Multiple sequence alignment - TraesCS7D01G495900

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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 TraesCS7D01G495900 chr7D 100.000 2501 0 0 1 2501 602775408 602777908 0.000000e+00 4619.0
1 TraesCS7D01G495900 chr7D 95.363 1294 51 8 849 2135 590072350 590071059 0.000000e+00 2049.0
2 TraesCS7D01G495900 chr7D 96.185 367 14 0 2135 2501 590071029 590070663 3.560000e-168 601.0
3 TraesCS7D01G495900 chr7D 95.455 110 3 1 221 328 602775518 602775627 9.200000e-40 174.0
4 TraesCS7D01G495900 chr7D 95.455 110 3 1 111 220 602775628 602775735 9.200000e-40 174.0
5 TraesCS7D01G495900 chr3D 94.998 2219 68 14 319 2501 585903860 585901649 0.000000e+00 3443.0
6 TraesCS7D01G495900 chr3D 93.684 1615 85 11 370 1972 46539861 46541470 0.000000e+00 2401.0
7 TraesCS7D01G495900 chr3D 97.548 367 9 0 2135 2501 46541632 46541998 1.630000e-176 628.0
8 TraesCS7D01G495900 chr5A 95.944 1701 53 4 448 2135 426307145 426305448 0.000000e+00 2745.0
9 TraesCS7D01G495900 chr5A 97.003 367 11 0 2135 2501 426305418 426305052 3.530000e-173 617.0
10 TraesCS7D01G495900 chr5A 96.000 50 2 0 1058 1107 426306289 426306240 5.730000e-12 82.4
11 TraesCS7D01G495900 chr1D 95.272 1671 59 9 318 1972 467457348 467455682 0.000000e+00 2630.0
12 TraesCS7D01G495900 chr1D 92.314 1184 58 13 961 2135 122263780 122262621 0.000000e+00 1652.0
13 TraesCS7D01G495900 chr1D 97.260 365 10 0 2135 2499 467455520 467455156 9.830000e-174 619.0
14 TraesCS7D01G495900 chr1D 96.458 367 13 0 2135 2501 122262591 122262225 7.650000e-170 606.0
15 TraesCS7D01G495900 chr6D 93.564 1616 78 14 376 1972 110324261 110322653 0.000000e+00 2385.0
16 TraesCS7D01G495900 chr6D 92.798 1569 77 12 425 1972 80068593 80070146 0.000000e+00 2239.0
17 TraesCS7D01G495900 chr6D 97.003 367 11 0 2135 2501 80081969 80082335 3.530000e-173 617.0
18 TraesCS7D01G495900 chr6D 96.730 367 12 0 2135 2501 110322491 110322125 1.640000e-171 612.0
19 TraesCS7D01G495900 chr5D 92.593 1620 76 22 370 1972 495476204 495477796 0.000000e+00 2287.0
20 TraesCS7D01G495900 chr3B 91.237 1415 102 10 1103 2501 241928756 241927348 0.000000e+00 1906.0
21 TraesCS7D01G495900 chr2B 92.365 537 35 6 318 851 18196190 18195657 0.000000e+00 760.0
22 TraesCS7D01G495900 chr2D 90.261 575 47 9 373 943 590221127 590221696 0.000000e+00 743.0
23 TraesCS7D01G495900 chr2D 89.575 259 21 3 1881 2135 41959312 41959568 8.630000e-85 324.0
24 TraesCS7D01G495900 chr5B 85.232 474 29 12 1881 2324 472291715 472292177 1.360000e-122 449.0
25 TraesCS7D01G495900 chr4D 91.506 259 18 2 1881 2135 417406822 417407080 1.100000e-93 353.0
26 TraesCS7D01G495900 chr1B 91.339 254 18 2 1886 2135 470442596 470442849 6.620000e-91 344.0


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 TraesCS7D01G495900 chr7D 602775408 602777908 2500 False 1655.666667 4619 96.970000 1 2501 3 chr7D.!!$F1 2500
1 TraesCS7D01G495900 chr7D 590070663 590072350 1687 True 1325.000000 2049 95.774000 849 2501 2 chr7D.!!$R1 1652
2 TraesCS7D01G495900 chr3D 585901649 585903860 2211 True 3443.000000 3443 94.998000 319 2501 1 chr3D.!!$R1 2182
3 TraesCS7D01G495900 chr3D 46539861 46541998 2137 False 1514.500000 2401 95.616000 370 2501 2 chr3D.!!$F1 2131
4 TraesCS7D01G495900 chr5A 426305052 426307145 2093 True 1148.133333 2745 96.315667 448 2501 3 chr5A.!!$R1 2053
5 TraesCS7D01G495900 chr1D 467455156 467457348 2192 True 1624.500000 2630 96.266000 318 2499 2 chr1D.!!$R2 2181
6 TraesCS7D01G495900 chr1D 122262225 122263780 1555 True 1129.000000 1652 94.386000 961 2501 2 chr1D.!!$R1 1540
7 TraesCS7D01G495900 chr6D 80068593 80070146 1553 False 2239.000000 2239 92.798000 425 1972 1 chr6D.!!$F1 1547
8 TraesCS7D01G495900 chr6D 110322125 110324261 2136 True 1498.500000 2385 95.147000 376 2501 2 chr6D.!!$R1 2125
9 TraesCS7D01G495900 chr5D 495476204 495477796 1592 False 2287.000000 2287 92.593000 370 1972 1 chr5D.!!$F1 1602
10 TraesCS7D01G495900 chr3B 241927348 241928756 1408 True 1906.000000 1906 91.237000 1103 2501 1 chr3B.!!$R1 1398
