Multiple sequence alignment - TraesCS2A01G417200

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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 TraesCS2A01G417200 chr2A 100.000 3011 0 0 1 3011 673278485 673275475 0.000000e+00 5561
1 TraesCS2A01G417200 chr2A 91.581 879 74 0 2133 3011 179275158 179276036 0.000000e+00 1214
2 TraesCS2A01G417200 chr2A 87.893 1049 97 17 1000 2019 673196134 673195087 0.000000e+00 1206
3 TraesCS2A01G417200 chr2A 96.528 288 8 2 1 286 79464642 79464355 2.720000e-130 475
4 TraesCS2A01G417200 chr2A 94.631 298 12 4 1 296 752305932 752305637 2.740000e-125 459
5 TraesCS2A01G417200 chr2B 92.229 1853 96 23 280 2126 626884976 626883166 0.000000e+00 2580
6 TraesCS2A01G417200 chr2B 88.953 1032 93 9 1000 2013 626651901 626650873 0.000000e+00 1254
7 TraesCS2A01G417200 chr2B 81.111 180 23 7 386 563 626652456 626652286 1.880000e-27 134
8 TraesCS2A01G417200 chr2B 82.895 152 22 4 1448 1597 627073521 627073670 1.880000e-27 134
9 TraesCS2A01G417200 chr2D 91.492 1857 115 14 280 2126 528590751 528588928 0.000000e+00 2514
10 TraesCS2A01G417200 chr2D 86.977 1052 112 13 1000 2028 528473772 528472723 0.000000e+00 1160
11 TraesCS2A01G417200 chr2D 79.592 245 29 16 325 563 528474364 528474135 4.020000e-34 156
12 TraesCS2A01G417200 chr3A 92.150 879 69 0 2133 3011 702516789 702515911 0.000000e+00 1242
13 TraesCS2A01G417200 chr4A 90.557 879 83 0 2133 3011 632629975 632630853 0.000000e+00 1164
14 TraesCS2A01G417200 chr4A 86.689 879 116 1 2133 3011 700975008 700975885 0.000000e+00 974
15 TraesCS2A01G417200 chr4A 95.819 287 10 2 1 286 95596657 95596372 2.110000e-126 462
16 TraesCS2A01G417200 chr4A 94.333 300 16 1 1 299 13248088 13247789 2.740000e-125 459
17 TraesCS2A01G417200 chr5B 89.192 879 95 0 2133 3011 364100658 364099780 0.000000e+00 1098
18 TraesCS2A01G417200 chr7B 87.927 878 100 6 2137 3011 484929807 484928933 0.000000e+00 1029
19 TraesCS2A01G417200 chr6B 87.827 879 99 8 2137 3011 18601392 18600518 0.000000e+00 1024
20 TraesCS2A01G417200 chr6B 87.358 878 103 7 2137 3011 573337784 573338656 0.000000e+00 1000
21 TraesCS2A01G417200 chr6B 88.152 211 23 2 1436 1645 506835964 506835755 1.790000e-62 250
22 TraesCS2A01G417200 chr3B 87.486 879 110 0 2133 3011 629908045 629908923 0.000000e+00 1014
23 TraesCS2A01G417200 chr5A 96.864 287 8 1 1 286 47961386 47961672 2.100000e-131 479
24 TraesCS2A01G417200 chr5A 95.819 287 11 1 1 286 23891207 23890921 2.110000e-126 462
25 TraesCS2A01G417200 chr7A 96.167 287 10 1 1 286 452624847 452624561 4.550000e-128 468
26 TraesCS2A01G417200 chr1A 95.833 288 10 2 1 286 278675366 278675079 5.880000e-127 464
27 TraesCS2A01G417200 chr6A 94.613 297 14 2 1 295 16353555 16353259 2.740000e-125 459
28 TraesCS2A01G417200 chr6A 88.626 211 22 2 1436 1645 454934506 454934715 3.850000e-64 255
29 TraesCS2A01G417200 chr6D 88.152 211 23 2 1436 1645 317414354 317414563 1.790000e-62 250


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 TraesCS2A01G417200 chr2A 673275475 673278485 3010 True 5561 5561 100.0000 1 3011 1 chr2A.!!$R3 3010
1 TraesCS2A01G417200 chr2A 179275158 179276036 878 False 1214 1214 91.5810 2133 3011 1 chr2A.!!$F1 878
2 TraesCS2A01G417200 chr2A 673195087 673196134 1047 True 1206 1206 87.8930 1000 2019 1 chr2A.!!$R2 1019
3 TraesCS2A01G417200 chr2B 626883166 626884976 1810 True 2580 2580 92.2290 280 2126 1 chr2B.!!$R1 1846
4 TraesCS2A01G417200 chr2B 626650873 626652456 1583 True 694 1254 85.0320 386 2013 2 chr2B.!!$R2 1627
5 TraesCS2A01G417200 chr2D 528588928 528590751 1823 True 2514 2514 91.4920 280 2126 1 chr2D.!!$R1 1846
6 TraesCS2A01G417200 chr2D 528472723 528474364 1641 True 658 1160 83.2845 325 2028 2 chr2D.!!$R2 1703
7 TraesCS2A01G417200 chr3A 702515911 702516789 878 True 1242 1242 92.1500 2133 3011 1 chr3A.!!$R1 878
8 TraesCS2A01G417200 chr4A 632629975 632630853 878 False 1164 1164 90.5570 2133 3011 1 chr4A.!!$F1 878
9 TraesCS2A01G417200 chr4A 700975008 700975885 877 False 974 974 86.6890 2133 3011 1 chr4A.!!$F2 878
10 TraesCS2A01G417200 chr5B 364099780 364100658 878 True 1098 1098 89.1920 2133 3011 1 chr5B.!!$R1 878
11 TraesCS2A01G417200 chr7B 484928933 484929807 874 True 1029 1029 87.9270 2137 3011 1 chr7B.!!$R1 874
