Multiple sequence alignment - TraesCS3D01G470000

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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 TraesCS3D01G470000 chr3D 100.000 2703 0 0 1 2703 571821230 571823932 0.000000e+00 4992.0
1 TraesCS3D01G470000 chr3D 86.667 390 37 7 1157 1532 571816221 571816609 4.160000e-113 418.0
2 TraesCS3D01G470000 chr3D 87.739 261 25 4 127 380 151444898 151445158 5.660000e-77 298.0
3 TraesCS3D01G470000 chr3D 81.818 121 12 5 2593 2703 571867889 571868009 2.870000e-15 93.5
4 TraesCS3D01G470000 chr3A 89.984 1268 80 22 399 1632 704343697 704344951 0.000000e+00 1594.0
5 TraesCS3D01G470000 chr3A 77.901 629 106 24 893 1504 704113700 704114312 7.110000e-96 361.0
6 TraesCS3D01G470000 chr3A 78.323 632 76 31 1659 2255 704345005 704345610 4.280000e-93 351.0
7 TraesCS3D01G470000 chr3A 97.073 205 3 1 2499 2703 704345901 704346102 2.580000e-90 342.0
8 TraesCS3D01G470000 chr3A 88.722 266 22 6 122 380 162081724 162081988 4.340000e-83 318.0
9 TraesCS3D01G470000 chr3A 80.760 421 50 14 1959 2354 704369398 704369812 1.570000e-77 300.0
10 TraesCS3D01G470000 chr3A 90.286 175 14 2 2499 2673 704456481 704456652 2.710000e-55 226.0
11 TraesCS3D01G470000 chr3A 85.446 213 15 5 2501 2703 704468138 704468344 9.810000e-50 207.0
12 TraesCS3D01G470000 chr3A 90.604 149 11 2 2356 2501 704345694 704345842 7.640000e-46 195.0
13 TraesCS3D01G470000 chr3A 77.812 329 35 22 1923 2215 704455753 704456079 4.630000e-38 169.0
14 TraesCS3D01G470000 chr3A 77.619 210 25 11 1923 2119 704350482 704350682 1.020000e-19 108.0
15 TraesCS3D01G470000 chr3B 83.124 1434 128 37 452 1810 758639260 758640654 0.000000e+00 1203.0
16 TraesCS3D01G470000 chr3B 83.097 775 81 15 402 1134 758555200 758555966 0.000000e+00 660.0
17 TraesCS3D01G470000 chr3B 86.980 553 49 11 398 933 758561717 758562263 3.850000e-168 601.0
18 TraesCS3D01G470000 chr3B 84.757 597 62 13 1923 2501 758640795 758641380 3.020000e-159 571.0
19 TraesCS3D01G470000 chr3B 84.158 606 53 15 1939 2501 758724835 758725440 5.090000e-152 547.0
20 TraesCS3D01G470000 chr3B 83.564 578 51 12 1939 2473 758766118 758766694 4.020000e-138 501.0
21 TraesCS3D01G470000 chr3B 83.178 428 58 5 725 1142 758523709 758524132 1.960000e-101 379.0
22 TraesCS3D01G470000 chr3B 82.984 429 59 5 725 1143 758527756 758528180 2.540000e-100 375.0
23 TraesCS3D01G470000 chr3B 82.217 433 61 7 725 1147 758519666 758520092 2.560000e-95 359.0
24 TraesCS3D01G470000 chr3B 82.020 406 58 7 1207 1603 758613370 758613769 5.580000e-87 331.0
25 TraesCS3D01G470000 chr3B 78.761 565 69 31 1658 2211 759072120 759072644 5.580000e-87 331.0
26 TraesCS3D01G470000 chr3B 90.438 251 20 3 478 727 758613045 758613292 7.220000e-86 327.0
27 TraesCS3D01G470000 chr3B 95.531 179 8 0 2525 2703 758725519 758725697 1.220000e-73 287.0
28 TraesCS3D01G470000 chr3B 91.477 176 7 4 2501 2673 758641443 758641613 4.500000e-58 235.0
29 TraesCS3D01G470000 chr3B 93.056 144 10 0 2525 2668 759098845 759098988 7.580000e-51 211.0
30 TraesCS3D01G470000 chr3B 89.017 173 13 4 2499 2671 758851985 758852151 2.730000e-50 209.0
31 TraesCS3D01G470000 chr3B 89.510 143 8 1 2531 2673 758641860 758641995 9.950000e-40 174.0
32 TraesCS3D01G470000 chr3B 88.811 143 9 1 2531 2673 759073896 759074031 4.630000e-38 169.0
33 TraesCS3D01G470000 chr3B 79.290 169 22 8 1476 1632 759071902 759072069 3.680000e-19 106.0
34 TraesCS3D01G470000 chr3B 80.263 152 10 4 2276 2415 759072676 759072819 2.220000e-16 97.1
35 TraesCS3D01G470000 chr3B 77.778 180 22 10 1102 1265 764520940 764521117 7.970000e-16 95.3
36 TraesCS3D01G470000 chr3B 79.167 120 12 7 1158 1265 764453740 764453858 1.340000e-08 71.3
37 TraesCS3D01G470000 chr3B 96.970 33 1 0 2671 2703 758642041 758642073 3.760000e-04 56.5
38 TraesCS3D01G470000 chr2A 91.221 262 16 5 127 381 203902736 203902475 1.540000e-92 350.0
39 TraesCS3D01G470000 chr7A 90.335 269 17 5 123 384 724081889 724081623 7.170000e-91 344.0
40 TraesCS3D01G470000 chr5D 88.889 261 22 3 127 380 421314825 421314565 5.620000e-82 315.0
41 TraesCS3D01G470000 chr5A 89.412 255 19 4 127 374 9609315 9609062 5.620000e-82 315.0
42 TraesCS3D01G470000 chr4A 87.636 275 22 9 118 381 547311498 547311771 2.610000e-80 309.0
43 TraesCS3D01G470000 chr7D 87.879 264 23 7 124 380 122823104 122823365 4.370000e-78 302.0
44 TraesCS3D01G470000 chr4D 87.405 262 26 3 126 380 114579218 114578957 7.320000e-76 294.0


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 TraesCS3D01G470000 chr3D 571821230 571823932 2702 False 4992.0 4992 100.0000 1 2703 1 chr3D.!!$F3 2702
1 TraesCS3D01G470000 chr3A 704343697 704346102 2405 False 620.5 1594 88.9960 399 2703 4 chr3A.!!$F6 2304
2 TraesCS3D01G470000 chr3A 704113700 704114312 612 False 361.0 361 77.9010 893 1504 1 chr3A.!!$F2 611
3 TraesCS3D01G470000 chr3B 758555200 758555966 766 False 660.0 660 83.0970 402 1134 1 chr3B.!!$F1 732
4 TraesCS3D01G470000 chr3B 758561717 758562263 546 False 601.0 601 86.9800 398 933 1 chr3B.!!$F2 535
5 TraesCS3D01G470000 chr3B 758766118 758766694 576 False 501.0 501 83.5640 1939 2473 1 chr3B.!!$F3 534
6 TraesCS3D01G470000 chr3B 758639260 758642073 2813 False 447.9 1203 89.1676 452 2703 5 chr3B.!!$F10 2251
7 TraesCS3D01G470000 chr3B 758724835 758725697 862 False 417.0 547 89.8445 1939 2703 2 chr3B.!!$F11 764
