Multiple sequence alignment - TraesCS3B01G114100

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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 TraesCS3B01G114100 chr3B 100.000 2084 0 0 715 2798 80162887 80164970 0.000000e+00 3849.0
1 TraesCS3B01G114100 chr3B 85.205 926 74 33 882 1800 80102793 80103662 0.000000e+00 893.0
2 TraesCS3B01G114100 chr3B 100.000 423 0 0 1 423 80162173 80162595 0.000000e+00 782.0
3 TraesCS3B01G114100 chr3D 92.308 2041 89 24 785 2795 50549729 50551731 0.000000e+00 2837.0
4 TraesCS3B01G114100 chr3D 90.172 641 39 10 1163 1800 50536232 50536851 0.000000e+00 813.0
5 TraesCS3B01G114100 chr3D 86.879 282 32 5 885 1161 50515441 50515722 7.530000e-81 311.0
6 TraesCS3B01G114100 chr3D 97.987 149 3 0 275 423 50549403 50549551 2.760000e-65 259.0
7 TraesCS3B01G114100 chr3D 94.545 55 3 0 715 769 50549598 50549652 4.970000e-13 86.1
8 TraesCS3B01G114100 chr3A 90.386 1113 44 28 805 1910 63558044 63559100 0.000000e+00 1404.0
9 TraesCS3B01G114100 chr3A 91.973 897 51 10 1906 2789 63559612 63560500 0.000000e+00 1238.0
10 TraesCS3B01G114100 chr3A 97.561 41 1 0 277 317 63557742 63557782 1.390000e-08 71.3
11 TraesCS3B01G114100 chr1B 81.895 591 84 16 1180 1769 44849438 44850006 7.010000e-131 477.0
12 TraesCS3B01G114100 chr1B 92.369 249 17 2 1 247 575734182 575733934 1.230000e-93 353.0
13 TraesCS3B01G114100 chr2D 80.775 619 92 15 1173 1786 467147671 467148267 2.540000e-125 459.0
14 TraesCS3B01G114100 chr4A 94.758 248 12 1 1 247 739879888 739879641 4.370000e-103 385.0
15 TraesCS3B01G114100 chr6A 78.862 615 94 18 1173 1785 270738824 270739404 1.570000e-102 383.0
16 TraesCS3B01G114100 chr2B 93.574 249 14 2 1 247 59007276 59007524 1.220000e-98 370.0
17 TraesCS3B01G114100 chr7B 93.574 249 13 3 1 247 635043121 635043368 4.400000e-98 368.0
18 TraesCS3B01G114100 chr7B 92.713 247 15 3 1 245 668358630 668358385 1.230000e-93 353.0
19 TraesCS3B01G114100 chr4B 93.522 247 14 2 1 245 565730875 565731121 1.580000e-97 366.0
20 TraesCS3B01G114100 chr4B 92.771 249 16 2 1 247 67507174 67507422 2.650000e-95 359.0
21 TraesCS3B01G114100 chr5B 92.742 248 17 1 1 247 588756554 588756801 9.530000e-95 357.0
22 TraesCS3B01G114100 chr5B 92.369 249 16 3 1 247 585273449 585273696 4.430000e-93 351.0
23 TraesCS3B01G114100 chr1D 77.224 562 104 12 1173 1731 448960306 448960846 9.740000e-80 307.0
24 TraesCS3B01G114100 chr7A 78.167 371 56 15 1214 1582 47770724 47771071 2.180000e-51 213.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G114100 chr3B 80162173 80164970 2797 False 2315.500000 3849 100.000000 1 2798 2 chr3B.!!$F2 2797
1 TraesCS3B01G114100 chr3B 80102793 80103662 869 False 893.000000 893 85.205000 882 1800 1 chr3B.!!$F1 918
2 TraesCS3B01G114100 chr3D 50549403 50551731 2328 False 1060.700000 2837 94.946667 275 2795 3 chr3D.!!$F3 2520
3 TraesCS3B01G114100 chr3D 50536232 50536851 619 False 813.000000 813 90.172000 1163 1800 1 chr3D.!!$F2 637
4 TraesCS3B01G114100 chr3A 63557742 63560500 2758 False 904.433333 1404 93.306667 277 2789 3 chr3A.!!$F1 2512
5 TraesCS3B01G114100 chr1B 44849438 44850006 568 False 477.000000 477 81.895000 1180 1769 1 chr1B.!!$F1 589
6 TraesCS3B01G114100 chr2D 467147671 467148267 596 False 459.000000 459 80.775000 1173 1786 1 chr2D.!!$F1 613
7 TraesCS3B01G114100 chr6A 270738824 270739404 580 False 383.000000 383 78.862000 1173 1785 1 chr6A.!!$F1 612
8 TraesCS3B01G114100 chr1D 448960306 448960846 540 False 307.000000 307 77.224000 1173 1731 1 chr1D.!!$F1 558

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
271 272 0.107831 TTTGAGGTCGGTGGAGTTGG 59.892 55.0 0.00 0.00 0.0 3.77 F
755 814 0.320073 TCACGGCAAGTTAACTCGGG 60.320 55.0 8.95 9.77 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 1623 2.496817 GAGTAGCTGCCCTGGTCG 59.503 66.667 0.0 0.0 0.00 4.79 R
2360 3057 0.109689 GCGGGATCTTATCGAGGACG 60.110 60.000 0.0 0.0 41.26 4.79 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
32 33 4.916293 GCTGATGCCGGCGATGGA 62.916 66.667 23.90 3.26 34.60 3.41
33 34 2.969238 CTGATGCCGGCGATGGAC 60.969 66.667 23.90 9.49 0.00 4.02
