Multiple sequence alignment - TraesCS3D01G022700

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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 TraesCS3D01G022700 chr3D 100.000 3380 0 0 1 3380 7245977 7242598 0.000000e+00 6242
1 TraesCS3D01G022700 chr3B 97.561 1763 33 6 436 2189 8862673 8860912 0.000000e+00 3009
2 TraesCS3D01G022700 chr3B 94.328 1146 57 5 2236 3380 8860907 8859769 0.000000e+00 1749
3 TraesCS3D01G022700 chr3B 81.485 983 139 18 1270 2237 8833612 8832658 0.000000e+00 767
4 TraesCS3D01G022700 chr3B 83.559 590 82 10 2758 3346 8832001 8831426 3.840000e-149 538
5 TraesCS3D01G022700 chr3B 94.304 158 8 1 253 409 8863091 8862934 1.210000e-59 241
6 TraesCS3D01G022700 chr2B 94.937 158 7 1 28 184 142654831 142654674 2.600000e-61 246
7 TraesCS3D01G022700 chr5D 94.340 159 7 2 26 183 451618103 451618260 3.370000e-60 243
8 TraesCS3D01G022700 chr2D 94.340 159 7 2 28 184 632759376 632759534 3.370000e-60 243
9 TraesCS3D01G022700 chr6B 93.711 159 9 1 22 179 675395921 675396079 1.570000e-58 237
10 TraesCS3D01G022700 chr4D 93.711 159 8 2 26 183 20077421 20077264 1.570000e-58 237
11 TraesCS3D01G022700 chr4D 88.710 186 16 5 1 184 21685362 21685544 4.390000e-54 222
12 TraesCS3D01G022700 chr5A 91.667 168 12 2 18 183 64980829 64980662 7.290000e-57 231
13 TraesCS3D01G022700 chr6A 91.228 171 12 3 14 183 601962191 601962023 2.620000e-56 230
14 TraesCS3D01G022700 chr2A 89.944 179 15 3 6 183 611294286 611294110 9.430000e-56 228


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 TraesCS3D01G022700 chr3D 7242598 7245977 3379 True 6242.000000 6242 100.000000 1 3380 1 chr3D.!!$R1 3379
1 TraesCS3D01G022700 chr3B 8859769 8863091 3322 True 1666.333333 3009 95.397667 253 3380 3 chr3B.!!$R2 3127
2 TraesCS3D01G022700 chr3B 8831426 8833612 2186 True 652.500000 767 82.522000 1270 3346 2 chr3B.!!$R1 2076

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
90 91 0.028642 ATCCCCAGCCTATCAGGGTT 60.029 55.0 0.00 0.0 45.25 4.11 F
209 210 0.034198 TGCAACTAGGCGCAACTACA 59.966 50.0 10.83 0.0 34.59 2.74 F
216 217 0.321671 AGGCGCAACTACATGTCTGT 59.678 50.0 10.83 0.0 39.49 3.41 F
1835 2085 0.473326 AGGAATGCATCAGAGAGGCC 59.527 55.0 0.00 0.0 38.67 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2061 0.182061 TGGCCTCTCTGATGCATTCC 59.818 55.000 3.32 0.0 0.00 3.01 R
1957 2212 4.371681 ACTCCCTTGGTATGTATCCACTT 58.628 43.478 0.00 0.0 34.45 3.16 R
2213 2469 2.797156 CAGACCGAATGCACAGTATAGC 59.203 50.000 0.00 0.0 0.00 2.97 R
3085 3557 0.107508 CTCCCGTCATGCTTCATGGT 60.108 55.000 6.92 0.0 41.66 3.55 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
22 23 5.749596 CAACTACTGTTTCAACCACATCA 57.250 39.130 0.00 0.00 33.52 3.07
23 24 6.130298 CAACTACTGTTTCAACCACATCAA 57.870 37.500 0.00 0.00 33.52 2.57
24 25 5.751243 ACTACTGTTTCAACCACATCAAC 57.249 39.130 0.00 0.00 0.00 3.18
25 26 4.578928 ACTACTGTTTCAACCACATCAACC 59.421 41.667 0.00 0.00 0.00 3.77
26 27 3.631250 ACTGTTTCAACCACATCAACCT 58.369 40.909 0.00 0.00 0.00 3.50
27 28 4.787551 ACTGTTTCAACCACATCAACCTA 58.212 39.130 0.00 0.00 0.00 3.08
28 29 4.821805 ACTGTTTCAACCACATCAACCTAG 59.178 41.667 0.00 0.00 0.00 3.02
29 30 5.042463 TGTTTCAACCACATCAACCTAGA 57.958 39.130 0.00 0.00 0.00 2.43
30 31 5.063204 TGTTTCAACCACATCAACCTAGAG 58.937 41.667 0.00 0.00 0.00 2.43
31 32 3.981071 TCAACCACATCAACCTAGAGG 57.019 47.619 0.00 0.00 42.17 3.69
32 33 2.027192 TCAACCACATCAACCTAGAGGC 60.027 50.000 0.00 0.00 39.32 4.70
33 34 0.537188 ACCACATCAACCTAGAGGCG 59.463 55.000 0.00 0.00 39.32 5.52
34 35 0.824109 CCACATCAACCTAGAGGCGA 59.176 55.000 0.00 0.00 39.32 5.54
35 36 1.207089 CCACATCAACCTAGAGGCGAA 59.793 52.381 0.00 0.00 39.32 4.70
36 37 2.271800 CACATCAACCTAGAGGCGAAC 58.728 52.381 0.00 0.00 39.32 3.95
37 38 1.207329 ACATCAACCTAGAGGCGAACC 59.793 52.381 0.00 0.00 39.32 3.62
38 39 1.207089 CATCAACCTAGAGGCGAACCA 59.793 52.381 0.00 0.00 39.06 3.67
39 40 1.344065 TCAACCTAGAGGCGAACCAA 58.656 50.000 0.00 0.00 39.06 3.67
40 41 1.001633 TCAACCTAGAGGCGAACCAAC 59.998 52.381 0.00 0.00 39.06 3.77
41 42 0.323957 AACCTAGAGGCGAACCAACC 59.676 55.000 0.00 0.00 39.06 3.77
42 43 0.544595 ACCTAGAGGCGAACCAACCT 60.545 55.000 0.00 0.00 39.65 3.50
43 44 0.108138 CCTAGAGGCGAACCAACCTG 60.108 60.000 0.00 0.00 36.05 4.00
44 45 0.741221 CTAGAGGCGAACCAACCTGC 60.741 60.000 0.00 0.00 36.05 4.85
45 46 2.501223 TAGAGGCGAACCAACCTGCG 62.501 60.000 0.00 0.00 36.05 5.18
55 56 2.843545 AACCTGCGGTTGGATGGT 59.156 55.556 11.39 0.00 45.07 3.55
56 57 1.152830 AACCTGCGGTTGGATGGTT 59.847 52.632 11.39 0.00 45.07 3.67
57 58 0.402504 AACCTGCGGTTGGATGGTTA 59.597 50.000 11.39 0.00 45.07 2.85
58 59 0.035439 ACCTGCGGTTGGATGGTTAG 60.035 55.000 0.00 0.00 27.29 2.34
59 60 0.251916 CCTGCGGTTGGATGGTTAGA 59.748 55.000 0.00 0.00 0.00 2.10
60 61 1.656652 CTGCGGTTGGATGGTTAGAG 58.343 55.000 0.00 0.00 0.00 2.43