8 TraesCS3D01G470000 chr3B 758519666 758528180 8514 False 371.0 379 82.7930 725 1147 3 chr3B.!!$F8 422
9 TraesCS3D01G470000 chr3B 758613045 758613769 724 False 329.0 331 86.2290 478 1603 2 chr3B.!!$F9 1125

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
137 138 0.105039 GACAATGCTACTCCCTCCGG 59.895 60.0 0.0 0.0 0.0 5.14 F
884 4554 0.401738 TGGCAAGGTTGAGGAGAAGG 59.598 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 5342 0.259647 ATGCAAATCCAGCCTAGCCA 59.740 50.0 0.00 0.0 0.0 4.75 R
2354 6303 0.315251 CAGGACACGTGAGCTTCTGA 59.685 55.0 25.01 0.0 0.0 3.27 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
29 30 4.341487 GGGGTGCCCAACTATAAATATCC 58.659 47.826 9.76 0.00 44.65 2.59
30 31 4.044191 GGGGTGCCCAACTATAAATATCCT 59.956 45.833 9.76 0.00 44.65 3.24
31 32 5.254115 GGGTGCCCAACTATAAATATCCTC 58.746 45.833 1.66 0.00 35.81 3.71
32 33 5.254115 GGTGCCCAACTATAAATATCCTCC 58.746 45.833 0.00 0.00 0.00 4.30
33 34 5.222048 GGTGCCCAACTATAAATATCCTCCA 60.222 44.000 0.00 0.00 0.00 3.86
34 35 6.303839 GTGCCCAACTATAAATATCCTCCAA 58.696 40.000 0.00 0.00 0.00 3.53
35 36 6.775629 GTGCCCAACTATAAATATCCTCCAAA 59.224 38.462 0.00 0.00 0.00 3.28
36 37 7.286775 GTGCCCAACTATAAATATCCTCCAAAA 59.713 37.037 0.00 0.00 0.00 2.44
37 38 7.286775 TGCCCAACTATAAATATCCTCCAAAAC 59.713 37.037 0.00 0.00 0.00 2.43
38 39 7.255836 GCCCAACTATAAATATCCTCCAAAACC 60.256 40.741 0.00 0.00 0.00 3.27
39 40 7.782644 CCCAACTATAAATATCCTCCAAAACCA 59.217 37.037 0.00 0.00 0.00 3.67
40 41 9.196139 CCAACTATAAATATCCTCCAAAACCAA 57.804 33.333 0.00 0.00 0.00 3.67
48 49 4.750833 TCCTCCAAAACCAATTAAGGGA 57.249 40.909 3.13 0.00 0.00 4.20
49 50 4.412843 TCCTCCAAAACCAATTAAGGGAC 58.587 43.478 3.13 0.00 0.00 4.46
50 51 3.513912 CCTCCAAAACCAATTAAGGGACC 59.486 47.826 3.13 0.00 0.00 4.46
51 52 4.416516 CTCCAAAACCAATTAAGGGACCT 58.583 43.478 3.13 0.00 0.00 3.85
53 54 4.140900 TCCAAAACCAATTAAGGGACCTGA 60.141 41.667 3.13 0.00 0.00 3.86
54 55 4.777366 CCAAAACCAATTAAGGGACCTGAT 59.223 41.667 3.13 0.00 0.00 2.90
57 58 5.789574 AACCAATTAAGGGACCTGATGTA 57.210 39.130 3.13 0.00 0.00 2.29
58 59 5.373812 ACCAATTAAGGGACCTGATGTAG 57.626 43.478 3.13 0.00 0.00 2.74
59 60 5.036916 ACCAATTAAGGGACCTGATGTAGA 58.963 41.667 3.13 0.00 0.00 2.59
60 61 5.491078 ACCAATTAAGGGACCTGATGTAGAA 59.509 40.000 3.13 0.00 0.00 2.10
62 63 7.062957 CCAATTAAGGGACCTGATGTAGAATT 58.937 38.462 0.00 0.00 0.00 2.17
63 64 7.561356 CCAATTAAGGGACCTGATGTAGAATTT 59.439 37.037 0.00 0.00 0.00 1.82
64 65 8.971073 CAATTAAGGGACCTGATGTAGAATTTT 58.029 33.333 0.00 0.00 0.00 1.82
66 67 9.853177 ATTAAGGGACCTGATGTAGAATTTTAG 57.147 33.333 0.00 0.00 0.00 1.85
68 69 6.653989 AGGGACCTGATGTAGAATTTTAGTG 58.346 40.000 0.00 0.00 0.00 2.74
69 70 6.443849 AGGGACCTGATGTAGAATTTTAGTGA 59.556 38.462 0.00 0.00 0.00 3.41
71 72 7.065923 GGGACCTGATGTAGAATTTTAGTGAAC 59.934 40.741 0.00 0.00 0.00 3.18
72 73 7.824779 GGACCTGATGTAGAATTTTAGTGAACT 59.175 37.037 0.00 0.00 0.00 3.01
73 74 9.220767 GACCTGATGTAGAATTTTAGTGAACTT 57.779 33.333 0.00 0.00 0.00 2.66
77 78 9.667107 TGATGTAGAATTTTAGTGAACTTAGGG 57.333 33.333 0.00 0.00 0.00 3.53
79 80 8.209802 TGTAGAATTTTAGTGAACTTAGGGGA 57.790 34.615 0.00 0.00 0.00 4.81
118 119 8.560576 TTTTCTCTTCAAGCAAAAGATAAACG 57.439 30.769 6.08 0.00 32.12 3.60
119 120 7.490962 TTCTCTTCAAGCAAAAGATAAACGA 57.509 32.000 0.00 0.00 32.56 3.85
120 121 6.888430 TCTCTTCAAGCAAAAGATAAACGAC 58.112 36.000 0.00 0.00 32.56 4.34
121 122 6.481976 TCTCTTCAAGCAAAAGATAAACGACA 59.518 34.615 0.00 0.00 32.56 4.35
122 123 7.011950 TCTCTTCAAGCAAAAGATAAACGACAA 59.988 33.333 0.00 0.00 32.56 3.18
125 126 5.629020 TCAAGCAAAAGATAAACGACAATGC 59.371 36.000 0.00 0.00 0.00 3.56
126 127 5.376854 AGCAAAAGATAAACGACAATGCT 57.623 34.783 0.00 0.00 36.83 3.79
130 131 6.466097 GCAAAAGATAAACGACAATGCTACTC 59.534 38.462 0.00 0.00 0.00 2.59
131 132 6.663944 AAAGATAAACGACAATGCTACTCC 57.336 37.500 0.00 0.00 0.00 3.85
132 133 4.694339 AGATAAACGACAATGCTACTCCC 58.306 43.478 0.00 0.00 0.00 4.30
133 134 4.406003 AGATAAACGACAATGCTACTCCCT 59.594 41.667 0.00 0.00 0.00 4.20
134 135 2.674796 AACGACAATGCTACTCCCTC 57.325 50.000 0.00 0.00 0.00 4.30
135 136 0.824759 ACGACAATGCTACTCCCTCC 59.175 55.000 0.00 0.00 0.00 4.30
136 137 0.249073 CGACAATGCTACTCCCTCCG 60.249 60.000 0.00 0.00 0.00 4.63
137 138 0.105039 GACAATGCTACTCCCTCCGG 59.895 60.000 0.00 0.00 0.00 5.14
140 141 1.049289 AATGCTACTCCCTCCGGTCC 61.049 60.000 0.00 0.00 0.00 4.46
143 144 0.976590 GCTACTCCCTCCGGTCCTTT 60.977 60.000 0.00 0.00 0.00 3.11
145 146 1.907255 CTACTCCCTCCGGTCCTTTTT 59.093 52.381 0.00 0.00 0.00 1.94
146 147 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
147 148 1.907255 ACTCCCTCCGGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
148 149 1.907255 CTCCCTCCGGTCCTTTTTAGT 59.093 52.381 0.00 0.00 0.00 2.24
149 150 1.904537 TCCCTCCGGTCCTTTTTAGTC 59.095 52.381 0.00 0.00 0.00 2.59
151 152 2.354805 CCCTCCGGTCCTTTTTAGTCTG 60.355 54.545 0.00 0.00 0.00 3.51
152 153 2.347731 CTCCGGTCCTTTTTAGTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
154 155 2.304761 TCCGGTCCTTTTTAGTCTGCAT 59.695 45.455 0.00 0.00 0.00 3.96
155 156 3.516300 TCCGGTCCTTTTTAGTCTGCATA 59.484 43.478 0.00 0.00 0.00 3.14
156 157 4.163458 TCCGGTCCTTTTTAGTCTGCATAT 59.837 41.667 0.00 0.00 0.00 1.78
157 158 5.364446 TCCGGTCCTTTTTAGTCTGCATATA 59.636 40.000 0.00 0.00 0.00 0.86
159 160 6.202954 CCGGTCCTTTTTAGTCTGCATATAAG 59.797 42.308 0.00 0.00 0.00 1.73
