Multiple sequence alignment - TraesCS5D01G425800

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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 TraesCS5D01G425800 chr5D 100.000 4239 0 0 1 4239 484429874 484425636 0.000000e+00 7829.0
1 TraesCS5D01G425800 chr5D 84.468 1204 158 18 2048 3231 444711795 444712989 0.000000e+00 1160.0
2 TraesCS5D01G425800 chr5D 84.815 540 70 10 909 1438 444710542 444711079 2.240000e-147 532.0
3 TraesCS5D01G425800 chr5D 98.396 187 3 0 2 188 543579370 543579184 3.160000e-86 329.0
4 TraesCS5D01G425800 chr5D 96.875 192 4 2 2 192 286500357 286500167 1.900000e-83 320.0
5 TraesCS5D01G425800 chr5B 87.396 3721 373 43 250 3928 595634021 595630355 0.000000e+00 4185.0
6 TraesCS5D01G425800 chr5B 92.800 1889 103 16 1702 3573 595645975 595644103 0.000000e+00 2704.0
7 TraesCS5D01G425800 chr5B 92.103 1469 90 14 251 1704 595651049 595649592 0.000000e+00 2047.0
8 TraesCS5D01G425800 chr5B 85.087 1207 148 22 2046 3231 541499466 541500661 0.000000e+00 1203.0
9 TraesCS5D01G425800 chr5B 84.481 1205 155 21 2046 3231 541528370 541529561 0.000000e+00 1160.0
10 TraesCS5D01G425800 chr5B 88.398 181 17 3 407 587 595640488 595640312 9.230000e-52 215.0
11 TraesCS5D01G425800 chr5B 96.491 57 2 0 189 245 278481826 278481770 1.250000e-15 95.3
12 TraesCS5D01G425800 chr5B 94.828 58 2 1 191 248 57936910 57936966 5.840000e-14 89.8
13 TraesCS5D01G425800 chr5B 94.828 58 2 1 189 246 111954233 111954177 5.840000e-14 89.8
14 TraesCS5D01G425800 chr5B 94.828 58 2 1 189 246 350417826 350417770 5.840000e-14 89.8
15 TraesCS5D01G425800 chr5A 91.583 1687 112 18 1905 3573 606059635 606057961 0.000000e+00 2302.0
16 TraesCS5D01G425800 chr5A 89.150 1576 125 29 263 1812 606061362 606059807 0.000000e+00 1921.0
17 TraesCS5D01G425800 chr5A 84.085 1175 164 20 2076 3236 561554064 561555229 0.000000e+00 1112.0
18 TraesCS5D01G425800 chr5A 85.463 681 50 22 3587 4238 606057976 606057316 0.000000e+00 664.0
19 TraesCS5D01G425800 chr5A 90.389 437 40 2 250 686 606061828 606061394 1.320000e-159 573.0
20 TraesCS5D01G425800 chr5A 86.310 504 60 6 246 743 606062295 606061795 1.340000e-149 540.0
21 TraesCS5D01G425800 chr5A 95.082 61 2 1 1550 1610 561553880 561553939 1.250000e-15 95.3
22 TraesCS5D01G425800 chr4D 80.263 912 152 20 2322 3219 52468995 52469892 0.000000e+00 662.0
23 TraesCS5D01G425800 chr4D 81.031 485 72 13 1034 1501 52467530 52468011 6.700000e-98 368.0
24 TraesCS5D01G425800 chr4B 79.585 916 152 26 2322 3219 76814925 76815823 1.290000e-174 623.0
25 TraesCS5D01G425800 chr4B 81.031 485 71 15 1034 1501 76813455 76813935 2.410000e-97 366.0
26 TraesCS5D01G425800 chr7B 79.310 551 91 12 915 1444 86139217 86139765 8.660000e-97 364.0
27 TraesCS5D01G425800 chr4A 80.361 499 70 18 1034 1511 544204235 544203744 1.870000e-93 353.0
28 TraesCS5D01G425800 chr4A 96.491 57 0 2 189 245 569450955 569450901 4.510000e-15 93.5
29 TraesCS5D01G425800 chr3D 98.421 190 3 0 2 191 220186386 220186575 6.790000e-88 335.0
30 TraesCS5D01G425800 chr3D 97.895 190 4 0 2 191 220132167 220132356 3.160000e-86 329.0
31 TraesCS5D01G425800 chr3D 97.340 188 5 0 2 189 499944549 499944736 1.900000e-83 320.0
32 TraesCS5D01G425800 chr2D 97.861 187 4 0 2 188 140686308 140686122 1.470000e-84 324.0
33 TraesCS5D01G425800 chr2D 97.340 188 5 0 2 189 256078377 256078564 1.900000e-83 320.0
34 TraesCS5D01G425800 chr1D 97.861 187 4 0 2 188 288430158 288429972 1.470000e-84 324.0
35 TraesCS5D01G425800 chrUn 95.455 198 8 1 1 197 67596607 67596410 8.850000e-82 315.0
36 TraesCS5D01G425800 chr6B 90.278 72 3 4 189 258 209197693 209197762 1.620000e-14 91.6
37 TraesCS5D01G425800 chr3B 96.429 56 1 1 189 244 80461697 80461643 1.620000e-14 91.6
38 TraesCS5D01G425800 chr3B 96.429 56 1 1 189 244 80496050 80495996 1.620000e-14 91.6
39 TraesCS5D01G425800 chr1B 94.828 58 2 1 189 246 364907607 364907663 5.840000e-14 89.8
40 TraesCS5D01G425800 chr2A 85.185 54 6 2 219 270 380910320 380910267 2.000000e-03 54.7


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 TraesCS5D01G425800 chr5D 484425636 484429874 4238 True 7829.000000 7829 100.000000 1 4239 1 chr5D.!!$R2 4238
1 TraesCS5D01G425800 chr5D 444710542 444712989 2447 False 846.000000 1160 84.641500 909 3231 2 chr5D.!!$F1 2322
2 TraesCS5D01G425800 chr5B 595630355 595634021 3666 True 4185.000000 4185 87.396000 250 3928 1 chr5B.!!$R4 3678
3 TraesCS5D01G425800 chr5B 595640312 595651049 10737 True 1655.333333 2704 91.100333 251 3573 3 chr5B.!!$R5 3322
4 TraesCS5D01G425800 chr5B 541499466 541500661 1195 False 1203.000000 1203 85.087000 2046 3231 1 chr5B.!!$F2 1185
5 TraesCS5D01G425800 chr5B 541528370 541529561 1191 False 1160.000000 1160 84.481000 2046 3231 1 chr5B.!!$F3 1185
6 TraesCS5D01G425800 chr5A 606057316 606062295 4979 True 1200.000000 2302 88.579000 246 4238 5 chr5A.!!$R1 3992
7 TraesCS5D01G425800 chr5A 561553880 561555229 1349 False 603.650000 1112 89.583500 1550 3236 2 chr5A.!!$F1 1686
8 TraesCS5D01G425800 chr4D 52467530 52469892 2362 False 515.000000 662 80.647000 1034 3219 2 chr4D.!!$F1 2185