34 35 4.889856 TGATGCCGGCGATGGACG 62.890 66.667 23.90 0.00 46.94 4.79
35 36 4.891727 GATGCCGGCGATGGACGT 62.892 66.667 23.90 0.00 45.55 4.34
38 39 4.501714 GCCGGCGATGGACGTGTA 62.502 66.667 12.58 0.00 45.55 2.90
39 40 2.278596 CCGGCGATGGACGTGTAG 60.279 66.667 9.30 0.00 45.55 2.74
40 41 2.278596 CGGCGATGGACGTGTAGG 60.279 66.667 0.00 0.00 40.74 3.18
41 42 2.585247 GGCGATGGACGTGTAGGC 60.585 66.667 0.00 0.00 44.60 3.93
47 48 4.814294 GGACGTGTAGGCCGCTGG 62.814 72.222 0.00 0.00 38.99 4.85
65 66 2.434884 CTCTGTTGCCGGCGTGAT 60.435 61.111 23.90 0.00 0.00 3.06
66 67 2.741985 TCTGTTGCCGGCGTGATG 60.742 61.111 23.90 10.88 0.00 3.07
67 68 2.741985 CTGTTGCCGGCGTGATGA 60.742 61.111 23.90 0.00 0.00 2.92
68 69 2.281139 TGTTGCCGGCGTGATGAA 60.281 55.556 23.90 6.19 0.00 2.57
69 70 2.175811 GTTGCCGGCGTGATGAAC 59.824 61.111 23.90 15.63 0.00 3.18
70 71 3.053291 TTGCCGGCGTGATGAACC 61.053 61.111 23.90 0.00 0.00 3.62
94 95 2.512515 GCCGCTGGCCTGAACTAG 60.513 66.667 14.77 0.00 44.06 2.57
102 103 4.645809 CCTGAACTAGGGCTTGGC 57.354 61.111 0.00 0.00 43.33 4.52
103 104 1.994463 CCTGAACTAGGGCTTGGCT 59.006 57.895 0.00 0.00 43.33 4.75
104 105 0.329596 CCTGAACTAGGGCTTGGCTT 59.670 55.000 0.00 0.00 43.33 4.35
105 106 1.272147 CCTGAACTAGGGCTTGGCTTT 60.272 52.381 0.00 0.00 43.33 3.51
106 107 1.815003 CTGAACTAGGGCTTGGCTTTG 59.185 52.381 0.00 0.00 0.00 2.77
107 108 1.423541 TGAACTAGGGCTTGGCTTTGA 59.576 47.619 0.00 0.00 0.00 2.69
108 109 2.158534 TGAACTAGGGCTTGGCTTTGAA 60.159 45.455 0.00 0.00 0.00 2.69
109 110 2.675658 ACTAGGGCTTGGCTTTGAAA 57.324 45.000 0.00 0.00 0.00 2.69
110 111 3.175438 ACTAGGGCTTGGCTTTGAAAT 57.825 42.857 0.00 0.00 0.00 2.17
111 112 2.827921 ACTAGGGCTTGGCTTTGAAATG 59.172 45.455 0.00 0.00 0.00 2.32
112 113 1.720781 AGGGCTTGGCTTTGAAATGT 58.279 45.000 0.00 0.00 0.00 2.71
113 114 2.049372 AGGGCTTGGCTTTGAAATGTT 58.951 42.857 0.00 0.00 0.00 2.71
114 115 2.145536 GGGCTTGGCTTTGAAATGTTG 58.854 47.619 0.00 0.00 0.00 3.33
115 116 1.532437 GGCTTGGCTTTGAAATGTTGC 59.468 47.619 0.00 0.00 0.00 4.17
116 117 2.486918 GCTTGGCTTTGAAATGTTGCT 58.513 42.857 0.00 0.00 0.00 3.91
117 118 2.874086 GCTTGGCTTTGAAATGTTGCTT 59.126 40.909 0.00 0.00 0.00 3.91
118 119 3.313249 GCTTGGCTTTGAAATGTTGCTTT 59.687 39.130 0.00 0.00 0.00 3.51
119 120 4.201940 GCTTGGCTTTGAAATGTTGCTTTT 60.202 37.500 0.00 0.00 0.00 2.27
120 121 5.007528 GCTTGGCTTTGAAATGTTGCTTTTA 59.992 36.000 0.00 0.00 0.00 1.52
121 122 6.601741 TTGGCTTTGAAATGTTGCTTTTAG 57.398 33.333 0.00 0.00 0.00 1.85
122 123 5.669477 TGGCTTTGAAATGTTGCTTTTAGT 58.331 33.333 0.00 0.00 0.00 2.24
123 124 6.112058 TGGCTTTGAAATGTTGCTTTTAGTT 58.888 32.000 0.00 0.00 0.00 2.24
124 125 6.597280 TGGCTTTGAAATGTTGCTTTTAGTTT 59.403 30.769 0.00 0.00 0.00 2.66
125 126 7.120432 TGGCTTTGAAATGTTGCTTTTAGTTTT 59.880 29.630 0.00 0.00 0.00 2.43
126 127 7.967854 GGCTTTGAAATGTTGCTTTTAGTTTTT 59.032 29.630 0.00 0.00 0.00 1.94
127 128 9.980780 GCTTTGAAATGTTGCTTTTAGTTTTTA 57.019 25.926 0.00 0.00 0.00 1.52
136 137 9.063739 TGTTGCTTTTAGTTTTTAAAGTGTACG 57.936 29.630 0.00 0.00 34.59 3.67
137 138 7.667984 TGCTTTTAGTTTTTAAAGTGTACGC 57.332 32.000 0.00 0.00 34.59 4.42
138 139 6.411492 TGCTTTTAGTTTTTAAAGTGTACGCG 59.589 34.615 3.53 3.53 34.59 6.01
139 140 6.628461 GCTTTTAGTTTTTAAAGTGTACGCGA 59.372 34.615 15.93 0.00 34.59 5.87
140 141 7.164008 GCTTTTAGTTTTTAAAGTGTACGCGAA 59.836 33.333 15.93 0.00 34.59 4.70
141 142 7.875306 TTTAGTTTTTAAAGTGTACGCGAAC 57.125 32.000 15.93 8.30 0.00 3.95
142 143 5.467902 AGTTTTTAAAGTGTACGCGAACA 57.532 34.783 15.93 0.00 0.00 3.18
143 144 5.495502 AGTTTTTAAAGTGTACGCGAACAG 58.504 37.500 15.93 0.00 0.00 3.16
144 145 4.455917 TTTTAAAGTGTACGCGAACAGG 57.544 40.909 15.93 0.00 0.00 4.00
145 146 3.367992 TTAAAGTGTACGCGAACAGGA 57.632 42.857 15.93 0.00 0.00 3.86
146 147 2.450609 AAAGTGTACGCGAACAGGAT 57.549 45.000 15.93 0.00 0.00 3.24
147 148 2.450609 AAGTGTACGCGAACAGGATT 57.549 45.000 15.93 0.00 0.00 3.01
148 149 1.710013 AGTGTACGCGAACAGGATTG 58.290 50.000 15.93 0.00 0.00 2.67
149 150 0.719465 GTGTACGCGAACAGGATTGG 59.281 55.000 15.93 0.00 0.00 3.16