12 TraesCS2A01G417200 chr6B 18600518 18601392 874 True 1024 1024 87.8270 2137 3011 1 chr6B.!!$R1 874
13 TraesCS2A01G417200 chr6B 573337784 573338656 872 False 1000 1000 87.3580 2137 3011 1 chr6B.!!$F1 874
14 TraesCS2A01G417200 chr3B 629908045 629908923 878 False 1014 1014 87.4860 2133 3011 1 chr3B.!!$F1 878

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
260 261 0.030235 GGGGGCGATTTTTATGCGTC 59.970 55.0 0.00 0.00 0.00 5.19 F
814 898 0.588252 GCGTACATGCATAGGCCTTG 59.412 55.0 12.58 10.73 40.13 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 1347 0.611200 CGTCAGGTCCATGTAACCCA 59.389 55.0 10.15 0.00 37.52 4.51 R
2351 2493 0.532417 GCATAGGAGGCTGCTCTGTG 60.532 60.0 13.31 11.39 35.49 3.66 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
69 70 9.885743 GAAATAATTGTGTTGATAATTGAACGC 57.114 29.630 0.00 0.00 33.96 4.84
70 71 7.985634 ATAATTGTGTTGATAATTGAACGCC 57.014 32.000 0.00 0.00 32.66 5.68
71 72 3.463533 TGTGTTGATAATTGAACGCCG 57.536 42.857 0.00 0.00 32.66 6.46
72 73 3.067833 TGTGTTGATAATTGAACGCCGA 58.932 40.909 0.00 0.00 32.66 5.54
73 74 3.498777 TGTGTTGATAATTGAACGCCGAA 59.501 39.130 0.00 0.00 32.66 4.30
74 75 4.023963 TGTGTTGATAATTGAACGCCGAAA 60.024 37.500 0.00 0.00 32.66 3.46
75 76 4.319901 GTGTTGATAATTGAACGCCGAAAC 59.680 41.667 0.00 0.00 0.00 2.78
76 77 4.023963 TGTTGATAATTGAACGCCGAAACA 60.024 37.500 0.00 0.00 0.00 2.83
77 78 4.073169 TGATAATTGAACGCCGAAACAC 57.927 40.909 0.00 0.00 0.00 3.32
78 79 2.580729 TAATTGAACGCCGAAACACG 57.419 45.000 0.00 0.00 42.18 4.49
87 88 3.015677 CGAAACACGGCGAAACCA 58.984 55.556 16.62 0.00 39.03 3.67
88 89 1.368374 CGAAACACGGCGAAACCAC 60.368 57.895 16.62 0.00 39.03 4.16
89 90 1.368374 GAAACACGGCGAAACCACG 60.368 57.895 16.62 0.00 39.03 4.94
98 99 3.798506 CGAAACCACGCCGAATATG 57.201 52.632 0.00 0.00 0.00 1.78
99 100 0.303493 CGAAACCACGCCGAATATGG 59.697 55.000 0.00 0.00 39.57 2.74
100 101 0.661020 GAAACCACGCCGAATATGGG 59.339 55.000 0.00 0.00 37.86 4.00
110 111 3.913089 GCCGAATATGGGCCTATTTTTG 58.087 45.455 7.02 9.68 44.97 2.44
111 112 3.320826 GCCGAATATGGGCCTATTTTTGT 59.679 43.478 7.02 0.00 44.97 2.83
112 113 4.558697 GCCGAATATGGGCCTATTTTTGTC 60.559 45.833 7.02 0.00 44.97 3.18
113 114 4.022329 CCGAATATGGGCCTATTTTTGTCC 60.022 45.833 7.02 0.00 0.00 4.02
114 115 4.582656 CGAATATGGGCCTATTTTTGTCCA 59.417 41.667 7.02 0.00 0.00 4.02
115 116 5.243730 CGAATATGGGCCTATTTTTGTCCAT 59.756 40.000 7.02 0.91 38.40 3.41
116 117 6.432783 CGAATATGGGCCTATTTTTGTCCATA 59.567 38.462 7.02 5.41 40.25 2.74
117 118 7.122650 CGAATATGGGCCTATTTTTGTCCATAT 59.877 37.037 7.02 9.28 44.86 1.78
118 119 7.722949 ATATGGGCCTATTTTTGTCCATATG 57.277 36.000 7.02 0.00 42.76 1.78
119 120 4.222336 TGGGCCTATTTTTGTCCATATGG 58.778 43.478 16.25 16.25 0.00 2.74
120 121 3.578282 GGGCCTATTTTTGTCCATATGGG 59.422 47.826 21.78 3.43 35.41 4.00
121 122 3.006859 GGCCTATTTTTGTCCATATGGGC 59.993 47.826 19.94 19.94 42.09 5.36
122 123 3.006859 GCCTATTTTTGTCCATATGGGCC 59.993 47.826 23.51 13.71 39.61 5.80
123 124 3.578282 CCTATTTTTGTCCATATGGGCCC 59.422 47.826 23.51 17.59 39.61 5.80
124 125 2.938428 TTTTTGTCCATATGGGCCCT 57.062 45.000 25.70 11.37 39.61 5.19
125 126 2.938428 TTTTGTCCATATGGGCCCTT 57.062 45.000 25.70 20.41 39.61 3.95
126 127 2.938428 TTTGTCCATATGGGCCCTTT 57.062 45.000 25.70 13.47 39.61 3.11
127 128 4.338795 TTTTGTCCATATGGGCCCTTTA 57.661 40.909 25.70 15.41 39.61 1.85
128 129 4.551215 TTTGTCCATATGGGCCCTTTAT 57.449 40.909 25.70 17.07 39.61 1.40
129 130 4.551215 TTGTCCATATGGGCCCTTTATT 57.449 40.909 25.70 5.15 39.61 1.40
130 131 4.112634 TGTCCATATGGGCCCTTTATTC 57.887 45.455 25.70 12.41 39.61 1.75
131 132 3.081804 GTCCATATGGGCCCTTTATTCG 58.918 50.000 25.70 11.96 36.21 3.34
132 133 2.714250 TCCATATGGGCCCTTTATTCGT 59.286 45.455 25.70 0.00 36.21 3.85
133 134 3.081804 CCATATGGGCCCTTTATTCGTC 58.918 50.000 25.70 0.00 0.00 4.20
134 135 2.536761 TATGGGCCCTTTATTCGTCG 57.463 50.000 25.70 0.00 0.00 5.12
135 136 0.834612 ATGGGCCCTTTATTCGTCGA 59.165 50.000 25.70 0.00 0.00 4.20
136 137 0.614294 TGGGCCCTTTATTCGTCGAA 59.386 50.000 25.70 10.61 0.00 3.71
137 138 1.003349 TGGGCCCTTTATTCGTCGAAA 59.997 47.619 25.70 0.00 0.00 3.46