9 TraesCS5D01G425800 chr4B 76813455 76815823 2368 False 494.500000 623 80.308000 1034 3219 2 chr4B.!!$F1 2185
10 TraesCS5D01G425800 chr7B 86139217 86139765 548 False 364.000000 364 79.310000 915 1444 1 chr7B.!!$F1 529

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
546 1228 0.033504 ACTACGAACCAGCTGTGTGG 59.966 55.0 13.81 9.8 44.01 4.17 F
1142 1868 0.035152 ACAATGCCGCATTCTCTCCA 60.035 50.0 15.85 0.0 31.05 3.86 F
1484 2227 0.671796 ACGGCAAGGTTTTTACCAGC 59.328 50.0 0.00 0.0 33.96 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 7498 1.593006 AGAAGTCGTCGCTTTGTGTTG 59.407 47.619 3.93 0.0 0.00 3.33 R
2668 7667 1.625818 AGACCACTTAGTGCTTCTGGG 59.374 52.381 6.88 0.0 31.34 4.45 R
3335 8363 0.038744 AACCACATCTGCCTCCCAAG 59.961 55.000 0.00 0.0 0.00 3.61 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
25 26 8.813643 AAAGCGCTACTATTAATTACCAGTAG 57.186 34.615 12.05 19.51 42.14 2.57
32 33 7.052142 ACTATTAATTACCAGTAGCGCTCTT 57.948 36.000 16.34 0.00 0.00 2.85
34 35 8.636213 ACTATTAATTACCAGTAGCGCTCTTTA 58.364 33.333 16.34 3.74 0.00 1.85
35 36 7.948278 ATTAATTACCAGTAGCGCTCTTTAG 57.052 36.000 16.34 2.53 0.00 1.85
37 38 2.656560 ACCAGTAGCGCTCTTTAGTG 57.343 50.000 16.34 9.77 36.25 2.74
38 39 2.168496 ACCAGTAGCGCTCTTTAGTGA 58.832 47.619 16.34 0.00 35.06 3.41
39 40 2.561419 ACCAGTAGCGCTCTTTAGTGAA 59.439 45.455 16.34 0.00 35.06 3.18
40 41 3.006537 ACCAGTAGCGCTCTTTAGTGAAA 59.993 43.478 16.34 0.00 35.06 2.69
42 43 3.061429 CAGTAGCGCTCTTTAGTGAAAGC 59.939 47.826 16.34 0.00 41.68 3.51
43 44 1.071605 AGCGCTCTTTAGTGAAAGCG 58.928 50.000 2.64 10.93 41.68 4.68
47 48 2.028165 CGCTCTTTAGTGAAAGCGCTAC 59.972 50.000 12.05 5.27 46.60 3.58
48 49 3.254892 GCTCTTTAGTGAAAGCGCTACT 58.745 45.455 12.05 14.04 45.74 2.57
50 51 4.265792 GCTCTTTAGTGAAAGCGCTACTAC 59.734 45.833 12.05 10.17 45.74 2.73
51 52 5.640189 TCTTTAGTGAAAGCGCTACTACT 57.360 39.130 12.05 17.25 41.68 2.57
53 54 7.149569 TCTTTAGTGAAAGCGCTACTACTAA 57.850 36.000 24.45 24.45 41.68 2.24
54 55 7.249147 TCTTTAGTGAAAGCGCTACTACTAAG 58.751 38.462 25.65 21.46 41.68 2.18
55 56 6.506500 TTAGTGAAAGCGCTACTACTAAGT 57.493 37.500 24.45 9.61 36.88 2.24
56 57 4.984205 AGTGAAAGCGCTACTACTAAGTC 58.016 43.478 12.05 0.00 37.15 3.01
57 58 3.784994 GTGAAAGCGCTACTACTAAGTCG 59.215 47.826 12.05 0.00 37.15 4.18
58 59 3.686241 TGAAAGCGCTACTACTAAGTCGA 59.314 43.478 12.05 0.00 37.15 4.20
59 60 4.334759 TGAAAGCGCTACTACTAAGTCGAT 59.665 41.667 12.05 0.00 37.15 3.59
61 62 6.204301 TGAAAGCGCTACTACTAAGTCGATAT 59.796 38.462 12.05 0.00 37.15 1.63
63 64 6.890663 AGCGCTACTACTAAGTCGATATAG 57.109 41.667 8.99 6.04 37.15 1.31
66 67 6.698107 CGCTACTACTAAGTCGATATAGCAG 58.302 44.000 7.21 6.71 37.15 4.24
67 68 6.310956 CGCTACTACTAAGTCGATATAGCAGT 59.689 42.308 14.23 14.23 37.15 4.40
68 69 7.487509 CGCTACTACTAAGTCGATATAGCAGTA 59.512 40.741 14.72 14.72 37.15 2.74
69 70 8.810427 GCTACTACTAAGTCGATATAGCAGTAG 58.190 40.741 25.56 25.56 43.15 2.57
70 71 7.599630 ACTACTAAGTCGATATAGCAGTAGC 57.400 40.000 10.66 0.00 38.23 3.58
71 72 7.487509 TACTACTAAGTCGATATAGCAGTAGCG 59.512 40.741 12.81 0.36 40.65 4.26
84 85 2.603560 GCAGTAGCGTGGATTAACAGAC 59.396 50.000 0.00 0.00 0.00 3.51
85 86 2.852413 CAGTAGCGTGGATTAACAGACG 59.148 50.000 0.00 0.00 34.93 4.18
90 91 3.146618 CGTGGATTAACAGACGCTACT 57.853 47.619 0.00 0.00 0.00 2.57
92 93 2.603560 GTGGATTAACAGACGCTACTGC 59.396 50.000 6.87 0.00 41.06 4.40
93 94 2.496070 TGGATTAACAGACGCTACTGCT 59.504 45.455 6.87 0.00 41.06 4.24
94 95 3.697542 TGGATTAACAGACGCTACTGCTA 59.302 43.478 6.87 0.00 41.06 3.49
95 96 4.158949 TGGATTAACAGACGCTACTGCTAA 59.841 41.667 6.87 6.24 41.06 3.09
96 97 4.503370 GGATTAACAGACGCTACTGCTAAC 59.497 45.833 6.87 2.61 41.06 2.34
97 98 2.365408 AACAGACGCTACTGCTAACC 57.635 50.000 6.87 0.00 41.06 2.85
98 99 1.546961 ACAGACGCTACTGCTAACCT 58.453 50.000 6.87 0.00 41.06 3.50
99 100 1.893801 ACAGACGCTACTGCTAACCTT 59.106 47.619 6.87 0.00 41.06 3.50
101 102 3.508793 ACAGACGCTACTGCTAACCTTTA 59.491 43.478 6.87 0.00 41.06 1.85
103 104 2.858941 GACGCTACTGCTAACCTTTAGC 59.141 50.000 10.42 10.42 40.76 3.09
104 105 2.496470 ACGCTACTGCTAACCTTTAGCT 59.504 45.455 16.71 0.00 40.95 3.32
105 106 2.860735 CGCTACTGCTAACCTTTAGCTG 59.139 50.000 18.11 18.11 42.67 4.24
107 108 4.439700 CGCTACTGCTAACCTTTAGCTGTA 60.440 45.833 24.39 24.39 46.16 2.74
110 111 3.676324 ACTGCTAACCTTTAGCTGTAGCG 60.676 47.826 21.85 7.09 46.16 4.26
111 112 7.894505 TACTGCTAACCTTTAGCTGTAGCGC 62.895 48.000 23.18 0.00 46.16 5.92
122 123 3.270962 GCTGTAGCGCCTTACTAGTAG 57.729 52.381 2.29 0.00 0.00 2.57
123 124 2.605097 GCTGTAGCGCCTTACTAGTAGC 60.605 54.545 2.29 2.45 0.00 3.58
126 127 4.630097 CGCCTTACTAGTAGCGCC 57.370 61.111 19.57 3.57 42.31 6.53
128 129 1.732308 GCCTTACTAGTAGCGCCGT 59.268 57.895 2.29 0.00 0.00 5.68
129 130 0.947244 GCCTTACTAGTAGCGCCGTA 59.053 55.000 2.29 0.00 0.00 4.02
131 132 1.265365 CCTTACTAGTAGCGCCGTACC 59.735 57.143 2.29 0.00 0.00 3.34
132 133 1.265365 CTTACTAGTAGCGCCGTACCC 59.735 57.143 2.29 0.00 0.00 3.69