11 TraesCS7D01G495900 chr2B 18195657 18196190 533 True 760.000000 760 92.365000 318 851 1 chr2B.!!$R1 533
12 TraesCS7D01G495900 chr2D 590221127 590221696 569 False 743.000000 743 90.261000 373 943 1 chr2D.!!$F2 570

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
169 170 0.031817 AGCAAAATGGGGAGATGGGG 60.032 55.0 0.0 0.0 0.0 4.96 F
280 281 0.031817 AAAATGGGGAGATGGGGCAG 60.032 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 1105 3.119096 GACGGCAAGAACGAGGGC 61.119 66.667 0.0 0.0 34.93 5.19 R
1771 1851 3.255642 GCAGCCTAACTCAAATGGACAAA 59.744 43.478 0.0 0.0 0.00 2.83 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
38 39 9.159254 AGAAATAAGAAAATTGGAAAAGGAGGT 57.841 29.630 0.00 0.00 0.00 3.85
39 40 9.778741 GAAATAAGAAAATTGGAAAAGGAGGTT 57.221 29.630 0.00 0.00 0.00 3.50
40 41 9.778741 AAATAAGAAAATTGGAAAAGGAGGTTC 57.221 29.630 0.00 0.00 0.00 3.62
41 42 6.806668 AAGAAAATTGGAAAAGGAGGTTCA 57.193 33.333 0.00 0.00 0.00 3.18
42 43 7.379059 AAGAAAATTGGAAAAGGAGGTTCAT 57.621 32.000 0.00 0.00 0.00 2.57
43 44 7.379059 AGAAAATTGGAAAAGGAGGTTCATT 57.621 32.000 0.00 0.00 0.00 2.57
44 45 8.491045 AGAAAATTGGAAAAGGAGGTTCATTA 57.509 30.769 0.00 0.00 0.00 1.90
45 46 9.104713 AGAAAATTGGAAAAGGAGGTTCATTAT 57.895 29.630 0.00 0.00 0.00 1.28
46 47 9.371136 GAAAATTGGAAAAGGAGGTTCATTATC 57.629 33.333 0.00 0.00 0.00 1.75
47 48 8.434589 AAATTGGAAAAGGAGGTTCATTATCA 57.565 30.769 0.00 0.00 0.00 2.15
48 49 8.434589 AATTGGAAAAGGAGGTTCATTATCAA 57.565 30.769 0.00 0.00 0.00 2.57
49 50 7.847711 TTGGAAAAGGAGGTTCATTATCAAA 57.152 32.000 0.00 0.00 0.00 2.69
50 51 8.434589 TTGGAAAAGGAGGTTCATTATCAAAT 57.565 30.769 0.00 0.00 0.00 2.32
51 52 8.434589 TGGAAAAGGAGGTTCATTATCAAATT 57.565 30.769 0.00 0.00 0.00 1.82
52 53 8.313292 TGGAAAAGGAGGTTCATTATCAAATTG 58.687 33.333 0.00 0.00 0.00 2.32
53 54 8.314021 GGAAAAGGAGGTTCATTATCAAATTGT 58.686 33.333 0.00 0.00 0.00 2.71
54 55 9.143631 GAAAAGGAGGTTCATTATCAAATTGTG 57.856 33.333 0.00 0.00 0.00 3.33
55 56 6.212888 AGGAGGTTCATTATCAAATTGTGC 57.787 37.500 0.00 0.00 0.00 4.57
56 57 5.716228 AGGAGGTTCATTATCAAATTGTGCA 59.284 36.000 0.00 0.00 0.00 4.57
57 58 6.381994 AGGAGGTTCATTATCAAATTGTGCAT 59.618 34.615 0.00 0.00 0.00 3.96
58 59 6.477688 GGAGGTTCATTATCAAATTGTGCATG 59.522 38.462 0.00 0.00 0.00 4.06
59 60 6.342906 AGGTTCATTATCAAATTGTGCATGG 58.657 36.000 0.00 0.00 0.00 3.66
60 61 6.070653 AGGTTCATTATCAAATTGTGCATGGT 60.071 34.615 0.00 0.00 0.00 3.55
61 62 6.036300 GGTTCATTATCAAATTGTGCATGGTG 59.964 38.462 0.00 0.00 0.00 4.17
62 63 5.662456 TCATTATCAAATTGTGCATGGTGG 58.338 37.500 0.00 0.00 0.00 4.61
63 64 2.389962 ATCAAATTGTGCATGGTGGC 57.610 45.000 0.00 0.00 0.00 5.01
64 65 0.321021 TCAAATTGTGCATGGTGGCC 59.679 50.000 0.00 0.00 0.00 5.36
65 66 0.322322 CAAATTGTGCATGGTGGCCT 59.678 50.000 3.32 0.00 0.00 5.19
66 67 0.322322 AAATTGTGCATGGTGGCCTG 59.678 50.000 3.32 0.00 0.00 4.85
67 68 0.832983 AATTGTGCATGGTGGCCTGT 60.833 50.000 3.32 0.00 0.00 4.00
68 69 1.537814 ATTGTGCATGGTGGCCTGTG 61.538 55.000 3.32 0.00 0.00 3.66
69 70 3.376078 GTGCATGGTGGCCTGTGG 61.376 66.667 3.32 0.00 0.00 4.17
70 71 3.900862 TGCATGGTGGCCTGTGGT 61.901 61.111 3.32 0.00 0.00 4.16
71 72 2.601367 GCATGGTGGCCTGTGGTT 60.601 61.111 3.32 0.00 0.00 3.67
72 73 1.304052 GCATGGTGGCCTGTGGTTA 60.304 57.895 3.32 0.00 0.00 2.85
73 74 1.595093 GCATGGTGGCCTGTGGTTAC 61.595 60.000 3.32 0.00 0.00 2.50
74 75 0.038166 CATGGTGGCCTGTGGTTACT 59.962 55.000 3.32 0.00 0.00 2.24
75 76 0.038166 ATGGTGGCCTGTGGTTACTG 59.962 55.000 3.32 0.00 0.00 2.74
76 77 1.349542 TGGTGGCCTGTGGTTACTGT 61.350 55.000 3.32 0.00 0.00 3.55
77 78 0.688487 GGTGGCCTGTGGTTACTGTA 59.312 55.000 3.32 0.00 0.00 2.74
78 79 1.338769 GGTGGCCTGTGGTTACTGTAG 60.339 57.143 3.32 0.00 0.00 2.74
79 80 0.323629 TGGCCTGTGGTTACTGTAGC 59.676 55.000 3.32 0.00 0.00 3.58
80 81 0.739813 GGCCTGTGGTTACTGTAGCG 60.740 60.000 0.00 0.00 0.00 4.26
81 82 0.037605 GCCTGTGGTTACTGTAGCGT 60.038 55.000 0.00 0.00 0.00 5.07
82 83 1.203052 GCCTGTGGTTACTGTAGCGTA 59.797 52.381 0.00 0.00 0.00 4.42
83 84 2.734492 GCCTGTGGTTACTGTAGCGTAG 60.734 54.545 0.00 0.00 0.00 3.51
108 109 2.872557 CGTAGGTCGCTGGTTCGA 59.127 61.111 0.00 0.00 35.95 3.71
