Multiple sequence alignment - TraesCS3B01G316600

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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 TraesCS3B01G316600 chr3B 100.000 3377 0 0 1 3377 508476053 508472677 0.000000e+00 6237.0
1 TraesCS3B01G316600 chr3D 93.312 2198 79 19 324 2499 391248114 391245963 0.000000e+00 3182.0
2 TraesCS3B01G316600 chr3D 86.280 656 61 11 2747 3377 391245278 391244627 0.000000e+00 686.0
3 TraesCS3B01G316600 chr3D 97.093 172 5 0 324 495 391253728 391253557 1.190000e-74 291.0
4 TraesCS3B01G316600 chr3D 82.745 255 28 7 4 244 391253977 391253725 2.640000e-51 213.0
5 TraesCS3B01G316600 chr3D 87.736 106 11 2 229 333 411724334 411724438 4.580000e-24 122.0
6 TraesCS3B01G316600 chr3D 90.541 74 2 4 176 244 391248184 391248111 3.590000e-15 93.5
7 TraesCS3B01G316600 chr3A 92.311 2198 101 31 318 2499 511599469 511597324 0.000000e+00 3061.0
8 TraesCS3B01G316600 chr3A 86.957 230 25 3 2652 2881 511596934 511596710 1.560000e-63 254.0
9 TraesCS3B01G316600 chr1D 80.752 1143 182 29 1060 2177 439216592 439215463 0.000000e+00 857.0
10 TraesCS3B01G316600 chr1D 91.667 96 6 2 240 334 363804257 363804163 7.600000e-27 132.0
11 TraesCS3B01G316600 chr1D 90.625 96 8 1 240 334 115989922 115990017 3.540000e-25 126.0
12 TraesCS3B01G316600 chr1A 79.983 1194 202 31 1060 2227 535436414 535435232 0.000000e+00 846.0
13 TraesCS3B01G316600 chr1B 80.141 1138 194 28 1060 2175 595638860 595637733 0.000000e+00 821.0
14 TraesCS3B01G316600 chr1B 79.188 394 78 3 2982 3374 311140008 311140398 1.540000e-68 270.0
15 TraesCS3B01G316600 chr2B 82.908 392 59 7 2983 3372 634653222 634652837 2.490000e-91 346.0
16 TraesCS3B01G316600 chr2B 80.323 371 64 7 3008 3376 478845911 478845548 4.290000e-69 272.0
17 TraesCS3B01G316600 chr7D 81.726 394 61 10 2982 3372 524552158 524551773 5.440000e-83 318.0
18 TraesCS3B01G316600 chr2D 80.612 392 66 8 2984 3371 436346057 436346442 9.160000e-76 294.0
19 TraesCS3B01G316600 chr2D 80.303 396 71 6 2982 3376 158672144 158671755 3.300000e-75 292.0
20 TraesCS3B01G316600 chr5D 80.101 397 72 7 2983 3377 41431755 41432146 4.260000e-74 289.0
21 TraesCS3B01G316600 chr5D 80.628 382 67 6 2993 3372 456846633 456847009 4.260000e-74 289.0
22 TraesCS3B01G316600 chr7B 90.099 101 10 0 238 338 718351008 718351108 7.600000e-27 132.0
23 TraesCS3B01G316600 chr4A 89.623 106 8 3 229 333 440964812 440964915 7.600000e-27 132.0
24 TraesCS3B01G316600 chr4A 88.235 102 11 1 241 342 21349215 21349115 1.650000e-23 121.0
25 TraesCS3B01G316600 chr6B 92.308 91 7 0 240 330 216509757 216509847 2.730000e-26 130.0
26 TraesCS3B01G316600 chr7A 90.000 100 8 1 240 337 522796135 522796234 9.840000e-26 128.0
27 TraesCS3B01G316600 chr7A 89.216 102 9 2 236 336 556767970 556768070 3.540000e-25 126.0


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 TraesCS3B01G316600 chr3B 508472677 508476053 3376 True 6237.0 6237 100.000000 1 3377 1 chr3B.!!$R1 3376
1 TraesCS3B01G316600 chr3D 391244627 391248184 3557 True 1320.5 3182 90.044333 176 3377 3 chr3D.!!$R1 3201
2 TraesCS3B01G316600 chr3A 511596710 511599469 2759 True 1657.5 3061 89.634000 318 2881 2 chr3A.!!$R1 2563
3 TraesCS3B01G316600 chr1D 439215463 439216592 1129 True 857.0 857 80.752000 1060 2177 1 chr1D.!!$R2 1117
4 TraesCS3B01G316600 chr1A 535435232 535436414 1182 True 846.0 846 79.983000 1060 2227 1 chr1A.!!$R1 1167
5 TraesCS3B01G316600 chr1B 595637733 595638860 1127 True 821.0 821 80.141000 1060 2175 1 chr1B.!!$R1 1115

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
852 878 0.108472 TTGCACGATGCTCTCTCTGG 60.108 55.0 10.54 0.0 45.31 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2645 2934 0.041238 TCGGAGGAGAGGTGTGGAAT 59.959 55.0 0.0 0.0 0.0 3.01 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 6.569179 TTTTGGTGTAGCTCTATTTCAACC 57.431 37.500 0.00 0.00 0.00 3.77
30 31 4.901197 TGGTGTAGCTCTATTTCAACCA 57.099 40.909 0.00 0.00 0.00 3.67
31 32 4.832248 TGGTGTAGCTCTATTTCAACCAG 58.168 43.478 0.00 0.00 0.00 4.00
32 33 4.530553 TGGTGTAGCTCTATTTCAACCAGA 59.469 41.667 0.00 0.00 0.00 3.86
33 34 5.012664 TGGTGTAGCTCTATTTCAACCAGAA 59.987 40.000 0.00 0.00 0.00 3.02
46 47 6.516739 TTCAACCAGAAAATTGTACACACA 57.483 33.333 0.00 0.00 32.05 3.72
47 48 6.707440 TCAACCAGAAAATTGTACACACAT 57.293 33.333 0.00 0.00 33.76 3.21
48 49 6.502652 TCAACCAGAAAATTGTACACACATG 58.497 36.000 0.00 0.00 33.76 3.21
49 50 4.870363 ACCAGAAAATTGTACACACATGC 58.130 39.130 0.00 0.00 33.76 4.06
50 51 4.236935 CCAGAAAATTGTACACACATGCC 58.763 43.478 0.00 0.00 33.76 4.40
51 52 4.236935 CAGAAAATTGTACACACATGCCC 58.763 43.478 0.00 0.00 33.76 5.36
52 53 3.057596 AGAAAATTGTACACACATGCCCG 60.058 43.478 0.00 0.00 33.76 6.13
53 54 1.904287 AATTGTACACACATGCCCGT 58.096 45.000 0.00 0.00 33.76 5.28
54 55 1.904287 ATTGTACACACATGCCCGTT 58.096 45.000 0.00 0.00 33.76 4.44
55 56 2.545537 TTGTACACACATGCCCGTTA 57.454 45.000 0.00 0.00 33.76 3.18
56 57 2.772077 TGTACACACATGCCCGTTAT 57.228 45.000 0.00 0.00 0.00 1.89
57 58 2.351455 TGTACACACATGCCCGTTATG 58.649 47.619 0.00 0.00 0.00 1.90