134 135 1.099879 ACTAGTAGCGCCGTACCCAG 61.100 60.000 2.29 4.25 0.00 4.45
135 136 2.403671 CTAGTAGCGCCGTACCCAGC 62.404 65.000 2.29 0.00 0.00 4.85
141 142 3.834799 GCCGTACCCAGCGCTACT 61.835 66.667 10.99 0.00 0.00 2.57
142 143 2.104331 CCGTACCCAGCGCTACTG 59.896 66.667 10.99 3.67 46.77 2.74
155 156 4.499183 AGCGCTACTGATAGGCATTATTC 58.501 43.478 8.99 0.00 30.92 1.75
156 157 3.619038 GCGCTACTGATAGGCATTATTCC 59.381 47.826 0.00 0.00 0.00 3.01
157 158 4.184629 CGCTACTGATAGGCATTATTCCC 58.815 47.826 0.00 0.00 0.00 3.97
160 161 2.002586 CTGATAGGCATTATTCCCGCG 58.997 52.381 0.00 0.00 0.00 6.46
162 163 0.324943 ATAGGCATTATTCCCGCGCT 59.675 50.000 5.56 0.00 0.00 5.92
163 164 0.970640 TAGGCATTATTCCCGCGCTA 59.029 50.000 5.56 0.00 0.00 4.26
164 165 0.602905 AGGCATTATTCCCGCGCTAC 60.603 55.000 5.56 0.00 0.00 3.58
165 166 0.602905 GGCATTATTCCCGCGCTACT 60.603 55.000 5.56 0.00 0.00 2.57
166 167 0.512952 GCATTATTCCCGCGCTACTG 59.487 55.000 5.56 0.00 0.00 2.74
168 169 0.393077 ATTATTCCCGCGCTACTGCT 59.607 50.000 5.56 0.00 36.97 4.24
170 171 0.596577 TATTCCCGCGCTACTGCTAG 59.403 55.000 5.56 0.00 36.97 3.42
173 174 3.528370 CCGCGCTACTGCTAGGGT 61.528 66.667 5.56 0.00 35.73 4.34
174 175 2.494918 CGCGCTACTGCTAGGGTT 59.505 61.111 5.56 0.00 35.73 4.11
175 176 1.153628 CGCGCTACTGCTAGGGTTT 60.154 57.895 5.56 0.00 35.73 3.27
176 177 0.739813 CGCGCTACTGCTAGGGTTTT 60.740 55.000 5.56 0.00 35.73 2.43
177 178 1.007580 GCGCTACTGCTAGGGTTTTC 58.992 55.000 0.00 0.00 35.73 2.29
178 179 1.653151 CGCTACTGCTAGGGTTTTCC 58.347 55.000 0.00 0.00 36.97 3.13
196 197 8.709272 GGTTTTCCCTAGTAGTGTAGATAGAT 57.291 38.462 0.00 0.00 0.00 1.98
197 198 8.795513 GGTTTTCCCTAGTAGTGTAGATAGATC 58.204 40.741 0.00 0.00 0.00 2.75
200 201 9.575868 TTTCCCTAGTAGTGTAGATAGATCTTG 57.424 37.037 0.00 0.00 38.32 3.02
201 202 8.277720 TCCCTAGTAGTGTAGATAGATCTTGT 57.722 38.462 0.00 0.00 38.32 3.16
202 203 8.158132 TCCCTAGTAGTGTAGATAGATCTTGTG 58.842 40.741 0.00 0.00 38.32 3.33
203 204 7.940137 CCCTAGTAGTGTAGATAGATCTTGTGT 59.060 40.741 0.00 0.00 38.32 3.72
204 205 8.779303 CCTAGTAGTGTAGATAGATCTTGTGTG 58.221 40.741 0.00 0.00 38.32 3.82
205 206 9.549078 CTAGTAGTGTAGATAGATCTTGTGTGA 57.451 37.037 0.00 0.00 38.32 3.58
206 207 8.988546 AGTAGTGTAGATAGATCTTGTGTGAT 57.011 34.615 0.00 0.00 38.32 3.06
207 208 9.415008 AGTAGTGTAGATAGATCTTGTGTGATT 57.585 33.333 0.00 0.00 38.32 2.57
208 209 9.457110 GTAGTGTAGATAGATCTTGTGTGATTG 57.543 37.037 0.00 0.00 38.32 2.67
209 210 8.072321 AGTGTAGATAGATCTTGTGTGATTGT 57.928 34.615 0.00 0.00 38.32 2.71
210 211 9.190317 AGTGTAGATAGATCTTGTGTGATTGTA 57.810 33.333 0.00 0.00 38.32 2.41
211 212 9.457110 GTGTAGATAGATCTTGTGTGATTGTAG 57.543 37.037 0.00 0.00 38.32 2.74
212 213 8.633561 TGTAGATAGATCTTGTGTGATTGTAGG 58.366 37.037 0.00 0.00 38.32 3.18
213 214 7.904558 AGATAGATCTTGTGTGATTGTAGGA 57.095 36.000 0.00 0.00 31.97 2.94
216 217 9.553064 GATAGATCTTGTGTGATTGTAGGAATT 57.447 33.333 0.00 0.00 0.00 2.17
217 218 7.621428 AGATCTTGTGTGATTGTAGGAATTG 57.379 36.000 0.00 0.00 0.00 2.32
218 219 7.170965 AGATCTTGTGTGATTGTAGGAATTGT 58.829 34.615 0.00 0.00 0.00 2.71
219 220 7.667219 AGATCTTGTGTGATTGTAGGAATTGTT 59.333 33.333 0.00 0.00 0.00 2.83
220 221 7.581213 TCTTGTGTGATTGTAGGAATTGTTT 57.419 32.000 0.00 0.00 0.00 2.83
221 222 8.006298 TCTTGTGTGATTGTAGGAATTGTTTT 57.994 30.769 0.00 0.00 0.00 2.43
222 223 8.474025 TCTTGTGTGATTGTAGGAATTGTTTTT 58.526 29.630 0.00 0.00 0.00 1.94
223 224 8.417780 TTGTGTGATTGTAGGAATTGTTTTTG 57.582 30.769 0.00 0.00 0.00 2.44
224 225 7.776107 TGTGTGATTGTAGGAATTGTTTTTGA 58.224 30.769 0.00 0.00 0.00 2.69
225 226 8.253810 TGTGTGATTGTAGGAATTGTTTTTGAA 58.746 29.630 0.00 0.00 0.00 2.69
226 227 9.092876 GTGTGATTGTAGGAATTGTTTTTGAAA 57.907 29.630 0.00 0.00 0.00 2.69
236 237 9.665719 AGGAATTGTTTTTGAAATTACTGTGTT 57.334 25.926 0.00 0.00 35.94 3.32
237 238 9.914923 GGAATTGTTTTTGAAATTACTGTGTTC 57.085 29.630 0.00 0.00 0.00 3.18
238 239 9.914923 GAATTGTTTTTGAAATTACTGTGTTCC 57.085 29.630 0.00 0.00 0.00 3.62
239 240 7.835634 TTGTTTTTGAAATTACTGTGTTCCC 57.164 32.000 0.00 0.00 0.00 3.97
241 242 6.070767 TGTTTTTGAAATTACTGTGTTCCCCA 60.071 34.615 0.00 0.00 0.00 4.96
242 243 6.546428 TTTTGAAATTACTGTGTTCCCCAA 57.454 33.333 0.00 0.00 0.00 4.12
243 244 5.523438 TTGAAATTACTGTGTTCCCCAAC 57.477 39.130 0.00 0.00 0.00 3.77
245 246 4.956700 TGAAATTACTGTGTTCCCCAACAA 59.043 37.500 0.00 0.00 44.32 2.83
274 493 6.348132 CGTGTAGCAAACTCCACATAAATCAA 60.348 38.462 0.00 0.00 32.52 2.57
286 505 7.410174 TCCACATAAATCAAATGTTCTAGGGT 58.590 34.615 0.00 0.00 35.39 4.34
312 531 3.374745 AGCAAAAGTGATGAAAAGCACG 58.625 40.909 0.00 0.00 39.88 5.34
340 567 6.627087 ATCAGTTTTGTCATCTTCTAGGGA 57.373 37.500 0.00 0.00 0.00 4.20
354 581 6.728411 TCTTCTAGGGATAGCGTTGGATATA 58.272 40.000 0.00 0.00 0.00 0.86
365 592 2.789339 CGTTGGATATACAGCAGTGTCG 59.211 50.000 2.44 0.00 38.19 4.35
424 1103 2.978010 CACACCCCACGGCAAGTC 60.978 66.667 0.00 0.00 0.00 3.01
496 1176 7.864379 TCTTTTCTAGTTAGGACTTTACACACG 59.136 37.037 0.00 0.00 37.33 4.49