61 62 0.251916 TGCGGTTGGATGGTTAGAGG 59.748 55.000 0.00 0.00 0.00 3.69
62 63 0.463833 GCGGTTGGATGGTTAGAGGG 60.464 60.000 0.00 0.00 0.00 4.30
63 64 1.200519 CGGTTGGATGGTTAGAGGGA 58.799 55.000 0.00 0.00 0.00 4.20
64 65 1.134491 CGGTTGGATGGTTAGAGGGAC 60.134 57.143 0.00 0.00 0.00 4.46
66 67 2.092914 GGTTGGATGGTTAGAGGGACTG 60.093 54.545 0.00 0.00 41.55 3.51
67 68 2.572104 GTTGGATGGTTAGAGGGACTGT 59.428 50.000 0.00 0.00 41.55 3.55
68 69 2.187958 TGGATGGTTAGAGGGACTGTG 58.812 52.381 0.00 0.00 41.55 3.66
69 70 1.486726 GGATGGTTAGAGGGACTGTGG 59.513 57.143 0.00 0.00 41.55 4.17
70 71 2.188817 GATGGTTAGAGGGACTGTGGT 58.811 52.381 0.00 0.00 41.55 4.16
71 72 3.371965 GATGGTTAGAGGGACTGTGGTA 58.628 50.000 0.00 0.00 41.55 3.25
72 73 3.484953 TGGTTAGAGGGACTGTGGTAT 57.515 47.619 0.00 0.00 41.55 2.73
73 74 3.371965 TGGTTAGAGGGACTGTGGTATC 58.628 50.000 0.00 0.00 41.55 2.24
74 75 2.699321 GGTTAGAGGGACTGTGGTATCC 59.301 54.545 0.00 0.00 41.55 2.59
79 80 1.527370 GGACTGTGGTATCCCCAGC 59.473 63.158 0.00 0.00 46.45 4.85
80 81 1.527370 GACTGTGGTATCCCCAGCC 59.473 63.158 0.00 0.00 46.45 4.85
81 82 0.983378 GACTGTGGTATCCCCAGCCT 60.983 60.000 0.00 0.00 46.45 4.58
82 83 0.341961 ACTGTGGTATCCCCAGCCTA 59.658 55.000 0.00 0.00 46.45 3.93
83 84 1.061346 ACTGTGGTATCCCCAGCCTAT 60.061 52.381 0.00 0.00 46.45 2.57
84 85 1.625818 CTGTGGTATCCCCAGCCTATC 59.374 57.143 0.00 0.00 46.45 2.08
85 86 1.061735 TGTGGTATCCCCAGCCTATCA 60.062 52.381 0.00 0.00 46.45 2.15
86 87 1.625818 GTGGTATCCCCAGCCTATCAG 59.374 57.143 0.00 0.00 46.45 2.90
87 88 1.280457 GGTATCCCCAGCCTATCAGG 58.720 60.000 0.00 0.00 38.80 3.86
88 89 1.280457 GTATCCCCAGCCTATCAGGG 58.720 60.000 0.00 0.00 40.98 4.45
90 91 0.028642 ATCCCCAGCCTATCAGGGTT 60.029 55.000 0.00 0.00 45.25 4.11
91 92 0.694444 TCCCCAGCCTATCAGGGTTC 60.694 60.000 0.00 0.00 45.25 3.62
92 93 0.988145 CCCCAGCCTATCAGGGTTCA 60.988 60.000 0.00 0.00 45.25 3.18
93 94 0.918983 CCCAGCCTATCAGGGTTCAA 59.081 55.000 0.00 0.00 45.25 2.69
94 95 1.284785 CCCAGCCTATCAGGGTTCAAA 59.715 52.381 0.00 0.00 45.25 2.69
95 96 2.091665 CCCAGCCTATCAGGGTTCAAAT 60.092 50.000 0.00 0.00 45.25 2.32
96 97 3.217626 CCAGCCTATCAGGGTTCAAATC 58.782 50.000 0.00 0.00 45.25 2.17
97 98 3.217626 CAGCCTATCAGGGTTCAAATCC 58.782 50.000 0.00 0.00 45.25 3.01
98 99 3.117738 CAGCCTATCAGGGTTCAAATCCT 60.118 47.826 0.00 0.00 45.25 3.24
105 106 3.010200 AGGGTTCAAATCCTGATGCTC 57.990 47.619 0.00 0.00 38.36 4.26
106 107 1.672881 GGGTTCAAATCCTGATGCTCG 59.327 52.381 0.00 0.00 32.78 5.03
107 108 1.064654 GGTTCAAATCCTGATGCTCGC 59.935 52.381 0.00 0.00 32.78 5.03
108 109 1.739466 GTTCAAATCCTGATGCTCGCA 59.261 47.619 0.00 0.00 32.78 5.10
109 110 2.336945 TCAAATCCTGATGCTCGCAT 57.663 45.000 3.70 3.70 39.69 4.73
110 111 2.646930 TCAAATCCTGATGCTCGCATT 58.353 42.857 5.79 0.00 36.70 3.56
111 112 3.018856 TCAAATCCTGATGCTCGCATTT 58.981 40.909 5.79 0.00 36.70 2.32
112 113 4.198530 TCAAATCCTGATGCTCGCATTTA 58.801 39.130 5.79 0.00 36.70 1.40
113 114 4.823442 TCAAATCCTGATGCTCGCATTTAT 59.177 37.500 5.79 0.00 36.70 1.40
114 115 5.300034 TCAAATCCTGATGCTCGCATTTATT 59.700 36.000 5.79 1.98 36.70 1.40
115 116 5.368256 AATCCTGATGCTCGCATTTATTC 57.632 39.130 5.79 0.00 36.70 1.75
116 117 3.141398 TCCTGATGCTCGCATTTATTCC 58.859 45.455 5.79 0.00 36.70 3.01
117 118 3.144506 CCTGATGCTCGCATTTATTCCT 58.855 45.455 5.79 0.00 36.70 3.36
118 119 3.058432 CCTGATGCTCGCATTTATTCCTG 60.058 47.826 5.79 0.00 36.70 3.86
119 120 2.880268 TGATGCTCGCATTTATTCCTGG 59.120 45.455 5.79 0.00 36.70 4.45
120 121 2.708216 TGCTCGCATTTATTCCTGGA 57.292 45.000 0.00 0.00 0.00 3.86
121 122 3.213206 TGCTCGCATTTATTCCTGGAT 57.787 42.857 0.00 0.00 0.00 3.41
122 123 3.554934 TGCTCGCATTTATTCCTGGATT 58.445 40.909 0.00 0.00 0.00 3.01
123 124 3.953612 TGCTCGCATTTATTCCTGGATTT 59.046 39.130 0.00 0.00 0.00 2.17
124 125 5.129634 TGCTCGCATTTATTCCTGGATTTA 58.870 37.500 0.00 0.00 0.00 1.40
125 126 5.769662 TGCTCGCATTTATTCCTGGATTTAT 59.230 36.000 0.00 0.00 0.00 1.40
126 127 6.265196 TGCTCGCATTTATTCCTGGATTTATT 59.735 34.615 0.00 0.00 0.00 1.40
127 128 7.147976 GCTCGCATTTATTCCTGGATTTATTT 58.852 34.615 0.00 0.00 0.00 1.40
128 129 7.327032 GCTCGCATTTATTCCTGGATTTATTTC 59.673 37.037 0.00 0.00 0.00 2.17
129 130 8.231692 TCGCATTTATTCCTGGATTTATTTCA 57.768 30.769 0.00 0.00 0.00 2.69
130 131 8.352201 TCGCATTTATTCCTGGATTTATTTCAG 58.648 33.333 0.00 0.00 0.00 3.02
131 132 7.596248 CGCATTTATTCCTGGATTTATTTCAGG 59.404 37.037 0.00 0.00 46.91 3.86
139 140 6.076981 CTGGATTTATTTCAGGATTTCCGG 57.923 41.667 0.00 0.00 42.08 5.14
140 141 4.340950 TGGATTTATTTCAGGATTTCCGGC 59.659 41.667 0.00 0.00 42.08 6.13
141 142 4.537015 GATTTATTTCAGGATTTCCGGCG 58.463 43.478 0.00 0.00 42.08 6.46
142 143 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
143 144 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
144 145 1.378531 TTTCAGGATTTCCGGCGATG 58.621 50.000 9.30 0.00 42.08 3.84