138 139 2.294979 GGGCCCTTTATTCGTCGAAAT 58.705 47.619 17.04 3.70 0.00 2.17
139 140 2.686405 GGGCCCTTTATTCGTCGAAATT 59.314 45.455 17.04 0.00 0.00 1.82
140 141 3.488553 GGGCCCTTTATTCGTCGAAATTG 60.489 47.826 17.04 3.10 0.00 2.32
141 142 3.488553 GGCCCTTTATTCGTCGAAATTGG 60.489 47.826 12.40 11.30 0.00 3.16
142 143 3.488553 GCCCTTTATTCGTCGAAATTGGG 60.489 47.826 23.01 23.01 0.00 4.12
143 144 3.488553 CCCTTTATTCGTCGAAATTGGGC 60.489 47.826 12.40 0.00 0.00 5.36
144 145 3.377172 CCTTTATTCGTCGAAATTGGGCT 59.623 43.478 12.40 0.00 0.00 5.19
145 146 4.342772 CTTTATTCGTCGAAATTGGGCTG 58.657 43.478 12.40 0.00 0.00 4.85
146 147 0.451783 ATTCGTCGAAATTGGGCTGC 59.548 50.000 12.40 0.00 0.00 5.25
147 148 0.886938 TTCGTCGAAATTGGGCTGCA 60.887 50.000 4.91 0.00 0.00 4.41
148 149 0.886938 TCGTCGAAATTGGGCTGCAA 60.887 50.000 0.50 0.00 0.00 4.08
149 150 0.039617 CGTCGAAATTGGGCTGCAAA 60.040 50.000 0.50 0.00 0.00 3.68
150 151 1.701704 GTCGAAATTGGGCTGCAAAG 58.298 50.000 0.50 0.00 0.00 2.77
151 152 1.000274 GTCGAAATTGGGCTGCAAAGT 60.000 47.619 0.50 0.00 0.00 2.66
152 153 1.000385 TCGAAATTGGGCTGCAAAGTG 60.000 47.619 0.50 0.00 0.00 3.16
153 154 1.799544 GAAATTGGGCTGCAAAGTGG 58.200 50.000 0.50 0.00 0.00 4.00
154 155 0.397564 AAATTGGGCTGCAAAGTGGG 59.602 50.000 0.50 0.00 0.00 4.61
155 156 2.115734 AATTGGGCTGCAAAGTGGGC 62.116 55.000 0.50 0.00 0.00 5.36
158 159 3.233231 GGCTGCAAAGTGGGCCAA 61.233 61.111 8.40 0.00 43.59 4.52
159 160 2.586293 GGCTGCAAAGTGGGCCAAT 61.586 57.895 8.40 3.05 43.59 3.16
160 161 1.372307 GCTGCAAAGTGGGCCAATT 59.628 52.632 14.45 14.45 0.00 2.32
161 162 0.250424 GCTGCAAAGTGGGCCAATTT 60.250 50.000 25.03 25.03 31.76 1.82
162 163 1.799544 CTGCAAAGTGGGCCAATTTC 58.200 50.000 27.50 21.06 29.07 2.17
163 164 0.033228 TGCAAAGTGGGCCAATTTCG 59.967 50.000 27.50 22.02 29.07 3.46
164 165 0.670239 GCAAAGTGGGCCAATTTCGG 60.670 55.000 27.50 18.68 29.07 4.30
171 172 4.496927 GCCAATTTCGGCGCCTGG 62.497 66.667 26.68 24.98 43.52 4.45
172 173 3.825611 CCAATTTCGGCGCCTGGG 61.826 66.667 26.68 8.93 0.00 4.45
173 174 3.825611 CAATTTCGGCGCCTGGGG 61.826 66.667 26.68 9.07 0.00 4.96
193 194 3.692406 GAGTTGGGGGCGACGACT 61.692 66.667 0.00 0.16 35.31 4.18
194 195 3.934391 GAGTTGGGGGCGACGACTG 62.934 68.421 0.00 0.00 32.81 3.51
203 204 3.342627 CGACGACTGGGCGCAAAA 61.343 61.111 10.83 0.00 33.86 2.44
204 205 2.251371 GACGACTGGGCGCAAAAC 59.749 61.111 10.83 0.00 33.86 2.43
205 206 3.249973 GACGACTGGGCGCAAAACC 62.250 63.158 10.83 0.47 33.86 3.27
206 207 4.383602 CGACTGGGCGCAAAACCG 62.384 66.667 10.83 2.69 0.00 4.44
223 224 2.345991 GCCCCAGCGCCGATTATA 59.654 61.111 2.29 0.00 0.00 0.98
224 225 1.078426 GCCCCAGCGCCGATTATAT 60.078 57.895 2.29 0.00 0.00 0.86
225 226 1.090052 GCCCCAGCGCCGATTATATC 61.090 60.000 2.29 0.00 0.00 1.63
234 235 2.566997 CGATTATATCGCCGGCTCG 58.433 57.895 26.68 20.74 46.55 5.03
235 236 1.472276 CGATTATATCGCCGGCTCGC 61.472 60.000 26.68 0.00 46.55 5.03
236 237 1.146358 GATTATATCGCCGGCTCGCC 61.146 60.000 26.68 0.00 0.00 5.54
237 238 2.573609 ATTATATCGCCGGCTCGCCC 62.574 60.000 26.68 0.00 0.00 6.13
255 256 3.531821 CCCAGGGGGCGATTTTTAT 57.468 52.632 0.00 0.00 35.35 1.40
256 257 1.039856 CCCAGGGGGCGATTTTTATG 58.960 55.000 0.00 0.00 35.35 1.90
257 258 0.389025 CCAGGGGGCGATTTTTATGC 59.611 55.000 0.00 0.00 0.00 3.14
258 259 0.030638 CAGGGGGCGATTTTTATGCG 59.969 55.000 0.00 0.00 0.00 4.73
259 260 0.395173 AGGGGGCGATTTTTATGCGT 60.395 50.000 0.00 0.00 0.00 5.24
260 261 0.030235 GGGGGCGATTTTTATGCGTC 59.970 55.000 0.00 0.00 0.00 5.19
261 262 3.544615 GGGCGATTTTTATGCGTCC 57.455 52.632 0.00 0.00 42.93 4.79
262 263 1.021968 GGGCGATTTTTATGCGTCCT 58.978 50.000 0.00 0.00 45.64 3.85
263 264 1.268539 GGGCGATTTTTATGCGTCCTG 60.269 52.381 0.00 0.00 45.64 3.86
264 265 1.268539 GGCGATTTTTATGCGTCCTGG 60.269 52.381 0.00 0.00 0.00 4.45
265 266 1.268539 GCGATTTTTATGCGTCCTGGG 60.269 52.381 0.00 0.00 0.00 4.45
266 267 1.333619 CGATTTTTATGCGTCCTGGGG 59.666 52.381 0.00 0.00 0.00 4.96
267 268 1.681264 GATTTTTATGCGTCCTGGGGG 59.319 52.381 0.00 0.00 0.00 5.40
287 288 4.308526 CAACGGCTGGAGATGCTT 57.691 55.556 0.00 0.00 0.00 3.91
289 290 0.883833 CAACGGCTGGAGATGCTTTT 59.116 50.000 0.00 0.00 0.00 2.27