532 1214 7.033791 TCTCAAGCTTGGAATTTAGTACTACG 58.966 38.462 25.73 0.00 0.00 3.51
539 1221 5.413499 TGGAATTTAGTACTACGAACCAGC 58.587 41.667 0.91 0.00 0.00 4.85
546 1228 0.033504 ACTACGAACCAGCTGTGTGG 59.966 55.000 13.81 9.80 44.01 4.17
547 1229 1.291877 CTACGAACCAGCTGTGTGGC 61.292 60.000 13.81 5.82 41.90 5.01
565 1247 3.004734 GTGGCGCAAATCCTAATTATGCT 59.995 43.478 10.83 0.00 34.93 3.79
672 1354 8.402472 TCAGTTGTGTGATTTTAAGAAAACGAT 58.598 29.630 0.00 0.00 32.37 3.73
796 1478 1.070134 AGCGCCACACTAACTTGAGAA 59.930 47.619 2.29 0.00 0.00 2.87
971 1691 3.181418 ACAACACTTCCCATTCATCCCTT 60.181 43.478 0.00 0.00 0.00 3.95
1009 1729 0.112412 AAAGCCCAACGAACCTCCAT 59.888 50.000 0.00 0.00 0.00 3.41
1012 1732 1.991230 CCCAACGAACCTCCATCCT 59.009 57.895 0.00 0.00 0.00 3.24
1142 1868 0.035152 ACAATGCCGCATTCTCTCCA 60.035 50.000 15.85 0.00 31.05 3.86
1163 1889 2.441348 TCCCTCCATGTCGCGCTA 60.441 61.111 5.56 0.00 0.00 4.26
1484 2227 0.671796 ACGGCAAGGTTTTTACCAGC 59.328 50.000 0.00 0.00 33.96 4.85
1781 6225 7.036829 CGGTTGGTTGGGTAAAATAAAATAGG 58.963 38.462 0.00 0.00 0.00 2.57
2043 6887 1.204704 TCTGTATGTGCTGAACTCCCG 59.795 52.381 0.00 0.00 0.00 5.14
2114 7090 9.616634 AATCATTTTCGTATGCACATATGATTC 57.383 29.630 10.38 0.00 38.63 2.52
2140 7118 2.852413 CTGTCATCCGTCGTTGTATGTC 59.148 50.000 0.00 0.00 0.00 3.06
2416 7412 2.930826 TCAAAGATATTCTCCCCGCC 57.069 50.000 0.00 0.00 0.00 6.13
2502 7498 2.813779 GATCAGTTTGATCCACGTGC 57.186 50.000 10.91 0.00 45.66 5.34
2507 7503 1.333619 AGTTTGATCCACGTGCAACAC 59.666 47.619 10.91 9.91 35.74 3.32
2516 7512 1.998257 CGTGCAACACAAAGCGACG 60.998 57.895 0.00 0.00 35.74 5.12
2608 7607 3.063510 TCTTCTGATGGCTTGAAGGTG 57.936 47.619 0.00 0.00 38.10 4.00
2668 7667 5.355596 CAGTTCTCCATGTACATCCTTCTC 58.644 45.833 5.07 0.00 0.00 2.87
2923 7922 7.555554 CAGAACCTCTACATCTCATCCATTTTT 59.444 37.037 0.00 0.00 0.00 1.94
3033 8035 2.418746 CCTCGGTCTTGGATTTCATCGT 60.419 50.000 0.00 0.00 0.00 3.73
3254 8262 8.481314 TCTATGCTTCTGATGAATTCTACACTT 58.519 33.333 7.05 0.00 0.00 3.16
3267 8275 5.878332 TTCTACACTTGTATGTTGGCATG 57.122 39.130 0.00 0.00 36.58 4.06
3287 8295 7.939039 TGGCATGTTATTTTTGTGGGAATTTTA 59.061 29.630 0.00 0.00 0.00 1.52
3332 8360 3.585289 TGACCCAAAATACTAGACCTGCA 59.415 43.478 0.00 0.00 0.00 4.41
3335 8363 3.378427 CCCAAAATACTAGACCTGCAAGC 59.622 47.826 0.00 0.00 0.00 4.01
3348 8376 1.379576 GCAAGCTTGGGAGGCAGAT 60.380 57.895 27.10 0.00 0.00 2.90
3350 8378 0.323178 CAAGCTTGGGAGGCAGATGT 60.323 55.000 19.14 0.00 0.00 3.06
3376 8404 6.034898 GGTTCAACACACTCATTTTGACTTTG 59.965 38.462 0.00 0.00 0.00 2.77
3377 8405 6.266168 TCAACACACTCATTTTGACTTTGT 57.734 33.333 0.00 0.00 0.00 2.83
3378 8406 6.686630 TCAACACACTCATTTTGACTTTGTT 58.313 32.000 0.00 0.00 0.00 2.83
3379 8407 7.151308 TCAACACACTCATTTTGACTTTGTTT 58.849 30.769 0.00 0.00 0.00 2.83
3380 8408 7.655328 TCAACACACTCATTTTGACTTTGTTTT 59.345 29.630 0.00 0.00 0.00 2.43
3381 8409 7.961325 ACACACTCATTTTGACTTTGTTTTT 57.039 28.000 0.00 0.00 0.00 1.94
3382 8410 7.795859 ACACACTCATTTTGACTTTGTTTTTG 58.204 30.769 0.00 0.00 0.00 2.44
3445 8474 6.901357 GTCAAAGTCAAAACACATGAAATTGC 59.099 34.615 0.00 0.00 30.60 3.56
3557 8590 4.648762 TCCACCTTTTCTTTGCTCAATTCA 59.351 37.500 0.00 0.00 0.00 2.57
3558 8591 5.305128 TCCACCTTTTCTTTGCTCAATTCAT 59.695 36.000 0.00 0.00 0.00 2.57
3559 8592 5.993441 CCACCTTTTCTTTGCTCAATTCATT 59.007 36.000 0.00 0.00 0.00 2.57
3560 8593 6.073440 CCACCTTTTCTTTGCTCAATTCATTG 60.073 38.462 0.00 0.00 39.10 2.82
3561 8594 6.702723 CACCTTTTCTTTGCTCAATTCATTGA 59.297 34.615 2.29 2.29 43.94 2.57
3562 8595 7.225145 CACCTTTTCTTTGCTCAATTCATTGAA 59.775 33.333 0.75 0.75 45.26 2.69
3563 8596 7.225341 ACCTTTTCTTTGCTCAATTCATTGAAC 59.775 33.333 0.15 0.40 45.26 3.18
3564 8597 7.307573 CCTTTTCTTTGCTCAATTCATTGAACC 60.308 37.037 0.15 0.00 45.26 3.62
3565 8598 5.787953 TCTTTGCTCAATTCATTGAACCA 57.212 34.783 0.15 2.05 45.26 3.67
3566 8599 6.159299 TCTTTGCTCAATTCATTGAACCAA 57.841 33.333 0.15 7.24 45.26 3.67
3567 8600 6.580788 TCTTTGCTCAATTCATTGAACCAAA 58.419 32.000 17.99 17.99 45.26 3.28
3568 8601 7.218614 TCTTTGCTCAATTCATTGAACCAAAT 58.781 30.769 18.70 0.00 45.26 2.32
3569 8602 8.366401 TCTTTGCTCAATTCATTGAACCAAATA 58.634 29.630 18.70 13.40 45.26 1.40
3570 8603 7.887996 TTGCTCAATTCATTGAACCAAATAC 57.112 32.000 0.15 0.00 45.26 1.89
3571 8604 6.990798 TGCTCAATTCATTGAACCAAATACA 58.009 32.000 0.15 0.00 45.26 2.29
3572 8605 7.613585 TGCTCAATTCATTGAACCAAATACAT 58.386 30.769 0.15 0.00 45.26 2.29
3573 8606 8.095792 TGCTCAATTCATTGAACCAAATACATT 58.904 29.630 0.15 0.00 45.26 2.71
3574 8607 8.938906 GCTCAATTCATTGAACCAAATACATTT 58.061 29.630 0.15 0.00 45.26 2.32
3605 8638 9.394477 GAGACAAACTGAACCAAATACATAAAC 57.606 33.333 0.00 0.00 0.00 2.01
3684 8742 0.036306 ACTGAACCACCAATCGTCCC 59.964 55.000 0.00 0.00 0.00 4.46
3727 8785 1.693062 CAGCTGCTGATAGGAGTGGAT 59.307 52.381 24.88 0.00 35.94 3.41
3733 8791 3.713248 TGCTGATAGGAGTGGATGTCAAT 59.287 43.478 0.00 0.00 0.00 2.57
3734 8792 4.063689 GCTGATAGGAGTGGATGTCAATG 58.936 47.826 0.00 0.00 0.00 2.82