145 146 1.095228 TTCAGGATTTCCGGCGATGC 61.095 55.000 9.30 0.00 42.08 3.91
146 147 2.588877 AGGATTTCCGGCGATGCG 60.589 61.111 9.30 0.00 42.08 4.73
157 158 2.711311 CGATGCGCATTCAGTGGG 59.289 61.111 26.12 4.47 43.21 4.61
158 159 1.815003 CGATGCGCATTCAGTGGGA 60.815 57.895 26.12 0.00 43.02 4.37
159 160 1.769098 CGATGCGCATTCAGTGGGAG 61.769 60.000 26.12 4.12 43.02 4.30
160 161 1.442526 GATGCGCATTCAGTGGGAGG 61.443 60.000 26.12 0.00 43.02 4.30
161 162 1.913951 ATGCGCATTCAGTGGGAGGA 61.914 55.000 19.28 0.00 43.02 3.71
162 163 1.817099 GCGCATTCAGTGGGAGGAG 60.817 63.158 0.30 0.00 43.02 3.69
163 164 1.900351 CGCATTCAGTGGGAGGAGA 59.100 57.895 0.00 0.00 43.02 3.71
164 165 0.467384 CGCATTCAGTGGGAGGAGAT 59.533 55.000 0.00 0.00 43.02 2.75
165 166 1.809271 CGCATTCAGTGGGAGGAGATG 60.809 57.143 0.00 0.00 43.02 2.90
166 167 1.211457 GCATTCAGTGGGAGGAGATGT 59.789 52.381 0.00 0.00 0.00 3.06
167 168 2.356535 GCATTCAGTGGGAGGAGATGTT 60.357 50.000 0.00 0.00 0.00 2.71
168 169 3.539604 CATTCAGTGGGAGGAGATGTTC 58.460 50.000 0.00 0.00 0.00 3.18
177 178 2.750815 GGAGATGTTCCCGTCAACG 58.249 57.895 0.00 0.00 40.37 4.10
178 179 0.245539 GGAGATGTTCCCGTCAACGA 59.754 55.000 3.71 0.00 40.37 3.85
179 180 1.630148 GAGATGTTCCCGTCAACGAG 58.370 55.000 3.71 0.00 43.02 4.18
180 181 1.201647 GAGATGTTCCCGTCAACGAGA 59.798 52.381 3.71 0.00 43.02 4.04
181 182 1.202582 AGATGTTCCCGTCAACGAGAG 59.797 52.381 3.71 0.00 43.02 3.20
182 183 0.246635 ATGTTCCCGTCAACGAGAGG 59.753 55.000 3.71 0.00 43.02 3.69
183 184 1.737008 GTTCCCGTCAACGAGAGGC 60.737 63.158 3.71 0.00 43.02 4.70
184 185 2.939261 TTCCCGTCAACGAGAGGCC 61.939 63.158 3.71 0.00 43.02 5.19
185 186 3.382832 CCCGTCAACGAGAGGCCT 61.383 66.667 3.86 3.86 43.02 5.19
186 187 2.182030 CCGTCAACGAGAGGCCTC 59.818 66.667 26.22 26.22 43.02 4.70
187 188 2.344203 CCGTCAACGAGAGGCCTCT 61.344 63.158 35.74 35.74 43.78 3.69
194 195 2.973899 GAGAGGCCTCTCGTGCAA 59.026 61.111 39.93 0.00 45.49 4.08
195 196 1.446966 GAGAGGCCTCTCGTGCAAC 60.447 63.158 39.93 21.27 45.49 4.17
196 197 1.882989 GAGAGGCCTCTCGTGCAACT 61.883 60.000 39.93 15.76 45.49 3.16
197 198 0.612174 AGAGGCCTCTCGTGCAACTA 60.612 55.000 30.40 0.00 44.47 2.24
198 199 0.179124 GAGGCCTCTCGTGCAACTAG 60.179 60.000 26.25 0.00 31.75 2.57
199 200 1.153549 GGCCTCTCGTGCAACTAGG 60.154 63.158 0.00 0.00 33.57 3.02
200 201 1.811679 GCCTCTCGTGCAACTAGGC 60.812 63.158 13.06 13.06 44.00 3.93
201 202 1.517257 CCTCTCGTGCAACTAGGCG 60.517 63.158 0.00 0.00 36.28 5.52
202 203 2.126071 TCTCGTGCAACTAGGCGC 60.126 61.111 0.00 0.00 40.79 6.53
203 204 2.432456 CTCGTGCAACTAGGCGCA 60.432 61.111 10.83 4.37 44.30 6.09
204 205 2.027073 CTCGTGCAACTAGGCGCAA 61.027 57.895 10.83 0.00 44.30 4.85
205 206 2.173382 CGTGCAACTAGGCGCAAC 59.827 61.111 10.83 0.00 44.30 4.17
206 207 2.317609 CGTGCAACTAGGCGCAACT 61.318 57.895 10.83 0.00 44.30 3.16
207 208 1.011968 CGTGCAACTAGGCGCAACTA 61.012 55.000 10.83 0.75 44.30 2.24
208 209 0.442699 GTGCAACTAGGCGCAACTAC 59.557 55.000 10.83 0.00 43.57 2.73
209 210 0.034198 TGCAACTAGGCGCAACTACA 59.966 50.000 10.83 0.00 34.59 2.74
210 211 1.338674 TGCAACTAGGCGCAACTACAT 60.339 47.619 10.83 0.00 34.59 2.29
211 212 1.062587 GCAACTAGGCGCAACTACATG 59.937 52.381 10.83 3.47 0.00 3.21
212 213 2.346803 CAACTAGGCGCAACTACATGT 58.653 47.619 10.83 2.69 0.00 3.21
213 214 2.295253 ACTAGGCGCAACTACATGTC 57.705 50.000 10.83 0.00 0.00 3.06
214 215 1.825474 ACTAGGCGCAACTACATGTCT 59.175 47.619 10.83 0.00 0.00 3.41
215 216 2.196749 CTAGGCGCAACTACATGTCTG 58.803 52.381 10.83 0.00 0.00 3.51
216 217 0.321671 AGGCGCAACTACATGTCTGT 59.678 50.000 10.83 0.00 39.49 3.41
217 218 1.156736 GGCGCAACTACATGTCTGTT 58.843 50.000 10.83 6.47 36.79 3.16
218 219 1.535462 GGCGCAACTACATGTCTGTTT 59.465 47.619 10.83 0.00 36.79 2.83
219 220 2.412847 GGCGCAACTACATGTCTGTTTC 60.413 50.000 10.83 3.01 36.79 2.78
220 221 2.480419 GCGCAACTACATGTCTGTTTCT 59.520 45.455 0.00 0.00 36.79 2.52
221 222 3.423645 GCGCAACTACATGTCTGTTTCTC 60.424 47.826 0.00 0.00 36.79 2.87
222 223 3.740832 CGCAACTACATGTCTGTTTCTCA 59.259 43.478 0.00 0.00 36.79 3.27
223 224 4.376413 CGCAACTACATGTCTGTTTCTCAC 60.376 45.833 0.00 0.00 36.79 3.51
224 225 4.376413 GCAACTACATGTCTGTTTCTCACG 60.376 45.833 0.00 0.00 36.79 4.35
225 226 3.318017 ACTACATGTCTGTTTCTCACGC 58.682 45.455 0.00 0.00 36.79 5.34
226 227 2.238942 ACATGTCTGTTTCTCACGCA 57.761 45.000 0.00 0.00 28.70 5.24
227 228 1.867233 ACATGTCTGTTTCTCACGCAC 59.133 47.619 0.00 0.00 28.70 5.34
228 229 1.866601 CATGTCTGTTTCTCACGCACA 59.133 47.619 0.00 0.00 0.00 4.57
229 230 2.017138 TGTCTGTTTCTCACGCACAA 57.983 45.000 0.00 0.00 0.00 3.33
230 231 1.663643 TGTCTGTTTCTCACGCACAAC 59.336 47.619 0.00 0.00 0.00 3.32
231 232 1.933853 GTCTGTTTCTCACGCACAACT 59.066 47.619 0.00 0.00 0.00 3.16
232 233 3.120792 GTCTGTTTCTCACGCACAACTA 58.879 45.455 0.00 0.00 0.00 2.24