304 305 2.093711 TGCTTTTAGCTGATGGACGCTA 60.094 45.455 0.00 0.00 42.97 4.26
305 306 2.541762 GCTTTTAGCTGATGGACGCTAG 59.458 50.000 0.00 0.00 39.62 3.42
317 318 4.931661 TGGACGCTAGGAATACTAAAGG 57.068 45.455 0.00 0.00 0.00 3.11
400 407 4.000988 GAGAGAGAGAGAGAGAAACACGT 58.999 47.826 0.00 0.00 0.00 4.49
432 439 2.104792 GGCAAGCTCTGGTATGTATGGA 59.895 50.000 0.00 0.00 0.00 3.41
515 522 1.276138 TGGTCGATGCTCTTGTCATGT 59.724 47.619 0.00 0.00 0.00 3.21
516 523 1.929836 GGTCGATGCTCTTGTCATGTC 59.070 52.381 0.00 0.00 0.00 3.06
517 524 2.610433 GTCGATGCTCTTGTCATGTCA 58.390 47.619 0.00 0.00 0.00 3.58
518 525 3.193263 GTCGATGCTCTTGTCATGTCAT 58.807 45.455 0.00 0.00 0.00 3.06
519 526 3.001026 GTCGATGCTCTTGTCATGTCATG 59.999 47.826 6.47 6.47 0.00 3.07
538 550 2.516930 ATGTATGCGCACCCCTGC 60.517 61.111 14.90 0.00 40.38 4.85
542 554 1.760480 TATGCGCACCCCTGCTCTA 60.760 57.895 14.90 0.00 41.77 2.43
578 590 2.221055 CGGAAATATCTTGCCGTGTAGC 59.779 50.000 2.02 0.00 46.87 3.58
579 591 3.467803 GGAAATATCTTGCCGTGTAGCT 58.532 45.455 0.00 0.00 0.00 3.32
588 603 3.114668 TGCCGTGTAGCTAGTCAAAAA 57.885 42.857 0.00 0.00 0.00 1.94
618 633 5.351465 ACTGCCTATATGTTTGAGTTTGACG 59.649 40.000 0.00 0.00 0.00 4.35
627 642 6.347270 TGTTTGAGTTTGACGACGAAAATA 57.653 33.333 0.00 0.00 0.00 1.40
695 725 1.176527 AGGATGTGGGTGCAAAATCG 58.823 50.000 0.00 0.00 0.00 3.34
706 736 3.000727 GTGCAAAATCGCTGGTACTACT 58.999 45.455 0.00 0.00 0.00 2.57
707 737 3.062234 GTGCAAAATCGCTGGTACTACTC 59.938 47.826 0.00 0.00 0.00 2.59
708 738 3.056107 TGCAAAATCGCTGGTACTACTCT 60.056 43.478 0.00 0.00 0.00 3.24
713 743 6.616774 AAATCGCTGGTACTACTCTACTAC 57.383 41.667 0.00 0.00 0.00 2.73
714 744 3.711086 TCGCTGGTACTACTCTACTACG 58.289 50.000 0.00 0.00 0.00 3.51
715 745 3.131223 TCGCTGGTACTACTCTACTACGT 59.869 47.826 0.00 0.00 0.00 3.57
716 746 3.244814 CGCTGGTACTACTCTACTACGTG 59.755 52.174 0.00 0.00 0.00 4.49
732 777 3.286751 TGCAGCAACGTGAAGCCC 61.287 61.111 0.00 0.00 0.00 5.19
742 787 1.671379 GTGAAGCCCTTCCACGGAC 60.671 63.158 5.64 0.00 38.77 4.79
776 823 1.456892 TACGACCCCGATGCCTCAT 60.457 57.895 0.00 0.00 39.50 2.90
790 837 1.146263 CTCATAAGTGGGTCCCGCC 59.854 63.158 18.36 3.38 33.99 6.13
791 838 1.306654 TCATAAGTGGGTCCCGCCT 60.307 57.895 18.36 7.93 33.99 5.52
792 839 1.146263 CATAAGTGGGTCCCGCCTC 59.854 63.158 18.36 1.08 33.99 4.70
793 840 2.070650 ATAAGTGGGTCCCGCCTCC 61.071 63.158 18.36 0.00 33.99 4.30
814 898 0.588252 GCGTACATGCATAGGCCTTG 59.412 55.000 12.58 10.73 40.13 3.61
867 967 6.049790 CCTATAAGTACTTTTGTCCTCAGGC 58.950 44.000 14.49 0.00 0.00 4.85
873 973 3.565307 ACTTTTGTCCTCAGGCAAATCA 58.435 40.909 12.38 1.18 34.99 2.57
878 978 3.499338 TGTCCTCAGGCAAATCAAACAT 58.501 40.909 0.00 0.00 0.00 2.71
883 995 2.752354 TCAGGCAAATCAAACATACCCG 59.248 45.455 0.00 0.00 0.00 5.28
985 1100 1.787012 GACTGAAAGGCGAACCGTAA 58.213 50.000 0.00 0.00 42.76 3.18
1169 1287 2.570181 CGAACCGGAAGCGTACCT 59.430 61.111 9.46 0.00 0.00 3.08
1266 1393 0.104304 ACGTGAACTCATATCCGGCC 59.896 55.000 0.00 0.00 0.00 6.13
1270 1397 3.178540 AACTCATATCCGGCCGCCC 62.179 63.158 22.85 0.00 0.00 6.13
1314 1450 1.538204 CCGGTGATGATACAGTTCGGG 60.538 57.143 0.00 0.00 33.47 5.14
1506 1645 0.391130 CTGAGATCCGCGACCCAAAA 60.391 55.000 8.23 0.00 0.00 2.44
2013 2155 5.447279 CCCGCAGCTTAGTGTTAGTTAATTG 60.447 44.000 0.00 0.00 0.00 2.32
2055 2197 6.307155 CGATAGAATGTTTCCTGTGTTTGTC 58.693 40.000 0.00 0.00 39.76 3.18
2158 2300 4.574674 TCCAGCAGAATTCTACCAACAT 57.425 40.909 7.86 0.00 0.00 2.71
2173 2315 3.966665 ACCAACATTGTTGGGAGATTGTT 59.033 39.130 38.50 20.89 43.71 2.83
2176 2318 6.098982 ACCAACATTGTTGGGAGATTGTTAAA 59.901 34.615 38.50 0.00 43.71 1.52
2177 2319 6.989169 CCAACATTGTTGGGAGATTGTTAAAA 59.011 34.615 32.30 0.00 35.96 1.52
2178 2320 7.497249 CCAACATTGTTGGGAGATTGTTAAAAA 59.503 33.333 32.30 0.00 35.96 1.94
2221 2363 2.357154 GGCCATGTATGAGGGAACACTT 60.357 50.000 0.00 0.00 0.00 3.16
2347 2489 7.970061 CCATATAAGTTGATCACAAAGGTGTTG 59.030 37.037 0.00 0.00 45.45 3.33
2350 2492 4.473444 AGTTGATCACAAAGGTGTTGGAT 58.527 39.130 0.00 0.00 45.45 3.41
2351 2493 4.520492 AGTTGATCACAAAGGTGTTGGATC 59.480 41.667 0.00 0.00 45.45 3.36