109 110 1.432251 CGTAGGTCGCTGGTTCGAT 59.568 57.895 0.00 0.00 40.84 3.59
110 111 0.591741 CGTAGGTCGCTGGTTCGATC 60.592 60.000 0.00 0.00 40.84 3.69
111 112 0.248949 GTAGGTCGCTGGTTCGATCC 60.249 60.000 5.52 5.52 40.24 3.36
112 113 1.389609 TAGGTCGCTGGTTCGATCCC 61.390 60.000 10.02 2.41 40.24 3.85
113 114 2.202892 GTCGCTGGTTCGATCCCC 60.203 66.667 10.02 0.00 40.84 4.81
114 115 2.363795 TCGCTGGTTCGATCCCCT 60.364 61.111 10.02 0.00 33.02 4.79
115 116 2.202932 CGCTGGTTCGATCCCCTG 60.203 66.667 10.02 4.73 0.00 4.45
116 117 2.990479 GCTGGTTCGATCCCCTGT 59.010 61.111 10.02 0.00 0.00 4.00
117 118 1.450312 GCTGGTTCGATCCCCTGTG 60.450 63.158 10.02 0.00 0.00 3.66
118 119 1.221840 CTGGTTCGATCCCCTGTGG 59.778 63.158 10.02 0.00 0.00 4.17
132 133 3.874392 CCTGTGGGATTGCCTTTTTAG 57.126 47.619 0.00 0.00 33.58 1.85
133 134 3.165071 CCTGTGGGATTGCCTTTTTAGT 58.835 45.455 0.00 0.00 33.58 2.24
134 135 3.578282 CCTGTGGGATTGCCTTTTTAGTT 59.422 43.478 0.00 0.00 33.58 2.24
135 136 4.770010 CCTGTGGGATTGCCTTTTTAGTTA 59.230 41.667 0.00 0.00 33.58 2.24
136 137 5.422012 CCTGTGGGATTGCCTTTTTAGTTAT 59.578 40.000 0.00 0.00 33.58 1.89
137 138 6.070824 CCTGTGGGATTGCCTTTTTAGTTATT 60.071 38.462 0.00 0.00 33.58 1.40
138 139 7.123547 CCTGTGGGATTGCCTTTTTAGTTATTA 59.876 37.037 0.00 0.00 33.58 0.98
139 140 8.423906 TGTGGGATTGCCTTTTTAGTTATTAA 57.576 30.769 0.00 0.00 0.00 1.40
140 141 8.871125 TGTGGGATTGCCTTTTTAGTTATTAAA 58.129 29.630 0.00 0.00 0.00 1.52
141 142 9.713713 GTGGGATTGCCTTTTTAGTTATTAAAA 57.286 29.630 0.00 0.00 38.99 1.52
162 163 4.769345 AAAACAGAAAGCAAAATGGGGA 57.231 36.364 0.00 0.00 0.00 4.81
163 164 4.341366 AAACAGAAAGCAAAATGGGGAG 57.659 40.909 0.00 0.00 0.00 4.30
164 165 3.243359 ACAGAAAGCAAAATGGGGAGA 57.757 42.857 0.00 0.00 0.00 3.71
165 166 3.782992 ACAGAAAGCAAAATGGGGAGAT 58.217 40.909 0.00 0.00 0.00 2.75
166 167 3.512724 ACAGAAAGCAAAATGGGGAGATG 59.487 43.478 0.00 0.00 0.00 2.90
167 168 3.102204 AGAAAGCAAAATGGGGAGATGG 58.898 45.455 0.00 0.00 0.00 3.51
168 169 1.870064 AAGCAAAATGGGGAGATGGG 58.130 50.000 0.00 0.00 0.00 4.00
169 170 0.031817 AGCAAAATGGGGAGATGGGG 60.032 55.000 0.00 0.00 0.00 4.96
170 171 1.689243 GCAAAATGGGGAGATGGGGC 61.689 60.000 0.00 0.00 0.00 5.80
171 172 0.325484 CAAAATGGGGAGATGGGGCA 60.325 55.000 0.00 0.00 0.00 5.36
172 173 0.031817 AAAATGGGGAGATGGGGCAG 60.032 55.000 0.00 0.00 0.00 4.85
173 174 2.594365 AAATGGGGAGATGGGGCAGC 62.594 60.000 0.00 0.00 0.00 5.25
181 182 4.511246 ATGGGGCAGCCCATCACG 62.511 66.667 32.58 0.00 46.53 4.35
184 185 4.864334 GGGCAGCCCATCACGGAG 62.864 72.222 27.33 0.00 44.65 4.63
185 186 4.864334 GGCAGCCCATCACGGAGG 62.864 72.222 0.00 0.00 36.56 4.30
186 187 4.101448 GCAGCCCATCACGGAGGT 62.101 66.667 0.00 0.00 36.56 3.85
187 188 2.124983 CAGCCCATCACGGAGGTG 60.125 66.667 0.00 0.00 45.78 4.00
197 198 2.932663 ACGGAGGTGATTTGTGCAG 58.067 52.632 0.00 0.00 0.00 4.41
198 199 1.237285 ACGGAGGTGATTTGTGCAGC 61.237 55.000 0.00 0.00 0.00 5.25
199 200 1.885871 GGAGGTGATTTGTGCAGCC 59.114 57.895 0.00 0.00 34.46 4.85
200 201 1.503542 GAGGTGATTTGTGCAGCCG 59.496 57.895 0.00 0.00 34.46 5.52
201 202 1.228245 AGGTGATTTGTGCAGCCGT 60.228 52.632 0.00 0.00 34.46 5.68
202 203 0.823356 AGGTGATTTGTGCAGCCGTT 60.823 50.000 0.00 0.00 34.46 4.44
203 204 0.031994 GGTGATTTGTGCAGCCGTTT 59.968 50.000 0.00 0.00 0.00 3.60
204 205 1.130955 GTGATTTGTGCAGCCGTTTG 58.869 50.000 0.00 0.00 0.00 2.93
205 206 0.597118 TGATTTGTGCAGCCGTTTGC 60.597 50.000 0.00 1.76 44.33 3.68
206 207 1.284297 GATTTGTGCAGCCGTTTGCC 61.284 55.000 6.00 0.00 43.43 4.52
207 208 2.025767 ATTTGTGCAGCCGTTTGCCA 62.026 50.000 6.00 1.88 43.43 4.92
208 209 2.230994 TTTGTGCAGCCGTTTGCCAA 62.231 50.000 6.00 6.94 43.43 4.52
209 210 2.105930 GTGCAGCCGTTTGCCAAA 59.894 55.556 6.00 0.00 43.43 3.28
210 211 1.300853 GTGCAGCCGTTTGCCAAAT 60.301 52.632 6.00 0.00 43.43 2.32
211 212 1.006337 TGCAGCCGTTTGCCAAATC 60.006 52.632 6.00 0.00 43.43 2.17
212 213 1.737735 GCAGCCGTTTGCCAAATCC 60.738 57.895 0.00 0.00 42.71 3.01
213 214 1.664873 CAGCCGTTTGCCAAATCCA 59.335 52.632 0.00 0.00 42.71 3.41