58 59 2.028020 TGTACACACATGCCCGTTATGA 60.028 45.455 0.00 0.00 0.00 2.15
59 60 1.448985 ACACACATGCCCGTTATGAC 58.551 50.000 0.00 0.00 0.00 3.06
60 61 1.003118 ACACACATGCCCGTTATGACT 59.997 47.619 0.00 0.00 0.00 3.41
61 62 1.665679 CACACATGCCCGTTATGACTC 59.334 52.381 0.00 0.00 0.00 3.36
62 63 1.555075 ACACATGCCCGTTATGACTCT 59.445 47.619 0.00 0.00 0.00 3.24
63 64 2.764010 ACACATGCCCGTTATGACTCTA 59.236 45.455 0.00 0.00 0.00 2.43
64 65 3.181475 ACACATGCCCGTTATGACTCTAG 60.181 47.826 0.00 0.00 0.00 2.43
65 66 2.365617 ACATGCCCGTTATGACTCTAGG 59.634 50.000 0.00 0.00 0.00 3.02
66 67 2.154567 TGCCCGTTATGACTCTAGGT 57.845 50.000 0.00 0.00 0.00 3.08
67 68 3.301794 TGCCCGTTATGACTCTAGGTA 57.698 47.619 0.00 0.00 0.00 3.08
68 69 3.840991 TGCCCGTTATGACTCTAGGTAT 58.159 45.455 0.00 0.00 0.00 2.73
69 70 4.989277 TGCCCGTTATGACTCTAGGTATA 58.011 43.478 0.00 0.00 0.00 1.47
70 71 5.577100 TGCCCGTTATGACTCTAGGTATAT 58.423 41.667 0.00 0.00 0.00 0.86
71 72 5.417894 TGCCCGTTATGACTCTAGGTATATG 59.582 44.000 0.00 0.00 0.00 1.78
72 73 5.418209 GCCCGTTATGACTCTAGGTATATGT 59.582 44.000 0.00 0.00 0.00 2.29
73 74 6.625300 GCCCGTTATGACTCTAGGTATATGTG 60.625 46.154 0.00 0.00 0.00 3.21
74 75 6.433404 CCCGTTATGACTCTAGGTATATGTGT 59.567 42.308 0.00 0.00 0.00 3.72
75 76 7.609146 CCCGTTATGACTCTAGGTATATGTGTA 59.391 40.741 0.00 0.00 0.00 2.90
76 77 8.449397 CCGTTATGACTCTAGGTATATGTGTAC 58.551 40.741 0.00 0.00 0.00 2.90
77 78 9.217278 CGTTATGACTCTAGGTATATGTGTACT 57.783 37.037 0.00 0.00 0.00 2.73
117 118 9.620660 TTTGAAACTAAAGAGTGAACTTTGAAC 57.379 29.630 0.00 0.00 39.86 3.18
118 119 8.561738 TGAAACTAAAGAGTGAACTTTGAACT 57.438 30.769 0.00 0.00 39.86 3.01
119 120 9.010029 TGAAACTAAAGAGTGAACTTTGAACTT 57.990 29.630 0.00 0.00 39.86 2.66
120 121 9.841880 GAAACTAAAGAGTGAACTTTGAACTTT 57.158 29.630 0.00 0.00 39.86 2.66
121 122 9.626045 AAACTAAAGAGTGAACTTTGAACTTTG 57.374 29.630 0.00 0.00 39.86 2.77
122 123 7.251281 ACTAAAGAGTGAACTTTGAACTTTGC 58.749 34.615 0.00 0.00 39.86 3.68
123 124 5.643379 AAGAGTGAACTTTGAACTTTGCA 57.357 34.783 0.00 0.00 0.00 4.08
124 125 5.643379 AGAGTGAACTTTGAACTTTGCAA 57.357 34.783 0.00 0.00 0.00 4.08
125 126 6.024552 AGAGTGAACTTTGAACTTTGCAAA 57.975 33.333 12.14 12.14 34.40 3.68
126 127 6.633856 AGAGTGAACTTTGAACTTTGCAAAT 58.366 32.000 13.23 0.00 35.00 2.32
127 128 7.099120 AGAGTGAACTTTGAACTTTGCAAATT 58.901 30.769 13.23 3.91 35.00 1.82
128 129 7.276438 AGAGTGAACTTTGAACTTTGCAAATTC 59.724 33.333 13.23 17.11 35.00 2.17
129 130 6.873076 AGTGAACTTTGAACTTTGCAAATTCA 59.127 30.769 22.25 22.25 35.00 2.57
130 131 7.063780 AGTGAACTTTGAACTTTGCAAATTCAG 59.936 33.333 23.58 18.99 35.72 3.02
131 132 5.723492 ACTTTGAACTTTGCAAATTCAGC 57.277 34.783 23.58 11.10 35.00 4.26
132 133 4.571984 ACTTTGAACTTTGCAAATTCAGCC 59.428 37.500 23.58 10.17 35.00 4.85
133 134 4.405116 TTGAACTTTGCAAATTCAGCCT 57.595 36.364 23.58 4.46 34.04 4.58
134 135 3.981211 TGAACTTTGCAAATTCAGCCTC 58.019 40.909 22.25 10.38 0.00 4.70
135 136 3.243839 TGAACTTTGCAAATTCAGCCTCC 60.244 43.478 22.25 6.52 0.00 4.30
136 137 2.318908 ACTTTGCAAATTCAGCCTCCA 58.681 42.857 13.23 0.00 0.00 3.86
137 138 2.901839 ACTTTGCAAATTCAGCCTCCAT 59.098 40.909 13.23 0.00 0.00 3.41
138 139 3.325716 ACTTTGCAAATTCAGCCTCCATT 59.674 39.130 13.23 0.00 0.00 3.16
139 140 4.202388 ACTTTGCAAATTCAGCCTCCATTT 60.202 37.500 13.23 0.00 0.00 2.32
140 141 3.322211 TGCAAATTCAGCCTCCATTTG 57.678 42.857 0.00 0.00 39.78 2.32
141 142 2.898612 TGCAAATTCAGCCTCCATTTGA 59.101 40.909 8.63 0.00 39.34 2.69
142 143 3.324268 TGCAAATTCAGCCTCCATTTGAA 59.676 39.130 8.63 0.00 39.34 2.69
143 144 4.020039 TGCAAATTCAGCCTCCATTTGAAT 60.020 37.500 8.63 1.88 41.84 2.57
179 180 9.898152 TTTAATTCCTTTTGAAATGTTTGTCCT 57.102 25.926 0.00 0.00 36.33 3.85
185 186 7.930865 TCCTTTTGAAATGTTTGTCCTAATTGG 59.069 33.333 0.00 0.00 37.10 3.16
188 189 9.454859 TTTTGAAATGTTTGTCCTAATTGGTTT 57.545 25.926 0.00 0.00 37.07 3.27
197 198 9.406828 GTTTGTCCTAATTGGTTTCTACATTTC 57.593 33.333 0.00 0.00 37.07 2.17
244 246 5.063880 AGTTCCTTTGTTTCGATGCTACTT 58.936 37.500 0.00 0.00 0.00 2.24
245 247 5.179555 AGTTCCTTTGTTTCGATGCTACTTC 59.820 40.000 0.00 0.00 0.00 3.01
246 248 4.000988 TCCTTTGTTTCGATGCTACTTCC 58.999 43.478 0.00 0.00 0.00 3.46
247 249 4.003648 CCTTTGTTTCGATGCTACTTCCT 58.996 43.478 0.00 0.00 0.00 3.36
248 250 4.093556 CCTTTGTTTCGATGCTACTTCCTC 59.906 45.833 0.00 0.00 0.00 3.71
249 251 4.537135 TTGTTTCGATGCTACTTCCTCT 57.463 40.909 0.00 0.00 0.00 3.69
250 252 3.849911 TGTTTCGATGCTACTTCCTCTG 58.150 45.455 0.00 0.00 0.00 3.35
251 253 3.258372 TGTTTCGATGCTACTTCCTCTGT 59.742 43.478 0.00 0.00 0.00 3.41
252 254 3.784701 TTCGATGCTACTTCCTCTGTC 57.215 47.619 0.00 0.00 0.00 3.51
253 255 3.006112 TCGATGCTACTTCCTCTGTCT 57.994 47.619 0.00 0.00 0.00 3.41
254 256 2.946329 TCGATGCTACTTCCTCTGTCTC 59.054 50.000 0.00 0.00 0.00 3.36
255 257 2.685388 CGATGCTACTTCCTCTGTCTCA 59.315 50.000 0.00 0.00 0.00 3.27
256 258 3.317711 CGATGCTACTTCCTCTGTCTCAT 59.682 47.826 0.00 0.00 0.00 2.90
257 259 4.517075 CGATGCTACTTCCTCTGTCTCATA 59.483 45.833 0.00 0.00 0.00 2.15