2363 2505 0.035630 GTTGGATCACAGAGCAGCCT 60.036 55.000 0.00 0.00 0.00 4.58
2398 2540 4.777140 CTTGTTTAGCAAGCACCAAAAC 57.223 40.909 0.00 0.89 46.68 2.43
2453 2595 6.071616 TGGGGTGCTTACTTTACATGAAATTC 60.072 38.462 0.00 0.00 0.00 2.17
2455 2597 7.338449 GGGGTGCTTACTTTACATGAAATTCTA 59.662 37.037 0.00 0.00 0.00 2.10
2509 2651 9.173939 GGCATCATTATTAAACTTGATTTCGAG 57.826 33.333 0.00 0.00 0.00 4.04
2539 2681 4.466827 ACGACAAGGTTAACTGGGATTTT 58.533 39.130 5.42 0.00 0.00 1.82
2573 2715 3.944015 CCTTGAGATTAGAGGCTTTGGTG 59.056 47.826 0.00 0.00 0.00 4.17
2599 2741 1.026718 GGTGCGGGTGGATGAAGAAG 61.027 60.000 0.00 0.00 0.00 2.85
2614 2756 3.588842 TGAAGAAGATCCTCCACAATGGT 59.411 43.478 0.00 0.00 39.03 3.55
2647 2789 7.043565 GTGTGAAACTAAATAATACCTCGGGA 58.956 38.462 0.00 0.00 38.04 5.14
2653 2795 8.502047 AACTAAATAATACCTCGGGACCTTAT 57.498 34.615 0.00 0.00 0.00 1.73
2689 2831 2.514824 GTGCGGCAAGGAGATCCC 60.515 66.667 3.23 0.00 36.42 3.85
2740 2882 4.067896 CTGAGTGCTTGTGTAAGATGGTT 58.932 43.478 0.00 0.00 35.92 3.67
2762 2904 1.950630 CAAGCACAAGCAAACGGGC 60.951 57.895 0.00 0.00 45.49 6.13
2848 2990 3.766151 CACAATCCTGTGCATTGATCAC 58.234 45.455 0.00 0.00 46.19 3.06
2870 3012 2.733956 ACCCTGAAAAAGCACTCAACA 58.266 42.857 0.00 0.00 0.00 3.33
2894 3036 9.230122 ACATGAAACTGTTGATGTATATGTTCA 57.770 29.630 13.80 2.24 39.46 3.18
2932 3074 8.335356 GGGTTGAAAATTAACTTTCAGAAAAGC 58.665 33.333 11.49 7.17 44.06 3.51
2935 3077 8.560576 TGAAAATTAACTTTCAGAAAAGCGAG 57.439 30.769 7.95 0.00 44.82 5.03
2962 3104 0.253327 GTGTGGGAGGGGATGAGAAC 59.747 60.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.885743 GCGTTCAATTATCAACACAATTATTTC 57.114 29.630 0.00 0.00 0.00 2.17
44 45 8.868916 GGCGTTCAATTATCAACACAATTATTT 58.131 29.630 0.00 0.00 0.00 1.40
45 46 7.219917 CGGCGTTCAATTATCAACACAATTATT 59.780 33.333 0.00 0.00 0.00 1.40
46 47 6.690957 CGGCGTTCAATTATCAACACAATTAT 59.309 34.615 0.00 0.00 0.00 1.28
47 48 6.024664 CGGCGTTCAATTATCAACACAATTA 58.975 36.000 0.00 0.00 0.00 1.40
48 49 4.856487 CGGCGTTCAATTATCAACACAATT 59.144 37.500 0.00 0.00 0.00 2.32
49 50 4.155099 TCGGCGTTCAATTATCAACACAAT 59.845 37.500 6.85 0.00 0.00 2.71
50 51 3.498777 TCGGCGTTCAATTATCAACACAA 59.501 39.130 6.85 0.00 0.00 3.33
51 52 3.067833 TCGGCGTTCAATTATCAACACA 58.932 40.909 6.85 0.00 0.00 3.72
52 53 3.733024 TCGGCGTTCAATTATCAACAC 57.267 42.857 6.85 0.00 0.00 3.32
53 54 4.023963 TGTTTCGGCGTTCAATTATCAACA 60.024 37.500 6.85 0.00 0.00 3.33
54 55 4.319901 GTGTTTCGGCGTTCAATTATCAAC 59.680 41.667 6.85 0.00 0.00 3.18
55 56 4.468643 GTGTTTCGGCGTTCAATTATCAA 58.531 39.130 6.85 0.00 0.00 2.57
56 57 3.423776 CGTGTTTCGGCGTTCAATTATCA 60.424 43.478 6.85 0.00 35.71 2.15
57 58 3.088552 CGTGTTTCGGCGTTCAATTATC 58.911 45.455 6.85 0.00 35.71 1.75
58 59 3.111958 CGTGTTTCGGCGTTCAATTAT 57.888 42.857 6.85 0.00 35.71 1.28
59 60 2.580729 CGTGTTTCGGCGTTCAATTA 57.419 45.000 6.85 0.00 35.71 1.40
60 61 3.448076 CGTGTTTCGGCGTTCAATT 57.552 47.368 6.85 0.00 35.71 2.32
70 71 1.368374 GTGGTTTCGCCGTGTTTCG 60.368 57.895 0.00 0.00 41.21 3.46
71 72 1.368374 CGTGGTTTCGCCGTGTTTC 60.368 57.895 0.00 0.00 41.21 2.78
72 73 2.710698 CGTGGTTTCGCCGTGTTT 59.289 55.556 0.00 0.00 41.21 2.83
80 81 0.303493 CCATATTCGGCGTGGTTTCG 59.697 55.000 6.85 0.00 0.00 3.46
81 82 0.661020 CCCATATTCGGCGTGGTTTC 59.339 55.000 6.85 0.00 0.00 2.78
82 83 1.381165 GCCCATATTCGGCGTGGTTT 61.381 55.000 6.85 0.00 36.47 3.27
83 84 1.822186 GCCCATATTCGGCGTGGTT 60.822 57.895 6.85 0.00 36.47 3.67
84 85 2.203153 GCCCATATTCGGCGTGGT 60.203 61.111 6.85 0.00 36.47 4.16
89 90 3.320826 ACAAAAATAGGCCCATATTCGGC 59.679 43.478 0.00 2.38 46.29 5.54
90 91 4.022329 GGACAAAAATAGGCCCATATTCGG 60.022 45.833 0.00 0.00 0.00 4.30
91 92 4.582656 TGGACAAAAATAGGCCCATATTCG 59.417 41.667 0.00 0.00 0.00 3.34
92 93 6.670695 ATGGACAAAAATAGGCCCATATTC 57.329 37.500 0.00 0.00 33.10 1.75
93 94 7.180766 CCATATGGACAAAAATAGGCCCATATT 59.819 37.037 17.49 0.00 42.31 1.28
94 95 6.669154 CCATATGGACAAAAATAGGCCCATAT 59.331 38.462 17.49 0.00 43.97 1.78
95 96 6.015918 CCATATGGACAAAAATAGGCCCATA 58.984 40.000 17.49 0.00 39.89 2.74
96 97 4.840115 CCATATGGACAAAAATAGGCCCAT 59.160 41.667 17.49 0.00 37.98 4.00