233 234 3.060473 GTCTGTTTCTCACGCACAACTAC 60.060 47.826 0.00 0.00 0.00 2.73
234 235 2.863740 CTGTTTCTCACGCACAACTACA 59.136 45.455 0.00 0.00 0.00 2.74
235 236 2.863740 TGTTTCTCACGCACAACTACAG 59.136 45.455 0.00 0.00 0.00 2.74
236 237 2.864343 GTTTCTCACGCACAACTACAGT 59.136 45.455 0.00 0.00 0.00 3.55
237 238 2.882927 TCTCACGCACAACTACAGTT 57.117 45.000 0.00 0.00 39.12 3.16
250 251 4.585955 ACTACAGTTGTATATCCGCTGG 57.414 45.455 0.00 0.00 0.00 4.85
251 252 3.958798 ACTACAGTTGTATATCCGCTGGT 59.041 43.478 0.00 0.00 0.00 4.00
252 253 3.454371 ACAGTTGTATATCCGCTGGTC 57.546 47.619 0.00 0.00 0.00 4.02
253 254 2.764010 ACAGTTGTATATCCGCTGGTCA 59.236 45.455 0.00 0.00 0.00 4.02
254 255 3.123804 CAGTTGTATATCCGCTGGTCAC 58.876 50.000 0.00 0.00 0.00 3.67
255 256 2.764010 AGTTGTATATCCGCTGGTCACA 59.236 45.455 0.00 0.00 0.00 3.58
256 257 2.864343 GTTGTATATCCGCTGGTCACAC 59.136 50.000 0.00 0.00 0.00 3.82
261 262 0.907704 ATCCGCTGGTCACACCCTAA 60.908 55.000 0.00 0.00 37.50 2.69
276 277 2.357760 TAAACGTCTGCCGGCCAC 60.358 61.111 26.77 19.64 42.24 5.01
319 320 4.424566 GCCCATGTGCAACTGCCG 62.425 66.667 0.00 0.00 41.18 5.69
327 328 1.153269 TGCAACTGCCGACTCAACA 60.153 52.632 0.00 0.00 41.18 3.33
332 333 2.805671 CAACTGCCGACTCAACATAACA 59.194 45.455 0.00 0.00 0.00 2.41
373 374 1.778334 CGCCTGCGTGCAACTATATA 58.222 50.000 2.83 0.00 34.35 0.86
409 410 5.073554 TGGGTGATGGAAAGCACTGATATAT 59.926 40.000 0.00 0.00 35.43 0.86
410 411 5.413833 GGGTGATGGAAAGCACTGATATATG 59.586 44.000 0.00 0.00 35.43 1.78
411 412 5.106396 GGTGATGGAAAGCACTGATATATGC 60.106 44.000 0.00 0.00 42.39 3.14
433 493 5.263185 GCTATGTGCATGGTTTAAAGTACG 58.737 41.667 0.00 0.00 42.31 3.67
434 494 5.163794 GCTATGTGCATGGTTTAAAGTACGT 60.164 40.000 0.00 0.00 42.31 3.57
455 690 2.028778 CCCTAGCTAGCTGCAGCG 59.971 66.667 31.78 20.25 46.52 5.18
489 724 0.749818 TGTGAGTGCGGGCTTTTTCA 60.750 50.000 0.00 0.00 0.00 2.69
494 729 1.963515 AGTGCGGGCTTTTTCATTCTT 59.036 42.857 0.00 0.00 0.00 2.52
495 730 2.029918 AGTGCGGGCTTTTTCATTCTTC 60.030 45.455 0.00 0.00 0.00 2.87
508 743 6.515272 TTTCATTCTTCCAGTTGGATTAGC 57.485 37.500 0.93 0.00 44.98 3.09
570 805 0.621571 TCAGAGGCAAGGTAGGGCAT 60.622 55.000 0.00 0.00 0.00 4.40
618 853 3.738282 GGAAGATGAATAGTGCTAGTGCG 59.262 47.826 0.00 0.00 43.34 5.34
782 1017 9.862371 AAATATATCTATGAAGTAGTCTTGCGG 57.138 33.333 0.00 0.00 33.64 5.69
879 1114 9.715119 AGTATGCATAATCTATACCATACTCCA 57.285 33.333 8.28 0.00 37.83 3.86
946 1181 1.556911 TGGCTAGAGGAAGAGGCAAAG 59.443 52.381 0.00 0.00 44.43 2.77
1202 1437 2.292192 CCCCACACCCCAATCTTATTGT 60.292 50.000 0.00 0.00 0.00 2.71
1253 1488 9.779237 CACTTTACGTTATCAAATTATAGAGCG 57.221 33.333 0.00 0.00 0.00 5.03
1255 1490 7.933728 TTACGTTATCAAATTATAGAGCGCA 57.066 32.000 11.47 0.00 0.00 6.09
1267 1508 6.828502 TTATAGAGCGCATCTTACAAAGTG 57.171 37.500 11.47 0.00 39.64 3.16
1346 1588 1.396653 CTGCCATTCAGGATTGGGAC 58.603 55.000 11.09 0.00 41.22 4.46
1365 1607 4.012374 GGACTGATGAGAAGCAATTCCAA 58.988 43.478 0.00 0.00 0.00 3.53
1561 1803 8.055181 ACTATCTTCATGGTATGTTGGTGATTT 58.945 33.333 0.00 0.00 0.00 2.17
1567 1809 6.597672 TCATGGTATGTTGGTGATTTCACTAC 59.402 38.462 10.32 9.29 45.73 2.73
1589 1832 2.613474 GGGTACGTTGGTCAGCATGTAA 60.613 50.000 0.00 0.00 37.40 2.41
1651 1895 5.709631 TGCTTGCAGAAAAATATACTGGACA 59.290 36.000 0.00 0.00 32.32 4.02
1809 2053 5.562890 GCGGATTTTGGAATATCAAGGCTAC 60.563 44.000 0.00 0.00 0.00 3.58
1817 2061 4.551388 GAATATCAAGGCTACTGGTCGAG 58.449 47.826 0.00 0.00 0.00 4.04
1835 2085 0.473326 AGGAATGCATCAGAGAGGCC 59.527 55.000 0.00 0.00 38.67 5.19
2194 2450 6.732896 AGTTTAGTACATCATCTAGGGTGG 57.267 41.667 0.00 0.00 0.00 4.61
2196 2452 6.324254 AGTTTAGTACATCATCTAGGGTGGAC 59.676 42.308 0.00 0.00 0.00 4.02
2205 2461 0.831307 CTAGGGTGGACTTAGGCACC 59.169 60.000 0.00 0.00 37.01 5.01
2219 2475 6.270156 CTTAGGCACCTAAGGTAGCTATAC 57.730 45.833 23.43 0.00 46.99 1.47
2220 2476 4.472690 AGGCACCTAAGGTAGCTATACT 57.527 45.455 0.00 0.00 32.11 2.12
2232 2502 3.099267 AGCTATACTGTGCATTCGGTC 57.901 47.619 0.00 0.00 0.00 4.79
2233 2503 2.695666 AGCTATACTGTGCATTCGGTCT 59.304 45.455 0.00 0.00 0.00 3.85
2234 2504 2.797156 GCTATACTGTGCATTCGGTCTG 59.203 50.000 0.00 0.00 0.00 3.51
2315 2652 6.627395 TTGATTTTGAAGGTACACGACAAT 57.373 33.333 0.00 0.00 0.00 2.71
2318 2655 6.261158 TGATTTTGAAGGTACACGACAATTGA 59.739 34.615 13.59 0.00 0.00 2.57
2344 2681 5.515008 GGAAAAGGTTTGAGGAGATACCACT 60.515 44.000 0.00 0.00 42.04 4.00
2404 2741 4.352039 ACTTGTATTGAGATCGCACTACG 58.648 43.478 17.72 9.93 45.62 3.51
2422 2759 0.668535 CGATGTACGGATCCTGAGCA 59.331 55.000 10.75 3.99 38.46 4.26
2423 2760 1.270826 CGATGTACGGATCCTGAGCAT 59.729 52.381 10.75 8.72 38.46 3.79
2488 2825 6.456003 TTCCAATACGAAGGATAGGGGTACC 61.456 48.000 2.17 2.17 40.43 3.34
2511 2848 3.787001 GGCCCGCTACAGCCTCTT 61.787 66.667 0.00 0.00 46.14 2.85