150 151 1.017177 TGTACGCGAACAGGATTGGC 61.017 55.000 15.93 0.00 0.00 4.52
151 152 1.017177 GTACGCGAACAGGATTGGCA 61.017 55.000 15.93 0.00 0.00 4.92
152 153 0.320858 TACGCGAACAGGATTGGCAA 60.321 50.000 15.93 0.68 0.00 4.52
153 154 1.169661 ACGCGAACAGGATTGGCAAA 61.170 50.000 15.93 0.00 0.00 3.68
154 155 0.171007 CGCGAACAGGATTGGCAAAT 59.829 50.000 3.01 0.00 0.00 2.32
155 156 1.632422 GCGAACAGGATTGGCAAATG 58.368 50.000 3.01 6.46 0.00 2.32
156 157 1.202114 GCGAACAGGATTGGCAAATGA 59.798 47.619 3.01 0.00 0.00 2.57
157 158 2.352617 GCGAACAGGATTGGCAAATGAA 60.353 45.455 3.01 0.00 0.00 2.57
158 159 3.676873 GCGAACAGGATTGGCAAATGAAT 60.677 43.478 3.01 0.00 0.00 2.57
159 160 3.861113 CGAACAGGATTGGCAAATGAATG 59.139 43.478 3.01 1.97 0.00 2.67
160 161 3.255969 ACAGGATTGGCAAATGAATGC 57.744 42.857 3.01 0.00 45.67 3.56
166 167 3.256833 GCAAATGAATGCGGCCGC 61.257 61.111 42.35 42.35 36.45 6.53
167 168 2.950710 CAAATGAATGCGGCCGCG 60.951 61.111 41.73 23.24 45.51 6.46
168 169 4.852963 AAATGAATGCGGCCGCGC 62.853 61.111 41.73 32.56 45.51 6.86
197 198 4.424711 GGCCACCGCATCCCAGAA 62.425 66.667 0.00 0.00 36.38 3.02
198 199 3.134127 GCCACCGCATCCCAGAAC 61.134 66.667 0.00 0.00 34.03 3.01
199 200 2.350895 CCACCGCATCCCAGAACA 59.649 61.111 0.00 0.00 0.00 3.18
200 201 1.746615 CCACCGCATCCCAGAACAG 60.747 63.158 0.00 0.00 0.00 3.16
201 202 1.296392 CACCGCATCCCAGAACAGA 59.704 57.895 0.00 0.00 0.00 3.41
202 203 1.021390 CACCGCATCCCAGAACAGAC 61.021 60.000 0.00 0.00 0.00 3.51
203 204 1.450312 CCGCATCCCAGAACAGACC 60.450 63.158 0.00 0.00 0.00 3.85
204 205 1.450312 CGCATCCCAGAACAGACCC 60.450 63.158 0.00 0.00 0.00 4.46
205 206 1.450312 GCATCCCAGAACAGACCCG 60.450 63.158 0.00 0.00 0.00 5.28
206 207 1.221840 CATCCCAGAACAGACCCGG 59.778 63.158 0.00 0.00 0.00 5.73
207 208 1.080354 ATCCCAGAACAGACCCGGA 59.920 57.895 0.73 0.00 0.00 5.14
208 209 1.265454 ATCCCAGAACAGACCCGGAC 61.265 60.000 0.73 0.00 0.00 4.79
209 210 2.214216 CCCAGAACAGACCCGGACA 61.214 63.158 0.73 0.00 0.00 4.02
210 211 1.004918 CCAGAACAGACCCGGACAC 60.005 63.158 0.73 0.00 0.00 3.67
211 212 1.372997 CAGAACAGACCCGGACACG 60.373 63.158 0.73 0.00 40.55 4.49
212 213 1.529948 AGAACAGACCCGGACACGA 60.530 57.895 0.73 0.00 44.60 4.35
213 214 1.372623 GAACAGACCCGGACACGAC 60.373 63.158 0.73 0.00 44.60 4.34
214 215 2.760387 GAACAGACCCGGACACGACC 62.760 65.000 0.73 0.00 44.60 4.79
215 216 4.065281 CAGACCCGGACACGACCC 62.065 72.222 0.73 0.00 44.60 4.46
219 220 3.943691 CCCGGACACGACCCCAAA 61.944 66.667 0.73 0.00 44.60 3.28
220 221 2.349755 CCGGACACGACCCCAAAT 59.650 61.111 0.00 0.00 44.60 2.32
221 222 1.743995 CCGGACACGACCCCAAATC 60.744 63.158 0.00 0.00 44.60 2.17
222 223 1.743995 CGGACACGACCCCAAATCC 60.744 63.158 0.00 0.00 44.60 3.01
223 224 1.378119 GGACACGACCCCAAATCCC 60.378 63.158 0.00 0.00 0.00 3.85
224 225 1.683441 GACACGACCCCAAATCCCT 59.317 57.895 0.00 0.00 0.00 4.20
225 226 0.906775 GACACGACCCCAAATCCCTA 59.093 55.000 0.00 0.00 0.00 3.53
226 227 1.279846 GACACGACCCCAAATCCCTAA 59.720 52.381 0.00 0.00 0.00 2.69
227 228 1.003928 ACACGACCCCAAATCCCTAAC 59.996 52.381 0.00 0.00 0.00 2.34
228 229 0.622136 ACGACCCCAAATCCCTAACC 59.378 55.000 0.00 0.00 0.00 2.85
229 230 0.621609 CGACCCCAAATCCCTAACCA 59.378 55.000 0.00 0.00 0.00 3.67
230 231 1.004979 CGACCCCAAATCCCTAACCAA 59.995 52.381 0.00 0.00 0.00 3.67
231 232 2.555670 CGACCCCAAATCCCTAACCAAA 60.556 50.000 0.00 0.00 0.00 3.28
232 233 2.829720 GACCCCAAATCCCTAACCAAAC 59.170 50.000 0.00 0.00 0.00 2.93
233 234 1.822371 CCCCAAATCCCTAACCAAACG 59.178 52.381 0.00 0.00 0.00 3.60
234 235 1.822371 CCCAAATCCCTAACCAAACGG 59.178 52.381 0.00 0.00 0.00 4.44
235 236 2.555670 CCCAAATCCCTAACCAAACGGA 60.556 50.000 0.00 0.00 0.00 4.69
236 237 3.361786 CCAAATCCCTAACCAAACGGAT 58.638 45.455 0.00 0.00 36.66 4.18
237 238 4.528920 CCAAATCCCTAACCAAACGGATA 58.471 43.478 0.00 0.00 33.92 2.59
238 239 4.578928 CCAAATCCCTAACCAAACGGATAG 59.421 45.833 0.00 0.00 33.92 2.08
239 240 5.433526 CAAATCCCTAACCAAACGGATAGA 58.566 41.667 0.00 0.00 33.92 1.98
240 241 5.703730 AATCCCTAACCAAACGGATAGAA 57.296 39.130 0.00 0.00 33.92 2.10