160 161 6.984474 CGGTCCTTTTTAGTCTGCATATAAGA 59.016 38.462 0.00 0.00 0.00 2.10
161 162 7.657761 CGGTCCTTTTTAGTCTGCATATAAGAT 59.342 37.037 0.00 0.00 0.00 2.40
162 163 9.343539 GGTCCTTTTTAGTCTGCATATAAGATT 57.656 33.333 0.00 0.00 0.00 2.40
168 169 9.679661 TTTTAGTCTGCATATAAGATTTGTCCA 57.320 29.630 0.00 0.00 0.00 4.02
169 170 9.679661 TTTAGTCTGCATATAAGATTTGTCCAA 57.320 29.630 0.00 0.00 0.00 3.53
170 171 9.679661 TTAGTCTGCATATAAGATTTGTCCAAA 57.320 29.630 0.00 0.00 34.46 3.28
172 173 7.831193 AGTCTGCATATAAGATTTGTCCAAAGT 59.169 33.333 0.00 0.00 33.32 2.66
173 174 8.462016 GTCTGCATATAAGATTTGTCCAAAGTT 58.538 33.333 0.00 0.00 33.32 2.66
174 175 9.679661 TCTGCATATAAGATTTGTCCAAAGTTA 57.320 29.630 0.00 0.53 33.32 2.24
183 184 8.349568 AGATTTGTCCAAAGTTAAAGTATCCC 57.650 34.615 0.00 0.00 33.32 3.85
184 185 7.947890 AGATTTGTCCAAAGTTAAAGTATCCCA 59.052 33.333 0.00 0.00 33.32 4.37
186 187 6.887626 TGTCCAAAGTTAAAGTATCCCAAC 57.112 37.500 0.00 0.00 0.00 3.77
187 188 6.607019 TGTCCAAAGTTAAAGTATCCCAACT 58.393 36.000 0.00 0.00 32.73 3.16
188 189 7.064229 TGTCCAAAGTTAAAGTATCCCAACTT 58.936 34.615 0.00 0.00 41.67 2.66
189 190 7.562088 TGTCCAAAGTTAAAGTATCCCAACTTT 59.438 33.333 7.12 7.12 46.67 2.66
194 195 6.887626 GTTAAAGTATCCCAACTTTGACCA 57.112 37.500 11.25 0.00 46.49 4.02
196 197 7.718525 GTTAAAGTATCCCAACTTTGACCAAA 58.281 34.615 11.25 0.00 46.49 3.28
197 198 5.784578 AAGTATCCCAACTTTGACCAAAC 57.215 39.130 0.00 0.00 36.26 2.93
200 201 6.607019 AGTATCCCAACTTTGACCAAACTTA 58.393 36.000 0.00 0.00 0.00 2.24
201 202 7.238710 AGTATCCCAACTTTGACCAAACTTAT 58.761 34.615 0.00 0.00 0.00 1.73
202 203 8.387813 AGTATCCCAACTTTGACCAAACTTATA 58.612 33.333 0.00 0.00 0.00 0.98
204 205 6.843752 TCCCAACTTTGACCAAACTTATAGA 58.156 36.000 0.00 0.00 0.00 1.98
205 206 7.291566 TCCCAACTTTGACCAAACTTATAGAA 58.708 34.615 0.00 0.00 0.00 2.10
206 207 7.780745 TCCCAACTTTGACCAAACTTATAGAAA 59.219 33.333 0.00 0.00 0.00 2.52
207 208 8.417884 CCCAACTTTGACCAAACTTATAGAAAA 58.582 33.333 0.00 0.00 0.00 2.29
208 209 9.810545 CCAACTTTGACCAAACTTATAGAAAAA 57.189 29.630 0.00 0.00 0.00 1.94
228 229 9.401873 AGAAAAAGTATTAACGTTTACAATGCC 57.598 29.630 5.91 0.00 36.46 4.40
230 231 9.530633 AAAAAGTATTAACGTTTACAATGCCAA 57.469 25.926 5.91 0.00 36.46 4.52
231 232 9.530633 AAAAGTATTAACGTTTACAATGCCAAA 57.469 25.926 5.91 0.00 35.84 3.28
232 233 9.699703 AAAGTATTAACGTTTACAATGCCAAAT 57.300 25.926 5.91 0.00 0.00 2.32
233 234 8.905103 AGTATTAACGTTTACAATGCCAAATC 57.095 30.769 5.91 0.00 0.00 2.17
234 235 8.516234 AGTATTAACGTTTACAATGCCAAATCA 58.484 29.630 5.91 0.00 0.00 2.57
235 236 9.130312 GTATTAACGTTTACAATGCCAAATCAA 57.870 29.630 5.91 0.00 0.00 2.57
236 237 5.898630 AACGTTTACAATGCCAAATCAAC 57.101 34.783 0.00 0.00 0.00 3.18
237 238 4.938080 ACGTTTACAATGCCAAATCAACA 58.062 34.783 0.00 0.00 0.00 3.33
238 239 5.537188 ACGTTTACAATGCCAAATCAACAT 58.463 33.333 0.00 0.00 0.00 2.71
239 240 5.988561 ACGTTTACAATGCCAAATCAACATT 59.011 32.000 0.00 0.00 34.42 2.71
246 247 7.837202 CAATGCCAAATCAACATTGTTAGAT 57.163 32.000 0.86 5.39 43.53 1.98
247 248 8.259049 CAATGCCAAATCAACATTGTTAGATT 57.741 30.769 15.44 15.44 43.53 2.40
250 251 7.613585 TGCCAAATCAACATTGTTAGATTCAT 58.386 30.769 18.76 8.84 30.87 2.57
251 252 8.095792 TGCCAAATCAACATTGTTAGATTCATT 58.904 29.630 18.76 8.39 30.87 2.57
252 253 9.585099 GCCAAATCAACATTGTTAGATTCATTA 57.415 29.630 18.76 0.00 30.87 1.90
341 342 6.827586 ACTTTACAAAGTTTGACCTGACAA 57.172 33.333 22.23 3.42 46.52 3.18
342 343 7.222000 ACTTTACAAAGTTTGACCTGACAAA 57.778 32.000 22.23 8.68 46.52 2.83
344 345 8.145122 ACTTTACAAAGTTTGACCTGACAAAAA 58.855 29.630 22.23 6.99 46.52 1.94
345 346 9.150348 CTTTACAAAGTTTGACCTGACAAAAAT 57.850 29.630 22.23 0.00 40.62 1.82
346 347 8.696410 TTACAAAGTTTGACCTGACAAAAATC 57.304 30.769 22.23 0.00 40.62 2.17
348 349 8.062065 ACAAAGTTTGACCTGACAAAAATCTA 57.938 30.769 22.23 0.00 40.62 1.98
349 350 8.527810 ACAAAGTTTGACCTGACAAAAATCTAA 58.472 29.630 22.23 0.00 40.62 2.10
350 351 9.533253 CAAAGTTTGACCTGACAAAAATCTAAT 57.467 29.630 10.19 0.00 40.62 1.73
354 355 9.076596 GTTTGACCTGACAAAAATCTAATATGC 57.923 33.333 0.00 0.00 40.62 3.14
355 356 7.015226 TGACCTGACAAAAATCTAATATGCG 57.985 36.000 0.00 0.00 0.00 4.73
356 357 6.821160 TGACCTGACAAAAATCTAATATGCGA 59.179 34.615 0.00 0.00 0.00 5.10
359 360 7.336931 ACCTGACAAAAATCTAATATGCGAAGT 59.663 33.333 0.00 0.00 0.00 3.01
371 372 8.836413 TCTAATATGCGAAGTAAAAAGGATTGG 58.164 33.333 0.00 0.00 0.00 3.16
373 374 5.567138 ATGCGAAGTAAAAAGGATTGGAG 57.433 39.130 0.00 0.00 0.00 3.86
375 376 3.128764 GCGAAGTAAAAAGGATTGGAGGG 59.871 47.826 0.00 0.00 0.00 4.30
376 377 4.585879 CGAAGTAAAAAGGATTGGAGGGA 58.414 43.478 0.00 0.00 0.00 4.20
377 378 4.636206 CGAAGTAAAAAGGATTGGAGGGAG 59.364 45.833 0.00 0.00 0.00 4.30
379 380 6.575649 CGAAGTAAAAAGGATTGGAGGGAGTA 60.576 42.308 0.00 0.00 0.00 2.59
381 382 7.285340 AGTAAAAAGGATTGGAGGGAGTATT 57.715 36.000 0.00 0.00 0.00 1.89
382 383 7.709601 AGTAAAAAGGATTGGAGGGAGTATTT 58.290 34.615 0.00 0.00 0.00 1.40
385 386 4.423625 AGGATTGGAGGGAGTATTTTCG 57.576 45.455 0.00 0.00 0.00 3.46
387 388 4.227527 AGGATTGGAGGGAGTATTTTCGTT 59.772 41.667 0.00 0.00 0.00 3.85
388 389 5.427481 AGGATTGGAGGGAGTATTTTCGTTA 59.573 40.000 0.00 0.00 0.00 3.18
389 390 5.758784 GGATTGGAGGGAGTATTTTCGTTAG 59.241 44.000 0.00 0.00 0.00 2.34
391 392 3.516300 TGGAGGGAGTATTTTCGTTAGCA 59.484 43.478 0.00 0.00 0.00 3.49