214 215 0.388907 CAGCCGTTTGCCAAATCCAG 60.389 55.000 0.00 0.00 42.71 3.86
215 216 0.539438 AGCCGTTTGCCAAATCCAGA 60.539 50.000 0.00 0.00 42.71 3.86
216 217 0.316841 GCCGTTTGCCAAATCCAGAA 59.683 50.000 0.00 0.00 0.00 3.02
217 218 1.270041 GCCGTTTGCCAAATCCAGAAA 60.270 47.619 0.00 0.00 0.00 2.52
218 219 2.612721 GCCGTTTGCCAAATCCAGAAAT 60.613 45.455 0.00 0.00 0.00 2.17
219 220 3.367910 GCCGTTTGCCAAATCCAGAAATA 60.368 43.478 0.00 0.00 0.00 1.40
220 221 4.173256 CCGTTTGCCAAATCCAGAAATAC 58.827 43.478 0.00 0.00 0.00 1.89
221 222 4.173256 CGTTTGCCAAATCCAGAAATACC 58.827 43.478 0.00 0.00 0.00 2.73
222 223 4.503910 GTTTGCCAAATCCAGAAATACCC 58.496 43.478 0.00 0.00 0.00 3.69
223 224 2.745968 TGCCAAATCCAGAAATACCCC 58.254 47.619 0.00 0.00 0.00 4.95
224 225 2.314549 TGCCAAATCCAGAAATACCCCT 59.685 45.455 0.00 0.00 0.00 4.79
225 226 2.695147 GCCAAATCCAGAAATACCCCTG 59.305 50.000 0.00 0.00 0.00 4.45
226 227 3.881713 GCCAAATCCAGAAATACCCCTGT 60.882 47.826 0.00 0.00 0.00 4.00
227 228 3.701040 CCAAATCCAGAAATACCCCTGTG 59.299 47.826 0.00 0.00 0.00 3.66
228 229 3.669939 AATCCAGAAATACCCCTGTGG 57.330 47.619 0.00 0.00 41.37 4.17
242 243 3.874392 CCTGTGGGATTGCCTTTTTAG 57.126 47.619 0.00 0.00 33.58 1.85
243 244 3.165071 CCTGTGGGATTGCCTTTTTAGT 58.835 45.455 0.00 0.00 33.58 2.24
244 245 3.578282 CCTGTGGGATTGCCTTTTTAGTT 59.422 43.478 0.00 0.00 33.58 2.24
245 246 4.770010 CCTGTGGGATTGCCTTTTTAGTTA 59.230 41.667 0.00 0.00 33.58 2.24
246 247 5.245075 CCTGTGGGATTGCCTTTTTAGTTAA 59.755 40.000 0.00 0.00 33.58 2.01
247 248 6.239458 CCTGTGGGATTGCCTTTTTAGTTAAA 60.239 38.462 0.00 0.00 33.58 1.52
248 249 7.125792 TGTGGGATTGCCTTTTTAGTTAAAA 57.874 32.000 0.00 0.00 34.64 1.52
249 250 7.565680 TGTGGGATTGCCTTTTTAGTTAAAAA 58.434 30.769 8.90 8.90 41.36 1.94
270 271 4.769345 AAAACAGAAAGCAAAATGGGGA 57.231 36.364 0.00 0.00 0.00 4.81
271 272 4.341366 AAACAGAAAGCAAAATGGGGAG 57.659 40.909 0.00 0.00 0.00 4.30
272 273 3.243359 ACAGAAAGCAAAATGGGGAGA 57.757 42.857 0.00 0.00 0.00 3.71
273 274 3.782992 ACAGAAAGCAAAATGGGGAGAT 58.217 40.909 0.00 0.00 0.00 2.75
274 275 3.512724 ACAGAAAGCAAAATGGGGAGATG 59.487 43.478 0.00 0.00 0.00 2.90
275 276 3.102204 AGAAAGCAAAATGGGGAGATGG 58.898 45.455 0.00 0.00 0.00 3.51
276 277 1.870064 AAGCAAAATGGGGAGATGGG 58.130 50.000 0.00 0.00 0.00 4.00
277 278 0.031817 AGCAAAATGGGGAGATGGGG 60.032 55.000 0.00 0.00 0.00 4.96
278 279 1.689243 GCAAAATGGGGAGATGGGGC 61.689 60.000 0.00 0.00 0.00 5.80
279 280 0.325484 CAAAATGGGGAGATGGGGCA 60.325 55.000 0.00 0.00 0.00 5.36
280 281 0.031817 AAAATGGGGAGATGGGGCAG 60.032 55.000 0.00 0.00 0.00 4.85
281 282 2.594365 AAATGGGGAGATGGGGCAGC 62.594 60.000 0.00 0.00 0.00 5.25
289 290 4.511246 ATGGGGCAGCCCATCACG 62.511 66.667 32.58 0.00 46.53 4.35
292 293 4.864334 GGGCAGCCCATCACGGAG 62.864 72.222 27.33 0.00 44.65 4.63
293 294 4.864334 GGCAGCCCATCACGGAGG 62.864 72.222 0.00 0.00 36.56 4.30
294 295 4.101448 GCAGCCCATCACGGAGGT 62.101 66.667 0.00 0.00 36.56 3.85
295 296 2.124983 CAGCCCATCACGGAGGTG 60.125 66.667 0.00 0.00 45.78 4.00
305 306 2.629002 ACGGAGGTGATTTGTGCAC 58.371 52.632 10.75 10.75 35.56 4.57
311 312 3.957383 GTGATTTGTGCACCCGTTT 57.043 47.368 15.69 0.00 0.00 3.60
312 313 1.486439 GTGATTTGTGCACCCGTTTG 58.514 50.000 15.69 0.00 0.00 2.93
313 314 1.107114 TGATTTGTGCACCCGTTTGT 58.893 45.000 15.69 0.00 0.00 2.83
314 315 1.202348 TGATTTGTGCACCCGTTTGTG 60.202 47.619 15.69 0.00 39.29 3.33
315 316 1.066303 GATTTGTGCACCCGTTTGTGA 59.934 47.619 15.69 0.00 38.55 3.58
316 317 0.888619 TTTGTGCACCCGTTTGTGAA 59.111 45.000 15.69 0.00 38.55 3.18
412 413 1.227973 GATGGATCTTGGGCCGTCC 60.228 63.158 0.00 4.55 34.76 4.79
560 563 2.424379 GCTTCCTGGGGGTATAAAAGGG 60.424 54.545 0.00 0.00 0.00 3.95
607 610 2.573869 CTCGCTCCCTTTCTCGCA 59.426 61.111 0.00 0.00 0.00 5.10
898 929 2.580815 CTGCCATGGACGAGCTCA 59.419 61.111 18.40 0.17 0.00 4.26
1015 1066 4.096003 CGATGGGGGAGCAACGGT 62.096 66.667 0.00 0.00 0.00 4.83
1016 1067 2.355115 GATGGGGGAGCAACGGTT 59.645 61.111 0.00 0.00 0.00 4.44
1054 1105 1.147153 GGGGAGGAAGAAGATGGCG 59.853 63.158 0.00 0.00 0.00 5.69