97 98 4.222336 CCATATGGACAAAAATAGGCCCA 58.778 43.478 17.49 0.00 37.39 5.36
98 99 3.578282 CCCATATGGACAAAAATAGGCCC 59.422 47.826 24.00 0.00 37.39 5.80
99 100 3.006859 GCCCATATGGACAAAAATAGGCC 59.993 47.826 24.00 0.00 37.39 5.19
100 101 3.006859 GGCCCATATGGACAAAAATAGGC 59.993 47.826 24.00 12.88 44.36 3.93
101 102 4.871933 GGCCCATATGGACAAAAATAGG 57.128 45.455 24.00 3.18 44.36 2.57
110 111 3.081804 CGAATAAAGGGCCCATATGGAC 58.918 50.000 27.56 11.97 44.14 4.02
111 112 2.714250 ACGAATAAAGGGCCCATATGGA 59.286 45.455 27.56 2.49 37.39 3.41
112 113 3.081804 GACGAATAAAGGGCCCATATGG 58.918 50.000 27.56 15.41 37.09 2.74
113 114 2.742053 CGACGAATAAAGGGCCCATATG 59.258 50.000 27.56 13.06 0.00 1.78
114 115 2.635915 TCGACGAATAAAGGGCCCATAT 59.364 45.455 27.56 19.09 0.00 1.78
115 116 2.040939 TCGACGAATAAAGGGCCCATA 58.959 47.619 27.56 17.50 0.00 2.74
116 117 0.834612 TCGACGAATAAAGGGCCCAT 59.165 50.000 27.56 10.06 0.00 4.00
117 118 0.614294 TTCGACGAATAAAGGGCCCA 59.386 50.000 27.56 2.74 0.00 5.36
118 119 1.741528 TTTCGACGAATAAAGGGCCC 58.258 50.000 16.46 16.46 0.00 5.80
119 120 3.488553 CCAATTTCGACGAATAAAGGGCC 60.489 47.826 11.71 0.00 0.00 5.80
120 121 3.488553 CCCAATTTCGACGAATAAAGGGC 60.489 47.826 11.71 0.00 0.00 5.19
121 122 3.488553 GCCCAATTTCGACGAATAAAGGG 60.489 47.826 23.04 23.04 32.85 3.95
122 123 3.377172 AGCCCAATTTCGACGAATAAAGG 59.623 43.478 11.71 11.28 0.00 3.11
123 124 4.342772 CAGCCCAATTTCGACGAATAAAG 58.657 43.478 11.71 2.34 0.00 1.85
124 125 3.426963 GCAGCCCAATTTCGACGAATAAA 60.427 43.478 11.71 0.00 0.00 1.40
125 126 2.096819 GCAGCCCAATTTCGACGAATAA 59.903 45.455 11.71 0.00 0.00 1.40
126 127 1.668751 GCAGCCCAATTTCGACGAATA 59.331 47.619 11.71 3.16 0.00 1.75
127 128 0.451783 GCAGCCCAATTTCGACGAAT 59.548 50.000 11.71 0.00 0.00 3.34
128 129 0.886938 TGCAGCCCAATTTCGACGAA 60.887 50.000 6.10 6.10 0.00 3.85
129 130 0.886938 TTGCAGCCCAATTTCGACGA 60.887 50.000 0.00 0.00 0.00 4.20
130 131 0.039617 TTTGCAGCCCAATTTCGACG 60.040 50.000 0.00 0.00 32.49 5.12
131 132 1.000274 ACTTTGCAGCCCAATTTCGAC 60.000 47.619 0.00 0.00 32.49 4.20
132 133 1.000385 CACTTTGCAGCCCAATTTCGA 60.000 47.619 0.00 0.00 32.49 3.71
133 134 1.421382 CACTTTGCAGCCCAATTTCG 58.579 50.000 0.00 0.00 32.49 3.46
134 135 1.608801 CCCACTTTGCAGCCCAATTTC 60.609 52.381 0.00 0.00 32.49 2.17
135 136 0.397564 CCCACTTTGCAGCCCAATTT 59.602 50.000 0.00 0.00 32.49 1.82
136 137 2.060370 CCCACTTTGCAGCCCAATT 58.940 52.632 0.00 0.00 32.49 2.32
137 138 2.586293 GCCCACTTTGCAGCCCAAT 61.586 57.895 0.00 0.00 32.49 3.16
138 139 3.233231 GCCCACTTTGCAGCCCAA 61.233 61.111 0.00 0.00 0.00 4.12
141 142 2.115734 AATTGGCCCACTTTGCAGCC 62.116 55.000 0.00 5.48 45.96 4.85
142 143 0.250424 AAATTGGCCCACTTTGCAGC 60.250 50.000 0.00 0.00 0.00 5.25
143 144 1.799544 GAAATTGGCCCACTTTGCAG 58.200 50.000 3.51 0.00 0.00 4.41
144 145 0.033228 CGAAATTGGCCCACTTTGCA 59.967 50.000 3.51 0.00 0.00 4.08
145 146 0.670239 CCGAAATTGGCCCACTTTGC 60.670 55.000 3.51 0.00 0.00 3.68
146 147 3.512978 CCGAAATTGGCCCACTTTG 57.487 52.632 3.51 0.00 0.00 2.77
155 156 3.825611 CCCAGGCGCCGAAATTGG 61.826 66.667 23.20 22.32 0.00 3.16
156 157 3.825611 CCCCAGGCGCCGAAATTG 61.826 66.667 23.20 13.64 0.00 2.32
176 177 3.692406 AGTCGTCGCCCCCAACTC 61.692 66.667 0.00 0.00 0.00 3.01
177 178 4.003788 CAGTCGTCGCCCCCAACT 62.004 66.667 0.00 0.00 0.00 3.16
186 187 3.342627 TTTTGCGCCCAGTCGTCG 61.343 61.111 4.18 0.00 0.00 5.12
187 188 2.251371 GTTTTGCGCCCAGTCGTC 59.749 61.111 4.18 0.00 0.00 4.20
188 189 3.284449 GGTTTTGCGCCCAGTCGT 61.284 61.111 4.18 0.00 0.00 4.34
189 190 4.383602 CGGTTTTGCGCCCAGTCG 62.384 66.667 4.18 0.00 0.00 4.18
190 191 4.700365 GCGGTTTTGCGCCCAGTC 62.700 66.667 4.18 0.00 0.00 3.51
206 207 1.078426 ATATAATCGGCGCTGGGGC 60.078 57.895 17.88 8.28 37.98 5.80
207 208 3.065575 GATATAATCGGCGCTGGGG 57.934 57.895 17.88 0.00 0.00 4.96
217 218 1.146358 GGCGAGCCGGCGATATAATC 61.146 60.000 23.20 10.39 43.33 1.75
218 219 1.153628 GGCGAGCCGGCGATATAAT 60.154 57.895 23.20 0.00 43.33 1.28
219 220 2.260434 GGCGAGCCGGCGATATAA 59.740 61.111 23.20 0.00 43.33 0.98
238 239 0.389025 GCATAAAAATCGCCCCCTGG 59.611 55.000 0.00 0.00 0.00 4.45
239 240 0.030638 CGCATAAAAATCGCCCCCTG 59.969 55.000 0.00 0.00 0.00 4.45