3805 8863 0.593128 GCTGTGGGTTGCTGTACAAG 59.407 55.000 0.00 0.00 39.50 3.16
3835 8896 1.471676 CGAAGCTCGTCCTAAGCCAAT 60.472 52.381 0.00 0.00 40.75 3.16
3881 8942 2.545532 CCACCAGCAGAGATTCGAGATC 60.546 54.545 0.00 0.00 0.00 2.75
3908 8969 1.811965 TCCACACAGCATACAACATGC 59.188 47.619 0.95 0.95 44.85 4.06
3928 8989 2.030893 GCAAACACAGAGCATAAGCACA 60.031 45.455 0.00 0.00 45.49 4.57
3929 8990 3.550639 GCAAACACAGAGCATAAGCACAA 60.551 43.478 0.00 0.00 45.49 3.33
3930 8991 4.609947 CAAACACAGAGCATAAGCACAAA 58.390 39.130 0.00 0.00 45.49 2.83
3933 8994 3.822735 ACACAGAGCATAAGCACAAATGT 59.177 39.130 0.00 0.00 45.49 2.71
3934 8995 4.279169 ACACAGAGCATAAGCACAAATGTT 59.721 37.500 0.00 0.00 45.49 2.71
3935 8996 5.473162 ACACAGAGCATAAGCACAAATGTTA 59.527 36.000 0.00 0.00 45.49 2.41
3936 8997 5.796935 CACAGAGCATAAGCACAAATGTTAC 59.203 40.000 0.00 0.00 45.49 2.50
3937 8998 5.106157 ACAGAGCATAAGCACAAATGTTACC 60.106 40.000 0.00 0.00 45.49 2.85
3938 8999 4.399303 AGAGCATAAGCACAAATGTTACCC 59.601 41.667 0.00 0.00 45.49 3.69
3940 9001 4.526262 AGCATAAGCACAAATGTTACCCAA 59.474 37.500 0.00 0.00 45.49 4.12
3941 9002 4.864247 GCATAAGCACAAATGTTACCCAAG 59.136 41.667 0.00 0.00 41.58 3.61
3943 9004 4.853924 AAGCACAAATGTTACCCAAGAG 57.146 40.909 0.00 0.00 0.00 2.85
3960 10144 4.380233 CCAAGAGACCAATCAGTTGAATGC 60.380 45.833 0.00 0.00 37.53 3.56
3962 10146 4.597004 AGAGACCAATCAGTTGAATGCAT 58.403 39.130 0.00 0.00 37.53 3.96
3965 10149 4.954202 AGACCAATCAGTTGAATGCATGAT 59.046 37.500 0.00 0.00 37.53 2.45
3966 10150 5.067413 AGACCAATCAGTTGAATGCATGATC 59.933 40.000 0.00 0.00 37.53 2.92
4004 10222 2.025981 TGCCACTGCCTTATTCATGAGT 60.026 45.455 0.00 0.00 36.33 3.41
4043 10338 7.573710 TGCTTGTCCTACAATTATTCAGGTAT 58.426 34.615 3.04 0.00 37.48 2.73
4075 10370 9.406828 GAAGTTACCAAACTGGACAAATAAATC 57.593 33.333 0.00 0.00 45.37 2.17
4080 10375 6.098982 ACCAAACTGGACAAATAAATCAACCA 59.901 34.615 0.00 0.00 40.96 3.67
4105 10400 5.005740 TCCTACAAGTCTACTTCGCAGTTA 58.994 41.667 0.00 0.00 34.06 2.24
4107 10402 5.572126 CCTACAAGTCTACTTCGCAGTTAAC 59.428 44.000 0.00 0.00 34.06 2.01
4129 10424 1.004044 AGAACATGCTTGCTGCCTACT 59.996 47.619 0.00 0.00 42.00 2.57
4130 10425 2.237143 AGAACATGCTTGCTGCCTACTA 59.763 45.455 0.00 0.00 42.00 1.82
4136 10431 2.093973 TGCTTGCTGCCTACTAGAAGAC 60.094 50.000 0.00 0.00 42.00 3.01
4194 10489 0.254747 CCCAGCAACCCGAATAGGAA 59.745 55.000 0.00 0.00 45.00 3.36
4217 10512 4.400884 ACTCTAGATACCTGCAGAACAGTG 59.599 45.833 17.39 0.00 45.68 3.66
4238 10533 5.811613 AGTGTCATTTGTCAAACCAATTGTG 59.188 36.000 4.43 0.00 40.11 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.818642 AGAGCGCTACTGGTAATTAATAGTAG 58.181 38.462 11.50 21.76 43.32 2.57
7 8 7.756395 AGAGCGCTACTGGTAATTAATAGTA 57.244 36.000 11.50 8.82 0.00 1.82
8 9 6.651975 AGAGCGCTACTGGTAATTAATAGT 57.348 37.500 11.50 7.71 0.00 2.12
9 10 7.948278 AAAGAGCGCTACTGGTAATTAATAG 57.052 36.000 11.50 0.00 0.00 1.73
10 11 8.636213 ACTAAAGAGCGCTACTGGTAATTAATA 58.364 33.333 11.50 0.00 0.00 0.98
11 12 7.438459 CACTAAAGAGCGCTACTGGTAATTAAT 59.562 37.037 11.50 0.00 0.00 1.40
12 13 6.755141 CACTAAAGAGCGCTACTGGTAATTAA 59.245 38.462 11.50 0.00 0.00 1.40
13 14 6.095860 TCACTAAAGAGCGCTACTGGTAATTA 59.904 38.462 11.50 4.16 0.00 1.40
15 16 4.401519 TCACTAAAGAGCGCTACTGGTAAT 59.598 41.667 11.50 0.00 0.00 1.89
16 17 3.760151 TCACTAAAGAGCGCTACTGGTAA 59.240 43.478 11.50 0.00 0.00 2.85
17 18 3.349927 TCACTAAAGAGCGCTACTGGTA 58.650 45.455 11.50 5.31 0.00 3.25
18 19 2.168496 TCACTAAAGAGCGCTACTGGT 58.832 47.619 11.50 2.54 0.00 4.00
19 20 2.941453 TCACTAAAGAGCGCTACTGG 57.059 50.000 11.50 1.79 0.00 4.00
22 23 2.028165 CGCTTTCACTAAAGAGCGCTAC 59.972 50.000 11.50 4.00 44.14 3.58
23 24 2.259618 CGCTTTCACTAAAGAGCGCTA 58.740 47.619 11.50 0.00 44.14 4.26
25 26 3.569957 CGCTTTCACTAAAGAGCGC 57.430 52.632 0.00 0.00 44.14 5.92
28 29 5.642686 AGTAGTAGCGCTTTCACTAAAGAG 58.357 41.667 18.68 0.09 44.14 2.85
29 30 5.640189 AGTAGTAGCGCTTTCACTAAAGA 57.360 39.130 18.68 0.00 44.14 2.52
30 31 7.028361 ACTTAGTAGTAGCGCTTTCACTAAAG 58.972 38.462 24.92 22.23 38.03 1.85
32 33 6.506500 ACTTAGTAGTAGCGCTTTCACTAA 57.493 37.500 18.68 22.52 31.21 2.24
34 35 4.437121 CGACTTAGTAGTAGCGCTTTCACT 60.437 45.833 18.68 16.54 33.84 3.41
35 36 3.784994 CGACTTAGTAGTAGCGCTTTCAC 59.215 47.826 18.68 8.24 33.84 3.18
37 38 4.270178 TCGACTTAGTAGTAGCGCTTTC 57.730 45.455 18.68 9.96 33.84 2.62
38 39 4.897025 ATCGACTTAGTAGTAGCGCTTT 57.103 40.909 18.68 7.38 33.84 3.51
39 40 6.183360 GCTATATCGACTTAGTAGTAGCGCTT 60.183 42.308 18.68 0.00 33.84 4.68
40 41 5.291614 GCTATATCGACTTAGTAGTAGCGCT 59.708 44.000 17.26 17.26 33.84 5.92
42 43 6.310956 ACTGCTATATCGACTTAGTAGTAGCG 59.689 42.308 19.14 9.49 38.90 4.26
43 44 7.599630 ACTGCTATATCGACTTAGTAGTAGC 57.400 40.000 19.14 10.78 38.90 3.58
47 48 6.310956 ACGCTACTGCTATATCGACTTAGTAG 59.689 42.308 15.53 15.53 39.21 2.57
48 49 6.090493 CACGCTACTGCTATATCGACTTAGTA 59.910 42.308 0.00 0.00 36.97 1.82
50 51 5.317559 CACGCTACTGCTATATCGACTTAG 58.682 45.833 0.00 0.00 36.97 2.18
