.00 0.00 38.74 3.08
2292 2342 3.764885 AACAAACAAGCAGTGACAGTC 57.235 42.857 0.00 0.00 0.00 3.51
2294 2344 4.882671 ACTAACAAACAAGCAGTGACAG 57.117 40.909 0.00 0.00 0.00 3.51
2295 2345 4.457603 ACAACTAACAAACAAGCAGTGACA 59.542 37.500 0.00 0.00 0.00 3.58
2296 2346 4.981794 ACAACTAACAAACAAGCAGTGAC 58.018 39.130 0.00 0.00 0.00 3.67
2298 2348 7.515059 GCATTAACAACTAACAAACAAGCAGTG 60.515 37.037 0.00 0.00 0.00 3.66
2462 2727 9.269453 CTGATATTTGCAGAATGAACTGATCTA 57.731 33.333 0.00 0.00 39.69 1.98
3073 3629 8.697846 ATCATGAATTACTTTCACAGCATTTG 57.302 30.769 0.00 0.00 46.80 2.32


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

AutoCloner maintained by Alex Coulton.