241 242 5.906772 ATCCCTAACCAAACGGATAGAAT 57.093 39.130 0.00 0.00 33.26 2.40
242 243 5.286267 TCCCTAACCAAACGGATAGAATC 57.714 43.478 0.00 0.00 32.03 2.52
243 244 4.102054 TCCCTAACCAAACGGATAGAATCC 59.898 45.833 0.00 0.00 46.22 3.01
254 255 4.625607 GGATAGAATCCGGATCCTGTTT 57.374 45.455 19.43 0.28 40.13 2.83
255 256 4.319177 GGATAGAATCCGGATCCTGTTTG 58.681 47.826 19.43 0.00 40.13 2.93
256 257 4.040461 GGATAGAATCCGGATCCTGTTTGA 59.960 45.833 19.43 0.00 40.13 2.69
257 258 3.550437 AGAATCCGGATCCTGTTTGAG 57.450 47.619 19.43 0.00 0.00 3.02
258 259 2.171448 AGAATCCGGATCCTGTTTGAGG 59.829 50.000 19.43 1.38 44.45 3.86
259 260 1.584724 ATCCGGATCCTGTTTGAGGT 58.415 50.000 12.38 0.00 43.37 3.85
260 261 0.902531 TCCGGATCCTGTTTGAGGTC 59.097 55.000 10.75 0.00 43.37 3.85
261 262 0.460284 CCGGATCCTGTTTGAGGTCG 60.460 60.000 10.75 0.00 43.37 4.79
262 263 0.460284 CGGATCCTGTTTGAGGTCGG 60.460 60.000 10.75 0.00 43.37 4.79
263 264 0.613777 GGATCCTGTTTGAGGTCGGT 59.386 55.000 3.84 0.00 43.37 4.69
264 265 1.676014 GGATCCTGTTTGAGGTCGGTG 60.676 57.143 3.84 0.00 43.37 4.94
265 266 0.324943 ATCCTGTTTGAGGTCGGTGG 59.675 55.000 0.00 0.00 43.37 4.61
266 267 0.761323 TCCTGTTTGAGGTCGGTGGA 60.761 55.000 0.00 0.00 43.37 4.02
267 268 0.320771 CCTGTTTGAGGTCGGTGGAG 60.321 60.000 0.00 0.00 37.02 3.86
268 269 0.393077 CTGTTTGAGGTCGGTGGAGT 59.607 55.000 0.00 0.00 0.00 3.85
269 270 0.834612 TGTTTGAGGTCGGTGGAGTT 59.165 50.000 0.00 0.00 0.00 3.01
270 271 1.226746 GTTTGAGGTCGGTGGAGTTG 58.773 55.000 0.00 0.00 0.00 3.16
271 272 0.107831 TTTGAGGTCGGTGGAGTTGG 59.892 55.000 0.00 0.00 0.00 3.77
272 273 2.047179 GAGGTCGGTGGAGTTGGC 60.047 66.667 0.00 0.00 0.00 4.52
273 274 3.607370 GAGGTCGGTGGAGTTGGCC 62.607 68.421 0.00 0.00 0.00 5.36
340 399 1.447314 CTGATGAGTCTGCGCTGCA 60.447 57.895 9.73 1.84 36.92 4.41
391 450 0.325933 TCATCCTGCTCAACACTGGG 59.674 55.000 0.00 0.00 0.00 4.45
755 814 0.320073 TCACGGCAAGTTAACTCGGG 60.320 55.000 8.95 9.77 0.00 5.14
756 815 1.670083 ACGGCAAGTTAACTCGGGC 60.670 57.895 8.95 14.90 0.00 6.13
757 816 1.669760 CGGCAAGTTAACTCGGGCA 60.670 57.895 24.12 0.00 0.00 5.36
769 828 1.618343 ACTCGGGCAAAATCTTTTGGG 59.382 47.619 15.17 0.00 45.73 4.12
770 829 0.972883 TCGGGCAAAATCTTTTGGGG 59.027 50.000 15.17 0.00 45.73 4.96
780 860 0.893270 TCTTTTGGGGCATGGACACG 60.893 55.000 0.00 0.00 0.00 4.49
789 869 1.668793 CATGGACACGCTGCTCACA 60.669 57.895 0.00 0.00 0.00 3.58
791 871 2.280119 GGACACGCTGCTCACACA 60.280 61.111 0.00 0.00 0.00 3.72
799 919 3.227372 CTGCTCACACAACGCACGG 62.227 63.158 0.00 0.00 0.00 4.94
825 945 2.203480 GAGCAGCCAACCCAACCA 60.203 61.111 0.00 0.00 0.00 3.67
897 1023 2.185350 CGCTGCTACCACCTCCAG 59.815 66.667 0.00 0.00 0.00 3.86
898 1024 2.586792 GCTGCTACCACCTCCAGG 59.413 66.667 0.00 0.00 42.17 4.45
899 1025 2.586792 CTGCTACCACCTCCAGGC 59.413 66.667 0.00 0.00 39.32 4.85
900 1026 1.992277 CTGCTACCACCTCCAGGCT 60.992 63.158 0.00 0.00 39.32 4.58
901 1027 1.965754 CTGCTACCACCTCCAGGCTC 61.966 65.000 0.00 0.00 39.32 4.70
902 1028 2.736826 GCTACCACCTCCAGGCTCC 61.737 68.421 0.00 0.00 39.32 4.70
903 1029 1.306141 CTACCACCTCCAGGCTCCA 60.306 63.158 0.00 0.00 39.32 3.86
940 1066 2.752238 CGCCTCCTCGTCCTCAGT 60.752 66.667 0.00 0.00 0.00 3.41
949 1075 3.827898 GTCCTCAGTCCTCGCCGG 61.828 72.222 0.00 0.00 0.00 6.13
1845 1995 3.281341 TGCGATTTCTCGTGCATTTTT 57.719 38.095 0.00 0.00 46.71 1.94
1846 1996 2.979151 TGCGATTTCTCGTGCATTTTTG 59.021 40.909 0.00 0.00 46.71 2.44
1847 1997 2.222354 GCGATTTCTCGTGCATTTTTGC 60.222 45.455 0.00 0.00 46.71 3.68
1848 1998 3.236816 CGATTTCTCGTGCATTTTTGCT 58.763 40.909 0.00 0.00 40.07 3.91
1849 1999 3.058520 CGATTTCTCGTGCATTTTTGCTG 59.941 43.478 0.00 0.00 40.07 4.41
1850 2000 1.769733 TTCTCGTGCATTTTTGCTGC 58.230 45.000 0.00 0.00 40.10 5.25
1851 2001 0.953727 TCTCGTGCATTTTTGCTGCT 59.046 45.000 0.00 0.00 40.34 4.24
1852 2002 2.150390 TCTCGTGCATTTTTGCTGCTA 58.850 42.857 0.00 0.00 40.34 3.49
1853 2003 2.160219 TCTCGTGCATTTTTGCTGCTAG 59.840 45.455 0.00 0.00 40.34 3.42
1862 2012 5.335191 GCATTTTTGCTGCTAGTAGAACTGT 60.335 40.000 12.54 0.00 36.68 3.55