1303 1355 1.141657 TGCAGGTGCTTGTTCTTCTCT 59.858 47.619 3.18 0.00 42.66 3.10
1577 1649 6.575244 AATTCCTGGATTATAGGTGTGTGA 57.425 37.500 0.00 0.00 36.67 3.58
1662 1741 5.046663 TCTGGGTGCTTTTGTTCTTTTCTTT 60.047 36.000 0.00 0.00 0.00 2.52
1663 1742 4.934602 TGGGTGCTTTTGTTCTTTTCTTTG 59.065 37.500 0.00 0.00 0.00 2.77
1664 1743 4.935205 GGGTGCTTTTGTTCTTTTCTTTGT 59.065 37.500 0.00 0.00 0.00 2.83
1755 1835 3.628942 TCTGTTGTGATATTGAGGCATGC 59.371 43.478 9.90 9.90 0.00 4.06
1771 1851 3.368739 GGCATGCAGGCTTCAATTTACTT 60.369 43.478 24.04 0.00 40.24 2.24
1911 1994 5.598417 TGCTACCTATTCAGTCAATGCTCTA 59.402 40.000 0.00 0.00 0.00 2.43
1936 2019 6.775629 ACTCAGTTTTAGTTTCTTTGGGCATA 59.224 34.615 0.00 0.00 0.00 3.14
2119 2233 7.180051 AGTCTGATTAGAGAAAGGTCAGTTCAT 59.820 37.037 0.00 0.00 37.96 2.57
2349 2523 2.094545 GGGAAAGCAGGTAAGCACATTG 60.095 50.000 0.00 0.00 36.85 2.82
2445 2619 5.700832 TGACTGACAGCGAGTTCATAAATTT 59.299 36.000 1.25 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.159254 ACCTCCTTTTCCAATTTTCTTATTTCT 57.841 29.630 0.00 0.00 0.00 2.52
13 14 9.778741 AACCTCCTTTTCCAATTTTCTTATTTC 57.221 29.630 0.00 0.00 0.00 2.17
14 15 9.778741 GAACCTCCTTTTCCAATTTTCTTATTT 57.221 29.630 0.00 0.00 0.00 1.40
15 16 8.933653 TGAACCTCCTTTTCCAATTTTCTTATT 58.066 29.630 0.00 0.00 0.00 1.40
16 17 8.491045 TGAACCTCCTTTTCCAATTTTCTTAT 57.509 30.769 0.00 0.00 0.00 1.73
17 18 7.906199 TGAACCTCCTTTTCCAATTTTCTTA 57.094 32.000 0.00 0.00 0.00 2.10
18 19 6.806668 TGAACCTCCTTTTCCAATTTTCTT 57.193 33.333 0.00 0.00 0.00 2.52
19 20 7.379059 AATGAACCTCCTTTTCCAATTTTCT 57.621 32.000 0.00 0.00 0.00 2.52
20 21 9.371136 GATAATGAACCTCCTTTTCCAATTTTC 57.629 33.333 0.00 0.00 0.00 2.29
21 22 8.879227 TGATAATGAACCTCCTTTTCCAATTTT 58.121 29.630 0.00 0.00 0.00 1.82
22 23 8.434589 TGATAATGAACCTCCTTTTCCAATTT 57.565 30.769 0.00 0.00 0.00 1.82
23 24 8.434589 TTGATAATGAACCTCCTTTTCCAATT 57.565 30.769 0.00 0.00 0.00 2.32
24 25 8.434589 TTTGATAATGAACCTCCTTTTCCAAT 57.565 30.769 0.00 0.00 0.00 3.16
25 26 7.847711 TTTGATAATGAACCTCCTTTTCCAA 57.152 32.000 0.00 0.00 0.00 3.53
26 27 8.313292 CAATTTGATAATGAACCTCCTTTTCCA 58.687 33.333 0.00 0.00 0.00 3.53
27 28 8.314021 ACAATTTGATAATGAACCTCCTTTTCC 58.686 33.333 2.79 0.00 0.00 3.13
28 29 9.143631 CACAATTTGATAATGAACCTCCTTTTC 57.856 33.333 2.79 0.00 0.00 2.29
29 30 7.603784 GCACAATTTGATAATGAACCTCCTTTT 59.396 33.333 2.79 0.00 0.00 2.27
30 31 7.099120 GCACAATTTGATAATGAACCTCCTTT 58.901 34.615 2.79 0.00 0.00 3.11
31 32 6.211184 TGCACAATTTGATAATGAACCTCCTT 59.789 34.615 2.79 0.00 0.00 3.36
32 33 5.716228 TGCACAATTTGATAATGAACCTCCT 59.284 36.000 2.79 0.00 0.00 3.69
33 34 5.964758 TGCACAATTTGATAATGAACCTCC 58.035 37.500 2.79 0.00 0.00 4.30
34 35 6.477688 CCATGCACAATTTGATAATGAACCTC 59.522 38.462 2.79 0.00 0.00 3.85
35 36 6.070653 ACCATGCACAATTTGATAATGAACCT 60.071 34.615 2.79 0.00 0.00 3.50
36 37 6.036300 CACCATGCACAATTTGATAATGAACC 59.964 38.462 2.79 0.00 0.00 3.62
37 38 6.036300 CCACCATGCACAATTTGATAATGAAC 59.964 38.462 2.79 0.00 0.00 3.18
38 39 6.107343 CCACCATGCACAATTTGATAATGAA 58.893 36.000 2.79 0.00 0.00 2.57
39 40 5.662456 CCACCATGCACAATTTGATAATGA 58.338 37.500 2.79 0.00 0.00 2.57
40 41 4.271533 GCCACCATGCACAATTTGATAATG 59.728 41.667 2.79 3.70 0.00 1.90
41 42 4.444536 GCCACCATGCACAATTTGATAAT 58.555 39.130 2.79 0.00 0.00 1.28
42 43 3.369261 GGCCACCATGCACAATTTGATAA 60.369 43.478 0.00 0.00 0.00 1.75
43 44 2.168106 GGCCACCATGCACAATTTGATA 59.832 45.455 0.00 0.00 0.00 2.15
44 45 1.065998 GGCCACCATGCACAATTTGAT 60.066 47.619 0.00 0.00 0.00 2.57
45 46 0.321021 GGCCACCATGCACAATTTGA 59.679 50.000 0.00 0.00 0.00 2.69
46 47 0.322322 AGGCCACCATGCACAATTTG 59.678 50.000 5.01 0.00 0.00 2.32
47 48 0.322322 CAGGCCACCATGCACAATTT 59.678 50.000 5.01 0.00 0.00 1.82
48 49 0.832983 ACAGGCCACCATGCACAATT 60.833 50.000 5.01 0.00 0.00 2.32
49 50 1.228956 ACAGGCCACCATGCACAAT 60.229 52.632 5.01 0.00 0.00 2.71
50 51 2.198150 ACAGGCCACCATGCACAA 59.802 55.556 5.01 0.00 0.00 3.33
51 52 2.598099 CACAGGCCACCATGCACA 60.598 61.111 5.01 0.00 0.00 4.57
52 53 3.376078 CCACAGGCCACCATGCAC 61.376 66.667 5.01 0.00 0.00 4.57