51 52 4.153655 CCACGCTACTGCTATATCGACTTA 59.846 45.833 0.00 0.00 36.97 2.24
53 54 2.484651 CCACGCTACTGCTATATCGACT 59.515 50.000 0.00 0.00 36.97 4.18
54 55 2.483106 TCCACGCTACTGCTATATCGAC 59.517 50.000 0.00 0.00 36.97 4.20
55 56 2.774687 TCCACGCTACTGCTATATCGA 58.225 47.619 0.00 0.00 36.97 3.59
56 57 3.766676 ATCCACGCTACTGCTATATCG 57.233 47.619 0.00 0.00 36.97 2.92
57 58 6.387465 TGTTAATCCACGCTACTGCTATATC 58.613 40.000 0.00 0.00 36.97 1.63
58 59 6.208797 TCTGTTAATCCACGCTACTGCTATAT 59.791 38.462 0.00 0.00 36.97 0.86
59 60 5.533528 TCTGTTAATCCACGCTACTGCTATA 59.466 40.000 0.00 0.00 36.97 1.31
61 62 3.697542 TCTGTTAATCCACGCTACTGCTA 59.302 43.478 0.00 0.00 36.97 3.49
63 64 2.603560 GTCTGTTAATCCACGCTACTGC 59.396 50.000 0.00 0.00 0.00 4.40
70 71 2.852413 CAGTAGCGTCTGTTAATCCACG 59.148 50.000 3.60 0.00 35.32 4.94
71 72 2.603560 GCAGTAGCGTCTGTTAATCCAC 59.396 50.000 11.53 0.00 37.70 4.02
72 73 2.888594 GCAGTAGCGTCTGTTAATCCA 58.111 47.619 11.53 0.00 37.70 3.41
84 85 6.238416 CTACAGCTAAAGGTTAGCAGTAGCG 61.238 48.000 26.08 13.98 46.14 4.26
85 86 3.863041 ACAGCTAAAGGTTAGCAGTAGC 58.137 45.455 19.26 7.87 42.68 3.58
88 89 3.676324 CGCTACAGCTAAAGGTTAGCAGT 60.676 47.826 19.26 18.71 42.68 4.40
89 90 2.860735 CGCTACAGCTAAAGGTTAGCAG 59.139 50.000 19.26 14.60 42.68 4.24
90 91 2.888594 CGCTACAGCTAAAGGTTAGCA 58.111 47.619 19.26 1.60 42.68 3.49
92 93 2.159085 AGGCGCTACAGCTAAAGGTTAG 60.159 50.000 7.64 0.00 39.32 2.34
93 94 1.829222 AGGCGCTACAGCTAAAGGTTA 59.171 47.619 7.64 0.00 39.32 2.85
94 95 0.613777 AGGCGCTACAGCTAAAGGTT 59.386 50.000 7.64 0.00 39.32 3.50
95 96 0.613777 AAGGCGCTACAGCTAAAGGT 59.386 50.000 7.64 0.00 39.32 3.50
96 97 2.159085 AGTAAGGCGCTACAGCTAAAGG 60.159 50.000 7.64 0.00 39.32 3.11
97 98 3.166489 AGTAAGGCGCTACAGCTAAAG 57.834 47.619 7.64 0.00 39.32 1.85
98 99 3.698040 ACTAGTAAGGCGCTACAGCTAAA 59.302 43.478 7.64 0.00 39.32 1.85
99 100 3.285484 ACTAGTAAGGCGCTACAGCTAA 58.715 45.455 7.64 0.00 39.32 3.09
101 102 1.765230 ACTAGTAAGGCGCTACAGCT 58.235 50.000 7.64 2.26 39.32 4.24
103 104 2.349627 CGCTACTAGTAAGGCGCTACAG 60.350 54.545 19.57 6.11 41.08 2.74
104 105 1.600957 CGCTACTAGTAAGGCGCTACA 59.399 52.381 19.57 0.00 41.08 2.74
105 106 2.313004 CGCTACTAGTAAGGCGCTAC 57.687 55.000 19.57 2.47 41.08 3.58
110 111 0.947244 TACGGCGCTACTAGTAAGGC 59.053 55.000 6.90 16.71 0.00 4.35
111 112 1.265365 GGTACGGCGCTACTAGTAAGG 59.735 57.143 6.90 0.00 0.00 2.69
113 114 1.308998 GGGTACGGCGCTACTAGTAA 58.691 55.000 6.90 0.00 0.00 2.24
114 115 0.180171 TGGGTACGGCGCTACTAGTA 59.820 55.000 6.90 1.89 0.00 1.82
115 116 1.077501 TGGGTACGGCGCTACTAGT 60.078 57.895 6.90 0.00 0.00 2.57
116 117 1.653115 CTGGGTACGGCGCTACTAG 59.347 63.158 6.90 0.00 0.00 2.57
118 119 3.834799 GCTGGGTACGGCGCTACT 61.835 66.667 6.90 0.00 39.57 2.57
128 129 1.617322 CCTATCAGTAGCGCTGGGTA 58.383 55.000 22.90 9.22 45.08 3.69
129 130 1.749334 GCCTATCAGTAGCGCTGGGT 61.749 60.000 22.90 8.44 45.08 4.51
131 132 0.319728 ATGCCTATCAGTAGCGCTGG 59.680 55.000 22.90 12.12 45.08 4.85
132 133 2.160822 AATGCCTATCAGTAGCGCTG 57.839 50.000 22.90 4.05 46.34 5.18
134 135 3.619038 GGAATAATGCCTATCAGTAGCGC 59.381 47.826 0.00 0.00 0.00 5.92
135 136 4.184629 GGGAATAATGCCTATCAGTAGCG 58.815 47.826 0.00 0.00 33.47 4.26
136 137 4.184629 CGGGAATAATGCCTATCAGTAGC 58.815 47.826 0.00 0.00 34.24 3.58
137 138 4.184629 GCGGGAATAATGCCTATCAGTAG 58.815 47.826 0.00 0.00 34.24 2.57
139 140 2.612972 CGCGGGAATAATGCCTATCAGT 60.613 50.000 0.00 0.00 34.24 3.41
140 141 2.002586 CGCGGGAATAATGCCTATCAG 58.997 52.381 0.00 0.00 34.24 2.90
141 142 1.943968 GCGCGGGAATAATGCCTATCA 60.944 52.381 8.83 0.00 34.24 2.15
142 143 0.727398 GCGCGGGAATAATGCCTATC 59.273 55.000 8.83 0.00 34.24 2.08
143 144 0.324943 AGCGCGGGAATAATGCCTAT 59.675 50.000 8.83 0.00 34.24 2.57
144 145 0.970640 TAGCGCGGGAATAATGCCTA 59.029 50.000 8.83 0.00 34.24 3.93
145 146 0.602905 GTAGCGCGGGAATAATGCCT 60.603 55.000 8.83 0.00 34.24 4.75
146 147 0.602905 AGTAGCGCGGGAATAATGCC 60.603 55.000 8.83 0.00 0.00 4.40
147 148 0.512952 CAGTAGCGCGGGAATAATGC 59.487 55.000 8.83 0.00 0.00 3.56
150 151 4.431035 GCAGTAGCGCGGGAATAA 57.569 55.556 8.83 0.00 0.00 1.40
160 161 1.560146 AGGGAAAACCCTAGCAGTAGC 59.440 52.381 5.97 0.00 41.63 3.58
168 169 6.407320 TCTACACTACTAGGGAAAACCCTA 57.593 41.667 13.44 13.44 41.63 3.53
170 171 7.065504 TCTATCTACACTACTAGGGAAAACCC 58.934 42.308 0.00 0.00 41.63 4.11
174 175 9.575868 CAAGATCTATCTACACTACTAGGGAAA 57.424 37.037 0.00 0.00 35.76 3.13
175 176 8.725256 ACAAGATCTATCTACACTACTAGGGAA 58.275 37.037 0.00 0.00 35.76 3.97
176 177 8.158132 CACAAGATCTATCTACACTACTAGGGA 58.842 40.741 0.00 0.00 35.76 4.20
177 178 7.940137 ACACAAGATCTATCTACACTACTAGGG 59.060 40.741 0.00 0.00 35.76 3.53
178 179 8.779303 CACACAAGATCTATCTACACTACTAGG 58.221 40.741 0.00 0.00 35.76 3.02
179 180 9.549078 TCACACAAGATCTATCTACACTACTAG 57.451 37.037 0.00 0.00 35.76 2.57
181 182 8.988546 ATCACACAAGATCTATCTACACTACT 57.011 34.615 0.00 0.00 35.76 2.57
182 183 9.457110 CAATCACACAAGATCTATCTACACTAC 57.543 37.037 0.00 0.00 35.76 2.73