1879 2029 5.931146 AGAACTGTTGAAGCAGATCAAGTAG 59.069 40.000 0.00 5.24 39.84 2.57
1950 2622 4.822036 TTCTAGTTAGCTGCTCGAGATC 57.178 45.455 18.75 3.63 0.00 2.75
1963 2638 4.872124 TGCTCGAGATCAAGTACTACGTAA 59.128 41.667 18.75 0.00 0.00 3.18
2072 2757 5.624159 TCAAACTTGACCATGAATCTGACT 58.376 37.500 0.00 0.00 31.01 3.41
2075 2760 6.365970 AACTTGACCATGAATCTGACTAGT 57.634 37.500 0.00 0.00 0.00 2.57
2076 2761 7.482169 AACTTGACCATGAATCTGACTAGTA 57.518 36.000 0.00 0.00 0.00 1.82
2162 2854 9.740239 TGCTTCTAACTATAACCTACAATTACG 57.260 33.333 0.00 0.00 0.00 3.18
2222 2919 0.038310 CCAACCTCCCCTCAGAAACC 59.962 60.000 0.00 0.00 0.00 3.27
2228 2925 2.592993 CCCCTCAGAAACCGCTGGA 61.593 63.158 1.50 0.00 36.55 3.86
2271 2968 6.316140 TGAACCTTGTACTGCATCATCATAAC 59.684 38.462 0.00 0.00 0.00 1.89
2294 2991 4.202367 CCAGGGAAAACTACTGACTGAAGT 60.202 45.833 0.00 0.00 34.21 3.01
2316 3013 0.249398 AGGCGCGATCTTGTTAACCT 59.751 50.000 12.10 0.00 0.00 3.50
2343 3040 0.459489 TGTTGCTTCCCACAAACTGC 59.541 50.000 0.00 0.00 0.00 4.40
2441 3138 1.996191 GCAGCCTCTTGTAACTTCTCG 59.004 52.381 0.00 0.00 0.00 4.04
2466 3163 1.977854 TGCTGCTCCCTCTTACTTTGA 59.022 47.619 0.00 0.00 0.00 2.69
2485 3182 6.648725 ACTTTGACTTTCATGAGCTTCTCTAC 59.351 38.462 0.00 0.00 0.00 2.59
2503 3200 1.276622 ACCATGTCCAGTACCTCCAC 58.723 55.000 0.00 0.00 0.00 4.02
2574 3271 5.647658 TGCAAGGATAGTTTGGATAACAGTG 59.352 40.000 0.00 0.00 0.00 3.66
2591 3288 3.069289 CAGTGTTACAGCATGCAAGAGA 58.931 45.455 21.98 3.18 42.53 3.10
2604 3301 0.809241 CAAGAGAGACGCCTCCATGC 60.809 60.000 0.00 0.00 40.30 4.06
2616 3313 3.615155 GCCTCCATGCTTCTATAATCCC 58.385 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.916293 TCCATCGCCGGCATCAGC 62.916 66.667 28.98 0.00 41.10 4.26
16 17 2.969238 GTCCATCGCCGGCATCAG 60.969 66.667 28.98 12.41 0.00 2.90
17 18 4.889856 CGTCCATCGCCGGCATCA 62.890 66.667 28.98 10.08 0.00 3.07
18 19 4.891727 ACGTCCATCGCCGGCATC 62.892 66.667 28.98 8.26 44.19 3.91
21 22 4.501714 TACACGTCCATCGCCGGC 62.502 66.667 19.07 19.07 44.19 6.13
22 23 2.278596 CTACACGTCCATCGCCGG 60.279 66.667 0.00 0.00 44.19 6.13
23 24 2.278596 CCTACACGTCCATCGCCG 60.279 66.667 0.00 0.00 44.19 6.46
24 25 2.585247 GCCTACACGTCCATCGCC 60.585 66.667 0.00 0.00 44.19 5.54
25 26 2.585247 GGCCTACACGTCCATCGC 60.585 66.667 0.00 0.00 44.19 4.58
26 27 2.278596 CGGCCTACACGTCCATCG 60.279 66.667 0.00 0.00 46.00 3.84
27 28 2.585247 GCGGCCTACACGTCCATC 60.585 66.667 0.00 0.00 0.00 3.51
28 29 3.075005 AGCGGCCTACACGTCCAT 61.075 61.111 0.00 0.00 0.00 3.41
29 30 4.063967 CAGCGGCCTACACGTCCA 62.064 66.667 0.00 0.00 0.00 4.02
30 31 4.814294 CCAGCGGCCTACACGTCC 62.814 72.222 0.00 0.00 0.00 4.79
48 49 2.434884 ATCACGCCGGCAACAGAG 60.435 61.111 28.98 11.60 0.00 3.35
49 50 2.723586 TTCATCACGCCGGCAACAGA 62.724 55.000 28.98 17.92 0.00 3.41
50 51 2.324330 TTCATCACGCCGGCAACAG 61.324 57.895 28.98 12.87 0.00 3.16
51 52 2.281139 TTCATCACGCCGGCAACA 60.281 55.556 28.98 9.22 0.00 3.33
52 53 2.175811 GTTCATCACGCCGGCAAC 59.824 61.111 28.98 18.07 0.00 4.17
53 54 3.053291 GGTTCATCACGCCGGCAA 61.053 61.111 28.98 11.85 0.00 4.52
78 79 2.187946 CCTAGTTCAGGCCAGCGG 59.812 66.667 5.01 0.00 37.70 5.52
79 80 2.187946 CCCTAGTTCAGGCCAGCG 59.812 66.667 5.01 0.00 43.98 5.18
80 81 2.124529 GCCCTAGTTCAGGCCAGC 60.125 66.667 5.01 0.00 43.98 4.85
85 86 0.329596 AAGCCAAGCCCTAGTTCAGG 59.670 55.000 0.00 0.00 45.07 3.86
86 87 1.815003 CAAAGCCAAGCCCTAGTTCAG 59.185 52.381 0.00 0.00 0.00 3.02
87 88 1.423541 TCAAAGCCAAGCCCTAGTTCA 59.576 47.619 0.00 0.00 0.00 3.18
88 89 2.200373 TCAAAGCCAAGCCCTAGTTC 57.800 50.000 0.00 0.00 0.00 3.01
89 90 2.675658 TTCAAAGCCAAGCCCTAGTT 57.324 45.000 0.00 0.00 0.00 2.24
90 91 2.675658 TTTCAAAGCCAAGCCCTAGT 57.324 45.000 0.00 0.00 0.00 2.57
91 92 2.827921 ACATTTCAAAGCCAAGCCCTAG 59.172 45.455 0.00 0.00 0.00 3.02
92 93 2.888212 ACATTTCAAAGCCAAGCCCTA 58.112 42.857 0.00 0.00 0.00 3.53
93 94 1.720781 ACATTTCAAAGCCAAGCCCT 58.279 45.000 0.00 0.00 0.00 5.19
94 95 2.145536 CAACATTTCAAAGCCAAGCCC 58.854 47.619 0.00 0.00 0.00 5.19