393 394 4.501071 GAGGGAGTATTTTCGTTAGCACA 58.499 43.478 0.00 0.00 0.00 4.57
395 396 4.020485 AGGGAGTATTTTCGTTAGCACAGT 60.020 41.667 0.00 0.00 0.00 3.55
396 397 4.329256 GGGAGTATTTTCGTTAGCACAGTC 59.671 45.833 0.00 0.00 0.00 3.51
398 399 4.890088 AGTATTTTCGTTAGCACAGTCCA 58.110 39.130 0.00 0.00 0.00 4.02
399 400 5.302360 AGTATTTTCGTTAGCACAGTCCAA 58.698 37.500 0.00 0.00 0.00 3.53
400 401 5.761234 AGTATTTTCGTTAGCACAGTCCAAA 59.239 36.000 0.00 0.00 0.00 3.28
427 428 5.432885 AATGGTCTTAACGTTTGTTGGAG 57.567 39.130 5.91 0.00 39.12 3.86
434 435 2.088950 ACGTTTGTTGGAGGGATACG 57.911 50.000 0.00 0.00 37.60 3.06
635 657 1.654105 CACGAGAAGTTGGATACGTGC 59.346 52.381 0.00 0.00 42.73 5.34
638 660 3.380637 ACGAGAAGTTGGATACGTGCTAT 59.619 43.478 0.00 0.00 42.51 2.97
639 661 4.577693 ACGAGAAGTTGGATACGTGCTATA 59.422 41.667 0.00 0.00 42.51 1.31
669 696 4.972875 GGAGGCATCCAGGAACAG 57.027 61.111 13.69 0.00 45.87 3.16
682 709 1.290324 GAACAGTCAGCTGCCTCGA 59.710 57.895 9.47 0.00 46.30 4.04
830 4499 4.096532 CCGTATGAGTAGAGAAACTGCTGA 59.903 45.833 0.00 0.00 41.40 4.26
884 4554 0.401738 TGGCAAGGTTGAGGAGAAGG 59.598 55.000 0.00 0.00 0.00 3.46
985 4672 1.221840 CAATCCCTCCTCACACCCG 59.778 63.158 0.00 0.00 0.00 5.28
1453 5166 2.105128 GTCTCCGGGATGCAGTCG 59.895 66.667 0.00 0.00 0.00 4.18
1592 5328 2.278330 GCAGGGGAAAGTTGGCCAG 61.278 63.158 5.11 0.00 0.00 4.85
1593 5329 2.118294 AGGGGAAAGTTGGCCAGC 59.882 61.111 12.39 12.39 0.00 4.85
1606 5342 4.636435 CCAGCGGGTTGGTCGGTT 62.636 66.667 0.00 0.00 36.14 4.44
1611 5348 2.751688 GGGTTGGTCGGTTGGCTA 59.248 61.111 0.00 0.00 0.00 3.93
1615 5352 2.221299 TTGGTCGGTTGGCTAGGCT 61.221 57.895 18.18 0.00 0.00 4.58
1632 5475 2.001361 GCTGGATTTGCATGCGCTCT 62.001 55.000 14.09 0.00 39.64 4.09
1633 5476 0.454600 CTGGATTTGCATGCGCTCTT 59.545 50.000 14.09 0.00 39.64 2.85
1635 5478 2.090760 TGGATTTGCATGCGCTCTTTA 58.909 42.857 14.09 0.00 39.64 1.85
1636 5479 2.689471 TGGATTTGCATGCGCTCTTTAT 59.311 40.909 14.09 0.00 39.64 1.40
1637 5480 3.130869 TGGATTTGCATGCGCTCTTTATT 59.869 39.130 14.09 0.00 39.64 1.40
1645 5508 5.464722 TGCATGCGCTCTTTATTTTTGAAAA 59.535 32.000 14.09 0.00 39.64 2.29
1648 5511 7.566709 CATGCGCTCTTTATTTTTGAAAAGTT 58.433 30.769 9.73 0.00 34.88 2.66
1650 5513 7.617557 TGCGCTCTTTATTTTTGAAAAGTTTC 58.382 30.769 9.73 0.00 34.88 2.78
1708 5578 1.398692 TTGTTTCCCAGGTGCTTCAC 58.601 50.000 0.00 0.00 0.00 3.18
1711 5581 0.110486 TTTCCCAGGTGCTTCACTCC 59.890 55.000 0.00 0.00 34.40 3.85
1753 5623 7.872483 GGTTTGTGATTTTTGTTATGTGGAGAT 59.128 33.333 0.00 0.00 0.00 2.75
1754 5624 9.260002 GTTTGTGATTTTTGTTATGTGGAGATT 57.740 29.630 0.00 0.00 0.00 2.40
1766 5636 7.453126 TGTTATGTGGAGATTAATTGTTTGGGT 59.547 33.333 0.00 0.00 0.00 4.51
1774 5644 8.314021 GGAGATTAATTGTTTGGGTCATTCTTT 58.686 33.333 0.00 0.00 0.00 2.52
1807 5683 7.805163 ACTGGATGGATTGTTAGTTGATGATA 58.195 34.615 0.00 0.00 0.00 2.15
1808 5684 8.274322 ACTGGATGGATTGTTAGTTGATGATAA 58.726 33.333 0.00 0.00 0.00 1.75
1809 5685 9.293404 CTGGATGGATTGTTAGTTGATGATAAT 57.707 33.333 0.00 0.00 0.00 1.28
1810 5686 9.645128 TGGATGGATTGTTAGTTGATGATAATT 57.355 29.630 0.00 0.00 0.00 1.40
1850 5726 4.343231 TGCACTATCATTTTGTGGGATGT 58.657 39.130 0.00 0.00 32.85 3.06
1851 5727 4.771577 TGCACTATCATTTTGTGGGATGTT 59.228 37.500 0.00 0.00 32.85 2.71
1852 5728 5.245751 TGCACTATCATTTTGTGGGATGTTT 59.754 36.000 0.00 0.00 32.85 2.83
1853 5729 5.577945 GCACTATCATTTTGTGGGATGTTTG 59.422 40.000 0.00 0.00 32.85 2.93
1854 5730 6.572119 GCACTATCATTTTGTGGGATGTTTGA 60.572 38.462 0.00 0.00 32.85 2.69
1855 5731 7.377398 CACTATCATTTTGTGGGATGTTTGAA 58.623 34.615 0.00 0.00 0.00 2.69
1856 5732 7.871973 CACTATCATTTTGTGGGATGTTTGAAA 59.128 33.333 0.00 0.00 0.00 2.69
1857 5733 8.428063 ACTATCATTTTGTGGGATGTTTGAAAA 58.572 29.630 0.00 0.00 0.00 2.29
1858 5734 9.270640 CTATCATTTTGTGGGATGTTTGAAAAA 57.729 29.630 0.00 0.00 0.00 1.94
1859 5735 8.694581 ATCATTTTGTGGGATGTTTGAAAAAT 57.305 26.923 0.00 0.00 0.00 1.82
1860 5736 8.152309 TCATTTTGTGGGATGTTTGAAAAATC 57.848 30.769 0.00 0.00 0.00 2.17
1861 5737 6.934048 TTTTGTGGGATGTTTGAAAAATCC 57.066 33.333 17.12 17.12 39.38 3.01
1871 5771 8.344831 GGATGTTTGAAAAATCCCAAGAAAAAG 58.655 33.333 14.95 0.00 34.89 2.27
1874 5774 8.052141 TGTTTGAAAAATCCCAAGAAAAAGGAT 58.948 29.630 0.00 0.00 42.30 3.24
1885 5785 7.037438 CCCAAGAAAAAGGATGTGTATGATTG 58.963 38.462 0.00 0.00 0.00 2.67
1889 5789 9.480053 AAGAAAAAGGATGTGTATGATTGTTTG 57.520 29.630 0.00 0.00 0.00 2.93
1894 5794 6.418101 AGGATGTGTATGATTGTTTGCTACT 58.582 36.000 0.00 0.00 0.00 2.57
1895 5795 6.540189 AGGATGTGTATGATTGTTTGCTACTC 59.460 38.462 0.00 0.00 0.00 2.59
1896 5796 6.540189 GGATGTGTATGATTGTTTGCTACTCT 59.460 38.462 0.00 0.00 0.00 3.24
1897 5797 6.726258 TGTGTATGATTGTTTGCTACTCTG 57.274 37.500 0.00 0.00 0.00 3.35
1898 5798 5.643348 TGTGTATGATTGTTTGCTACTCTGG 59.357 40.000 0.00 0.00 0.00 3.86
1907 5807 4.177783 GTTTGCTACTCTGGTCTAGCTTC 58.822 47.826 0.00 0.00 36.58 3.86
1920 5820 4.867608 GGTCTAGCTTCACTGTTGATTCTC 59.132 45.833 0.00 0.00 0.00 2.87
1921 5821 5.473931 GTCTAGCTTCACTGTTGATTCTCA 58.526 41.667 0.00 0.00 0.00 3.27
1922 5822 5.576384 GTCTAGCTTCACTGTTGATTCTCAG 59.424 44.000 0.00 7.51 37.65 3.35
1923 5823 3.072944 AGCTTCACTGTTGATTCTCAGC 58.927 45.455 8.54 0.00 35.37 4.26
1924 5824 2.810274 GCTTCACTGTTGATTCTCAGCA 59.190 45.455 8.54 0.00 35.22 4.41