53 54 2.074113 TAACCACAGGCCACCATGCA 62.074 55.000 5.01 0.00 0.00 3.96
54 55 1.304052 TAACCACAGGCCACCATGC 60.304 57.895 5.01 0.00 0.00 4.06
55 56 0.038166 AGTAACCACAGGCCACCATG 59.962 55.000 5.01 0.00 0.00 3.66
56 57 0.038166 CAGTAACCACAGGCCACCAT 59.962 55.000 5.01 0.00 0.00 3.55
57 58 1.349542 ACAGTAACCACAGGCCACCA 61.350 55.000 5.01 0.00 0.00 4.17
58 59 0.688487 TACAGTAACCACAGGCCACC 59.312 55.000 5.01 0.00 0.00 4.61
59 60 1.944430 GCTACAGTAACCACAGGCCAC 60.944 57.143 5.01 0.00 0.00 5.01
60 61 0.323629 GCTACAGTAACCACAGGCCA 59.676 55.000 5.01 0.00 0.00 5.36
61 62 0.739813 CGCTACAGTAACCACAGGCC 60.740 60.000 0.00 0.00 0.00 5.19
62 63 0.037605 ACGCTACAGTAACCACAGGC 60.038 55.000 0.00 0.00 0.00 4.85
63 64 2.734492 GCTACGCTACAGTAACCACAGG 60.734 54.545 0.00 0.00 0.00 4.00
64 65 2.527100 GCTACGCTACAGTAACCACAG 58.473 52.381 0.00 0.00 0.00 3.66
65 66 1.203052 GGCTACGCTACAGTAACCACA 59.797 52.381 0.00 0.00 34.05 4.17
66 67 1.470458 GGGCTACGCTACAGTAACCAC 60.470 57.143 0.03 0.00 35.20 4.16
67 68 0.819582 GGGCTACGCTACAGTAACCA 59.180 55.000 0.03 0.00 35.20 3.67
68 69 0.248784 CGGGCTACGCTACAGTAACC 60.249 60.000 0.00 0.00 33.32 2.85
69 70 0.734889 TCGGGCTACGCTACAGTAAC 59.265 55.000 0.00 0.00 43.86 2.50
70 71 1.335810 CATCGGGCTACGCTACAGTAA 59.664 52.381 0.00 0.00 43.86 2.24
71 72 0.949397 CATCGGGCTACGCTACAGTA 59.051 55.000 0.00 0.00 43.86 2.74
72 73 1.734137 CATCGGGCTACGCTACAGT 59.266 57.895 0.00 0.00 43.86 3.55
73 74 1.661821 GCATCGGGCTACGCTACAG 60.662 63.158 0.00 0.00 43.86 2.74
74 75 2.415843 GCATCGGGCTACGCTACA 59.584 61.111 0.00 0.00 43.86 2.74
75 76 2.121564 TACGCATCGGGCTACGCTAC 62.122 60.000 0.00 0.00 43.86 3.58
76 77 1.848932 CTACGCATCGGGCTACGCTA 61.849 60.000 0.00 0.00 43.86 4.26
77 78 3.195591 CTACGCATCGGGCTACGCT 62.196 63.158 0.00 0.00 43.86 5.07
78 79 2.729862 CTACGCATCGGGCTACGC 60.730 66.667 0.00 0.00 43.86 4.42
79 80 2.050351 CCTACGCATCGGGCTACG 60.050 66.667 0.00 0.00 46.11 3.51
80 81 1.007618 GACCTACGCATCGGGCTAC 60.008 63.158 0.00 0.00 41.67 3.58
81 82 2.549198 CGACCTACGCATCGGGCTA 61.549 63.158 0.00 0.00 41.67 3.93
82 83 3.900892 CGACCTACGCATCGGGCT 61.901 66.667 0.00 0.00 41.67 5.19
91 92 0.591741 GATCGAACCAGCGACCTACG 60.592 60.000 0.00 0.00 43.79 3.51
92 93 0.248949 GGATCGAACCAGCGACCTAC 60.249 60.000 6.88 0.00 43.79 3.18
93 94 1.389609 GGGATCGAACCAGCGACCTA 61.390 60.000 14.28 0.00 43.79 3.08
94 95 2.722201 GGGATCGAACCAGCGACCT 61.722 63.158 14.28 0.00 43.79 3.85
95 96 2.202892 GGGATCGAACCAGCGACC 60.203 66.667 14.28 0.00 43.79 4.79
96 97 2.202892 GGGGATCGAACCAGCGAC 60.203 66.667 14.28 0.00 43.79 5.19
97 98 2.363795 AGGGGATCGAACCAGCGA 60.364 61.111 14.28 0.00 45.22 4.93
98 99 2.202932 CAGGGGATCGAACCAGCG 60.203 66.667 14.28 0.00 0.00 5.18
99 100 1.450312 CACAGGGGATCGAACCAGC 60.450 63.158 14.28 0.00 0.00 4.85
100 101 1.221840 CCACAGGGGATCGAACCAG 59.778 63.158 14.28 5.37 40.01 4.00
101 102 3.399046 CCACAGGGGATCGAACCA 58.601 61.111 14.28 0.00 40.01 3.67
111 112 1.351076 AAAAAGGCAATCCCACAGGG 58.649 50.000 0.00 0.00 46.11 4.45
112 113 3.165071 ACTAAAAAGGCAATCCCACAGG 58.835 45.455 0.00 0.00 35.39 4.00
113 114 4.871933 AACTAAAAAGGCAATCCCACAG 57.128 40.909 0.00 0.00 35.39 3.66
114 115 6.926630 AATAACTAAAAAGGCAATCCCACA 57.073 33.333 0.00 0.00 35.39 4.17
115 116 9.713713 TTTTAATAACTAAAAAGGCAATCCCAC 57.286 29.630 0.00 0.00 36.70 4.61
140 141 5.104569 TCTCCCCATTTTGCTTTCTGTTTTT 60.105 36.000 0.00 0.00 0.00 1.94
141 142 4.408596 TCTCCCCATTTTGCTTTCTGTTTT 59.591 37.500 0.00 0.00 0.00 2.43
142 143 3.966665 TCTCCCCATTTTGCTTTCTGTTT 59.033 39.130 0.00 0.00 0.00 2.83
143 144 3.575805 TCTCCCCATTTTGCTTTCTGTT 58.424 40.909 0.00 0.00 0.00 3.16
144 145 3.243359 TCTCCCCATTTTGCTTTCTGT 57.757 42.857 0.00 0.00 0.00 3.41
145 146 3.118884 CCATCTCCCCATTTTGCTTTCTG 60.119 47.826 0.00 0.00 0.00 3.02
146 147 3.102204 CCATCTCCCCATTTTGCTTTCT 58.898 45.455 0.00 0.00 0.00 2.52
147 148 2.169144 CCCATCTCCCCATTTTGCTTTC 59.831 50.000 0.00 0.00 0.00 2.62
148 149 2.190538 CCCATCTCCCCATTTTGCTTT 58.809 47.619 0.00 0.00 0.00 3.51