2515 2852 0.804989 CCCGCTACAGCCTCTTTTTG 59.195 55.000 0.00 0.00 37.91 2.44
2714 3186 7.636359 CGTGAACTGCTATAGCTTATTTGTTTC 59.364 37.037 24.61 14.24 42.66 2.78
2741 3213 3.417069 ACCGGAAGATTCACACATTCA 57.583 42.857 9.46 0.00 0.00 2.57
2770 3242 2.981859 ACCGCCATTCGAGTTTCTAT 57.018 45.000 0.00 0.00 41.67 1.98
2781 3253 9.098355 CCATTCGAGTTTCTATGAGAAATTACA 57.902 33.333 5.03 0.00 44.94 2.41
2817 3289 5.803020 AGGAACGAATAGTTTCTGAATGC 57.197 39.130 0.00 0.00 46.61 3.56
2825 3297 2.430465 AGTTTCTGAATGCGCATCTGT 58.570 42.857 25.53 8.32 0.00 3.41
2986 3458 9.967346 GATTTAGGGCAAGTAAAAAGGATATTC 57.033 33.333 0.00 0.00 0.00 1.75
3077 3549 4.142600 ACTCGGCTATTGCAATGAAAAGAC 60.143 41.667 22.27 12.18 41.91 3.01
3085 3557 3.218453 TGCAATGAAAAGACGAGGGAAA 58.782 40.909 0.00 0.00 0.00 3.13
3177 3649 5.450550 GCCAAATAGAAGCCTTGACCAATAC 60.451 44.000 0.00 0.00 0.00 1.89
3289 3761 1.364171 CAAGTAGGCCCTCGATCGG 59.636 63.158 16.41 5.93 0.00 4.18
3309 3781 7.810282 CGATCGGTCTATCATGTTCTAAGAAAT 59.190 37.037 7.38 0.00 0.00 2.17
3310 3782 9.482627 GATCGGTCTATCATGTTCTAAGAAATT 57.517 33.333 0.00 0.00 0.00 1.82
3311 3783 9.838339 ATCGGTCTATCATGTTCTAAGAAATTT 57.162 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.578928 GGTTGATGTGGTTGAAACAGTAGT 59.421 41.667 0.00 0.00 0.00 2.73
3 4 4.821805 AGGTTGATGTGGTTGAAACAGTAG 59.178 41.667 0.00 0.00 0.00 2.57
4 5 4.787551 AGGTTGATGTGGTTGAAACAGTA 58.212 39.130 0.00 0.00 0.00 2.74
5 6 3.631250 AGGTTGATGTGGTTGAAACAGT 58.369 40.909 0.00 0.00 0.00 3.55
6 7 5.063204 TCTAGGTTGATGTGGTTGAAACAG 58.937 41.667 0.00 0.00 0.00 3.16
7 8 5.042463 TCTAGGTTGATGTGGTTGAAACA 57.958 39.130 0.00 0.00 0.00 2.83
8 9 4.455877 CCTCTAGGTTGATGTGGTTGAAAC 59.544 45.833 0.00 0.00 0.00 2.78
9 10 4.651778 CCTCTAGGTTGATGTGGTTGAAA 58.348 43.478 0.00 0.00 0.00 2.69
10 11 3.559171 GCCTCTAGGTTGATGTGGTTGAA 60.559 47.826 0.00 0.00 37.57 2.69
11 12 2.027192 GCCTCTAGGTTGATGTGGTTGA 60.027 50.000 0.00 0.00 37.57 3.18
12 13 2.359900 GCCTCTAGGTTGATGTGGTTG 58.640 52.381 0.00 0.00 37.57 3.77
13 14 1.066143 CGCCTCTAGGTTGATGTGGTT 60.066 52.381 0.00 0.00 37.57 3.67
14 15 0.537188 CGCCTCTAGGTTGATGTGGT 59.463 55.000 0.00 0.00 37.57 4.16
15 16 0.824109 TCGCCTCTAGGTTGATGTGG 59.176 55.000 0.00 0.00 37.57 4.17
16 17 2.271800 GTTCGCCTCTAGGTTGATGTG 58.728 52.381 0.00 0.00 37.57 3.21
17 18 1.207329 GGTTCGCCTCTAGGTTGATGT 59.793 52.381 0.00 0.00 37.57 3.06
18 19 1.207089 TGGTTCGCCTCTAGGTTGATG 59.793 52.381 0.00 0.00 38.36 3.07
19 20 1.568504 TGGTTCGCCTCTAGGTTGAT 58.431 50.000 0.00 0.00 38.36 2.57
20 21 1.001633 GTTGGTTCGCCTCTAGGTTGA 59.998 52.381 0.00 0.00 38.36 3.18
21 22 1.439679 GTTGGTTCGCCTCTAGGTTG 58.560 55.000 0.00 0.00 38.36 3.77
22 23 0.323957 GGTTGGTTCGCCTCTAGGTT 59.676 55.000 0.00 0.00 38.36 3.50
23 24 0.544595 AGGTTGGTTCGCCTCTAGGT 60.545 55.000 0.00 0.00 38.36 3.08
24 25 0.108138 CAGGTTGGTTCGCCTCTAGG 60.108 60.000 0.00 0.00 38.36 3.02
25 26 0.741221 GCAGGTTGGTTCGCCTCTAG 60.741 60.000 0.00 0.00 38.36 2.43
26 27 1.295423 GCAGGTTGGTTCGCCTCTA 59.705 57.895 0.00 0.00 38.36 2.43
27 28 2.032681 GCAGGTTGGTTCGCCTCT 59.967 61.111 0.00 0.00 38.36 3.69
28 29 3.423154 CGCAGGTTGGTTCGCCTC 61.423 66.667 0.00 0.00 38.36 4.70
41 42 1.656652 CTCTAACCATCCAACCGCAG 58.343 55.000 0.00 0.00 0.00 5.18
42 43 0.251916 CCTCTAACCATCCAACCGCA 59.748 55.000 0.00 0.00 0.00 5.69
43 44 0.463833 CCCTCTAACCATCCAACCGC 60.464 60.000 0.00 0.00 0.00 5.68
44 45 1.134491 GTCCCTCTAACCATCCAACCG 60.134 57.143 0.00 0.00 0.00 4.44
45 46 2.092914 CAGTCCCTCTAACCATCCAACC 60.093 54.545 0.00 0.00 0.00 3.77
46 47 2.572104 ACAGTCCCTCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
47 48 2.571653 CACAGTCCCTCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
48 49 2.187958 CACAGTCCCTCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
49 50 1.486726 CCACAGTCCCTCTAACCATCC 59.513 57.143 0.00 0.00 0.00 3.51
50 51 2.188817 ACCACAGTCCCTCTAACCATC 58.811 52.381 0.00 0.00 0.00 3.51
51 52 2.344093 ACCACAGTCCCTCTAACCAT 57.656 50.000 0.00 0.00 0.00 3.55
52 53 3.371965 GATACCACAGTCCCTCTAACCA 58.628 50.000 0.00 0.00 0.00 3.67
53 54 2.699321 GGATACCACAGTCCCTCTAACC 59.301 54.545 0.00 0.00 0.00 2.85
75 76 2.806945 TTTGAACCCTGATAGGCTGG 57.193 50.000 0.00 0.00 32.73 4.85
76 77 3.117738 AGGATTTGAACCCTGATAGGCTG 60.118 47.826 0.00 0.00 32.73 4.85
77 78 3.126453 AGGATTTGAACCCTGATAGGCT 58.874 45.455 0.00 0.00 32.73 4.58
78 79 3.584733 AGGATTTGAACCCTGATAGGC 57.415 47.619 0.00 0.00 32.73 3.93
85 86 2.681976 CGAGCATCAGGATTTGAACCCT 60.682 50.000 0.00 0.00 39.77 4.34
86 87 1.672881 CGAGCATCAGGATTTGAACCC 59.327 52.381 0.00 0.00 39.77 4.11
87 88 1.064654 GCGAGCATCAGGATTTGAACC 59.935 52.381 0.00 0.00 39.77 3.62
88 89 1.739466 TGCGAGCATCAGGATTTGAAC 59.261 47.619 0.00 0.00 39.77 3.18
89 90 2.112380 TGCGAGCATCAGGATTTGAA 57.888 45.000 0.00 0.00 39.77 2.69