1928 5828 2.896243 CTGTTGATTCTCAGCAGTGC 57.104 50.000 7.13 7.13 46.36 4.40
1929 5829 2.424557 CTGTTGATTCTCAGCAGTGCT 58.575 47.619 13.14 13.14 46.36 4.40
1930 5830 2.812591 CTGTTGATTCTCAGCAGTGCTT 59.187 45.455 16.89 0.00 46.36 3.91
1931 5831 2.551032 TGTTGATTCTCAGCAGTGCTTG 59.449 45.455 16.89 11.70 36.40 4.01
1932 5832 2.810274 GTTGATTCTCAGCAGTGCTTGA 59.190 45.455 16.89 14.00 36.40 3.02
1933 5833 2.696506 TGATTCTCAGCAGTGCTTGAG 58.303 47.619 26.00 26.00 36.40 3.02
1934 5834 2.008329 GATTCTCAGCAGTGCTTGAGG 58.992 52.381 28.69 15.98 36.40 3.86
1935 5835 0.761187 TTCTCAGCAGTGCTTGAGGT 59.239 50.000 28.69 5.77 36.40 3.85
1936 5836 0.761187 TCTCAGCAGTGCTTGAGGTT 59.239 50.000 28.69 5.13 36.40 3.50
1937 5837 0.873054 CTCAGCAGTGCTTGAGGTTG 59.127 55.000 25.01 12.43 36.40 3.77
2025 5951 9.319143 CTCAAGAAATTATTGGTACTAGGAGTG 57.681 37.037 0.24 0.00 0.00 3.51
2044 5980 7.924541 AGGAGTGGTACTTGTTAATTATTCCA 58.075 34.615 0.00 0.00 0.00 3.53
2106 6044 4.019174 ACATCAATTTCCTTGCCACTAGG 58.981 43.478 0.00 0.00 34.66 3.02
2107 6045 3.085952 TCAATTTCCTTGCCACTAGGG 57.914 47.619 0.00 0.00 40.85 3.53
2119 6059 2.807676 CCACTAGGGCCTTTGTGAATT 58.192 47.619 29.12 1.62 32.72 2.17
2126 6066 7.877612 CACTAGGGCCTTTGTGAATTTAAAAAT 59.122 33.333 25.59 0.00 32.72 1.82
2170 6118 5.551760 ACAGCATAAAGTGAACTACATGC 57.448 39.130 16.01 16.01 40.62 4.06
2174 6122 4.788100 GCATAAAGTGAACTACATGCAACG 59.212 41.667 17.72 0.00 40.31 4.10
2176 6124 2.543777 AGTGAACTACATGCAACGGT 57.456 45.000 0.00 0.00 0.00 4.83
2213 6162 8.579863 CAGAATTTTCTATTCTCACCCTTTTGT 58.420 33.333 0.00 0.00 36.32 2.83
2214 6163 8.579863 AGAATTTTCTATTCTCACCCTTTTGTG 58.420 33.333 0.00 0.00 33.43 3.33
2218 6167 3.806949 ATTCTCACCCTTTTGTGCCTA 57.193 42.857 0.00 0.00 36.17 3.93
2222 6171 3.844211 TCTCACCCTTTTGTGCCTATAGT 59.156 43.478 0.00 0.00 36.17 2.12
2258 6207 4.574013 CACAGTTTAGCTTCATCATCTCCC 59.426 45.833 0.00 0.00 0.00 4.30
2354 6303 0.330604 AAGTGCAGGGCATGTGATCT 59.669 50.000 0.00 0.00 41.91 2.75
2373 6473 0.315251 TCAGAAGCTCACGTGTCCTG 59.685 55.000 16.51 15.10 0.00 3.86
2374 6474 1.005630 AGAAGCTCACGTGTCCTGC 60.006 57.895 16.51 15.03 0.00 4.85
2404 6504 3.374042 TTGACTGTTGTCCCTGGAAAA 57.626 42.857 0.00 0.00 42.28 2.29
2406 6506 1.954382 GACTGTTGTCCCTGGAAAACC 59.046 52.381 15.11 0.00 40.62 3.27
2407 6507 1.328279 CTGTTGTCCCTGGAAAACCC 58.672 55.000 15.11 0.00 40.62 4.11
2408 6508 0.930726 TGTTGTCCCTGGAAAACCCT 59.069 50.000 15.11 0.00 40.62 4.34
2523 6689 6.484818 TTTTTACCGCTTGGATTGTACTAC 57.515 37.500 0.00 0.00 36.26 2.73
2524 6690 5.410355 TTTACCGCTTGGATTGTACTACT 57.590 39.130 0.00 0.00 36.26 2.57
2525 6691 6.528537 TTTACCGCTTGGATTGTACTACTA 57.471 37.500 0.00 0.00 36.26 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.876357 TGGAGGATATTTATAGTTGGGCAC 58.124 41.667 0.00 0.00 0.00 5.01
12 13 7.255836 GGTTTTGGAGGATATTTATAGTTGGGC 60.256 40.741 0.00 0.00 0.00 5.36
14 15 8.760980 TGGTTTTGGAGGATATTTATAGTTGG 57.239 34.615 0.00 0.00 0.00 3.77
21 22 9.207868 CCCTTAATTGGTTTTGGAGGATATTTA 57.792 33.333 0.00 0.00 0.00 1.40
22 23 7.904022 TCCCTTAATTGGTTTTGGAGGATATTT 59.096 33.333 0.00 0.00 0.00 1.40
24 25 6.839134 GTCCCTTAATTGGTTTTGGAGGATAT 59.161 38.462 0.00 0.00 0.00 1.63
25 26 6.192044 GTCCCTTAATTGGTTTTGGAGGATA 58.808 40.000 0.00 0.00 0.00 2.59
28 29 3.513912 GGTCCCTTAATTGGTTTTGGAGG 59.486 47.826 0.00 0.00 0.00 4.30
29 30 4.220602 CAGGTCCCTTAATTGGTTTTGGAG 59.779 45.833 0.00 0.00 0.00 3.86
30 31 4.140900 TCAGGTCCCTTAATTGGTTTTGGA 60.141 41.667 0.00 0.00 0.00 3.53
31 32 4.156477 TCAGGTCCCTTAATTGGTTTTGG 58.844 43.478 0.00 0.00 0.00 3.28
32 33 5.245977 ACATCAGGTCCCTTAATTGGTTTTG 59.754 40.000 0.00 0.00 0.00 2.44
33 34 5.402630 ACATCAGGTCCCTTAATTGGTTTT 58.597 37.500 0.00 0.00 0.00 2.43
34 35 5.010708 ACATCAGGTCCCTTAATTGGTTT 57.989 39.130 0.00 0.00 0.00 3.27
35 36 4.675063 ACATCAGGTCCCTTAATTGGTT 57.325 40.909 0.00 0.00 0.00 3.67
36 37 5.036916 TCTACATCAGGTCCCTTAATTGGT 58.963 41.667 0.00 0.00 0.00 3.67
37 38 5.630415 TCTACATCAGGTCCCTTAATTGG 57.370 43.478 0.00 0.00 0.00 3.16
38 39 8.525290 AAATTCTACATCAGGTCCCTTAATTG 57.475 34.615 0.00 0.00 0.00 2.32
40 41 9.853177 CTAAAATTCTACATCAGGTCCCTTAAT 57.147 33.333 0.00 0.00 0.00 1.40
41 42 8.832735 ACTAAAATTCTACATCAGGTCCCTTAA 58.167 33.333 0.00 0.00 0.00 1.85
42 43 8.265055 CACTAAAATTCTACATCAGGTCCCTTA 58.735 37.037 0.00 0.00 0.00 2.69
43 44 7.037586 TCACTAAAATTCTACATCAGGTCCCTT 60.038 37.037 0.00 0.00 0.00 3.95
44 45 6.443849 TCACTAAAATTCTACATCAGGTCCCT 59.556 38.462 0.00 0.00 0.00 4.20
51 52 9.667107 CCCTAAGTTCACTAAAATTCTACATCA 57.333 33.333 0.00 0.00 0.00 3.07
53 54 8.832735 TCCCCTAAGTTCACTAAAATTCTACAT 58.167 33.333 0.00 0.00 0.00 2.29
54 55 8.098912 GTCCCCTAAGTTCACTAAAATTCTACA 58.901 37.037 0.00 0.00 0.00 2.74
57 58 6.045106 TGGTCCCCTAAGTTCACTAAAATTCT 59.955 38.462 0.00 0.00 0.00 2.40
58 59 6.243148 TGGTCCCCTAAGTTCACTAAAATTC 58.757 40.000 0.00 0.00 0.00 2.17
59 60 6.208840 TGGTCCCCTAAGTTCACTAAAATT 57.791 37.500 0.00 0.00 0.00 1.82
60 61 5.853572 TGGTCCCCTAAGTTCACTAAAAT 57.146 39.130 0.00 0.00 0.00 1.82
62 63 5.649970 TTTGGTCCCCTAAGTTCACTAAA 57.350 39.130 0.00 0.00 0.00 1.85
63 64 5.649970 TTTTGGTCCCCTAAGTTCACTAA 57.350 39.130 0.00 0.00 0.00 2.24
64 65 5.649970 TTTTTGGTCCCCTAAGTTCACTA 57.350 39.130 0.00 0.00 0.00 2.74
93 94 8.402472 TCGTTTATCTTTTGCTTGAAGAGAAAA 58.598 29.630 14.19 0.00 42.48 2.29