95 96 1.532437 GCAACATTTCAAAGCCAAGCC 59.468 47.619 0.00 0.00 0.00 4.35
96 97 2.486918 AGCAACATTTCAAAGCCAAGC 58.513 42.857 0.00 0.00 0.00 4.01
97 98 5.488645 AAAAGCAACATTTCAAAGCCAAG 57.511 34.783 0.00 0.00 0.00 3.61
98 99 6.112058 ACTAAAAGCAACATTTCAAAGCCAA 58.888 32.000 0.00 0.00 0.00 4.52
99 100 5.669477 ACTAAAAGCAACATTTCAAAGCCA 58.331 33.333 0.00 0.00 0.00 4.75
100 101 6.603237 AACTAAAAGCAACATTTCAAAGCC 57.397 33.333 0.00 0.00 0.00 4.35
101 102 8.894409 AAAAACTAAAAGCAACATTTCAAAGC 57.106 26.923 0.00 0.00 0.00 3.51
110 111 9.063739 CGTACACTTTAAAAACTAAAAGCAACA 57.936 29.630 0.00 0.00 36.39 3.33
111 112 8.046132 GCGTACACTTTAAAAACTAAAAGCAAC 58.954 33.333 0.00 0.00 36.39 4.17
112 113 7.044836 CGCGTACACTTTAAAAACTAAAAGCAA 60.045 33.333 0.00 0.00 36.39 3.91
113 114 6.411492 CGCGTACACTTTAAAAACTAAAAGCA 59.589 34.615 0.00 0.00 36.39 3.91
114 115 6.628461 TCGCGTACACTTTAAAAACTAAAAGC 59.372 34.615 5.77 0.00 36.39 3.51
115 116 8.456032 GTTCGCGTACACTTTAAAAACTAAAAG 58.544 33.333 11.25 0.00 38.41 2.27
116 117 7.959651 TGTTCGCGTACACTTTAAAAACTAAAA 59.040 29.630 14.93 0.00 0.00 1.52
117 118 7.459486 TGTTCGCGTACACTTTAAAAACTAAA 58.541 30.769 14.93 0.00 0.00 1.85
118 119 6.998338 TGTTCGCGTACACTTTAAAAACTAA 58.002 32.000 14.93 0.00 0.00 2.24
119 120 6.292274 CCTGTTCGCGTACACTTTAAAAACTA 60.292 38.462 14.93 0.00 0.00 2.24
120 121 5.467902 TGTTCGCGTACACTTTAAAAACT 57.532 34.783 14.93 0.00 0.00 2.66
121 122 4.667504 CCTGTTCGCGTACACTTTAAAAAC 59.332 41.667 14.93 3.27 0.00 2.43
122 123 4.569966 TCCTGTTCGCGTACACTTTAAAAA 59.430 37.500 14.93 0.00 0.00 1.94
123 124 4.118410 TCCTGTTCGCGTACACTTTAAAA 58.882 39.130 14.93 0.00 0.00 1.52
124 125 3.715495 TCCTGTTCGCGTACACTTTAAA 58.285 40.909 14.93 0.00 0.00 1.52
125 126 3.367992 TCCTGTTCGCGTACACTTTAA 57.632 42.857 14.93 0.00 0.00 1.52
126 127 3.581024 ATCCTGTTCGCGTACACTTTA 57.419 42.857 14.93 1.22 0.00 1.85
127 128 2.450609 ATCCTGTTCGCGTACACTTT 57.549 45.000 14.93 0.00 0.00 2.66
128 129 2.066262 CAATCCTGTTCGCGTACACTT 58.934 47.619 14.93 6.17 0.00 3.16
129 130 1.671850 CCAATCCTGTTCGCGTACACT 60.672 52.381 14.93 0.00 0.00 3.55
130 131 0.719465 CCAATCCTGTTCGCGTACAC 59.281 55.000 14.93 6.68 0.00 2.90
131 132 1.017177 GCCAATCCTGTTCGCGTACA 61.017 55.000 17.78 17.78 0.00 2.90
132 133 1.017177 TGCCAATCCTGTTCGCGTAC 61.017 55.000 9.12 9.12 0.00 3.67
133 134 0.320858 TTGCCAATCCTGTTCGCGTA 60.321 50.000 5.77 0.00 0.00 4.42
134 135 1.169661 TTTGCCAATCCTGTTCGCGT 61.170 50.000 5.77 0.00 0.00 6.01
135 136 0.171007 ATTTGCCAATCCTGTTCGCG 59.829 50.000 0.00 0.00 0.00 5.87
136 137 1.202114 TCATTTGCCAATCCTGTTCGC 59.798 47.619 0.00 0.00 0.00 4.70
137 138 3.574284 TTCATTTGCCAATCCTGTTCG 57.426 42.857 0.00 0.00 0.00 3.95
138 139 3.619929 GCATTCATTTGCCAATCCTGTTC 59.380 43.478 0.00 0.00 36.60 3.18
139 140 3.602483 GCATTCATTTGCCAATCCTGTT 58.398 40.909 0.00 0.00 36.60 3.16
140 141 2.417651 CGCATTCATTTGCCAATCCTGT 60.418 45.455 0.00 0.00 39.52 4.00
141 142 2.198406 CGCATTCATTTGCCAATCCTG 58.802 47.619 0.00 0.00 39.52 3.86
142 143 1.137479 CCGCATTCATTTGCCAATCCT 59.863 47.619 0.00 0.00 39.52 3.24
143 144 1.574134 CCGCATTCATTTGCCAATCC 58.426 50.000 0.00 0.00 39.52 3.01
144 145 0.932399 GCCGCATTCATTTGCCAATC 59.068 50.000 0.00 0.00 39.52 2.67
145 146 0.462403 GGCCGCATTCATTTGCCAAT 60.462 50.000 0.00 0.00 41.76 3.16
146 147 1.079266 GGCCGCATTCATTTGCCAA 60.079 52.632 0.00 0.00 41.76 4.52
147 148 2.578128 GGCCGCATTCATTTGCCA 59.422 55.556 0.00 0.00 41.76 4.92
148 149 2.583045 CGGCCGCATTCATTTGCC 60.583 61.111 14.67 0.00 39.52 4.52
149 150 3.256833 GCGGCCGCATTCATTTGC 61.257 61.111 43.55 11.07 41.49 3.68
150 151 2.950710 CGCGGCCGCATTCATTTG 60.951 61.111 45.26 25.41 42.06 2.32
180 181 4.424711 TTCTGGGATGCGGTGGCC 62.425 66.667 0.00 0.00 38.85 5.36
181 182 3.134127 GTTCTGGGATGCGGTGGC 61.134 66.667 0.00 0.00 40.52 5.01
182 183 1.746615 CTGTTCTGGGATGCGGTGG 60.747 63.158 0.00 0.00 0.00 4.61
183 184 1.021390 GTCTGTTCTGGGATGCGGTG 61.021 60.000 0.00 0.00 0.00 4.94
184 185 1.296715 GTCTGTTCTGGGATGCGGT 59.703 57.895 0.00 0.00 0.00 5.68
185 186 1.450312 GGTCTGTTCTGGGATGCGG 60.450 63.158 0.00 0.00 0.00 5.69