149 150 1.623279 CCCCATCTCCCCATTTTGCTT 60.623 52.381 0.00 0.00 0.00 3.91
150 151 0.031817 CCCCATCTCCCCATTTTGCT 60.032 55.000 0.00 0.00 0.00 3.91
151 152 1.689243 GCCCCATCTCCCCATTTTGC 61.689 60.000 0.00 0.00 0.00 3.68
152 153 0.325484 TGCCCCATCTCCCCATTTTG 60.325 55.000 0.00 0.00 0.00 2.44
153 154 0.031817 CTGCCCCATCTCCCCATTTT 60.032 55.000 0.00 0.00 0.00 1.82
154 155 1.622499 CTGCCCCATCTCCCCATTT 59.378 57.895 0.00 0.00 0.00 2.32
155 156 3.078843 GCTGCCCCATCTCCCCATT 62.079 63.158 0.00 0.00 0.00 3.16
156 157 3.505773 GCTGCCCCATCTCCCCAT 61.506 66.667 0.00 0.00 0.00 4.00
167 168 4.864334 CTCCGTGATGGGCTGCCC 62.864 72.222 30.97 30.97 45.71 5.36
168 169 4.864334 CCTCCGTGATGGGCTGCC 62.864 72.222 11.05 11.05 38.76 4.85
169 170 4.101448 ACCTCCGTGATGGGCTGC 62.101 66.667 0.00 0.00 38.76 5.25
170 171 2.124983 CACCTCCGTGATGGGCTG 60.125 66.667 0.00 0.00 43.14 4.85
171 172 2.284625 TCACCTCCGTGATGGGCT 60.285 61.111 0.00 0.00 44.20 5.19
178 179 0.518636 CTGCACAAATCACCTCCGTG 59.481 55.000 0.00 0.00 41.72 4.94
179 180 1.237285 GCTGCACAAATCACCTCCGT 61.237 55.000 0.00 0.00 0.00 4.69
180 181 1.503542 GCTGCACAAATCACCTCCG 59.496 57.895 0.00 0.00 0.00 4.63
181 182 1.885871 GGCTGCACAAATCACCTCC 59.114 57.895 0.50 0.00 0.00 4.30
182 183 1.237285 ACGGCTGCACAAATCACCTC 61.237 55.000 0.50 0.00 0.00 3.85
183 184 0.823356 AACGGCTGCACAAATCACCT 60.823 50.000 0.50 0.00 0.00 4.00
184 185 0.031994 AAACGGCTGCACAAATCACC 59.968 50.000 0.50 0.00 0.00 4.02
185 186 1.130955 CAAACGGCTGCACAAATCAC 58.869 50.000 0.50 0.00 0.00 3.06
186 187 0.597118 GCAAACGGCTGCACAAATCA 60.597 50.000 0.50 0.00 42.17 2.57
187 188 1.284297 GGCAAACGGCTGCACAAATC 61.284 55.000 12.34 0.00 44.52 2.17
188 189 1.300853 GGCAAACGGCTGCACAAAT 60.301 52.632 12.34 0.00 44.52 2.32
189 190 2.105930 GGCAAACGGCTGCACAAA 59.894 55.556 12.34 0.00 44.52 2.83
190 191 2.230994 TTTGGCAAACGGCTGCACAA 62.231 50.000 8.93 10.61 44.52 3.33
191 192 2.025767 ATTTGGCAAACGGCTGCACA 62.026 50.000 16.00 5.89 44.52 4.57
192 193 1.284297 GATTTGGCAAACGGCTGCAC 61.284 55.000 16.00 3.67 44.52 4.57
193 194 1.006337 GATTTGGCAAACGGCTGCA 60.006 52.632 16.00 0.00 44.52 4.41
194 195 1.737735 GGATTTGGCAAACGGCTGC 60.738 57.895 16.00 0.49 44.01 5.25
195 196 0.388907 CTGGATTTGGCAAACGGCTG 60.389 55.000 16.00 1.37 44.01 4.85
196 197 0.539438 TCTGGATTTGGCAAACGGCT 60.539 50.000 16.00 0.00 44.01 5.52
197 198 0.316841 TTCTGGATTTGGCAAACGGC 59.683 50.000 16.00 7.72 43.74 5.68
198 199 2.810439 TTTCTGGATTTGGCAAACGG 57.190 45.000 16.00 8.87 0.00 4.44
199 200 4.173256 GGTATTTCTGGATTTGGCAAACG 58.827 43.478 16.00 4.56 0.00 3.60
200 201 4.503910 GGGTATTTCTGGATTTGGCAAAC 58.496 43.478 16.00 9.19 0.00 2.93
201 202 3.517500 GGGGTATTTCTGGATTTGGCAAA 59.482 43.478 16.01 16.01 0.00 3.68
202 203 3.103742 GGGGTATTTCTGGATTTGGCAA 58.896 45.455 0.00 0.00 0.00 4.52
203 204 2.314549 AGGGGTATTTCTGGATTTGGCA 59.685 45.455 0.00 0.00 0.00 4.92
204 205 2.695147 CAGGGGTATTTCTGGATTTGGC 59.305 50.000 0.00 0.00 0.00 4.52
205 206 3.701040 CACAGGGGTATTTCTGGATTTGG 59.299 47.826 0.00 0.00 35.47 3.28
206 207 3.701040 CCACAGGGGTATTTCTGGATTTG 59.299 47.826 0.00 0.00 35.47 2.32
207 208 3.981212 CCACAGGGGTATTTCTGGATTT 58.019 45.455 0.00 0.00 35.47 2.17
208 209 3.669939 CCACAGGGGTATTTCTGGATT 57.330 47.619 0.00 0.00 35.47 3.01
221 222 1.351076 AAAAAGGCAATCCCACAGGG 58.649 50.000 0.00 0.00 46.11 4.45
222 223 3.165071 ACTAAAAAGGCAATCCCACAGG 58.835 45.455 0.00 0.00 35.39 4.00
223 224 4.871933 AACTAAAAAGGCAATCCCACAG 57.128 40.909 0.00 0.00 35.39 3.66
224 225 6.732896 TTTAACTAAAAAGGCAATCCCACA 57.267 33.333 0.00 0.00 35.39 4.17
248 249 5.104569 TCTCCCCATTTTGCTTTCTGTTTTT 60.105 36.000 0.00 0.00 0.00 1.94
249 250 4.408596 TCTCCCCATTTTGCTTTCTGTTTT 59.591 37.500 0.00 0.00 0.00 2.43
250 251 3.966665 TCTCCCCATTTTGCTTTCTGTTT 59.033 39.130 0.00 0.00 0.00 2.83
251 252 3.575805 TCTCCCCATTTTGCTTTCTGTT 58.424 40.909 0.00 0.00 0.00 3.16
252 253 3.243359 TCTCCCCATTTTGCTTTCTGT 57.757 42.857 0.00 0.00 0.00 3.41
253 254 3.118884 CCATCTCCCCATTTTGCTTTCTG 60.119 47.826 0.00 0.00 0.00 3.02
254 255 3.102204 CCATCTCCCCATTTTGCTTTCT 58.898 45.455 0.00 0.00 0.00 2.52