90 91 2.336945 ATGCGAGCATCAGGATTTGA 57.663 45.000 4.52 0.00 40.85 2.69
91 92 3.431922 AAATGCGAGCATCAGGATTTG 57.568 42.857 11.26 0.00 37.87 2.32
92 93 5.278660 GGAATAAATGCGAGCATCAGGATTT 60.279 40.000 11.26 4.40 40.41 2.17
93 94 4.217118 GGAATAAATGCGAGCATCAGGATT 59.783 41.667 11.26 8.31 35.31 3.01
94 95 3.755378 GGAATAAATGCGAGCATCAGGAT 59.245 43.478 11.26 0.39 35.31 3.24
95 96 3.141398 GGAATAAATGCGAGCATCAGGA 58.859 45.455 11.26 0.00 35.31 3.86
96 97 3.058432 CAGGAATAAATGCGAGCATCAGG 60.058 47.826 11.26 0.00 35.31 3.86
97 98 3.058432 CCAGGAATAAATGCGAGCATCAG 60.058 47.826 11.26 0.00 35.31 2.90
98 99 2.880268 CCAGGAATAAATGCGAGCATCA 59.120 45.455 11.26 3.11 35.31 3.07
99 100 3.141398 TCCAGGAATAAATGCGAGCATC 58.859 45.455 11.26 0.00 35.31 3.91
100 101 3.213206 TCCAGGAATAAATGCGAGCAT 57.787 42.857 4.52 4.52 38.46 3.79
101 102 2.708216 TCCAGGAATAAATGCGAGCA 57.292 45.000 0.00 0.00 0.00 4.26
102 103 4.574599 AAATCCAGGAATAAATGCGAGC 57.425 40.909 0.00 0.00 0.00 5.03
103 104 8.352201 TGAAATAAATCCAGGAATAAATGCGAG 58.648 33.333 0.00 0.00 0.00 5.03
104 105 8.231692 TGAAATAAATCCAGGAATAAATGCGA 57.768 30.769 0.00 0.00 0.00 5.10
105 106 8.511465 CTGAAATAAATCCAGGAATAAATGCG 57.489 34.615 0.00 0.00 0.00 4.73
115 116 5.010012 CCGGAAATCCTGAAATAAATCCAGG 59.990 44.000 0.00 0.00 46.64 4.45
116 117 5.507985 GCCGGAAATCCTGAAATAAATCCAG 60.508 44.000 5.05 0.00 0.00 3.86
117 118 4.340950 GCCGGAAATCCTGAAATAAATCCA 59.659 41.667 5.05 0.00 0.00 3.41
118 119 4.556699 CGCCGGAAATCCTGAAATAAATCC 60.557 45.833 5.05 0.00 0.00 3.01
119 120 4.274950 TCGCCGGAAATCCTGAAATAAATC 59.725 41.667 5.05 0.00 0.00 2.17
120 121 4.204012 TCGCCGGAAATCCTGAAATAAAT 58.796 39.130 5.05 0.00 0.00 1.40
121 122 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
122 123 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
123 124 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
124 125 1.949525 CATCGCCGGAAATCCTGAAAT 59.050 47.619 5.05 0.00 0.00 2.17
125 126 1.378531 CATCGCCGGAAATCCTGAAA 58.621 50.000 5.05 0.00 0.00 2.69
126 127 1.095228 GCATCGCCGGAAATCCTGAA 61.095 55.000 5.05 0.00 0.00 3.02
127 128 1.523711 GCATCGCCGGAAATCCTGA 60.524 57.895 5.05 0.00 0.00 3.86
128 129 2.885676 CGCATCGCCGGAAATCCTG 61.886 63.158 5.05 0.00 0.00 3.86
129 130 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
140 141 1.769098 CTCCCACTGAATGCGCATCG 61.769 60.000 25.53 17.09 0.00 3.84
141 142 1.442526 CCTCCCACTGAATGCGCATC 61.443 60.000 25.53 17.12 0.00 3.91
142 143 1.452651 CCTCCCACTGAATGCGCAT 60.453 57.895 19.28 19.28 0.00 4.73
143 144 2.046023 CCTCCCACTGAATGCGCA 60.046 61.111 14.96 14.96 0.00 6.09
144 145 1.817099 CTCCTCCCACTGAATGCGC 60.817 63.158 0.00 0.00 0.00 6.09
145 146 0.467384 ATCTCCTCCCACTGAATGCG 59.533 55.000 0.00 0.00 0.00 4.73
146 147 1.211457 ACATCTCCTCCCACTGAATGC 59.789 52.381 0.00 0.00 0.00 3.56
147 148 3.539604 GAACATCTCCTCCCACTGAATG 58.460 50.000 0.00 0.00 0.00 2.67
148 149 2.507471 GGAACATCTCCTCCCACTGAAT 59.493 50.000 0.00 0.00 41.61 2.57
149 150 1.909302 GGAACATCTCCTCCCACTGAA 59.091 52.381 0.00 0.00 41.61 3.02
150 151 1.573108 GGAACATCTCCTCCCACTGA 58.427 55.000 0.00 0.00 41.61 3.41
155 156 0.976073 TGACGGGAACATCTCCTCCC 60.976 60.000 0.00 0.00 46.97 4.30
156 157 0.902531 TTGACGGGAACATCTCCTCC 59.097 55.000 0.00 0.00 44.68 4.30
157 158 1.736032 CGTTGACGGGAACATCTCCTC 60.736 57.143 0.00 0.00 44.68 3.71
158 159 0.246635 CGTTGACGGGAACATCTCCT 59.753 55.000 0.00 0.00 44.68 3.69
159 160 0.245539 TCGTTGACGGGAACATCTCC 59.754 55.000 3.48 0.00 44.54 3.71
160 161 1.630148 CTCGTTGACGGGAACATCTC 58.370 55.000 0.00 0.00 43.86 2.75
161 162 3.814577 CTCGTTGACGGGAACATCT 57.185 52.632 0.00 0.00 43.86 2.90
168 169 3.358076 GAGGCCTCTCGTTGACGGG 62.358 68.421 26.25 0.00 42.17 5.28
169 170 2.182030 GAGGCCTCTCGTTGACGG 59.818 66.667 26.25 0.00 40.29 4.79
170 171 1.137825 GAGAGGCCTCTCGTTGACG 59.862 63.158 39.93 0.00 45.49 4.35
178 179 0.612174 TAGTTGCACGAGAGGCCTCT 60.612 55.000 35.74 35.74 43.78 3.69
179 180 0.179124 CTAGTTGCACGAGAGGCCTC 60.179 60.000 26.22 26.22 36.08 4.70
180 181 1.608717 CCTAGTTGCACGAGAGGCCT 61.609 60.000 3.86 3.86 0.00 5.19
181 182 1.153549 CCTAGTTGCACGAGAGGCC 60.154 63.158 0.00 0.00 0.00 5.19
182 183 1.811679 GCCTAGTTGCACGAGAGGC 60.812 63.158 11.22 11.22 45.48 4.70
183 184 1.517257 CGCCTAGTTGCACGAGAGG 60.517 63.158 0.00 0.00 0.00 3.69
184 185 2.161486 GCGCCTAGTTGCACGAGAG 61.161 63.158 0.00 0.00 0.00 3.20
185 186 2.126071 GCGCCTAGTTGCACGAGA 60.126 61.111 0.00 0.00 0.00 4.04
186 187 2.027073 TTGCGCCTAGTTGCACGAG 61.027 57.895 4.18 0.00 41.57 4.18
187 188 2.029815 TTGCGCCTAGTTGCACGA 59.970 55.556 4.18 0.00 41.57 4.35
188 189 1.011968 TAGTTGCGCCTAGTTGCACG 61.012 55.000 4.18 0.00 41.57 5.34
189 190 0.442699 GTAGTTGCGCCTAGTTGCAC 59.557 55.000 4.18 2.84 41.57 4.57
190 191 0.034198 TGTAGTTGCGCCTAGTTGCA 59.966 50.000 4.18 2.26 39.81 4.08