258 260 5.009110 CGATGCTACTTCCTCTGTCTCATAA 59.991 44.000 0.00 0.00 0.00 1.90
259 261 6.294453 CGATGCTACTTCCTCTGTCTCATAAT 60.294 42.308 0.00 0.00 0.00 1.28
260 262 7.094592 CGATGCTACTTCCTCTGTCTCATAATA 60.095 40.741 0.00 0.00 0.00 0.98
261 263 8.663209 ATGCTACTTCCTCTGTCTCATAATAT 57.337 34.615 0.00 0.00 0.00 1.28
262 264 9.760926 ATGCTACTTCCTCTGTCTCATAATATA 57.239 33.333 0.00 0.00 0.00 0.86
263 265 9.588096 TGCTACTTCCTCTGTCTCATAATATAA 57.412 33.333 0.00 0.00 0.00 0.98
267 269 8.802267 ACTTCCTCTGTCTCATAATATAAGAGC 58.198 37.037 0.00 0.00 0.00 4.09
268 270 8.948401 TTCCTCTGTCTCATAATATAAGAGCT 57.052 34.615 0.00 0.00 0.00 4.09
269 271 8.948401 TCCTCTGTCTCATAATATAAGAGCTT 57.052 34.615 0.00 0.00 0.00 3.74
270 272 9.373450 TCCTCTGTCTCATAATATAAGAGCTTT 57.627 33.333 0.00 0.00 0.00 3.51
271 273 9.995003 CCTCTGTCTCATAATATAAGAGCTTTT 57.005 33.333 0.00 0.00 0.00 2.27
283 285 8.934507 ATATAAGAGCTTTTCTGACACTACAC 57.065 34.615 0.00 0.00 35.91 2.90
284 286 4.946478 AGAGCTTTTCTGACACTACACT 57.054 40.909 0.00 0.00 33.93 3.55
285 287 6.406692 AAGAGCTTTTCTGACACTACACTA 57.593 37.500 0.00 0.00 35.91 2.74
286 288 6.019779 AGAGCTTTTCTGACACTACACTAG 57.980 41.667 0.00 0.00 33.93 2.57
287 289 5.536916 AGAGCTTTTCTGACACTACACTAGT 59.463 40.000 0.00 0.00 35.33 2.57
288 290 6.515862 AGAGCTTTTCTGACACTACACTAGTG 60.516 42.308 21.44 21.44 46.88 2.74
299 301 5.793030 ACTACACTAGTGTCAGAAAAGCT 57.207 39.130 31.11 10.25 43.74 3.74
300 302 5.774630 ACTACACTAGTGTCAGAAAAGCTC 58.225 41.667 31.11 0.00 43.74 4.09
301 303 4.946478 ACACTAGTGTCAGAAAAGCTCT 57.054 40.909 22.95 0.00 40.24 4.09
302 304 5.283457 ACACTAGTGTCAGAAAAGCTCTT 57.717 39.130 22.95 0.00 40.24 2.85
303 305 6.406692 ACACTAGTGTCAGAAAAGCTCTTA 57.593 37.500 22.95 0.00 40.24 2.10
304 306 6.998802 ACACTAGTGTCAGAAAAGCTCTTAT 58.001 36.000 22.95 0.00 40.24 1.73
305 307 8.123639 ACACTAGTGTCAGAAAAGCTCTTATA 57.876 34.615 22.95 0.00 40.24 0.98
306 308 8.754080 ACACTAGTGTCAGAAAAGCTCTTATAT 58.246 33.333 22.95 0.00 40.24 0.86
307 309 9.593134 CACTAGTGTCAGAAAAGCTCTTATATT 57.407 33.333 15.06 0.00 29.07 1.28
311 313 9.553064 AGTGTCAGAAAAGCTCTTATATTATGG 57.447 33.333 0.00 0.00 29.07 2.74
312 314 8.778358 GTGTCAGAAAAGCTCTTATATTATGGG 58.222 37.037 0.00 0.00 29.07 4.00
313 315 8.713971 TGTCAGAAAAGCTCTTATATTATGGGA 58.286 33.333 0.00 0.00 29.07 4.37
314 316 8.994170 GTCAGAAAAGCTCTTATATTATGGGAC 58.006 37.037 0.00 0.00 29.07 4.46
315 317 7.872993 TCAGAAAAGCTCTTATATTATGGGACG 59.127 37.037 0.00 0.00 29.07 4.79
316 318 7.118390 CAGAAAAGCTCTTATATTATGGGACGG 59.882 40.741 0.00 0.00 29.07 4.79
325 327 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
331 333 3.205056 TGGGACGGAGGGAGTACTATTTA 59.795 47.826 0.00 0.00 0.00 1.40
409 416 3.825143 AAACATGTTTCCTTTGCTGCT 57.175 38.095 18.13 0.00 0.00 4.24
466 474 1.102809 TCAGCAGCACCACACCTTTG 61.103 55.000 0.00 0.00 0.00 2.77
467 475 1.102809 CAGCAGCACCACACCTTTGA 61.103 55.000 0.00 0.00 0.00 2.69
476 484 2.291153 ACCACACCTTTGAGATGGATGG 60.291 50.000 0.00 0.00 38.32 3.51
526 544 2.806608 TTACTCGTCCAAAACTCGCT 57.193 45.000 0.00 0.00 0.00 4.93
538 556 5.761234 TCCAAAACTCGCTGTGTAATAAGTT 59.239 36.000 0.00 0.00 0.00 2.66
539 557 6.930164 TCCAAAACTCGCTGTGTAATAAGTTA 59.070 34.615 0.00 0.00 0.00 2.24
541 559 7.692291 CCAAAACTCGCTGTGTAATAAGTTATG 59.308 37.037 0.00 0.00 0.00 1.90
543 561 6.216801 ACTCGCTGTGTAATAAGTTATGGA 57.783 37.500 0.00 0.00 0.00 3.41
544 562 6.273825 ACTCGCTGTGTAATAAGTTATGGAG 58.726 40.000 0.00 0.00 0.00 3.86
545 563 5.047847 TCGCTGTGTAATAAGTTATGGAGC 58.952 41.667 0.00 0.12 0.00 4.70
546 564 4.085055 CGCTGTGTAATAAGTTATGGAGCG 60.085 45.833 14.50 14.50 35.77 5.03
547 565 5.047847 GCTGTGTAATAAGTTATGGAGCGA 58.952 41.667 0.00 0.00 0.00 4.93
548 566 5.050972 GCTGTGTAATAAGTTATGGAGCGAC 60.051 44.000 0.00 0.00 0.00 5.19
580 600 4.843728 TCCTTTGTACTTGGCCTGATAAG 58.156 43.478 3.32 0.83 0.00 1.73
595 615 5.491982 CCTGATAAGCCAGTTTTACTCAGT 58.508 41.667 0.00 0.00 32.43 3.41
640 665 7.223582 CCAGTCAACTTATCTTATGTAGCAGTG 59.776 40.741 0.00 0.00 0.00 3.66
644 669 8.924303 TCAACTTATCTTATGTAGCAGTGGTAT 58.076 33.333 5.16 0.00 0.00 2.73
657 682 1.486726 AGTGGTATTGCTAGCCCTGTC 59.513 52.381 13.29 0.00 0.00 3.51
784 810 0.527817 GCGCTGCTCGTACCACTAAT 60.528 55.000 0.00 0.00 41.07 1.73
790 816 2.229543 TGCTCGTACCACTAATTCGTGT 59.770 45.455 9.06 1.11 33.07 4.49
817 843 2.595172 GTTTTTCCCGGCGTCCCA 60.595 61.111 6.01 0.00 0.00 4.37
852 878 0.108472 TTGCACGATGCTCTCTCTGG 60.108 55.000 10.54 0.00 45.31 3.86
871 897 2.815211 CATGGCCGGTCACGTCAG 60.815 66.667 13.07 0.00 38.78 3.51
874 900 3.771160 GGCCGGTCACGTCAGGAT 61.771 66.667 0.00 0.00 38.78 3.24
875 901 2.202756 GCCGGTCACGTCAGGATC 60.203 66.667 1.90 0.00 38.78 3.36
876 902 2.102357 CCGGTCACGTCAGGATCG 59.898 66.667 0.00 0.35 38.57 3.69
881 907 0.793478 GTCACGTCAGGATCGTCACG 60.793 60.000 10.36 10.36 39.55 4.35
882 908 1.209383 CACGTCAGGATCGTCACGT 59.791 57.895 11.80 11.80 46.05 4.49
883 909 0.793478 CACGTCAGGATCGTCACGTC 60.793 60.000 14.64 0.00 43.39 4.34
884 910 1.232621 ACGTCAGGATCGTCACGTCA 61.233 55.000 11.80 0.00 41.51 4.35