255 256 2.169144 CCCATCTCCCCATTTTGCTTTC 59.831 50.000 0.00 0.00 0.00 2.62
256 257 2.190538 CCCATCTCCCCATTTTGCTTT 58.809 47.619 0.00 0.00 0.00 3.51
257 258 1.623279 CCCCATCTCCCCATTTTGCTT 60.623 52.381 0.00 0.00 0.00 3.91
258 259 0.031817 CCCCATCTCCCCATTTTGCT 60.032 55.000 0.00 0.00 0.00 3.91
259 260 1.689243 GCCCCATCTCCCCATTTTGC 61.689 60.000 0.00 0.00 0.00 3.68
260 261 0.325484 TGCCCCATCTCCCCATTTTG 60.325 55.000 0.00 0.00 0.00 2.44
261 262 0.031817 CTGCCCCATCTCCCCATTTT 60.032 55.000 0.00 0.00 0.00 1.82
262 263 1.622499 CTGCCCCATCTCCCCATTT 59.378 57.895 0.00 0.00 0.00 2.32
263 264 3.078843 GCTGCCCCATCTCCCCATT 62.079 63.158 0.00 0.00 0.00 3.16
264 265 3.505773 GCTGCCCCATCTCCCCAT 61.506 66.667 0.00 0.00 0.00 4.00
275 276 4.864334 CTCCGTGATGGGCTGCCC 62.864 72.222 30.97 30.97 45.71 5.36
276 277 4.864334 CCTCCGTGATGGGCTGCC 62.864 72.222 11.05 11.05 38.76 4.85
277 278 4.101448 ACCTCCGTGATGGGCTGC 62.101 66.667 0.00 0.00 38.76 5.25
278 279 2.124983 CACCTCCGTGATGGGCTG 60.125 66.667 0.00 0.00 43.14 4.85
279 280 2.284625 TCACCTCCGTGATGGGCT 60.285 61.111 0.00 0.00 44.20 5.19
286 287 0.238289 GTGCACAAATCACCTCCGTG 59.762 55.000 13.17 0.00 41.72 4.94
287 288 2.629002 GTGCACAAATCACCTCCGT 58.371 52.632 13.17 0.00 0.00 4.69
293 294 1.202359 ACAAACGGGTGCACAAATCAC 60.202 47.619 20.43 0.00 0.00 3.06
294 295 1.107114 ACAAACGGGTGCACAAATCA 58.893 45.000 20.43 0.00 0.00 2.57
295 296 1.066303 TCACAAACGGGTGCACAAATC 59.934 47.619 20.43 0.00 38.66 2.17
296 297 1.107114 TCACAAACGGGTGCACAAAT 58.893 45.000 20.43 0.00 38.66 2.32
297 298 0.888619 TTCACAAACGGGTGCACAAA 59.111 45.000 20.43 0.00 38.66 2.83
298 299 0.888619 TTTCACAAACGGGTGCACAA 59.111 45.000 20.43 0.00 38.66 3.33
299 300 1.066303 GATTTCACAAACGGGTGCACA 59.934 47.619 20.43 0.00 38.66 4.57
300 301 1.601914 GGATTTCACAAACGGGTGCAC 60.602 52.381 8.80 8.80 38.66 4.57
301 302 0.671251 GGATTTCACAAACGGGTGCA 59.329 50.000 0.00 0.00 38.66 4.57
302 303 0.671251 TGGATTTCACAAACGGGTGC 59.329 50.000 0.00 0.00 38.66 5.01
303 304 2.226330 TCTGGATTTCACAAACGGGTG 58.774 47.619 0.00 0.00 40.16 4.61
304 305 2.649531 TCTGGATTTCACAAACGGGT 57.350 45.000 0.00 0.00 0.00 5.28
305 306 4.519540 ATTTCTGGATTTCACAAACGGG 57.480 40.909 0.00 0.00 0.00 5.28
306 307 6.908825 TCTTATTTCTGGATTTCACAAACGG 58.091 36.000 0.00 0.00 0.00 4.44
307 308 8.970691 ATTCTTATTTCTGGATTTCACAAACG 57.029 30.769 0.00 0.00 0.00 3.60
312 313 9.943163 GCTTCTATTCTTATTTCTGGATTTCAC 57.057 33.333 0.00 0.00 0.00 3.18
313 314 9.911788 AGCTTCTATTCTTATTTCTGGATTTCA 57.088 29.630 0.00 0.00 0.00 2.69
315 316 9.348476 GGAGCTTCTATTCTTATTTCTGGATTT 57.652 33.333 0.00 0.00 0.00 2.17
316 317 8.722422 AGGAGCTTCTATTCTTATTTCTGGATT 58.278 33.333 0.00 0.00 0.00 3.01
412 413 2.885644 CTTCCACGCGGTCCATCG 60.886 66.667 12.47 0.00 0.00 3.84
461 462 5.105635 ACGAGACGGTAACTATTCATTCCAA 60.106 40.000 0.00 0.00 0.00 3.53
682 685 1.223487 GGCGGCTAGGGTTCAATCA 59.777 57.895 0.00 0.00 0.00 2.57
1015 1066 2.693591 CCATAGCCTCACGTTCCTCTAA 59.306 50.000 0.00 0.00 0.00 2.10
1016 1067 2.307768 CCATAGCCTCACGTTCCTCTA 58.692 52.381 0.00 0.00 0.00 2.43
1054 1105 3.119096 GACGGCAAGAACGAGGGC 61.119 66.667 0.00 0.00 34.93 5.19
1577 1649 4.256920 CGATCCAGACAAGGAACAAGAAT 58.743 43.478 0.00 0.00 41.92 2.40
1621 1697 4.468510 ACCCAGAATCATGTGCAAATGAAT 59.531 37.500 23.17 15.51 39.90 2.57
1755 1835 5.841810 TGGACAAAAGTAAATTGAAGCCTG 58.158 37.500 0.00 0.00 0.00 4.85
1771 1851 3.255642 GCAGCCTAACTCAAATGGACAAA 59.744 43.478 0.00 0.00 0.00 2.83
1880 1963 4.080356 TGACTGAATAGGTAGCAAAGGCAT 60.080 41.667 0.00 0.00 44.61 4.40
1911 1994 4.953579 TGCCCAAAGAAACTAAAACTGAGT 59.046 37.500 0.00 0.00 0.00 3.41
1936 2019 7.972301 AGAGACCAGAAAGCTATATAAAGCAT 58.028 34.615 0.48 0.00 45.30 3.79
2119 2233 6.531503 ACTGCTATACAAAAGCTACAGAGA 57.468 37.500 0.00 0.00 40.73 3.10
2243 2417 6.297080 TGTGGGCAAAATTTATCATCATGT 57.703 33.333 0.00 0.00 0.00 3.21
2349 2523 1.620819 AGATCTGACACACCAGACACC 59.379 52.381 0.00 0.00 44.93 4.16


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

AutoCloner maintained by Alex Coulton.