191 192 1.062587 CATGTAGTTGCGCCTAGTTGC 59.937 52.381 4.18 0.00 0.00 4.17
192 193 2.346803 ACATGTAGTTGCGCCTAGTTG 58.653 47.619 4.18 3.37 0.00 3.16
193 194 2.233922 AGACATGTAGTTGCGCCTAGTT 59.766 45.455 4.18 0.00 0.00 2.24
194 195 1.825474 AGACATGTAGTTGCGCCTAGT 59.175 47.619 4.18 0.00 0.00 2.57
195 196 2.196749 CAGACATGTAGTTGCGCCTAG 58.803 52.381 4.18 0.00 0.00 3.02
196 197 1.548719 ACAGACATGTAGTTGCGCCTA 59.451 47.619 4.18 0.00 38.09 3.93
197 198 0.321671 ACAGACATGTAGTTGCGCCT 59.678 50.000 4.18 0.00 38.09 5.52
198 199 1.156736 AACAGACATGTAGTTGCGCC 58.843 50.000 13.59 0.00 39.29 6.53
199 200 2.480419 AGAAACAGACATGTAGTTGCGC 59.520 45.455 14.72 0.00 39.29 6.09
200 201 3.740832 TGAGAAACAGACATGTAGTTGCG 59.259 43.478 14.72 0.00 39.29 4.85
201 202 4.376413 CGTGAGAAACAGACATGTAGTTGC 60.376 45.833 14.72 13.26 39.29 4.17
202 203 4.376413 GCGTGAGAAACAGACATGTAGTTG 60.376 45.833 14.72 9.25 39.29 3.16
203 204 3.741344 GCGTGAGAAACAGACATGTAGTT 59.259 43.478 0.00 4.17 39.29 2.24
204 205 3.243737 TGCGTGAGAAACAGACATGTAGT 60.244 43.478 0.00 0.00 39.29 2.73
205 206 3.121944 GTGCGTGAGAAACAGACATGTAG 59.878 47.826 0.00 0.00 39.29 2.74
206 207 3.057019 GTGCGTGAGAAACAGACATGTA 58.943 45.455 0.00 0.00 39.29 2.29
207 208 1.867233 GTGCGTGAGAAACAGACATGT 59.133 47.619 0.00 0.00 43.15 3.21
208 209 1.866601 TGTGCGTGAGAAACAGACATG 59.133 47.619 0.00 0.00 0.00 3.21
209 210 2.238942 TGTGCGTGAGAAACAGACAT 57.761 45.000 0.00 0.00 0.00 3.06
210 211 1.663643 GTTGTGCGTGAGAAACAGACA 59.336 47.619 0.00 0.00 32.09 3.41
211 212 1.933853 AGTTGTGCGTGAGAAACAGAC 59.066 47.619 0.00 0.00 32.09 3.51
212 213 2.309528 AGTTGTGCGTGAGAAACAGA 57.690 45.000 0.00 0.00 32.09 3.41
213 214 2.863740 TGTAGTTGTGCGTGAGAAACAG 59.136 45.455 0.00 0.00 32.09 3.16
214 215 2.863740 CTGTAGTTGTGCGTGAGAAACA 59.136 45.455 0.00 0.00 0.00 2.83
215 216 2.864343 ACTGTAGTTGTGCGTGAGAAAC 59.136 45.455 0.00 0.00 0.00 2.78
216 217 3.173668 ACTGTAGTTGTGCGTGAGAAA 57.826 42.857 0.00 0.00 0.00 2.52
217 218 2.882927 ACTGTAGTTGTGCGTGAGAA 57.117 45.000 0.00 0.00 0.00 2.87
218 219 2.882927 AACTGTAGTTGTGCGTGAGA 57.117 45.000 0.00 0.00 36.80 3.27
228 229 4.404715 ACCAGCGGATATACAACTGTAGTT 59.595 41.667 4.67 0.00 39.12 2.24
229 230 3.958798 ACCAGCGGATATACAACTGTAGT 59.041 43.478 4.67 0.00 33.52 2.73
230 231 4.037565 TGACCAGCGGATATACAACTGTAG 59.962 45.833 4.67 0.00 33.52 2.74
231 232 3.955551 TGACCAGCGGATATACAACTGTA 59.044 43.478 4.67 0.00 34.67 2.74
232 233 2.764010 TGACCAGCGGATATACAACTGT 59.236 45.455 4.67 0.00 0.00 3.55
233 234 3.123804 GTGACCAGCGGATATACAACTG 58.876 50.000 1.50 0.00 0.00 3.16
234 235 2.764010 TGTGACCAGCGGATATACAACT 59.236 45.455 1.50 0.00 0.00 3.16
235 236 2.864343 GTGTGACCAGCGGATATACAAC 59.136 50.000 1.50 0.00 0.00 3.32
236 237 2.159014 GGTGTGACCAGCGGATATACAA 60.159 50.000 1.50 0.00 38.42 2.41
237 238 1.411246 GGTGTGACCAGCGGATATACA 59.589 52.381 1.50 0.00 38.42 2.29
238 239 1.270147 GGGTGTGACCAGCGGATATAC 60.270 57.143 1.50 0.00 41.02 1.47
239 240 1.045407 GGGTGTGACCAGCGGATATA 58.955 55.000 1.50 0.00 41.02 0.86
240 241 0.691078 AGGGTGTGACCAGCGGATAT 60.691 55.000 1.50 0.00 41.02 1.63
241 242 0.032912 TAGGGTGTGACCAGCGGATA 60.033 55.000 1.50 0.00 41.02 2.59
242 243 0.907704 TTAGGGTGTGACCAGCGGAT 60.908 55.000 1.50 0.00 41.02 4.18
243 244 1.122632 TTTAGGGTGTGACCAGCGGA 61.123 55.000 1.50 0.00 41.02 5.54
244 245 0.953960 GTTTAGGGTGTGACCAGCGG 60.954 60.000 0.00 0.00 41.02 5.52
245 246 1.289109 CGTTTAGGGTGTGACCAGCG 61.289 60.000 0.00 0.00 41.02 5.18
246 247 0.250166 ACGTTTAGGGTGTGACCAGC 60.250 55.000 0.00 0.00 41.02 4.85
247 248 1.343465 AGACGTTTAGGGTGTGACCAG 59.657 52.381 0.00 0.00 41.02 4.00
248 249 1.069513 CAGACGTTTAGGGTGTGACCA 59.930 52.381 0.00 0.00 41.02 4.02
249 250 1.792006 CAGACGTTTAGGGTGTGACC 58.208 55.000 0.00 0.00 37.60 4.02
250 251 1.145803 GCAGACGTTTAGGGTGTGAC 58.854 55.000 0.00 0.00 30.84 3.67
251 252 0.034337 GGCAGACGTTTAGGGTGTGA 59.966 55.000 0.00 0.00 30.84 3.58
252 253 1.289109 CGGCAGACGTTTAGGGTGTG 61.289 60.000 0.00 0.00 37.93 3.82
253 254 1.005394 CGGCAGACGTTTAGGGTGT 60.005 57.895 0.00 0.00 37.93 4.16
254 255 1.740296 CCGGCAGACGTTTAGGGTG 60.740 63.158 0.00 0.00 42.24 4.61
255 256 2.660802 CCGGCAGACGTTTAGGGT 59.339 61.111 0.00 0.00 42.24 4.34
256 257 2.818274 GCCGGCAGACGTTTAGGG 60.818 66.667 24.80 0.00 42.24 3.53
261 262 4.988598 CTGTGGCCGGCAGACGTT 62.989 66.667 30.85 0.00 42.24 3.99
276 277 1.300388 GTGCAGTTGCCTTTGCCTG 60.300 57.895 1.06 0.00 39.54 4.85
306 307 0.534877 TTGAGTCGGCAGTTGCACAT 60.535 50.000 6.43 0.00 44.36 3.21
319 320 6.738200 CGATGAATGTGTTGTTATGTTGAGTC 59.262 38.462 0.00 0.00 0.00 3.36
327 328 3.128589 GTGGCCGATGAATGTGTTGTTAT 59.871 43.478 0.00 0.00 0.00 1.89
332 333 2.566824 GGTGGCCGATGAATGTGTT 58.433 52.632 0.00 0.00 0.00 3.32
373 374 3.025978 CCATCACCCAATGTGCAACTAT 58.974 45.455 0.00 0.00 45.03 2.12