885 911 0.109919 CGTCAGGATCGTCACGTCAA 60.110 55.000 3.50 0.00 0.00 3.18
886 912 1.467543 CGTCAGGATCGTCACGTCAAT 60.468 52.381 3.50 0.00 0.00 2.57
973 999 1.674359 ACCACACTCATCAAACGCAA 58.326 45.000 0.00 0.00 0.00 4.85
1022 1048 2.660258 GATACCACGATGCCGGCCTT 62.660 60.000 26.77 12.10 40.78 4.35
1026 1052 2.114670 CACGATGCCGGCCTTCATT 61.115 57.895 26.77 7.83 40.78 2.57
1051 1077 3.596066 TTCCTGTGCCTGCTCTCGC 62.596 63.158 0.00 0.00 0.00 5.03
1420 1461 1.745489 CTGCAGCAGCTCAGCATCA 60.745 57.895 10.14 0.00 42.74 3.07
1725 1766 1.004044 CTGGACCTGAGCTCCAACAAT 59.996 52.381 12.15 0.00 37.36 2.71
1783 1824 3.322466 CCCTCACCTTCCTGGCGT 61.322 66.667 0.00 0.00 40.22 5.68
1869 1910 2.555006 CCTGATCATGGACAACAACCCA 60.555 50.000 0.00 0.00 36.79 4.51
1879 1920 0.237235 CAACAACCCAATGGACGTCG 59.763 55.000 9.92 0.00 34.81 5.12
1971 2012 4.397832 ATACCGGCGGCGTTTGGT 62.398 61.111 30.09 21.72 38.51 3.67
2250 2294 3.419759 GGTTCGTTGGCGCGTGAT 61.420 61.111 8.43 0.00 38.14 3.06
2266 2310 0.894835 TGATTCGGTGAGCAGTGCTA 59.105 50.000 19.77 0.58 39.88 3.49
2386 2433 3.504520 TGAGTATGCGTAGTGTTGACAGA 59.495 43.478 0.00 0.00 0.00 3.41
2393 2440 3.916172 GCGTAGTGTTGACAGAATTCGTA 59.084 43.478 0.00 0.00 0.00 3.43
2478 2528 2.094700 CGAGGCTTGTAGCAGAGTTGTA 60.095 50.000 0.67 0.00 44.75 2.41
2479 2529 3.254892 GAGGCTTGTAGCAGAGTTGTAC 58.745 50.000 0.67 0.00 44.75 2.90
2480 2530 1.993370 GGCTTGTAGCAGAGTTGTACG 59.007 52.381 0.67 0.00 44.75 3.67
2481 2531 2.609737 GGCTTGTAGCAGAGTTGTACGT 60.610 50.000 0.00 0.00 44.75 3.57
2502 2791 4.619336 CGTAGAAAGCTGTTGACTCTTCTC 59.381 45.833 0.00 0.00 0.00 2.87
2504 2793 3.389329 AGAAAGCTGTTGACTCTTCTCCA 59.611 43.478 0.00 0.00 0.00 3.86
2507 2796 4.363991 AGCTGTTGACTCTTCTCCATTT 57.636 40.909 0.00 0.00 0.00 2.32
2540 2829 2.815647 CTTCTTCGCCACCGCTCC 60.816 66.667 0.00 0.00 0.00 4.70
2597 2886 1.646189 GCAAGGAACTCGATGAGTCC 58.354 55.000 0.00 4.06 42.59 3.85
2606 2895 0.809385 TCGATGAGTCCGTCACCTTC 59.191 55.000 0.00 0.00 38.28 3.46
2608 2897 1.468224 CGATGAGTCCGTCACCTTCAG 60.468 57.143 0.00 0.00 38.28 3.02
2645 2934 4.742201 GCCGCTTCTCCGTCAGCA 62.742 66.667 0.00 0.00 35.60 4.41
2665 2954 0.178944 TTCCACACCTCTCCTCCGAA 60.179 55.000 0.00 0.00 0.00 4.30
2667 2956 1.185618 CCACACCTCTCCTCCGAACA 61.186 60.000 0.00 0.00 0.00 3.18
2675 3156 2.813474 CCTCCGAACATCGCGCAA 60.813 61.111 8.75 0.00 38.82 4.85
2683 3164 0.947180 AACATCGCGCAAGTACCGTT 60.947 50.000 8.75 0.00 41.68 4.44
2700 3181 2.157279 CCGTTAGCTCCTACGATACTCG 59.843 54.545 15.08 0.00 46.93 4.18
2744 3225 0.107654 AATGCCCGTGCTAAGAGGAC 60.108 55.000 0.00 0.00 38.71 3.85
2745 3226 0.978146 ATGCCCGTGCTAAGAGGACT 60.978 55.000 0.00 0.00 34.11 3.85
2765 3246 3.966665 ACTTTTGGATTGGTGTTGATGGT 59.033 39.130 0.00 0.00 0.00 3.55
2767 3248 5.600484 ACTTTTGGATTGGTGTTGATGGTTA 59.400 36.000 0.00 0.00 0.00 2.85
2775 3279 0.325602 TGTTGATGGTTACCCGACCC 59.674 55.000 0.00 0.00 39.01 4.46
2845 3349 0.107214 TATTTGGCTCGCCCCAAGAG 60.107 55.000 5.33 0.00 45.03 2.85
2951 3461 4.496336 GAGCGAGCAGGGGCCAAT 62.496 66.667 4.39 0.00 42.56 3.16
2952 3462 4.052518 AGCGAGCAGGGGCCAATT 62.053 61.111 4.39 0.00 42.56 2.32
2967 3477 3.554129 GGCCAATTCCAAACAACACCTAC 60.554 47.826 0.00 0.00 0.00 3.18
2971 3481 6.287525 CCAATTCCAAACAACACCTACATTT 58.712 36.000 0.00 0.00 0.00 2.32
3056 3584 3.549423 CGTCCGACAAAGAGAACTACACA 60.549 47.826 0.00 0.00 0.00 3.72
3058 3586 3.005472 TCCGACAAAGAGAACTACACAGG 59.995 47.826 0.00 0.00 0.00 4.00
3066 3594 2.812591 GAGAACTACACAGGTGAGACGA 59.187 50.000 6.40 0.00 0.00 4.20
3123 3651 3.316588 TGCGAAGGAGCATGTTTTTAACA 59.683 39.130 0.00 0.00 42.92 2.41
3150 3678 0.319040 ATCGATCAAGGGTCATCGCG 60.319 55.000 0.00 0.00 41.41 5.87
3158 3686 1.815421 GGGTCATCGCGTGCTCAAT 60.815 57.895 5.77 0.00 0.00 2.57
3169 3697 1.726853 GTGCTCAATCGCAACTAGGT 58.273 50.000 0.00 0.00 42.32 3.08
3170 3698 1.394917 GTGCTCAATCGCAACTAGGTG 59.605 52.381 2.45 2.45 42.32 4.00
3184 3712 4.776647 GGTGCGCGGCCATTTGAC 62.777 66.667 8.83 0.00 0.00 3.18
3209 3737 1.927487 TGGACGACTACTTTGCCCTA 58.073 50.000 0.00 0.00 0.00 3.53
3213 3741 3.887716 GGACGACTACTTTGCCCTAGATA 59.112 47.826 0.00 0.00 0.00 1.98
3216 3744 3.005578 CGACTACTTTGCCCTAGATACCC 59.994 52.174 0.00 0.00 0.00 3.69
3229 3757 4.585162 CCTAGATACCCTCTTCGTTGACAT 59.415 45.833 0.00 0.00 35.28 3.06
3243 3771 0.237235 TGACATTTTTCGCCTGCGTC 59.763 50.000 11.68 0.43 40.74 5.19
3247 3775 1.069296 CATTTTTCGCCTGCGTCTTCA 60.069 47.619 11.68 0.00 40.74 3.02
3252 3780 1.446792 CGCCTGCGTCTTCAGATGT 60.447 57.895 2.83 0.00 36.19 3.06
3260 3788 3.004629 TGCGTCTTCAGATGTGCAAAAAT 59.995 39.130 0.00 0.00 33.71 1.82
3266 3794 7.464444 CGTCTTCAGATGTGCAAAAATGTTTTT 60.464 33.333 0.00 0.00 40.75 1.94
3288 3816 0.393944 TCGTCTCTACCATGGCGTCT 60.394 55.000 13.04 0.00 0.00 4.18
3293 3821 0.324368 TCTACCATGGCGTCTGGTCT 60.324 55.000 13.04 0.00 43.59 3.85
3302 3830 2.290260 TGGCGTCTGGTCTTTTGATGAT 60.290 45.455 0.00 0.00 0.00 2.45
3337 3865 0.903454 AAGGACGTCGTGGGAAGGAT 60.903 55.000 12.13 0.00 0.00 3.24