240 241 0.395173 ACGCATAAAAATCGCCCCCT 60.395 50.000 0.00 0.00 0.00 4.79
241 242 0.030235 GACGCATAAAAATCGCCCCC 59.970 55.000 0.00 0.00 0.00 5.40
242 243 0.030235 GGACGCATAAAAATCGCCCC 59.970 55.000 0.00 0.00 0.00 5.80
243 244 1.021968 AGGACGCATAAAAATCGCCC 58.978 50.000 0.00 0.00 0.00 6.13
244 245 1.268539 CCAGGACGCATAAAAATCGCC 60.269 52.381 0.00 0.00 0.00 5.54
245 246 1.268539 CCCAGGACGCATAAAAATCGC 60.269 52.381 0.00 0.00 0.00 4.58
246 247 1.333619 CCCCAGGACGCATAAAAATCG 59.666 52.381 0.00 0.00 0.00 3.34
247 248 1.681264 CCCCCAGGACGCATAAAAATC 59.319 52.381 0.00 0.00 33.47 2.17
248 249 1.775385 CCCCCAGGACGCATAAAAAT 58.225 50.000 0.00 0.00 33.47 1.82
249 250 3.274601 CCCCCAGGACGCATAAAAA 57.725 52.632 0.00 0.00 33.47 1.94
270 271 0.883833 AAAAGCATCTCCAGCCGTTG 59.116 50.000 0.00 0.00 0.00 4.10
271 272 2.359900 CTAAAAGCATCTCCAGCCGTT 58.640 47.619 0.00 0.00 0.00 4.44
272 273 2.014068 GCTAAAAGCATCTCCAGCCGT 61.014 52.381 0.00 0.00 41.89 5.68
273 274 0.659957 GCTAAAAGCATCTCCAGCCG 59.340 55.000 0.00 0.00 41.89 5.52
274 275 1.674962 CAGCTAAAAGCATCTCCAGCC 59.325 52.381 1.22 0.00 45.56 4.85
275 276 2.636830 TCAGCTAAAAGCATCTCCAGC 58.363 47.619 1.22 0.00 45.56 4.85
276 277 3.564644 CCATCAGCTAAAAGCATCTCCAG 59.435 47.826 1.22 0.00 45.56 3.86
277 278 3.200605 TCCATCAGCTAAAAGCATCTCCA 59.799 43.478 1.22 0.00 45.56 3.86
278 279 3.563390 GTCCATCAGCTAAAAGCATCTCC 59.437 47.826 1.22 0.00 45.56 3.71
286 287 2.764010 TCCTAGCGTCCATCAGCTAAAA 59.236 45.455 0.00 0.00 44.22 1.52
287 288 2.384828 TCCTAGCGTCCATCAGCTAAA 58.615 47.619 0.00 0.00 44.22 1.85
289 290 2.067365 TTCCTAGCGTCCATCAGCTA 57.933 50.000 0.00 0.00 44.15 3.32
304 305 4.112331 ACTGAAGGGCCTTTAGTATTCCT 58.888 43.478 34.68 14.88 38.28 3.36
305 306 4.505324 ACTGAAGGGCCTTTAGTATTCC 57.495 45.455 34.68 14.93 38.28 3.01
317 318 8.910351 ATAGTTTCATTCTTATACTGAAGGGC 57.090 34.615 0.00 0.00 31.11 5.19
354 359 7.060421 TCTTTTCCTCATACACAAAAAGGAGT 58.940 34.615 0.00 0.00 37.43 3.85
355 360 7.445402 TCTCTTTTCCTCATACACAAAAAGGAG 59.555 37.037 0.00 0.00 37.43 3.69
400 407 2.938451 CAGAGCTTGCCATGAATCGTTA 59.062 45.455 0.00 0.00 0.00 3.18
432 439 0.181350 GGCTACCTATTGGCTGCTGT 59.819 55.000 0.00 0.00 35.91 4.40
515 522 0.534877 GGGTGCGCATACATCCATGA 60.535 55.000 15.91 0.00 40.83 3.07
516 523 1.518056 GGGGTGCGCATACATCCATG 61.518 60.000 15.91 0.00 43.13 3.66
517 524 1.228245 GGGGTGCGCATACATCCAT 60.228 57.895 15.91 0.00 43.13 3.41
518 525 2.191908 GGGGTGCGCATACATCCA 59.808 61.111 15.91 0.00 43.13 3.41
519 526 1.893808 CAGGGGTGCGCATACATCC 60.894 63.158 15.91 9.83 40.38 3.51
538 550 2.478031 CCGGAGTCGTGTCAATGTAGAG 60.478 54.545 0.00 0.00 33.95 2.43
542 554 0.677288 TTCCGGAGTCGTGTCAATGT 59.323 50.000 3.34 0.00 33.95 2.71
572 584 7.905493 GCAGTTGATATTTTTGACTAGCTACAC 59.095 37.037 0.00 0.00 0.00 2.90
577 589 6.442513 AGGCAGTTGATATTTTTGACTAGC 57.557 37.500 0.00 0.00 0.00 3.42
588 603 9.632638 AAACTCAAACATATAGGCAGTTGATAT 57.367 29.630 0.00 0.00 0.00 1.63
618 633 4.384547 GTGCAATTTGTGGGTATTTTCGTC 59.615 41.667 0.00 0.00 0.00 4.20
627 642 3.610637 GCATGTGCAATTTGTGGGT 57.389 47.368 0.00 0.00 41.59 4.51
655 673 2.505628 TTCAAATTTGCTGCGCTGAA 57.494 40.000 19.32 9.38 0.00 3.02
695 725 3.002144 GCACGTAGTAGAGTAGTACCAGC 59.998 52.174 0.00 0.00 41.61 4.85
706 736 3.394800 CGTTGCTGCACGTAGTAGA 57.605 52.632 0.00 0.00 41.61 2.59
713 743 2.425773 GCTTCACGTTGCTGCACG 60.426 61.111 18.29 18.29 46.04 5.34
714 744 2.050985 GGCTTCACGTTGCTGCAC 60.051 61.111 0.00 0.00 0.00 4.57
715 745 3.286751 GGGCTTCACGTTGCTGCA 61.287 61.111 0.00 0.00 0.00 4.41
716 746 2.463675 GAAGGGCTTCACGTTGCTGC 62.464 60.000 0.00 0.00 39.31 5.25
724 764 1.671379 GTCCGTGGAAGGGCTTCAC 60.671 63.158 0.00 0.00 42.91 3.18
732 777 0.387367 CTCGTCACTGTCCGTGGAAG 60.387 60.000 0.00 0.00 43.94 3.46
742 787 1.925185 TCGTACTCGATCTCGTCACTG 59.075 52.381 0.00 0.00 41.35 3.66
776 823 2.686106 GGAGGCGGGACCCACTTA 60.686 66.667 12.15 0.00 40.58 2.24
790 837 0.667487 CCTATGCATGTACGCGGGAG 60.667 60.000 12.47 0.00 33.35 4.30
791 838 1.365999 CCTATGCATGTACGCGGGA 59.634 57.895 12.47 0.00 33.35 5.14
792 839 2.317609 GCCTATGCATGTACGCGGG 61.318 63.158 12.47 0.00 37.47 6.13