384 385 1.144708 TCAGTGCTTTCCATCACCCAA 59.855 47.619 0.00 0.00 33.90 4.12
410 411 5.163794 ACGTACTTTAAACCATGCACATAGC 60.164 40.000 0.00 0.00 45.96 2.97
411 412 6.417191 ACGTACTTTAAACCATGCACATAG 57.583 37.500 0.00 0.00 0.00 2.23
455 690 3.065371 CACTCACACCTTTCAAGTTGGAC 59.935 47.826 2.34 0.00 0.00 4.02
494 729 3.186554 GCTCCGGCTAATCCAACTGGA 62.187 57.143 0.00 0.00 41.21 3.86
495 730 0.815615 GCTCCGGCTAATCCAACTGG 60.816 60.000 0.00 0.00 35.22 4.00
570 805 0.469331 ATGCCGATCTTCCCCGTCTA 60.469 55.000 0.00 0.00 0.00 2.59
618 853 2.415512 GGTTGGTGAATCTAACGACTGC 59.584 50.000 0.00 0.00 38.21 4.40
779 1014 1.821216 TTTGGAGAAATCTGGACCGC 58.179 50.000 0.00 0.00 0.00 5.68
782 1017 6.000840 AGAACTCTTTTGGAGAAATCTGGAC 58.999 40.000 0.00 0.00 44.45 4.02
879 1114 7.308589 GCAGAAACACACTGACCAATATAAACT 60.309 37.037 0.00 0.00 37.54 2.66
946 1181 1.138266 TGAGCAACGGGTATAGCTTCC 59.862 52.381 0.00 0.00 37.48 3.46
1226 1461 9.582223 GCTCTATAATTTGATAACGTAAAGTGC 57.418 33.333 0.00 0.00 0.00 4.40
1253 1488 4.096833 TCATGATGCCACTTTGTAAGATGC 59.903 41.667 0.00 0.00 0.00 3.91
1255 1490 8.408601 GTTATTCATGATGCCACTTTGTAAGAT 58.591 33.333 0.00 0.00 0.00 2.40
1267 1508 5.449588 CCTGTTCACAGTTATTCATGATGCC 60.450 44.000 6.22 0.00 42.27 4.40
1346 1588 4.855388 CGTTTTGGAATTGCTTCTCATCAG 59.145 41.667 0.00 0.00 0.00 2.90
1365 1607 5.636543 CCTCTTAAGGTGTTCGTATTCGTTT 59.363 40.000 1.85 0.00 37.94 3.60
1567 1809 1.079405 ATGCTGACCAACGTACCCG 60.079 57.895 0.00 0.00 40.83 5.28
1651 1895 1.519408 GAACCGTGTGTGCCAACTAT 58.481 50.000 0.00 0.00 0.00 2.12
1778 2022 7.769272 TGATATTCCAAAATCCGCAATTTTC 57.231 32.000 4.30 0.00 44.04 2.29
1809 2053 1.137675 TCTGATGCATTCCTCGACCAG 59.862 52.381 0.00 0.66 0.00 4.00
1817 2061 0.182061 TGGCCTCTCTGATGCATTCC 59.818 55.000 3.32 0.00 0.00 3.01
1835 2085 4.631813 GCTTACATTGTCCCTAACTGAGTG 59.368 45.833 0.00 0.00 0.00 3.51
1957 2212 4.371681 ACTCCCTTGGTATGTATCCACTT 58.628 43.478 0.00 0.00 34.45 3.16
2205 2461 5.859114 CGAATGCACAGTATAGCTACCTTAG 59.141 44.000 0.00 0.00 0.00 2.18
2210 2466 3.978687 ACCGAATGCACAGTATAGCTAC 58.021 45.455 0.00 0.00 0.00 3.58
2213 2469 2.797156 CAGACCGAATGCACAGTATAGC 59.203 50.000 0.00 0.00 0.00 2.97
2216 2472 2.233676 TGACAGACCGAATGCACAGTAT 59.766 45.455 0.00 0.00 0.00 2.12
2219 2475 1.073964 CTGACAGACCGAATGCACAG 58.926 55.000 0.00 0.00 0.00 3.66
2220 2476 0.392706 ACTGACAGACCGAATGCACA 59.607 50.000 10.08 0.00 0.00 4.57
2233 2503 4.034285 TCTATCACTGTCTCCACTGACA 57.966 45.455 0.00 0.00 43.72 3.58
2234 2504 4.400884 ACATCTATCACTGTCTCCACTGAC 59.599 45.833 0.00 0.00 37.47 3.51
2315 2652 5.124036 TCTCCTCAAACCTTTTCCTTCAA 57.876 39.130 0.00 0.00 0.00 2.69
2318 2655 5.074515 TGGTATCTCCTCAAACCTTTTCCTT 59.925 40.000 0.00 0.00 37.07 3.36
2344 2681 7.938490 TGCAATATTCTTCAAGCCATAGATACA 59.062 33.333 0.00 0.00 0.00 2.29
2404 2741 2.560542 AGATGCTCAGGATCCGTACATC 59.439 50.000 22.27 22.27 34.14 3.06
2410 2747 4.753233 CCTATTAAGATGCTCAGGATCCG 58.247 47.826 5.98 1.36 0.00 4.18
2415 2752 4.322567 GAAGGCCTATTAAGATGCTCAGG 58.677 47.826 5.16 0.00 0.00 3.86
2416 2753 3.993081 CGAAGGCCTATTAAGATGCTCAG 59.007 47.826 5.16 0.00 0.00 3.35
2422 2759 7.009179 TGATTCATCGAAGGCCTATTAAGAT 57.991 36.000 5.16 4.02 0.00 2.40
2423 2760 6.419484 TGATTCATCGAAGGCCTATTAAGA 57.581 37.500 5.16 1.37 0.00 2.10
2488 2825 0.037232 GGCTGTAGCGGGCCTATAAG 60.037 60.000 0.84 0.00 44.48 1.73
2497 2834 0.804989 CCAAAAAGAGGCTGTAGCGG 59.195 55.000 0.00 0.00 43.26 5.52
2511 2848 0.039035 AACCTAGATGCCGGCCAAAA 59.961 50.000 26.77 4.98 0.00 2.44
2515 2852 1.947456 CTTTAAACCTAGATGCCGGCC 59.053 52.381 26.77 9.73 0.00 6.13
2517 2854 4.761975 TGTACTTTAAACCTAGATGCCGG 58.238 43.478 0.00 0.00 0.00 6.13
2518 2855 6.920569 AATGTACTTTAAACCTAGATGCCG 57.079 37.500 0.00 0.00 0.00 5.69
2714 3186 3.372206 GTGTGAATCTTCCGGTTCTGATG 59.628 47.826 0.00 0.00 0.00 3.07
2741 3213 0.881118 GAATGGCGGTTCACATGTGT 59.119 50.000 24.63 2.49 0.00 3.72
2753 3225 3.706698 TCTCATAGAAACTCGAATGGCG 58.293 45.455 0.00 0.00 42.69 5.69
2781 3253 9.981114 ACTATTCGTTCCTTTGAAAAATCATTT 57.019 25.926 0.00 0.00 30.79 2.32
2817 3289 5.460646 ACCTTAAAAATTGTCACAGATGCG 58.539 37.500 0.00 0.00 0.00 4.73
2825 3297 7.817418 AGCAGAAGTACCTTAAAAATTGTCA 57.183 32.000 0.00 0.00 0.00 3.58
2884 3356 6.997476 TCTATCAGTAAATGCATGCATGGTAA 59.003 34.615 32.79 16.71 36.68 2.85
2951 3423 3.282885 CTTGCCCTAAATCTCTTCACCC 58.717 50.000 0.00 0.00 0.00 4.61
2986 3458 6.656693 ACTTCATTCTGAAACACCTTATCTGG 59.343 38.462 0.00 0.00 35.73 3.86
3077 3549 1.402968 CATGCTTCATGGTTTCCCTCG 59.597 52.381 0.00 0.00 38.11 4.63
3085 3557 0.107508 CTCCCGTCATGCTTCATGGT 60.108 55.000 6.92 0.00 41.66 3.55
3088 3560 5.946942 ATATATCTCCCGTCATGCTTCAT 57.053 39.130 0.00 0.00 0.00 2.57
3311 3783 6.723298 ACAAATGGGTCATCACTACAAAAA 57.277 33.333 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.