3348 3876 2.041755 GTGGGAAGGATTGGGTTCTCTT 59.958 50.000 0.00 0.00 0.00 2.85
3349 3877 3.265995 GTGGGAAGGATTGGGTTCTCTTA 59.734 47.826 0.00 0.00 0.00 2.10
3353 3881 6.062749 GGGAAGGATTGGGTTCTCTTATTAC 58.937 44.000 0.00 0.00 0.00 1.89
3357 3885 5.970640 AGGATTGGGTTCTCTTATTACCAGA 59.029 40.000 0.00 0.00 33.51 3.86
3372 3900 2.044650 AGAAGTGCATGGCCGCAT 60.045 55.556 8.65 0.00 45.26 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.065374 TGGTTGAAATAGAGCTACACCAAAA 58.935 36.000 0.00 0.00 0.00 2.44
7 8 5.626142 TGGTTGAAATAGAGCTACACCAAA 58.374 37.500 0.00 0.00 0.00 3.28
9 10 4.530553 TCTGGTTGAAATAGAGCTACACCA 59.469 41.667 0.00 0.00 0.00 4.17
12 13 8.514594 CAATTTTCTGGTTGAAATAGAGCTACA 58.485 33.333 0.00 0.00 43.34 2.74
13 14 8.515414 ACAATTTTCTGGTTGAAATAGAGCTAC 58.485 33.333 0.00 0.00 43.34 3.58
14 15 8.635765 ACAATTTTCTGGTTGAAATAGAGCTA 57.364 30.769 0.00 0.00 43.34 3.32
15 16 7.530426 ACAATTTTCTGGTTGAAATAGAGCT 57.470 32.000 0.00 0.00 43.34 4.09
16 17 8.296713 TGTACAATTTTCTGGTTGAAATAGAGC 58.703 33.333 0.00 0.00 43.34 4.09
17 18 9.612620 GTGTACAATTTTCTGGTTGAAATAGAG 57.387 33.333 0.00 0.00 43.34 2.43
18 19 9.126151 TGTGTACAATTTTCTGGTTGAAATAGA 57.874 29.630 0.00 0.00 43.34 1.98
19 20 9.180678 GTGTGTACAATTTTCTGGTTGAAATAG 57.819 33.333 0.00 0.00 43.34 1.73
20 21 8.687242 TGTGTGTACAATTTTCTGGTTGAAATA 58.313 29.630 0.00 0.00 37.91 1.40
21 22 7.551585 TGTGTGTACAATTTTCTGGTTGAAAT 58.448 30.769 0.00 0.00 37.91 2.17
22 23 6.925211 TGTGTGTACAATTTTCTGGTTGAAA 58.075 32.000 0.00 0.00 37.07 2.69
23 24 6.516739 TGTGTGTACAATTTTCTGGTTGAA 57.483 33.333 0.00 0.00 32.88 2.69
24 25 6.502652 CATGTGTGTACAATTTTCTGGTTGA 58.497 36.000 0.00 0.00 40.84 3.18
25 26 5.175491 GCATGTGTGTACAATTTTCTGGTTG 59.825 40.000 0.00 0.00 40.84 3.77
26 27 5.288804 GCATGTGTGTACAATTTTCTGGTT 58.711 37.500 0.00 0.00 40.84 3.67
27 28 4.261994 GGCATGTGTGTACAATTTTCTGGT 60.262 41.667 0.00 0.00 40.84 4.00
28 29 4.236935 GGCATGTGTGTACAATTTTCTGG 58.763 43.478 0.00 0.00 40.84 3.86
29 30 4.236935 GGGCATGTGTGTACAATTTTCTG 58.763 43.478 0.00 0.00 40.84 3.02
30 31 3.057596 CGGGCATGTGTGTACAATTTTCT 60.058 43.478 0.00 0.00 40.84 2.52
31 32 3.241701 CGGGCATGTGTGTACAATTTTC 58.758 45.455 0.00 0.00 40.84 2.29
32 33 2.625790 ACGGGCATGTGTGTACAATTTT 59.374 40.909 0.00 0.00 40.84 1.82
33 34 2.235016 ACGGGCATGTGTGTACAATTT 58.765 42.857 0.00 0.00 40.84 1.82
34 35 1.904287 ACGGGCATGTGTGTACAATT 58.096 45.000 0.00 0.00 40.84 2.32
35 36 1.904287 AACGGGCATGTGTGTACAAT 58.096 45.000 0.00 0.00 40.84 2.71
36 37 2.545537 TAACGGGCATGTGTGTACAA 57.454 45.000 0.00 0.00 40.84 2.41
37 38 2.028020 TCATAACGGGCATGTGTGTACA 60.028 45.455 0.00 0.00 41.89 2.90
38 39 2.350498 GTCATAACGGGCATGTGTGTAC 59.650 50.000 0.00 0.00 0.00 2.90
39 40 2.235155 AGTCATAACGGGCATGTGTGTA 59.765 45.455 0.00 0.00 0.00 2.90
40 41 1.003118 AGTCATAACGGGCATGTGTGT 59.997 47.619 0.00 0.00 0.00 3.72
41 42 1.665679 GAGTCATAACGGGCATGTGTG 59.334 52.381 0.00 0.00 0.00 3.82
42 43 1.555075 AGAGTCATAACGGGCATGTGT 59.445 47.619 0.00 0.00 0.00 3.72
43 44 2.315925 AGAGTCATAACGGGCATGTG 57.684 50.000 0.00 0.00 0.00 3.21
44 45 2.365617 CCTAGAGTCATAACGGGCATGT 59.634 50.000 0.00 0.00 0.00 3.21
45 46 2.365617 ACCTAGAGTCATAACGGGCATG 59.634 50.000 0.00 0.00 0.00 4.06
46 47 2.679082 ACCTAGAGTCATAACGGGCAT 58.321 47.619 0.00 0.00 0.00 4.40
47 48 2.154567 ACCTAGAGTCATAACGGGCA 57.845 50.000 0.00 0.00 0.00 5.36
48 49 5.418209 ACATATACCTAGAGTCATAACGGGC 59.582 44.000 0.00 0.00 0.00 6.13
49 50 6.433404 ACACATATACCTAGAGTCATAACGGG 59.567 42.308 0.00 0.00 0.00 5.28
50 51 7.450124 ACACATATACCTAGAGTCATAACGG 57.550 40.000 0.00 0.00 0.00 4.44
51 52 9.217278 AGTACACATATACCTAGAGTCATAACG 57.783 37.037 0.00 0.00 0.00 3.18
91 92 9.620660 GTTCAAAGTTCACTCTTTAGTTTCAAA 57.379 29.630 0.00 0.00 36.12 2.69
92 93 9.010029 AGTTCAAAGTTCACTCTTTAGTTTCAA 57.990 29.630 0.00 0.00 36.12 2.69
93 94 8.561738 AGTTCAAAGTTCACTCTTTAGTTTCA 57.438 30.769 0.00 0.00 36.12 2.69
94 95 9.841880 AAAGTTCAAAGTTCACTCTTTAGTTTC 57.158 29.630 0.00 0.00 36.12 2.78
95 96 9.626045 CAAAGTTCAAAGTTCACTCTTTAGTTT 57.374 29.630 0.00 0.00 36.12 2.66
96 97 7.755373 GCAAAGTTCAAAGTTCACTCTTTAGTT 59.245 33.333 0.00 0.00 36.12 2.24
97 98 7.094377 TGCAAAGTTCAAAGTTCACTCTTTAGT 60.094 33.333 0.00 0.00 36.12 2.24
98 99 7.250569 TGCAAAGTTCAAAGTTCACTCTTTAG 58.749 34.615 0.00 0.00 36.12 1.85
99 100 7.151999 TGCAAAGTTCAAAGTTCACTCTTTA 57.848 32.000 0.00 0.00 36.12 1.85
100 101 6.024552 TGCAAAGTTCAAAGTTCACTCTTT 57.975 33.333 0.00 0.00 38.04 2.52
101 102 5.643379 TGCAAAGTTCAAAGTTCACTCTT 57.357 34.783 0.00 0.00 0.00 2.85
102 103 5.643379 TTGCAAAGTTCAAAGTTCACTCT 57.357 34.783 0.00 0.00 0.00 3.24
103 104 6.892310 ATTTGCAAAGTTCAAAGTTCACTC 57.108 33.333 18.19 0.00 36.93 3.51
104 105 7.294676 GAATTTGCAAAGTTCAAAGTTCACT 57.705 32.000 18.19 0.00 41.58 3.41
114 115 3.243839 TGGAGGCTGAATTTGCAAAGTTC 60.244 43.478 18.19 18.78 42.21 3.01
115 116 2.699846 TGGAGGCTGAATTTGCAAAGTT 59.300 40.909 18.19 11.57 0.00 2.66
116 117 2.318908 TGGAGGCTGAATTTGCAAAGT 58.681 42.857 18.19 15.58 0.00 2.66
117 118 3.604875 ATGGAGGCTGAATTTGCAAAG 57.395 42.857 18.19 4.70 0.00 2.77