183 184 9.190317 ACAATCACACAAGATCTATCTACACTA 57.810 33.333 0.00 0.00 35.76 2.74
185 186 9.457110 CTACAATCACACAAGATCTATCTACAC 57.543 37.037 0.00 0.00 35.76 2.90
187 188 8.851145 TCCTACAATCACACAAGATCTATCTAC 58.149 37.037 0.00 0.00 35.76 2.59
188 189 8.996651 TCCTACAATCACACAAGATCTATCTA 57.003 34.615 0.00 0.00 35.76 1.98
189 190 7.904558 TCCTACAATCACACAAGATCTATCT 57.095 36.000 0.00 0.00 39.22 1.98
190 191 9.553064 AATTCCTACAATCACACAAGATCTATC 57.447 33.333 0.00 0.00 0.00 2.08
193 194 7.170965 ACAATTCCTACAATCACACAAGATCT 58.829 34.615 0.00 0.00 0.00 2.75
194 195 7.383102 ACAATTCCTACAATCACACAAGATC 57.617 36.000 0.00 0.00 0.00 2.75
195 196 7.765695 AACAATTCCTACAATCACACAAGAT 57.234 32.000 0.00 0.00 0.00 2.40
196 197 7.581213 AAACAATTCCTACAATCACACAAGA 57.419 32.000 0.00 0.00 0.00 3.02
197 198 8.542132 CAAAAACAATTCCTACAATCACACAAG 58.458 33.333 0.00 0.00 0.00 3.16
200 201 8.641499 TTCAAAAACAATTCCTACAATCACAC 57.359 30.769 0.00 0.00 0.00 3.82
201 202 9.829507 ATTTCAAAAACAATTCCTACAATCACA 57.170 25.926 0.00 0.00 0.00 3.58
210 211 9.665719 AACACAGTAATTTCAAAAACAATTCCT 57.334 25.926 0.00 0.00 0.00 3.36
211 212 9.914923 GAACACAGTAATTTCAAAAACAATTCC 57.085 29.630 0.00 0.00 0.00 3.01
212 213 9.914923 GGAACACAGTAATTTCAAAAACAATTC 57.085 29.630 0.00 0.00 0.00 2.17
213 214 8.888716 GGGAACACAGTAATTTCAAAAACAATT 58.111 29.630 0.00 0.00 0.00 2.32
216 217 6.070767 TGGGGAACACAGTAATTTCAAAAACA 60.071 34.615 0.00 0.00 0.00 2.83
217 218 6.342111 TGGGGAACACAGTAATTTCAAAAAC 58.658 36.000 0.00 0.00 0.00 2.43
218 219 6.546428 TGGGGAACACAGTAATTTCAAAAA 57.454 33.333 0.00 0.00 0.00 1.94
219 220 6.070767 TGTTGGGGAACACAGTAATTTCAAAA 60.071 34.615 0.00 0.00 0.00 2.44
220 221 5.422331 TGTTGGGGAACACAGTAATTTCAAA 59.578 36.000 0.00 0.00 0.00 2.69
221 222 4.956700 TGTTGGGGAACACAGTAATTTCAA 59.043 37.500 0.00 0.00 0.00 2.69
222 223 4.537751 TGTTGGGGAACACAGTAATTTCA 58.462 39.130 0.00 0.00 0.00 2.69
223 224 5.523438 TTGTTGGGGAACACAGTAATTTC 57.477 39.130 0.00 0.00 31.49 2.17
224 225 5.163353 CCTTTGTTGGGGAACACAGTAATTT 60.163 40.000 0.00 0.00 30.61 1.82
225 226 4.343814 CCTTTGTTGGGGAACACAGTAATT 59.656 41.667 0.00 0.00 30.61 1.40
226 227 3.895041 CCTTTGTTGGGGAACACAGTAAT 59.105 43.478 0.00 0.00 30.61 1.89
229 230 1.775385 CCTTTGTTGGGGAACACAGT 58.225 50.000 0.00 0.00 30.61 3.55
232 233 1.362355 CGCCTTTGTTGGGGAACAC 59.638 57.895 0.00 0.00 41.89 3.32
233 234 1.076632 ACGCCTTTGTTGGGGAACA 60.077 52.632 4.64 0.00 41.89 3.18
234 235 1.362355 CACGCCTTTGTTGGGGAAC 59.638 57.895 4.64 0.00 41.89 3.62
236 237 0.250553 CTACACGCCTTTGTTGGGGA 60.251 55.000 4.64 0.00 41.89 4.81
237 238 1.862602 GCTACACGCCTTTGTTGGGG 61.863 60.000 0.00 0.00 44.44 4.96
238 239 1.169661 TGCTACACGCCTTTGTTGGG 61.170 55.000 0.00 0.00 38.05 4.12
239 240 0.665835 TTGCTACACGCCTTTGTTGG 59.334 50.000 0.00 0.00 38.05 3.77
241 242 2.021457 AGTTTGCTACACGCCTTTGTT 58.979 42.857 0.00 0.00 38.05 2.83
242 243 1.602377 GAGTTTGCTACACGCCTTTGT 59.398 47.619 0.00 0.00 38.05 2.83
243 244 1.069227 GGAGTTTGCTACACGCCTTTG 60.069 52.381 0.00 0.00 38.05 2.77
245 246 0.107831 TGGAGTTTGCTACACGCCTT 59.892 50.000 5.24 0.00 35.27 4.35
247 248 1.866925 GTGGAGTTTGCTACACGCC 59.133 57.895 0.00 0.00 45.57 5.68
274 493 7.390718 CACTTTTGCTAGTTACCCTAGAACATT 59.609 37.037 0.00 0.00 45.21 2.71
286 505 7.138736 GTGCTTTTCATCACTTTTGCTAGTTA 58.861 34.615 0.00 0.00 0.00 2.24
340 567 4.039245 ACACTGCTGTATATCCAACGCTAT 59.961 41.667 0.00 0.00 0.00 2.97
354 581 1.591594 CAACGGACGACACTGCTGT 60.592 57.895 0.00 0.00 0.00 4.40
365 592 9.019764 CAAATTAATGTTTATGATCCAACGGAC 57.980 33.333 0.00 0.00 32.98 4.79
424 1103 4.411256 AAGCCTAATTGGGATTTGCATG 57.589 40.909 12.81 0.00 29.99 4.06
532 1214 4.030452 GCGCCACACAGCTGGTTC 62.030 66.667 19.93 6.50 33.30 3.62
539 1221 1.164411 TTAGGATTTGCGCCACACAG 58.836 50.000 4.18 0.00 0.00 3.66
546 1228 4.795278 GCATAGCATAATTAGGATTTGCGC 59.205 41.667 13.39 0.00 35.90 6.09
547 1229 5.106197 TGGCATAGCATAATTAGGATTTGCG 60.106 40.000 19.32 2.31 35.90 4.85
565 1247 5.439721 AGTAAAGAAGATGTGCATGGCATA 58.560 37.500 0.00 0.00 41.91 3.14
672 1354 6.801539 AACTGATCGTTTTAGAAGCATTGA 57.198 33.333 0.00 0.00 29.63 2.57
774 1456 1.873591 CTCAAGTTAGTGTGGCGCTTT 59.126 47.619 7.64 0.00 0.00 3.51
796 1478 6.374417 TGTAAGAAACCTGAGCTTATCCTT 57.626 37.500 0.00 0.00 0.00 3.36
1009 1729 1.302949 GTGGTTGCCATGGCTAGGA 59.697 57.895 35.53 14.65 42.51 2.94
1012 1732 2.210144 GAGGGTGGTTGCCATGGCTA 62.210 60.000 35.53 27.11 42.51 3.93
1142 1868 2.418910 CGCGACATGGAGGGAGACT 61.419 63.158 0.00 0.00 0.00 3.24
1163 1889 2.270205 CCAGCGGTGATGAGGCTT 59.730 61.111 17.83 0.00 34.13 4.35
1813 6258 8.364142 ACAAAAATAAATTGTACAAGCAGCCTA 58.636 29.630 14.65 0.00 39.14 3.93
2026 6870 2.481449 CCTACGGGAGTTCAGCACATAC 60.481 54.545 0.00 0.00 43.33 2.39
2114 7090 2.800544 ACAACGACGGATGACAGAAAAG 59.199 45.455 9.51 0.00 0.00 2.27
2140 7118 8.514594 AGGTTTCACACACATAGTAAAATCATG 58.485 33.333 0.00 0.00 0.00 3.07
2416 7412 7.040340 AGTCTAGTGGTATTGTCAATAGATCCG 60.040 40.741 5.49 0.00 41.64 4.18