793 840 2.317609 GGCCTATGCATGTACGCGG 61.318 63.158 12.47 1.31 40.13 6.46
794 841 0.880278 AAGGCCTATGCATGTACGCG 60.880 55.000 5.16 3.53 40.13 6.01
795 842 0.588252 CAAGGCCTATGCATGTACGC 59.412 55.000 5.16 5.05 40.13 4.42
796 843 0.588252 GCAAGGCCTATGCATGTACG 59.412 55.000 25.63 0.00 43.29 3.67
799 846 4.265206 GGCAAGGCCTATGCATGT 57.735 55.556 29.07 3.86 46.69 3.21
814 898 1.104577 AGAGAAGGAGATCCGACGGC 61.105 60.000 9.66 0.00 42.08 5.68
867 967 4.302455 TGTTTGCGGGTATGTTTGATTTG 58.698 39.130 0.00 0.00 0.00 2.32
873 973 4.116238 CAAGTTTGTTTGCGGGTATGTTT 58.884 39.130 0.00 0.00 0.00 2.83
878 978 3.949031 GCAAGTTTGTTTGCGGGTA 57.051 47.368 0.00 0.00 43.36 3.69
911 1023 3.138205 CACGGTAGAGAAGTGCTACTG 57.862 52.381 0.00 0.00 46.04 2.74
985 1100 4.443978 ACTCCATGGTGCTTATGCTTAT 57.556 40.909 12.58 0.00 40.48 1.73
1169 1287 1.228644 AAGAACATGGGCTGCTGCA 60.229 52.632 17.89 0.88 41.91 4.41
1220 1347 0.611200 CGTCAGGTCCATGTAACCCA 59.389 55.000 10.15 0.00 37.52 4.51
1221 1348 0.743345 GCGTCAGGTCCATGTAACCC 60.743 60.000 10.15 0.00 37.52 4.11
1290 1426 1.781786 ACTGTATCATCACCGGCTCT 58.218 50.000 0.00 0.00 0.00 4.09
1314 1450 3.394836 ACAGGAGAAGGCTCGCCC 61.395 66.667 3.92 0.00 42.27 6.13
1323 1459 2.604686 AGCGCCCTCACAGGAGAA 60.605 61.111 2.29 0.00 44.26 2.87
1488 1627 0.672401 GTTTTGGGTCGCGGATCTCA 60.672 55.000 6.13 0.11 0.00 3.27
1876 2015 1.305887 GAGGAAACCCTCCCTCCGA 60.306 63.158 0.00 0.00 46.81 4.55
2013 2155 6.223852 TCTATCGCTTAATGAACCATCCTTC 58.776 40.000 0.00 0.00 0.00 3.46
2055 2197 2.814336 GGGTGCCTACTCTGTTTTTCTG 59.186 50.000 0.00 0.00 0.00 3.02
2126 2268 5.705441 AGAATTCTGCTGGAACGTTCAATTA 59.295 36.000 28.24 11.63 36.70 1.40
2127 2269 4.520492 AGAATTCTGCTGGAACGTTCAATT 59.480 37.500 28.24 21.94 36.70 2.32
2128 2270 4.074970 AGAATTCTGCTGGAACGTTCAAT 58.925 39.130 28.24 15.51 36.70 2.57
2129 2271 3.476552 AGAATTCTGCTGGAACGTTCAA 58.523 40.909 28.24 17.90 36.70 2.69
2130 2272 3.126001 AGAATTCTGCTGGAACGTTCA 57.874 42.857 28.24 14.13 36.70 3.18
2131 2273 3.371285 GGTAGAATTCTGCTGGAACGTTC 59.629 47.826 20.14 20.14 36.70 3.95
2135 2277 4.072131 TGTTGGTAGAATTCTGCTGGAAC 58.928 43.478 20.91 19.14 36.70 3.62
2176 2318 8.146412 GCCTCAAAAAGCCTCATAATATCATTT 58.854 33.333 0.00 0.00 0.00 2.32
2177 2319 7.256083 GGCCTCAAAAAGCCTCATAATATCATT 60.256 37.037 0.00 0.00 46.14 2.57
2178 2320 6.210185 GGCCTCAAAAAGCCTCATAATATCAT 59.790 38.462 0.00 0.00 46.14 2.45
2221 2363 8.568676 TCCCGTAATTTAATCTTTGAACATCA 57.431 30.769 0.00 0.00 0.00 3.07
2239 2381 6.895782 AGGAATCAAAGTAATGATCCCGTAA 58.104 36.000 0.00 0.00 39.08 3.18
2347 2489 1.145819 GGAGGCTGCTCTGTGATCC 59.854 63.158 0.00 0.00 0.00 3.36
2350 2492 1.117994 CATAGGAGGCTGCTCTGTGA 58.882 55.000 13.31 0.00 0.00 3.58
2351 2493 0.532417 GCATAGGAGGCTGCTCTGTG 60.532 60.000 13.31 11.39 35.49 3.66
2363 2505 5.118990 GCTAAACAAGATGTCAGCATAGGA 58.881 41.667 10.46 0.00 35.07 2.94
2398 2540 9.950680 ATGATATTTCTGTGTTTAATAAAGGCG 57.049 29.630 0.00 0.00 0.00 5.52
2509 2651 5.333875 CCAGTTAACCTTGTCGTAAGCTTTC 60.334 44.000 3.20 0.00 37.18 2.62
2539 2681 7.148018 CCTCTAATCTCAAGGCATTTAAGCAAA 60.148 37.037 0.00 0.00 35.83 3.68
2560 2702 3.117663 ACCAAGTTTCACCAAAGCCTCTA 60.118 43.478 0.00 0.00 0.00 2.43
2573 2715 0.893727 ATCCACCCGCACCAAGTTTC 60.894 55.000 0.00 0.00 0.00 2.78
2599 2741 1.485066 ACCGTACCATTGTGGAGGATC 59.515 52.381 2.45 0.00 40.96 3.36
2647 2789 4.524328 CCTTTGTGGCTCTGAAAATAAGGT 59.476 41.667 0.00 0.00 0.00 3.50
2653 2795 1.063266 ACCCCTTTGTGGCTCTGAAAA 60.063 47.619 0.00 0.00 0.00 2.29
2689 2831 6.753107 ATATTAAACAAGAAAGGGGACACG 57.247 37.500 0.00 0.00 0.00 4.49
2740 2882 1.601903 CCGTTTGCTTGTGCTTGTAGA 59.398 47.619 0.00 0.00 40.48 2.59
2762 2904 1.396653 GAGGCCAACCCATCAATCAG 58.603 55.000 5.01 0.00 36.11 2.90
2845 2987 2.687935 GAGTGCTTTTTCAGGGTTGTGA 59.312 45.455 0.00 0.00 0.00 3.58
2848 2990 3.119173 TGTTGAGTGCTTTTTCAGGGTTG 60.119 43.478 0.00 0.00 0.00 3.77
2909 3051 8.918961 TCGCTTTTCTGAAAGTTAATTTTCAA 57.081 26.923 21.90 12.96 44.06 2.69
2932 3074 2.101582 CCCTCCCACACTAAGAATCTCG 59.898 54.545 0.00 0.00 0.00 4.04
2935 3077 2.478292 TCCCCTCCCACACTAAGAATC 58.522 52.381 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.