118 119 4.066490 CAAATGGAGGCTGAATTTGCAAA 58.934 39.130 15.44 15.44 35.27 3.68
119 120 3.324268 TCAAATGGAGGCTGAATTTGCAA 59.676 39.130 19.49 0.00 39.85 4.08
120 121 2.898612 TCAAATGGAGGCTGAATTTGCA 59.101 40.909 19.49 10.60 39.85 4.08
121 122 3.598019 TCAAATGGAGGCTGAATTTGC 57.402 42.857 19.49 0.00 39.85 3.68
153 154 9.898152 AGGACAAACATTTCAAAAGGAATTAAA 57.102 25.926 0.00 0.00 34.91 1.52
158 159 9.323985 CAATTAGGACAAACATTTCAAAAGGAA 57.676 29.630 0.00 0.00 0.00 3.36
159 160 7.930865 CCAATTAGGACAAACATTTCAAAAGGA 59.069 33.333 0.00 0.00 41.22 3.36
160 161 7.714813 ACCAATTAGGACAAACATTTCAAAAGG 59.285 33.333 1.54 0.00 41.22 3.11
161 162 8.661352 ACCAATTAGGACAAACATTTCAAAAG 57.339 30.769 1.54 0.00 41.22 2.27
162 163 9.454859 AAACCAATTAGGACAAACATTTCAAAA 57.545 25.926 1.54 0.00 41.22 2.44
163 164 9.103861 GAAACCAATTAGGACAAACATTTCAAA 57.896 29.630 1.54 0.00 41.22 2.69
164 165 8.482128 AGAAACCAATTAGGACAAACATTTCAA 58.518 29.630 0.00 0.00 41.22 2.69
165 166 8.017418 AGAAACCAATTAGGACAAACATTTCA 57.983 30.769 0.00 0.00 41.22 2.69
166 167 9.406828 GTAGAAACCAATTAGGACAAACATTTC 57.593 33.333 1.54 0.00 41.22 2.17
167 168 8.919145 TGTAGAAACCAATTAGGACAAACATTT 58.081 29.630 1.54 0.00 41.22 2.32
168 169 8.472007 TGTAGAAACCAATTAGGACAAACATT 57.528 30.769 1.54 0.00 41.22 2.71
169 170 8.650143 ATGTAGAAACCAATTAGGACAAACAT 57.350 30.769 1.54 0.00 41.22 2.71
170 171 8.472007 AATGTAGAAACCAATTAGGACAAACA 57.528 30.769 1.54 0.00 41.22 2.83
171 172 9.406828 GAAATGTAGAAACCAATTAGGACAAAC 57.593 33.333 1.54 0.00 41.22 2.93
172 173 8.293867 CGAAATGTAGAAACCAATTAGGACAAA 58.706 33.333 1.54 0.00 41.22 2.83
173 174 7.662258 TCGAAATGTAGAAACCAATTAGGACAA 59.338 33.333 1.54 0.00 41.22 3.18
174 175 7.162761 TCGAAATGTAGAAACCAATTAGGACA 58.837 34.615 1.54 0.00 41.22 4.02
175 176 7.605410 TCGAAATGTAGAAACCAATTAGGAC 57.395 36.000 1.54 0.00 41.22 3.85
176 177 8.801882 AATCGAAATGTAGAAACCAATTAGGA 57.198 30.769 0.00 0.00 41.22 2.94
177 178 8.893727 AGAATCGAAATGTAGAAACCAATTAGG 58.106 33.333 0.00 0.00 45.67 2.69
178 179 9.708222 CAGAATCGAAATGTAGAAACCAATTAG 57.292 33.333 0.00 0.00 0.00 1.73
179 180 9.226606 ACAGAATCGAAATGTAGAAACCAATTA 57.773 29.630 0.00 0.00 0.00 1.40
180 181 8.110860 ACAGAATCGAAATGTAGAAACCAATT 57.889 30.769 0.00 0.00 0.00 2.32
181 182 7.687941 ACAGAATCGAAATGTAGAAACCAAT 57.312 32.000 0.00 0.00 0.00 3.16
197 198 9.737427 ACTCAGATGTAAATAGTAACAGAATCG 57.263 33.333 0.00 0.00 0.00 3.34
244 246 8.948401 AAGCTCTTATATTATGAGACAGAGGA 57.052 34.615 0.00 0.00 33.20 3.71
245 247 9.995003 AAAAGCTCTTATATTATGAGACAGAGG 57.005 33.333 0.00 0.00 33.20 3.69
257 259 9.372369 GTGTAGTGTCAGAAAAGCTCTTATATT 57.628 33.333 0.00 0.00 29.07 1.28
258 260 8.754080 AGTGTAGTGTCAGAAAAGCTCTTATAT 58.246 33.333 0.00 0.00 29.07 0.86
259 261 8.123639 AGTGTAGTGTCAGAAAAGCTCTTATA 57.876 34.615 0.00 0.00 29.07 0.98
260 262 6.998802 AGTGTAGTGTCAGAAAAGCTCTTAT 58.001 36.000 0.00 0.00 29.07 1.73
261 263 6.406692 AGTGTAGTGTCAGAAAAGCTCTTA 57.593 37.500 0.00 0.00 29.07 2.10
262 264 5.283457 AGTGTAGTGTCAGAAAAGCTCTT 57.717 39.130 0.00 0.00 29.07 2.85
263 265 4.946478 AGTGTAGTGTCAGAAAAGCTCT 57.054 40.909 0.00 0.00 33.23 4.09
264 266 5.774630 ACTAGTGTAGTGTCAGAAAAGCTC 58.225 41.667 0.00 0.00 37.69 4.09
265 267 5.793030 ACTAGTGTAGTGTCAGAAAAGCT 57.207 39.130 0.00 0.00 37.69 3.74
276 278 6.515862 AGAGCTTTTCTGACACTAGTGTAGTG 60.516 42.308 27.98 19.31 46.88 2.74
277 279 5.536916 AGAGCTTTTCTGACACTAGTGTAGT 59.463 40.000 27.98 6.32 45.05 2.73
278 280 6.019779 AGAGCTTTTCTGACACTAGTGTAG 57.980 41.667 27.98 22.31 45.05 2.74
279 281 6.406692 AAGAGCTTTTCTGACACTAGTGTA 57.593 37.500 27.98 10.72 38.52 2.90
280 282 5.283457 AAGAGCTTTTCTGACACTAGTGT 57.717 39.130 28.27 28.27 40.21 3.55
281 283 9.593134 AATATAAGAGCTTTTCTGACACTAGTG 57.407 33.333 21.44 21.44 35.91 2.74
285 287 9.553064 CCATAATATAAGAGCTTTTCTGACACT 57.447 33.333 0.00 0.00 35.91 3.55
286 288 8.778358 CCCATAATATAAGAGCTTTTCTGACAC 58.222 37.037 0.00 0.00 35.91 3.67
287 289 8.713971 TCCCATAATATAAGAGCTTTTCTGACA 58.286 33.333 0.00 0.00 35.91 3.58
288 290 8.994170 GTCCCATAATATAAGAGCTTTTCTGAC 58.006 37.037 0.00 0.00 35.91 3.51
289 291 7.872993 CGTCCCATAATATAAGAGCTTTTCTGA 59.127 37.037 0.00 0.00 35.91 3.27
290 292 7.118390 CCGTCCCATAATATAAGAGCTTTTCTG 59.882 40.741 0.00 0.00 35.91 3.02
291 293 7.016268 TCCGTCCCATAATATAAGAGCTTTTCT 59.984 37.037 0.00 0.00 37.93 2.52
292 294 7.159372 TCCGTCCCATAATATAAGAGCTTTTC 58.841 38.462 0.00 0.00 0.00 2.29
293 295 7.074653 TCCGTCCCATAATATAAGAGCTTTT 57.925 36.000 0.00 0.00 0.00 2.27
294 296 6.295916 CCTCCGTCCCATAATATAAGAGCTTT 60.296 42.308 0.00 0.00 0.00 3.51
295 297 5.187967 CCTCCGTCCCATAATATAAGAGCTT 59.812 44.000 0.00 0.00 0.00 3.74
296 298 4.712337 CCTCCGTCCCATAATATAAGAGCT 59.288 45.833 0.00 0.00 0.00 4.09
297 299 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
298 300 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
299 301 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
300 302 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
301 303 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