94 95 7.855904 GTCGTTTATCTTTTGCTTGAAGAGAAA 59.144 33.333 0.00 10.72 40.19 2.52
95 96 7.011950 TGTCGTTTATCTTTTGCTTGAAGAGAA 59.988 33.333 0.00 2.94 36.64 2.87
96 97 6.481976 TGTCGTTTATCTTTTGCTTGAAGAGA 59.518 34.615 0.00 0.00 36.64 3.10
97 98 6.658831 TGTCGTTTATCTTTTGCTTGAAGAG 58.341 36.000 0.00 0.00 36.64 2.85
98 99 6.612247 TGTCGTTTATCTTTTGCTTGAAGA 57.388 33.333 0.00 0.69 37.52 2.87
99 100 7.617935 GCATTGTCGTTTATCTTTTGCTTGAAG 60.618 37.037 0.00 0.00 0.00 3.02
100 101 6.143758 GCATTGTCGTTTATCTTTTGCTTGAA 59.856 34.615 0.00 0.00 0.00 2.69
102 103 5.630680 AGCATTGTCGTTTATCTTTTGCTTG 59.369 36.000 0.00 0.00 34.47 4.01
103 104 5.772521 AGCATTGTCGTTTATCTTTTGCTT 58.227 33.333 0.00 0.00 34.47 3.91
104 105 5.376854 AGCATTGTCGTTTATCTTTTGCT 57.623 34.783 0.00 0.00 33.37 3.91
105 106 6.314784 AGTAGCATTGTCGTTTATCTTTTGC 58.685 36.000 0.00 0.00 0.00 3.68
107 108 6.093633 GGGAGTAGCATTGTCGTTTATCTTTT 59.906 38.462 0.00 0.00 0.00 2.27
110 111 4.406003 AGGGAGTAGCATTGTCGTTTATCT 59.594 41.667 0.00 0.00 0.00 1.98
111 112 4.694339 AGGGAGTAGCATTGTCGTTTATC 58.306 43.478 0.00 0.00 0.00 1.75
112 113 4.443034 GGAGGGAGTAGCATTGTCGTTTAT 60.443 45.833 0.00 0.00 0.00 1.40
114 115 2.354805 GGAGGGAGTAGCATTGTCGTTT 60.355 50.000 0.00 0.00 0.00 3.60
115 116 1.207329 GGAGGGAGTAGCATTGTCGTT 59.793 52.381 0.00 0.00 0.00 3.85
116 117 0.824759 GGAGGGAGTAGCATTGTCGT 59.175 55.000 0.00 0.00 0.00 4.34
117 118 0.249073 CGGAGGGAGTAGCATTGTCG 60.249 60.000 0.00 0.00 0.00 4.35
118 119 3.669354 CGGAGGGAGTAGCATTGTC 57.331 57.895 0.00 0.00 0.00 3.18
132 133 2.289444 TGCAGACTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
133 134 1.695242 TGCAGACTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
134 135 2.178912 TGCAGACTAAAAAGGACCGG 57.821 50.000 0.00 0.00 0.00 5.28
135 136 6.984474 TCTTATATGCAGACTAAAAAGGACCG 59.016 38.462 0.00 0.00 0.00 4.79
136 137 8.910351 ATCTTATATGCAGACTAAAAAGGACC 57.090 34.615 0.00 0.00 0.00 4.46
143 144 9.679661 TTGGACAAATCTTATATGCAGACTAAA 57.320 29.630 0.00 0.00 0.00 1.85
145 146 9.330063 CTTTGGACAAATCTTATATGCAGACTA 57.670 33.333 0.00 0.00 0.00 2.59
146 147 7.831193 ACTTTGGACAAATCTTATATGCAGACT 59.169 33.333 0.00 0.00 0.00 3.24
147 148 7.989826 ACTTTGGACAAATCTTATATGCAGAC 58.010 34.615 0.00 0.00 0.00 3.51
148 149 8.579850 AACTTTGGACAAATCTTATATGCAGA 57.420 30.769 0.00 0.00 0.00 4.26
157 158 8.803235 GGGATACTTTAACTTTGGACAAATCTT 58.197 33.333 0.00 0.00 0.00 2.40
159 160 8.117813 TGGGATACTTTAACTTTGGACAAATC 57.882 34.615 0.00 0.00 0.00 2.17
160 161 8.364894 GTTGGGATACTTTAACTTTGGACAAAT 58.635 33.333 0.00 0.00 0.00 2.32
161 162 7.562088 AGTTGGGATACTTTAACTTTGGACAAA 59.438 33.333 0.00 0.00 33.61 2.83
162 163 7.064229 AGTTGGGATACTTTAACTTTGGACAA 58.936 34.615 0.00 0.00 33.61 3.18
163 164 6.607019 AGTTGGGATACTTTAACTTTGGACA 58.393 36.000 0.00 0.00 33.61 4.02
164 165 7.520451 AAGTTGGGATACTTTAACTTTGGAC 57.480 36.000 0.00 0.00 39.97 4.02
168 169 7.562088 TGGTCAAAGTTGGGATACTTTAACTTT 59.438 33.333 0.00 0.00 44.33 2.66
169 170 7.064229 TGGTCAAAGTTGGGATACTTTAACTT 58.936 34.615 0.00 0.00 44.33 2.66
170 171 6.607019 TGGTCAAAGTTGGGATACTTTAACT 58.393 36.000 0.00 0.00 44.33 2.24
172 173 7.562088 AGTTTGGTCAAAGTTGGGATACTTTAA 59.438 33.333 0.00 0.00 44.33 1.52
173 174 7.064229 AGTTTGGTCAAAGTTGGGATACTTTA 58.936 34.615 0.00 0.00 44.33 1.85
174 175 5.897250 AGTTTGGTCAAAGTTGGGATACTTT 59.103 36.000 0.00 0.00 46.42 2.66
176 177 5.061721 AGTTTGGTCAAAGTTGGGATACT 57.938 39.130 0.00 0.00 30.25 2.12
178 179 8.607713 TCTATAAGTTTGGTCAAAGTTGGGATA 58.392 33.333 20.50 12.43 42.17 2.59
179 180 7.466804 TCTATAAGTTTGGTCAAAGTTGGGAT 58.533 34.615 20.50 12.08 42.17 3.85
180 181 6.843752 TCTATAAGTTTGGTCAAAGTTGGGA 58.156 36.000 20.50 14.21 42.17 4.37
181 182 7.519032 TTCTATAAGTTTGGTCAAAGTTGGG 57.481 36.000 20.50 12.78 42.17 4.12
182 183 9.810545 TTTTTCTATAAGTTTGGTCAAAGTTGG 57.189 29.630 20.50 13.03 42.17 3.77
202 203 9.401873 GGCATTGTAAACGTTAATACTTTTTCT 57.598 29.630 0.00 0.00 29.68 2.52
204 205 9.530633 TTGGCATTGTAAACGTTAATACTTTTT 57.469 25.926 0.00 0.00 29.68 1.94
205 206 9.530633 TTTGGCATTGTAAACGTTAATACTTTT 57.469 25.926 0.00 0.00 31.54 2.27
206 207 9.699703 ATTTGGCATTGTAAACGTTAATACTTT 57.300 25.926 0.00 0.00 0.00 2.66
207 208 9.349145 GATTTGGCATTGTAAACGTTAATACTT 57.651 29.630 0.00 0.00 0.00 2.24
208 209 8.516234 TGATTTGGCATTGTAAACGTTAATACT 58.484 29.630 0.00 0.00 0.00 2.12
209 210 8.676454 TGATTTGGCATTGTAAACGTTAATAC 57.324 30.769 0.00 1.80 0.00 1.89
210 211 9.130312 GTTGATTTGGCATTGTAAACGTTAATA 57.870 29.630 0.00 0.00 0.00 0.98
211 212 7.653713 TGTTGATTTGGCATTGTAAACGTTAAT 59.346 29.630 0.00 0.00 0.00 1.40
212 213 6.978659 TGTTGATTTGGCATTGTAAACGTTAA 59.021 30.769 0.00 0.00 0.00 2.01
213 214 6.504398 TGTTGATTTGGCATTGTAAACGTTA 58.496 32.000 0.00 0.00 0.00 3.18
214 215 5.352284 TGTTGATTTGGCATTGTAAACGTT 58.648 33.333 0.00 0.00 0.00 3.99
215 216 4.938080 TGTTGATTTGGCATTGTAAACGT 58.062 34.783 0.00 0.00 0.00 3.99
216 217 6.298103 CAATGTTGATTTGGCATTGTAAACG 58.702 36.000 7.96 0.00 42.41 3.60
223 224 8.095792 TGAATCTAACAATGTTGATTTGGCATT 58.904 29.630 17.90 0.00 33.64 3.56
224 225 7.613585 TGAATCTAACAATGTTGATTTGGCAT 58.386 30.769 17.90 3.27 30.41 4.40
225 226 6.990798 TGAATCTAACAATGTTGATTTGGCA 58.009 32.000 17.90 12.14 30.41 4.92
226 227 8.483307 AATGAATCTAACAATGTTGATTTGGC 57.517 30.769 17.90 10.56 30.41 4.52