186 187 1.450312 GGGTCTGTTCTGGGATGCG 60.450 63.158 0.00 0.00 0.00 4.73
187 188 1.450312 CGGGTCTGTTCTGGGATGC 60.450 63.158 0.00 0.00 0.00 3.91
188 189 1.221840 CCGGGTCTGTTCTGGGATG 59.778 63.158 0.00 0.00 0.00 3.51
189 190 1.080354 TCCGGGTCTGTTCTGGGAT 59.920 57.895 0.00 0.00 0.00 3.85
190 191 1.911766 GTCCGGGTCTGTTCTGGGA 60.912 63.158 0.00 0.00 0.00 4.37
191 192 2.214216 TGTCCGGGTCTGTTCTGGG 61.214 63.158 0.00 0.00 0.00 4.45
192 193 1.004918 GTGTCCGGGTCTGTTCTGG 60.005 63.158 0.00 0.00 0.00 3.86
193 194 1.372997 CGTGTCCGGGTCTGTTCTG 60.373 63.158 0.00 0.00 0.00 3.02
194 195 1.529948 TCGTGTCCGGGTCTGTTCT 60.530 57.895 0.00 0.00 33.95 3.01
195 196 1.372623 GTCGTGTCCGGGTCTGTTC 60.373 63.158 0.00 0.00 33.95 3.18
196 197 2.732658 GTCGTGTCCGGGTCTGTT 59.267 61.111 0.00 0.00 33.95 3.16
197 198 3.300765 GGTCGTGTCCGGGTCTGT 61.301 66.667 0.00 0.00 33.95 3.41
198 199 4.065281 GGGTCGTGTCCGGGTCTG 62.065 72.222 0.00 0.00 33.95 3.51
202 203 3.262448 ATTTGGGGTCGTGTCCGGG 62.262 63.158 0.00 0.00 33.95 5.73
203 204 1.743995 GATTTGGGGTCGTGTCCGG 60.744 63.158 0.00 0.00 33.95 5.14
204 205 1.743995 GGATTTGGGGTCGTGTCCG 60.744 63.158 0.00 0.00 0.00 4.79
205 206 1.378119 GGGATTTGGGGTCGTGTCC 60.378 63.158 0.00 0.00 0.00 4.02
206 207 0.906775 TAGGGATTTGGGGTCGTGTC 59.093 55.000 0.00 0.00 0.00 3.67
207 208 1.003928 GTTAGGGATTTGGGGTCGTGT 59.996 52.381 0.00 0.00 0.00 4.49
208 209 1.680860 GGTTAGGGATTTGGGGTCGTG 60.681 57.143 0.00 0.00 0.00 4.35
209 210 0.622136 GGTTAGGGATTTGGGGTCGT 59.378 55.000 0.00 0.00 0.00 4.34
210 211 0.621609 TGGTTAGGGATTTGGGGTCG 59.378 55.000 0.00 0.00 0.00 4.79
211 212 2.829720 GTTTGGTTAGGGATTTGGGGTC 59.170 50.000 0.00 0.00 0.00 4.46
212 213 2.820105 CGTTTGGTTAGGGATTTGGGGT 60.820 50.000 0.00 0.00 0.00 4.95
213 214 1.822371 CGTTTGGTTAGGGATTTGGGG 59.178 52.381 0.00 0.00 0.00 4.96
214 215 1.822371 CCGTTTGGTTAGGGATTTGGG 59.178 52.381 0.00 0.00 0.00 4.12
215 216 2.797786 TCCGTTTGGTTAGGGATTTGG 58.202 47.619 0.00 0.00 36.30 3.28
216 217 5.433526 TCTATCCGTTTGGTTAGGGATTTG 58.566 41.667 3.51 0.00 41.62 2.32
217 218 5.703730 TCTATCCGTTTGGTTAGGGATTT 57.296 39.130 3.51 0.00 41.62 2.17
218 219 5.703730 TTCTATCCGTTTGGTTAGGGATT 57.296 39.130 3.51 0.00 41.62 3.01
219 220 5.221864 GGATTCTATCCGTTTGGTTAGGGAT 60.222 44.000 0.00 0.00 43.31 3.85
220 221 4.102054 GGATTCTATCCGTTTGGTTAGGGA 59.898 45.833 0.00 0.00 40.13 4.20
221 222 4.386711 GGATTCTATCCGTTTGGTTAGGG 58.613 47.826 0.00 0.00 40.13 3.53
233 234 4.040461 TCAAACAGGATCCGGATTCTATCC 59.960 45.833 25.31 18.49 46.22 2.59
234 235 5.215252 TCAAACAGGATCCGGATTCTATC 57.785 43.478 25.31 9.32 0.00 2.08
235 236 5.220710 CTCAAACAGGATCCGGATTCTAT 57.779 43.478 25.31 12.07 0.00 1.98
236 237 4.672587 CTCAAACAGGATCCGGATTCTA 57.327 45.455 25.31 8.46 0.00 2.10
237 238 3.550437 CTCAAACAGGATCCGGATTCT 57.450 47.619 20.40 20.40 0.00 2.40
249 250 0.393077 ACTCCACCGACCTCAAACAG 59.607 55.000 0.00 0.00 0.00 3.16
250 251 0.834612 AACTCCACCGACCTCAAACA 59.165 50.000 0.00 0.00 0.00 2.83
251 252 1.226746 CAACTCCACCGACCTCAAAC 58.773 55.000 0.00 0.00 0.00 2.93
252 253 0.107831 CCAACTCCACCGACCTCAAA 59.892 55.000 0.00 0.00 0.00 2.69
253 254 1.752198 CCAACTCCACCGACCTCAA 59.248 57.895 0.00 0.00 0.00 3.02
254 255 2.879233 GCCAACTCCACCGACCTCA 61.879 63.158 0.00 0.00 0.00 3.86
255 256 2.047179 GCCAACTCCACCGACCTC 60.047 66.667 0.00 0.00 0.00 3.85
256 257 3.637273 GGCCAACTCCACCGACCT 61.637 66.667 0.00 0.00 0.00 3.85
257 258 1.833787 TAAGGCCAACTCCACCGACC 61.834 60.000 5.01 0.00 0.00 4.79
258 259 0.035739 TTAAGGCCAACTCCACCGAC 59.964 55.000 5.01 0.00 0.00 4.79
259 260 0.323629 CTTAAGGCCAACTCCACCGA 59.676 55.000 5.01 0.00 0.00 4.69
260 261 1.305930 GCTTAAGGCCAACTCCACCG 61.306 60.000 5.01 0.00 34.27 4.94
261 262 2.568003 GCTTAAGGCCAACTCCACC 58.432 57.895 5.01 0.00 34.27 4.61
271 272 5.105063 GTCATCAATCAAAAGGCTTAAGGC 58.895 41.667 20.84 20.84 41.43 4.35
272 273 6.271488 TGTCATCAATCAAAAGGCTTAAGG 57.729 37.500 0.00 0.00 0.00 2.69
273 274 7.540055 GTCTTGTCATCAATCAAAAGGCTTAAG 59.460 37.037 0.00 0.00 32.82 1.85