2502 7498 1.593006 AGAAGTCGTCGCTTTGTGTTG 59.407 47.619 3.93 0.00 0.00 3.33
2507 7503 2.349297 AGGTAGAAGTCGTCGCTTTG 57.651 50.000 3.93 0.00 0.00 2.77
2516 7512 4.682050 GCTCCCATCAAGAAGGTAGAAGTC 60.682 50.000 0.00 0.00 0.00 3.01
2608 7607 4.727475 CTTGCTTGTAAGGAAGCTTAAGC 58.273 43.478 20.09 20.09 45.29 3.09
2668 7667 1.625818 AGACCACTTAGTGCTTCTGGG 59.374 52.381 6.88 0.00 31.34 4.45
2679 7678 1.902508 CCAAGCTCCAGAGACCACTTA 59.097 52.381 0.00 0.00 0.00 2.24
3033 8035 1.916181 GGAAGAGGAAAGGGTGATCCA 59.084 52.381 0.00 0.00 38.23 3.41
3237 8245 8.393366 CCAACATACAAGTGTAGAATTCATCAG 58.607 37.037 8.44 0.00 33.52 2.90
3254 8262 6.648310 CCACAAAAATAACATGCCAACATACA 59.352 34.615 0.00 0.00 33.67 2.29
3287 8295 3.194005 GTGGTCCAATCCACGATACAT 57.806 47.619 0.00 0.00 46.38 2.29
3295 8303 0.404040 GGTCAAGGTGGTCCAATCCA 59.596 55.000 0.00 0.00 35.89 3.41
3332 8360 0.323178 CACATCTGCCTCCCAAGCTT 60.323 55.000 0.00 0.00 0.00 3.74
3335 8363 0.038744 AACCACATCTGCCTCCCAAG 59.961 55.000 0.00 0.00 0.00 3.61
3348 8376 4.460731 TCAAAATGAGTGTGTTGAACCACA 59.539 37.500 15.70 7.75 42.81 4.17
3350 8378 4.704540 AGTCAAAATGAGTGTGTTGAACCA 59.295 37.500 0.00 0.00 32.12 3.67
3415 8443 6.918626 TCATGTGTTTTGACTTTGACTTGAA 58.081 32.000 0.00 0.00 0.00 2.69
3445 8474 7.140705 TGCAATGTTTGACAAGAATCTAGTTG 58.859 34.615 0.00 0.00 0.00 3.16
3524 8556 2.721906 AGAAAAGGTGGAGGGAATTCCA 59.278 45.455 25.67 2.94 44.84 3.53
3574 8607 8.307483 TGTATTTGGTTCAGTTTGTCTCAAAAA 58.693 29.630 0.00 0.00 0.00 1.94
3575 8608 7.831753 TGTATTTGGTTCAGTTTGTCTCAAAA 58.168 30.769 0.00 0.00 0.00 2.44
3576 8609 7.397892 TGTATTTGGTTCAGTTTGTCTCAAA 57.602 32.000 0.00 0.00 0.00 2.69
3577 8610 7.581213 ATGTATTTGGTTCAGTTTGTCTCAA 57.419 32.000 0.00 0.00 0.00 3.02
3578 8611 8.684386 TTATGTATTTGGTTCAGTTTGTCTCA 57.316 30.769 0.00 0.00 0.00 3.27
3579 8612 9.394477 GTTTATGTATTTGGTTCAGTTTGTCTC 57.606 33.333 0.00 0.00 0.00 3.36
3580 8613 8.908903 TGTTTATGTATTTGGTTCAGTTTGTCT 58.091 29.630 0.00 0.00 0.00 3.41
3581 8614 9.180678 CTGTTTATGTATTTGGTTCAGTTTGTC 57.819 33.333 0.00 0.00 0.00 3.18
3582 8615 8.691797 ACTGTTTATGTATTTGGTTCAGTTTGT 58.308 29.630 0.00 0.00 31.02 2.83
3583 8616 8.967218 CACTGTTTATGTATTTGGTTCAGTTTG 58.033 33.333 0.00 0.00 32.48 2.93
3584 8617 7.651704 GCACTGTTTATGTATTTGGTTCAGTTT 59.348 33.333 0.00 0.00 32.48 2.66
3585 8618 7.014230 AGCACTGTTTATGTATTTGGTTCAGTT 59.986 33.333 0.00 0.00 32.48 3.16
3727 8785 2.076100 CTGCCGTTCTAAGCATTGACA 58.924 47.619 0.00 0.00 38.56 3.58
3733 8791 2.434185 CGGCTGCCGTTCTAAGCA 60.434 61.111 31.72 0.00 42.73 3.91
3755 8813 1.503542 CTTTTGCTGCCAGGTAGCG 59.496 57.895 23.14 6.42 43.95 4.26
3788 8846 2.171659 TCTTCTTGTACAGCAACCCACA 59.828 45.455 0.00 0.00 32.90 4.17
3789 8847 2.548480 GTCTTCTTGTACAGCAACCCAC 59.452 50.000 0.00 0.00 32.90 4.61
3805 8863 2.345942 GGACGAGCTTCGAAATGTCTTC 59.654 50.000 11.64 8.14 43.74 2.87
3863 8924 3.449528 TTGATCTCGAATCTCTGCTGG 57.550 47.619 0.00 0.00 0.00 4.85
3881 8942 3.402110 TGTATGCTGTGTGGAGACTTTG 58.598 45.455 0.00 0.00 0.00 2.77
3908 8969 3.902261 TGTGCTTATGCTCTGTGTTTG 57.098 42.857 1.96 0.00 40.48 2.93
3928 8989 5.640147 TGATTGGTCTCTTGGGTAACATTT 58.360 37.500 0.00 0.00 39.74 2.32
3929 8990 5.222130 ACTGATTGGTCTCTTGGGTAACATT 60.222 40.000 0.00 0.00 39.74 2.71
3930 8991 4.289672 ACTGATTGGTCTCTTGGGTAACAT 59.710 41.667 0.00 0.00 39.74 2.71
3933 8994 4.349636 TCAACTGATTGGTCTCTTGGGTAA 59.650 41.667 0.00 0.00 36.39 2.85
3934 8995 3.907474 TCAACTGATTGGTCTCTTGGGTA 59.093 43.478 0.00 0.00 36.39 3.69
3935 8996 2.711009 TCAACTGATTGGTCTCTTGGGT 59.289 45.455 0.00 0.00 36.39 4.51
3936 8997 3.423539 TCAACTGATTGGTCTCTTGGG 57.576 47.619 0.00 0.00 36.39 4.12
3937 8998 4.380233 GCATTCAACTGATTGGTCTCTTGG 60.380 45.833 4.32 0.00 36.39 3.61
3938 8999 4.216902 TGCATTCAACTGATTGGTCTCTTG 59.783 41.667 4.32 0.00 36.39 3.02
3940 9001 4.025040 TGCATTCAACTGATTGGTCTCT 57.975 40.909 4.32 0.00 36.39 3.10
3941 9002 4.397103 TCATGCATTCAACTGATTGGTCTC 59.603 41.667 0.00 0.00 36.39 3.36
3943 9004 4.707030 TCATGCATTCAACTGATTGGTC 57.293 40.909 0.00 0.00 36.39 4.02
3960 10144 4.061357 AGACTGTCAGCTCATGATCATG 57.939 45.455 26.79 26.79 40.92 3.07
3962 10146 4.501058 GCATAGACTGTCAGCTCATGATCA 60.501 45.833 10.88 0.00 40.92 2.92
3965 10149 2.102084 GGCATAGACTGTCAGCTCATGA 59.898 50.000 10.88 0.00 34.79 3.07
3966 10150 2.159000 TGGCATAGACTGTCAGCTCATG 60.159 50.000 10.88 6.34 33.57 3.07
4043 10338 2.955660 CCAGTTTGGTAACTTCCTTGCA 59.044 45.455 0.00 0.00 41.85 4.08
4075 10370 5.577164 CGAAGTAGACTTGTAGGATTGGTTG 59.423 44.000 0.00 0.00 36.11 3.77
4080 10375 4.463186 ACTGCGAAGTAGACTTGTAGGATT 59.537 41.667 0.00 0.00 45.23 3.01
4105 10400 0.316204 GCAGCAAGCATGTTCTGGTT 59.684 50.000 0.00 0.00 46.25 3.67
4107 10402 4.883026 GCAGCAAGCATGTTCTGG 57.117 55.556 0.00 0.00 44.79 3.86
4129 10424 1.030488 CAGGCTCCGTCCGTCTTCTA 61.030 60.000 0.00 0.00 0.00 2.10
4130 10425 2.035940 AGGCTCCGTCCGTCTTCT 59.964 61.111 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.