319 320 8.527567 TTTTTGTCAGGTCAAACTTTGTAAAG 57.472 30.769 2.94 2.94 41.73 1.85
320 321 9.145865 GATTTTTGTCAGGTCAAACTTTGTAAA 57.854 29.630 1.44 0.00 37.10 2.01
321 322 8.527810 AGATTTTTGTCAGGTCAAACTTTGTAA 58.472 29.630 1.44 0.00 37.10 2.41
322 323 8.062065 AGATTTTTGTCAGGTCAAACTTTGTA 57.938 30.769 1.44 0.00 37.10 2.41
323 324 6.935167 AGATTTTTGTCAGGTCAAACTTTGT 58.065 32.000 1.44 0.00 37.10 2.83
324 325 8.925161 TTAGATTTTTGTCAGGTCAAACTTTG 57.075 30.769 0.00 0.00 37.10 2.77
328 329 9.076596 GCATATTAGATTTTTGTCAGGTCAAAC 57.923 33.333 0.00 0.00 37.10 2.93
329 330 7.967854 CGCATATTAGATTTTTGTCAGGTCAAA 59.032 33.333 0.00 0.00 35.83 2.69
330 331 7.335673 TCGCATATTAGATTTTTGTCAGGTCAA 59.664 33.333 0.00 0.00 0.00 3.18
331 332 6.821160 TCGCATATTAGATTTTTGTCAGGTCA 59.179 34.615 0.00 0.00 0.00 4.02
332 333 7.246674 TCGCATATTAGATTTTTGTCAGGTC 57.753 36.000 0.00 0.00 0.00 3.85
333 334 7.336931 ACTTCGCATATTAGATTTTTGTCAGGT 59.663 33.333 0.00 0.00 0.00 4.00
334 335 7.697691 ACTTCGCATATTAGATTTTTGTCAGG 58.302 34.615 0.00 0.00 0.00 3.86
345 346 8.836413 CCAATCCTTTTTACTTCGCATATTAGA 58.164 33.333 0.00 0.00 0.00 2.10
346 347 8.836413 TCCAATCCTTTTTACTTCGCATATTAG 58.164 33.333 0.00 0.00 0.00 1.73
348 349 7.201821 CCTCCAATCCTTTTTACTTCGCATATT 60.202 37.037 0.00 0.00 0.00 1.28
349 350 6.263168 CCTCCAATCCTTTTTACTTCGCATAT 59.737 38.462 0.00 0.00 0.00 1.78
350 351 5.588648 CCTCCAATCCTTTTTACTTCGCATA 59.411 40.000 0.00 0.00 0.00 3.14
352 353 3.756434 CCTCCAATCCTTTTTACTTCGCA 59.244 43.478 0.00 0.00 0.00 5.10
354 355 4.585879 TCCCTCCAATCCTTTTTACTTCG 58.414 43.478 0.00 0.00 0.00 3.79
355 356 5.571285 ACTCCCTCCAATCCTTTTTACTTC 58.429 41.667 0.00 0.00 0.00 3.01
356 357 5.600669 ACTCCCTCCAATCCTTTTTACTT 57.399 39.130 0.00 0.00 0.00 2.24
359 360 7.338449 CGAAAATACTCCCTCCAATCCTTTTTA 59.662 37.037 0.00 0.00 0.00 1.52
361 362 5.652452 CGAAAATACTCCCTCCAATCCTTTT 59.348 40.000 0.00 0.00 0.00 2.27
362 363 5.193679 CGAAAATACTCCCTCCAATCCTTT 58.806 41.667 0.00 0.00 0.00 3.11
363 364 4.227527 ACGAAAATACTCCCTCCAATCCTT 59.772 41.667 0.00 0.00 0.00 3.36
364 365 3.780850 ACGAAAATACTCCCTCCAATCCT 59.219 43.478 0.00 0.00 0.00 3.24
366 367 5.236695 GCTAACGAAAATACTCCCTCCAATC 59.763 44.000 0.00 0.00 0.00 2.67
367 368 5.123936 GCTAACGAAAATACTCCCTCCAAT 58.876 41.667 0.00 0.00 0.00 3.16
368 369 4.020039 TGCTAACGAAAATACTCCCTCCAA 60.020 41.667 0.00 0.00 0.00 3.53
369 370 3.516300 TGCTAACGAAAATACTCCCTCCA 59.484 43.478 0.00 0.00 0.00 3.86
370 371 3.869832 GTGCTAACGAAAATACTCCCTCC 59.130 47.826 0.00 0.00 0.00 4.30
371 372 4.501071 TGTGCTAACGAAAATACTCCCTC 58.499 43.478 0.00 0.00 0.00 4.30
373 374 4.251268 ACTGTGCTAACGAAAATACTCCC 58.749 43.478 0.00 0.00 0.00 4.30
375 376 4.927425 TGGACTGTGCTAACGAAAATACTC 59.073 41.667 0.00 0.00 0.00 2.59
376 377 4.890088 TGGACTGTGCTAACGAAAATACT 58.110 39.130 0.00 0.00 0.00 2.12
377 378 5.600908 TTGGACTGTGCTAACGAAAATAC 57.399 39.130 0.00 0.00 0.00 1.89
379 380 4.819630 TCTTTGGACTGTGCTAACGAAAAT 59.180 37.500 0.00 0.00 0.00 1.82
381 382 3.799366 TCTTTGGACTGTGCTAACGAAA 58.201 40.909 0.00 0.00 0.00 3.46
382 383 3.462483 TCTTTGGACTGTGCTAACGAA 57.538 42.857 0.00 0.00 0.00 3.85
385 386 6.151144 ACCATTTATCTTTGGACTGTGCTAAC 59.849 38.462 0.00 0.00 36.79 2.34
387 388 5.815581 ACCATTTATCTTTGGACTGTGCTA 58.184 37.500 0.00 0.00 36.79 3.49
388 389 4.666512 ACCATTTATCTTTGGACTGTGCT 58.333 39.130 0.00 0.00 36.79 4.40
389 390 4.702131 AGACCATTTATCTTTGGACTGTGC 59.298 41.667 0.00 0.00 36.79 4.57
391 392 7.119262 CGTTAAGACCATTTATCTTTGGACTGT 59.881 37.037 0.00 0.00 37.92 3.55
393 394 7.166167 ACGTTAAGACCATTTATCTTTGGACT 58.834 34.615 0.00 0.00 39.23 3.85
395 396 7.989416 AACGTTAAGACCATTTATCTTTGGA 57.011 32.000 0.00 0.00 37.57 3.53
396 397 8.079809 ACAAACGTTAAGACCATTTATCTTTGG 58.920 33.333 0.00 0.00 37.57 3.28
398 399 9.458374 CAACAAACGTTAAGACCATTTATCTTT 57.542 29.630 0.00 0.00 37.57 2.52
399 400 8.079809 CCAACAAACGTTAAGACCATTTATCTT 58.920 33.333 0.00 0.00 39.70 2.40
400 401 7.446013 TCCAACAAACGTTAAGACCATTTATCT 59.554 33.333 0.00 0.00 0.00 1.98
427 428 1.944709 GGTGGTTGCATTACGTATCCC 59.055 52.381 0.00 0.00 0.00 3.85
434 435 2.427095 GGAAGGATGGTGGTTGCATTAC 59.573 50.000 0.00 0.00 0.00 1.89
523 525 6.046290 ACGGCAAGTAGGAAATAAGTAAGT 57.954 37.500 0.00 0.00 0.00 2.24
600 614 9.490663 CAACTTCTCGTGATTGTTATTATTTCC 57.509 33.333 6.21 0.00 0.00 3.13
635 657 4.284490 TGCCTCCTAATCCAAGCAGTATAG 59.716 45.833 0.00 0.00 0.00 1.31
638 660 2.477245 TGCCTCCTAATCCAAGCAGTA 58.523 47.619 0.00 0.00 0.00 2.74
639 661 1.289160 TGCCTCCTAATCCAAGCAGT 58.711 50.000 0.00 0.00 0.00 4.40
669 696 0.319900 TTCAACTCGAGGCAGCTGAC 60.320 55.000 20.43 17.00 0.00 3.51
701 728 1.839994 ACACCTCCCATCATCGAACAT 59.160 47.619 0.00 0.00 0.00 2.71
830 4499 4.911390 AGTTACAGCAGCAGGAACTATTT 58.089 39.130 13.64 0.00 36.02 1.40
985 4672 1.333931 TCGTGTGAGTGAGTGACTGAC 59.666 52.381 0.00 0.00 39.15 3.51
1062 4757 1.377202 GCTCCGGTTCTTGGCATCA 60.377 57.895 0.00 0.00 0.00 3.07
1439 5152 3.458163 GGACGACTGCATCCCGGA 61.458 66.667 0.73 0.00 0.00 5.14
1577 5313 3.373565 CGCTGGCCAACTTTCCCC 61.374 66.667 7.01 0.00 0.00 4.81
1593 5329 3.242897 TAGCCAACCGACCAACCCG 62.243 63.158 0.00 0.00 0.00 5.28
1606 5342 0.259647 ATGCAAATCCAGCCTAGCCA 59.740 50.000 0.00 0.00 0.00 4.75
1611 5348 3.072486 GCGCATGCAAATCCAGCCT 62.072 57.895 19.57 0.00 42.15 4.58
1615 5352 0.889994 AAAGAGCGCATGCAAATCCA 59.110 45.000 19.57 0.00 46.23 3.41