340 399 1.156736 GCAAGTGTACACCGAGCAAT 58.843 50.000 22.28 0.00 0.00 3.56
391 450 0.521735 GGATCGAAGGGCAACAACAC 59.478 55.000 0.00 0.00 39.74 3.32
755 814 2.086094 CCATGCCCCAAAAGATTTTGC 58.914 47.619 11.68 2.92 44.62 3.68
756 815 3.244491 TGTCCATGCCCCAAAAGATTTTG 60.244 43.478 10.43 10.43 45.34 2.44
757 816 2.978278 TGTCCATGCCCCAAAAGATTTT 59.022 40.909 0.00 0.00 0.00 1.82
769 828 3.503363 GAGCAGCGTGTCCATGCC 61.503 66.667 7.83 0.00 44.12 4.40
770 829 2.743538 TGAGCAGCGTGTCCATGC 60.744 61.111 3.26 3.26 43.42 4.06
780 860 2.051882 GTGCGTTGTGTGAGCAGC 60.052 61.111 0.00 0.00 41.93 5.25
799 919 2.650116 TTGGCTGCTCCTCGGAGAC 61.650 63.158 16.92 8.49 44.53 3.36
845 965 2.047655 TGGCATTGGACGACGGAC 60.048 61.111 0.00 0.00 0.00 4.79
880 1000 2.185350 CTGGAGGTGGTAGCAGCG 59.815 66.667 17.58 0.65 0.00 5.18
897 1023 3.706373 TGCCGAGGAGTTGGAGCC 61.706 66.667 0.00 0.00 0.00 4.70
898 1024 2.435059 GTGCCGAGGAGTTGGAGC 60.435 66.667 0.00 0.00 0.00 4.70
899 1025 1.374758 GTGTGCCGAGGAGTTGGAG 60.375 63.158 0.00 0.00 0.00 3.86
900 1026 1.691195 TTGTGTGCCGAGGAGTTGGA 61.691 55.000 0.00 0.00 0.00 3.53
901 1027 1.227823 TTGTGTGCCGAGGAGTTGG 60.228 57.895 0.00 0.00 0.00 3.77
902 1028 1.845809 GCTTGTGTGCCGAGGAGTTG 61.846 60.000 0.00 0.00 0.00 3.16
903 1029 1.598130 GCTTGTGTGCCGAGGAGTT 60.598 57.895 0.00 0.00 0.00 3.01
924 1050 2.419739 GGACTGAGGACGAGGAGGC 61.420 68.421 0.00 0.00 0.00 4.70
932 1058 3.827898 CCGGCGAGGACTGAGGAC 61.828 72.222 9.30 0.00 45.00 3.85
949 1075 4.479993 AGCAGGATCAGCCACCGC 62.480 66.667 5.84 0.00 40.02 5.68
953 1079 3.473647 CCCGAGCAGGATCAGCCA 61.474 66.667 5.84 0.00 45.00 4.75
1479 1623 2.496817 GAGTAGCTGCCCTGGTCG 59.503 66.667 0.00 0.00 0.00 4.79
1845 1995 4.560128 CTTCAACAGTTCTACTAGCAGCA 58.440 43.478 0.00 0.00 0.00 4.41
1846 1996 3.369451 GCTTCAACAGTTCTACTAGCAGC 59.631 47.826 0.00 0.00 28.17 5.25
1847 1997 4.560128 TGCTTCAACAGTTCTACTAGCAG 58.440 43.478 0.00 0.00 31.91 4.24
1848 1998 4.280929 TCTGCTTCAACAGTTCTACTAGCA 59.719 41.667 0.00 0.00 38.84 3.49
1849 1999 4.810790 TCTGCTTCAACAGTTCTACTAGC 58.189 43.478 0.00 0.00 38.84 3.42
1850 2000 6.625362 TGATCTGCTTCAACAGTTCTACTAG 58.375 40.000 0.00 0.00 37.31 2.57
1851 2001 6.590234 TGATCTGCTTCAACAGTTCTACTA 57.410 37.500 0.00 0.00 37.31 1.82
1852 2002 5.474578 TGATCTGCTTCAACAGTTCTACT 57.525 39.130 0.00 0.00 37.31 2.57
1853 2003 5.698545 ACTTGATCTGCTTCAACAGTTCTAC 59.301 40.000 0.00 0.00 37.31 2.59
1862 2012 5.246203 AGTGGTACTACTTGATCTGCTTCAA 59.754 40.000 5.98 0.00 34.55 2.69
1879 2029 4.272261 GCTAGGACGAACTAGTAGTGGTAC 59.728 50.000 2.90 6.25 41.93 3.34
1963 2638 8.978874 TCATGCCATAAATGTTGAACTAGTAT 57.021 30.769 0.00 0.00 0.00 2.12
1982 2657 7.924412 ACTGATACATCAATTTCATTTCATGCC 59.076 33.333 0.00 0.00 36.18 4.40
1983 2658 8.867112 ACTGATACATCAATTTCATTTCATGC 57.133 30.769 0.00 0.00 36.18 4.06
2116 2801 5.987098 AGCAGATGATTTCAGATGTACTGT 58.013 37.500 0.00 0.00 45.86 3.55
2117 2802 6.762187 AGAAGCAGATGATTTCAGATGTACTG 59.238 38.462 0.00 0.00 46.97 2.74
2228 2925 5.539955 AGGTTCACAAAGCAAGTTGGATATT 59.460 36.000 4.75 0.00 35.29 1.28
2271 2968 4.202367 ACTTCAGTCAGTAGTTTTCCCTGG 60.202 45.833 0.00 0.00 0.00 4.45
2294 2991 1.730064 GTTAACAAGATCGCGCCTTCA 59.270 47.619 0.00 0.00 0.00 3.02
2360 3057 0.109689 GCGGGATCTTATCGAGGACG 60.110 60.000 0.00 0.00 41.26 4.79
2441 3138 0.978146 TAAGAGGGAGCAGCAGGACC 60.978 60.000 0.00 0.00 0.00 4.46
2466 3163 5.046014 ACATGGTAGAGAAGCTCATGAAAGT 60.046 40.000 14.26 0.00 38.69 2.66
2485 3182 0.541863 GGTGGAGGTACTGGACATGG 59.458 60.000 0.00 0.00 41.55 3.66
2503 3200 1.156736 CGGTTTCAGTAAGCTGTGGG 58.843 55.000 0.00 0.00 43.05 4.61
2525 3222 3.376234 CACTCAATGATCTTTCGGCACAT 59.624 43.478 0.00 0.00 0.00 3.21
2574 3271 2.346847 CGTCTCTCTTGCATGCTGTAAC 59.653 50.000 20.33 7.08 0.00 2.50
2591 3288 3.719121 AGAAGCATGGAGGCGTCT 58.281 55.556 6.34 0.00 45.66 4.18
2604 3301 4.873746 TCTCGCCAAGGGATTATAGAAG 57.126 45.455 0.00 0.00 0.00 2.85
2616 3313 2.079158 TGCTCAGAATTTCTCGCCAAG 58.921 47.619 12.28 1.79 0.00 3.61


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

AutoCloner maintained by Alex Coulton.