302 304 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
303 305 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
304 306 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
305 307 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
306 308 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
307 309 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
308 310 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
309 311 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
310 312 2.378378 AATAGTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
311 313 4.831710 ACATAAATAGTACTCCCTCCGTCC 59.168 45.833 0.00 0.00 0.00 4.79
312 314 6.402456 AACATAAATAGTACTCCCTCCGTC 57.598 41.667 0.00 0.00 0.00 4.79
313 315 7.902920 TTAACATAAATAGTACTCCCTCCGT 57.097 36.000 0.00 0.00 0.00 4.69
314 316 8.365647 ACATTAACATAAATAGTACTCCCTCCG 58.634 37.037 0.00 0.00 0.00 4.63
331 333 6.371271 GCAAATAGCAAACCCAACATTAACAT 59.629 34.615 0.00 0.00 44.79 2.71
466 474 2.359900 GTGTTGGTGTCCATCCATCTC 58.640 52.381 0.00 0.00 34.75 2.75
467 475 1.339055 CGTGTTGGTGTCCATCCATCT 60.339 52.381 0.00 0.00 34.75 2.90
476 484 2.260869 ATGCCTGCGTGTTGGTGTC 61.261 57.895 0.00 0.00 0.00 3.67
526 544 5.038683 CGTCGCTCCATAACTTATTACACA 58.961 41.667 0.00 0.00 0.00 3.72
538 556 2.836360 GGGACCCGTCGCTCCATA 60.836 66.667 0.00 0.00 39.18 2.74
545 563 1.982938 AAAGGAGAGGGACCCGTCG 60.983 63.158 4.40 0.00 36.13 5.12
546 564 1.192803 ACAAAGGAGAGGGACCCGTC 61.193 60.000 4.40 6.11 0.00 4.79
547 565 0.115745 TACAAAGGAGAGGGACCCGT 59.884 55.000 4.40 0.00 0.00 5.28
548 566 0.535797 GTACAAAGGAGAGGGACCCG 59.464 60.000 4.40 0.00 0.00 5.28
560 580 4.622701 GCTTATCAGGCCAAGTACAAAG 57.377 45.455 5.01 0.00 0.00 2.77
580 600 5.758784 AGTTAAGTCACTGAGTAAAACTGGC 59.241 40.000 11.27 0.00 0.00 4.85
595 615 3.236047 TGGTCAGGCACTAGTTAAGTCA 58.764 45.455 0.00 0.00 35.76 3.41
640 665 1.132500 AGGACAGGGCTAGCAATACC 58.868 55.000 18.24 8.42 0.00 2.73
644 669 0.615331 CAGAAGGACAGGGCTAGCAA 59.385 55.000 18.24 0.00 0.00 3.91
657 682 1.115467 ATGGTCCTCGCTACAGAAGG 58.885 55.000 0.00 0.00 0.00 3.46
756 782 4.385405 GAGCAGCGCACAGGAGGT 62.385 66.667 11.47 0.00 0.00 3.85
784 810 2.035237 AAACCTCGGCCTCACACGAA 62.035 55.000 0.00 0.00 38.79 3.85
790 816 1.074248 GGGAAAAACCTCGGCCTCA 59.926 57.895 0.00 0.00 38.98 3.86
817 843 1.134848 TGCAAAGAAAGGCTTGCGTTT 60.135 42.857 12.19 12.19 36.80 3.60
825 851 2.729378 GCATCGTGCAAAGAAAGGC 58.271 52.632 0.00 0.00 44.26 4.35
871 897 1.278238 GGTGATTGACGTGACGATCC 58.722 55.000 13.70 0.57 31.65 3.36
873 899 1.076533 GCGGTGATTGACGTGACGAT 61.077 55.000 13.70 0.00 0.00 3.73
874 900 1.731613 GCGGTGATTGACGTGACGA 60.732 57.895 13.70 0.00 0.00 4.20
875 901 2.769617 GCGGTGATTGACGTGACG 59.230 61.111 2.24 2.24 0.00 4.35
876 902 2.769617 CGCGGTGATTGACGTGAC 59.230 61.111 0.00 0.00 42.67 3.67
881 907 2.476051 CAGTGCGCGGTGATTGAC 59.524 61.111 8.83 0.00 0.00 3.18
882 908 2.741985 CCAGTGCGCGGTGATTGA 60.742 61.111 8.83 0.00 0.00 2.57
883 909 4.465512 GCCAGTGCGCGGTGATTG 62.466 66.667 8.83 0.00 0.00 2.67
929 955 0.036388 CGGGGTTTAAGAGCAGCAGA 60.036 55.000 0.00 0.00 0.00 4.26
991 1017 1.299541 GTGGTATCCATTCGCCAGTG 58.700 55.000 0.00 0.00 35.28 3.66
994 1020 0.756294 ATCGTGGTATCCATTCGCCA 59.244 50.000 0.00 0.00 35.28 5.69
995 1021 1.148310 CATCGTGGTATCCATTCGCC 58.852 55.000 0.00 0.00 35.28 5.54
996 1022 0.512952 GCATCGTGGTATCCATTCGC 59.487 55.000 0.00 0.00 35.28 4.70
997 1023 1.148310 GGCATCGTGGTATCCATTCG 58.852 55.000 0.00 0.00 35.28 3.34
998 1024 1.148310 CGGCATCGTGGTATCCATTC 58.852 55.000 0.00 0.00 35.28 2.67
999 1025 0.250295 CCGGCATCGTGGTATCCATT 60.250 55.000 0.00 0.00 35.28 3.16
1000 1026 1.371183 CCGGCATCGTGGTATCCAT 59.629 57.895 0.00 0.00 35.28 3.41
1001 1027 2.818841 CCGGCATCGTGGTATCCA 59.181 61.111 0.00 0.00 33.95 3.41
1002 1028 2.665185 GCCGGCATCGTGGTATCC 60.665 66.667 24.80 0.00 33.95 2.59
1003 1029 2.660258 AAGGCCGGCATCGTGGTATC 62.660 60.000 30.85 6.30 33.95 2.24
1004 1030 2.660258 GAAGGCCGGCATCGTGGTAT 62.660 60.000 30.85 3.11 33.95 2.73
1005 1031 3.379865 GAAGGCCGGCATCGTGGTA 62.380 63.158 30.85 0.00 33.95 3.25
1022 1048 1.675310 CACAGGAAGGCCGCAATGA 60.675 57.895 0.00 0.00 39.96 2.57
1031 1057 1.078567 GAGAGCAGGCACAGGAAGG 60.079 63.158 0.00 0.00 0.00 3.46
1461 1502 1.610673 GAGGGACCTGAGCCTGACA 60.611 63.158 0.00 0.00 0.00 3.58
1542 1583 1.300931 GTGCACCAGCGACTTGAGA 60.301 57.895 5.22 0.00 46.23 3.27
1614 1655 2.750350 CCGACCAAGCCCTTGAGT 59.250 61.111 9.50 5.86 42.93 3.41
1725 1766 4.467084 GGAATGCCGCCGGTGAGA 62.467 66.667 18.79 1.88 0.00 3.27
1750 1791 2.670148 GGGAGGTGAGGTTGGCGAT 61.670 63.158 0.00 0.00 0.00 4.58
1783 1824 1.681538 TTGAGGCCGTTGTTGCTTAA 58.318 45.000 0.00 0.00 0.00 1.85
1827 1868 1.609501 CTGGAGGTTCCGGAGACCA 60.610 63.158 27.10 21.73 45.95 4.02
1971 2012 4.074526 GTCAGGCTCGCCAGCTGA 62.075 66.667 17.39 2.45 46.03 4.26
2238 2282 3.419759 ACCGAATCACGCGCCAAC 61.420 61.111 5.73 0.00 41.07 3.77
2250 2294 1.080772 CGTAGCACTGCTCACCGAA 60.081 57.895 6.86 0.00 40.44 4.30