1635 5478 9.190317 AGAGACTACTGGAAACTTTTCAAAAAT 57.810 29.630 4.18 0.00 38.92 1.82
1636 5479 8.575649 AGAGACTACTGGAAACTTTTCAAAAA 57.424 30.769 4.18 0.00 38.92 1.94
1637 5480 8.458843 CAAGAGACTACTGGAAACTTTTCAAAA 58.541 33.333 4.18 0.00 38.92 2.44
1645 5508 9.274206 GAAATTTACAAGAGACTACTGGAAACT 57.726 33.333 0.00 0.00 0.00 2.66
1648 5511 9.436957 GATGAAATTTACAAGAGACTACTGGAA 57.563 33.333 0.00 0.00 0.00 3.53
1650 5513 8.043710 AGGATGAAATTTACAAGAGACTACTGG 58.956 37.037 0.00 0.00 0.00 4.00
1655 5518 8.160106 ACTCAAGGATGAAATTTACAAGAGACT 58.840 33.333 0.00 0.00 34.49 3.24
1656 5519 8.329203 ACTCAAGGATGAAATTTACAAGAGAC 57.671 34.615 0.00 0.00 34.49 3.36
1742 5612 7.671819 TGACCCAAACAATTAATCTCCACATAA 59.328 33.333 0.00 0.00 0.00 1.90
1744 5614 6.015918 TGACCCAAACAATTAATCTCCACAT 58.984 36.000 0.00 0.00 0.00 3.21
1822 5698 8.938801 TCCCACAAAATGATAGTGCAATATAT 57.061 30.769 6.66 0.00 32.09 0.86
1827 5703 4.771577 ACATCCCACAAAATGATAGTGCAA 59.228 37.500 0.00 0.00 32.09 4.08
1830 5706 6.923012 TCAAACATCCCACAAAATGATAGTG 58.077 36.000 0.00 0.00 0.00 2.74
1832 5708 8.830201 TTTTCAAACATCCCACAAAATGATAG 57.170 30.769 0.00 0.00 0.00 2.08
1834 5710 8.694581 ATTTTTCAAACATCCCACAAAATGAT 57.305 26.923 0.00 0.00 0.00 2.45
1850 5726 8.052141 ACATCCTTTTTCTTGGGATTTTTCAAA 58.948 29.630 0.00 0.00 37.72 2.69
1851 5727 7.498570 CACATCCTTTTTCTTGGGATTTTTCAA 59.501 33.333 0.00 0.00 37.72 2.69
1852 5728 6.991531 CACATCCTTTTTCTTGGGATTTTTCA 59.008 34.615 0.00 0.00 37.72 2.69
1853 5729 6.992123 ACACATCCTTTTTCTTGGGATTTTTC 59.008 34.615 0.00 0.00 37.72 2.29
1854 5730 6.899089 ACACATCCTTTTTCTTGGGATTTTT 58.101 32.000 0.00 0.00 37.72 1.94
1855 5731 6.499106 ACACATCCTTTTTCTTGGGATTTT 57.501 33.333 0.00 0.00 37.72 1.82
1856 5732 7.454380 TCATACACATCCTTTTTCTTGGGATTT 59.546 33.333 0.00 0.00 37.72 2.17
1857 5733 6.953520 TCATACACATCCTTTTTCTTGGGATT 59.046 34.615 0.00 0.00 37.72 3.01
1858 5734 6.493166 TCATACACATCCTTTTTCTTGGGAT 58.507 36.000 0.00 0.00 40.10 3.85
1859 5735 5.886609 TCATACACATCCTTTTTCTTGGGA 58.113 37.500 0.00 0.00 0.00 4.37
1860 5736 6.780457 ATCATACACATCCTTTTTCTTGGG 57.220 37.500 0.00 0.00 0.00 4.12
1861 5737 7.605449 ACAATCATACACATCCTTTTTCTTGG 58.395 34.615 0.00 0.00 0.00 3.61
1862 5738 9.480053 AAACAATCATACACATCCTTTTTCTTG 57.520 29.630 0.00 0.00 0.00 3.02
1863 5739 9.480053 CAAACAATCATACACATCCTTTTTCTT 57.520 29.630 0.00 0.00 0.00 2.52
1864 5740 7.599998 GCAAACAATCATACACATCCTTTTTCT 59.400 33.333 0.00 0.00 0.00 2.52
1865 5741 7.599998 AGCAAACAATCATACACATCCTTTTTC 59.400 33.333 0.00 0.00 0.00 2.29
1866 5742 7.444299 AGCAAACAATCATACACATCCTTTTT 58.556 30.769 0.00 0.00 0.00 1.94
1871 5771 6.540189 AGAGTAGCAAACAATCATACACATCC 59.460 38.462 0.00 0.00 0.00 3.51
1874 5774 5.643348 CCAGAGTAGCAAACAATCATACACA 59.357 40.000 0.00 0.00 0.00 3.72
1885 5785 3.878160 AGCTAGACCAGAGTAGCAAAC 57.122 47.619 0.00 0.00 43.55 2.93
1889 5789 3.020984 AGTGAAGCTAGACCAGAGTAGC 58.979 50.000 0.00 0.00 41.77 3.58
1894 5794 3.230976 TCAACAGTGAAGCTAGACCAGA 58.769 45.455 0.00 0.00 0.00 3.86
1895 5795 3.667497 TCAACAGTGAAGCTAGACCAG 57.333 47.619 0.00 0.00 0.00 4.00
1896 5796 4.284490 AGAATCAACAGTGAAGCTAGACCA 59.716 41.667 0.00 0.00 37.30 4.02
1897 5797 4.826556 AGAATCAACAGTGAAGCTAGACC 58.173 43.478 0.00 0.00 37.30 3.85
1898 5798 5.473931 TGAGAATCAACAGTGAAGCTAGAC 58.526 41.667 0.00 0.00 45.97 2.59
1920 5820 1.285023 GCAACCTCAAGCACTGCTG 59.715 57.895 3.73 0.00 39.62 4.41
1921 5821 1.152902 TGCAACCTCAAGCACTGCT 60.153 52.632 0.00 0.00 42.56 4.24
1922 5822 1.285023 CTGCAACCTCAAGCACTGC 59.715 57.895 0.00 0.00 36.62 4.40
1923 5823 1.521450 CCCTGCAACCTCAAGCACTG 61.521 60.000 0.00 0.00 36.62 3.66
1924 5824 1.228367 CCCTGCAACCTCAAGCACT 60.228 57.895 0.00 0.00 36.62 4.40
1925 5825 2.924105 GCCCTGCAACCTCAAGCAC 61.924 63.158 0.00 0.00 36.62 4.40
1926 5826 2.598394 GCCCTGCAACCTCAAGCA 60.598 61.111 0.00 0.00 39.25 3.91
1928 5828 4.179361 TTGCCCTGCAACCTCAAG 57.821 55.556 0.00 0.00 43.99 3.02
2044 5980 6.550481 TGCATCTATGAGAACTGAGAAGAGAT 59.450 38.462 0.00 0.00 0.00 2.75
2131 6071 9.905713 TTTATGCTGTTCAGAGGTAAAATATCT 57.094 29.630 3.84 0.00 0.00 1.98
2140 6081 4.623932 TCACTTTATGCTGTTCAGAGGT 57.376 40.909 3.84 0.00 0.00 3.85
2151 6099 4.788100 CGTTGCATGTAGTTCACTTTATGC 59.212 41.667 15.74 15.74 40.91 3.14
2170 6118 2.828877 TCTGTTGTGGAGTTACCGTTG 58.171 47.619 0.00 0.00 42.61 4.10
2174 6122 6.635030 AGAAAATTCTGTTGTGGAGTTACC 57.365 37.500 0.00 0.00 35.89 2.85
2176 6124 9.793259 AGAATAGAAAATTCTGTTGTGGAGTTA 57.207 29.630 9.49 0.00 38.51 2.24
2213 6162 3.306989 GCTGGATGCACATACTATAGGCA 60.307 47.826 4.43 3.92 42.31 4.75
2214 6163 3.265791 GCTGGATGCACATACTATAGGC 58.734 50.000 4.43 0.00 42.31 3.93
2258 6207 3.555956 AGGCTTTACGCTAACAATCATCG 59.444 43.478 0.00 0.00 39.13 3.84
2282 6231 4.876701 TGCGAAGTGGCAAGAACT 57.123 50.000 0.00 0.00 40.59 3.01
2354 6303 0.315251 CAGGACACGTGAGCTTCTGA 59.685 55.000 25.01 0.00 0.00 3.27
2373 6473 2.290641 ACAACAGTCAATGGTTCTTCGC 59.709 45.455 0.00 0.00 0.00 4.70
2374 6474 3.058914 GGACAACAGTCAATGGTTCTTCG 60.059 47.826 0.00 0.00 33.90 3.79
2523 6689 4.117685 GCGGTACAAATTGGTAGGAGTAG 58.882 47.826 0.00 0.00 0.00 2.57
2524 6690 3.770933 AGCGGTACAAATTGGTAGGAGTA 59.229 43.478 0.00 0.00 0.00 2.59
2525 6691 2.570302 AGCGGTACAAATTGGTAGGAGT 59.430 45.455 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.