2266 2310 3.461773 CCTCGCCATCACTCCCGT 61.462 66.667 0.00 0.00 0.00 5.28
2386 2433 3.692593 GGGCAGTAACCAACATACGAATT 59.307 43.478 0.00 0.00 0.00 2.17
2393 2440 2.603075 ACATGGGCAGTAACCAACAT 57.397 45.000 0.00 0.00 42.17 2.71
2478 2528 4.038162 AGAAGAGTCAACAGCTTTCTACGT 59.962 41.667 0.00 0.00 0.00 3.57
2479 2529 4.551388 AGAAGAGTCAACAGCTTTCTACG 58.449 43.478 0.00 0.00 0.00 3.51
2480 2530 4.926832 GGAGAAGAGTCAACAGCTTTCTAC 59.073 45.833 0.00 0.00 0.00 2.59
2481 2531 4.588951 TGGAGAAGAGTCAACAGCTTTCTA 59.411 41.667 0.00 0.00 0.00 2.10
2572 2861 1.021390 ATCGAGTTCCTTGCGGCAAG 61.021 55.000 30.80 30.80 40.75 4.01
2573 2862 1.003839 ATCGAGTTCCTTGCGGCAA 60.004 52.632 15.55 15.55 0.00 4.52
2574 2863 1.741401 CATCGAGTTCCTTGCGGCA 60.741 57.895 0.00 0.00 0.00 5.69
2575 2864 1.424493 CTCATCGAGTTCCTTGCGGC 61.424 60.000 0.00 0.00 0.00 6.53
2576 2865 0.108615 ACTCATCGAGTTCCTTGCGG 60.109 55.000 0.00 0.00 40.28 5.69
2577 2866 1.272781 GACTCATCGAGTTCCTTGCG 58.727 55.000 0.00 0.00 43.53 4.85
2578 2867 1.646189 GGACTCATCGAGTTCCTTGC 58.354 55.000 0.00 0.00 43.53 4.01
2579 2868 1.202582 ACGGACTCATCGAGTTCCTTG 59.797 52.381 0.00 0.00 43.53 3.61
2580 2869 1.473278 GACGGACTCATCGAGTTCCTT 59.527 52.381 0.00 0.00 43.53 3.36
2581 2870 1.096416 GACGGACTCATCGAGTTCCT 58.904 55.000 0.00 0.00 43.53 3.36
2591 2880 1.666011 GCTGAAGGTGACGGACTCA 59.334 57.895 0.00 0.00 0.00 3.41
2597 2886 1.007336 GTGTACCGCTGAAGGTGACG 61.007 60.000 5.65 0.00 45.54 4.35
2606 2895 1.741770 GAGCCCAAGTGTACCGCTG 60.742 63.158 0.00 0.00 0.00 5.18
2608 2897 2.436115 GGAGCCCAAGTGTACCGC 60.436 66.667 0.00 0.00 0.00 5.68
2645 2934 0.041238 TCGGAGGAGAGGTGTGGAAT 59.959 55.000 0.00 0.00 0.00 3.01
2665 2954 0.109179 TAACGGTACTTGCGCGATGT 60.109 50.000 12.10 7.35 0.00 3.06
2667 2956 1.143969 GCTAACGGTACTTGCGCGAT 61.144 55.000 12.10 0.00 0.00 4.58
2675 3156 2.698855 TCGTAGGAGCTAACGGTACT 57.301 50.000 13.75 0.00 35.57 2.73
2744 3225 4.605640 ACCATCAACACCAATCCAAAAG 57.394 40.909 0.00 0.00 0.00 2.27
2745 3226 5.221541 GGTAACCATCAACACCAATCCAAAA 60.222 40.000 0.00 0.00 0.00 2.44
2775 3279 1.394618 TTGGTCGACCCCAAAGTTTG 58.605 50.000 31.19 8.73 41.47 2.93
2845 3349 2.642139 TGAATGCTAAAGCTTGCTGC 57.358 45.000 0.00 5.66 42.66 5.25
2890 3394 2.705312 TTTGGAATCGGCTGCCCACA 62.705 55.000 14.12 2.21 0.00 4.17
2934 3444 4.496336 ATTGGCCCCTGCTCGCTC 62.496 66.667 0.00 0.00 37.74 5.03
2935 3445 4.052518 AATTGGCCCCTGCTCGCT 62.053 61.111 0.00 0.00 37.74 4.93
2936 3446 3.521796 GAATTGGCCCCTGCTCGC 61.522 66.667 0.00 0.00 37.74 5.03
2977 3487 4.341487 ATGTACTCATATCCGAATCGGGA 58.659 43.478 22.53 10.74 38.91 5.14
2978 3488 4.720649 ATGTACTCATATCCGAATCGGG 57.279 45.455 22.53 6.84 38.91 5.14
3000 3528 7.368833 GTGGACTCAACGTAGTGCTTATATAT 58.631 38.462 10.75 0.00 45.00 0.86
3001 3529 6.238842 GGTGGACTCAACGTAGTGCTTATATA 60.239 42.308 10.75 0.00 45.00 0.86
3002 3530 5.451520 GGTGGACTCAACGTAGTGCTTATAT 60.452 44.000 10.75 0.00 45.00 0.86
3006 3534 1.270147 GGTGGACTCAACGTAGTGCTT 60.270 52.381 10.75 0.00 45.00 3.91
3041 3569 4.985409 GTCTCACCTGTGTAGTTCTCTTTG 59.015 45.833 0.00 0.00 0.00 2.77
3043 3571 3.253677 CGTCTCACCTGTGTAGTTCTCTT 59.746 47.826 0.00 0.00 0.00 2.85
3044 3572 2.814919 CGTCTCACCTGTGTAGTTCTCT 59.185 50.000 0.00 0.00 0.00 3.10
3045 3573 2.812591 TCGTCTCACCTGTGTAGTTCTC 59.187 50.000 0.00 0.00 0.00 2.87
3056 3584 1.276138 TGCATCATTGTCGTCTCACCT 59.724 47.619 0.00 0.00 0.00 4.00
3058 3586 2.475187 GCTTGCATCATTGTCGTCTCAC 60.475 50.000 0.00 0.00 0.00 3.51
3066 3594 0.322816 AGGACCGCTTGCATCATTGT 60.323 50.000 0.00 0.00 0.00 2.71
3117 3645 5.822519 CCTTGATCGATCCCTTGATGTTAAA 59.177 40.000 22.31 4.78 0.00 1.52
3119 3647 4.202357 CCCTTGATCGATCCCTTGATGTTA 60.202 45.833 22.31 0.00 0.00 2.41
3123 3651 2.370189 GACCCTTGATCGATCCCTTGAT 59.630 50.000 22.31 4.05 0.00 2.57
3165 3693 3.130819 CAAATGGCCGCGCACCTA 61.131 61.111 16.63 0.36 0.00 3.08
3170 3698 4.398598 AACGTCAAATGGCCGCGC 62.399 61.111 0.00 0.00 0.00 6.86
3175 3703 1.465689 CGTCCATCAACGTCAAATGGC 60.466 52.381 15.42 11.08 39.86 4.40
3184 3712 2.092211 GCAAAGTAGTCGTCCATCAACG 59.908 50.000 0.00 0.00 43.92 4.10
3209 3737 5.422214 AAATGTCAACGAAGAGGGTATCT 57.578 39.130 0.00 0.00 41.27 1.98
3213 3741 3.250040 CGAAAAATGTCAACGAAGAGGGT 59.750 43.478 0.00 0.00 0.00 4.34
3216 3744 3.058914 AGGCGAAAAATGTCAACGAAGAG 60.059 43.478 0.00 0.00 0.00 2.85
3229 3757 0.586319 CTGAAGACGCAGGCGAAAAA 59.414 50.000 21.62 1.04 42.83 1.94
3266 3794 2.292569 GACGCCATGGTAGAGACGATAA 59.707 50.000 14.67 0.00 0.00 1.75
3267 3795 1.878088 GACGCCATGGTAGAGACGATA 59.122 52.381 14.67 0.00 0.00 2.92
3271 3799 0.103208 CCAGACGCCATGGTAGAGAC 59.897 60.000 14.67 3.57 32.85 3.36
3337 3865 6.472887 CACTTCTGGTAATAAGAGAACCCAA 58.527 40.000 0.00 0.00 31.97 4.12
3348 3876 2.744823 CGGCCATGCACTTCTGGTAATA 60.745 50.000 2.24 0.00 34.86 0.98
3349 3877 1.767759 GGCCATGCACTTCTGGTAAT 58.232 50.000 0.00 0.00 34.86 1.89
3353 3881 3.818787 GCGGCCATGCACTTCTGG 61.819 66.667 2.24 0.00 35.53 3.86


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

AutoCloner maintained by Alex Coulton.