Multiple sequence alignment - TraesCS2B01G285800

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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 TraesCS2B01G285800 chr2B 100.000 8827 0 0 1 8827 393475571 393466745 0.000000e+00 16301
1 TraesCS2B01G285800 chr2B 93.966 232 14 0 6444 6675 393468897 393468666 1.410000e-92 351
2 TraesCS2B01G285800 chr2B 93.966 232 14 0 6675 6906 393469128 393468897 1.410000e-92 351
3 TraesCS2B01G285800 chr2B 79.817 218 42 2 170 387 25935718 25935933 3.300000e-34 158
4 TraesCS2B01G285800 chr2D 95.941 6874 226 17 169 7011 324605511 324598660 0.000000e+00 11099
5 TraesCS2B01G285800 chr2D 97.174 1840 35 8 7004 8827 324598637 324596799 0.000000e+00 3094
6 TraesCS2B01G285800 chr2D 92.672 232 17 0 6444 6675 324598996 324598765 1.420000e-87 335
7 TraesCS2B01G285800 chr2D 92.672 232 17 0 6675 6906 324599227 324598996 1.420000e-87 335
8 TraesCS2B01G285800 chr2D 92.857 168 10 1 1 166 45721069 45721236 8.850000e-60 243
9 TraesCS2B01G285800 chr2D 81.938 227 31 1 389 605 167003613 167003387 5.440000e-42 183
10 TraesCS2B01G285800 chr2D 96.875 96 3 0 4709 4804 324600869 324600774 2.550000e-35 161
11 TraesCS2B01G285800 chr2D 93.750 96 6 0 4805 4900 324600965 324600870 2.570000e-30 145
12 TraesCS2B01G285800 chr2D 77.169 219 40 7 169 383 178535031 178534819 1.560000e-22 119
13 TraesCS2B01G285800 chr2A 95.755 6878 235 18 175 7011 394010418 394017279 0.000000e+00 11031
14 TraesCS2B01G285800 chr2A 96.298 1837 50 10 7005 8827 394017303 394019135 0.000000e+00 3000
15 TraesCS2B01G285800 chr2A 93.103 232 16 0 6675 6906 394016712 394016943 3.050000e-89 340
16 TraesCS2B01G285800 chr2A 93.450 229 15 0 6444 6672 394016943 394017171 3.050000e-89 340
17 TraesCS2B01G285800 chr2A 80.967 331 56 7 5396 5721 724109749 724109421 1.140000e-63 255
18 TraesCS2B01G285800 chr2A 82.819 227 29 2 387 603 555806411 555806185 2.510000e-45 195
19 TraesCS2B01G285800 chr2A 95.833 96 4 0 4709 4804 394015071 394015166 1.190000e-33 156
20 TraesCS2B01G285800 chr2A 92.708 96 7 0 4805 4900 394014975 394015070 1.190000e-28 139
21 TraesCS2B01G285800 chr2A 78.453 181 30 9 169 346 82341816 82341990 9.370000e-20 110
22 TraesCS2B01G285800 chr6B 91.429 210 17 1 388 596 27120824 27120615 4.030000e-73 287
23 TraesCS2B01G285800 chr6B 92.216 167 11 1 1 165 603937304 603937138 1.480000e-57 235
24 TraesCS2B01G285800 chr5A 80.000 365 69 4 5396 5759 568571331 568571692 5.250000e-67 267
25 TraesCS2B01G285800 chrUn 80.665 331 57 7 5396 5721 69802415 69802087 5.290000e-62 250
26 TraesCS2B01G285800 chr4A 80.363 331 58 7 5396 5721 2619845 2620173 2.460000e-60 244
27 TraesCS2B01G285800 chr4A 85.022 227 22 3 387 602 685317454 685317679 4.150000e-53 220
28 TraesCS2B01G285800 chr5D 92.857 168 10 1 1 166 197484314 197484481 8.850000e-60 243
29 TraesCS2B01G285800 chr5D 92.216 167 11 1 2 166 88579128 88578962 1.480000e-57 235
30 TraesCS2B01G285800 chr4B 92.262 168 11 1 1 166 600227900 600228067 4.120000e-58 237
31 TraesCS2B01G285800 chr4B 91.813 171 10 4 1 168 38810166 38809997 1.480000e-57 235
32 TraesCS2B01G285800 chr4B 90.909 176 11 5 1 174 60705726 60705554 1.920000e-56 231
33 TraesCS2B01G285800 chr4B 86.923 130 17 0 471 600 467249488 467249617 7.140000e-31 147
34 TraesCS2B01G285800 chr1D 92.262 168 11 1 1 166 106855596 106855763 4.120000e-58 237
35 TraesCS2B01G285800 chr3D 92.216 167 11 1 1 165 198977380 198977546 1.480000e-57 235
36 TraesCS2B01G285800 chr3D 82.960 223 32 5 387 603 250915888 250916110 6.990000e-46 196
37 TraesCS2B01G285800 chr7A 79.697 330 62 5 5396 5721 619254372 619254044 5.330000e-57 233
38 TraesCS2B01G285800 chr3A 78.098 347 70 6 5417 5759 31814403 31814747 1.930000e-51 215
39 TraesCS2B01G285800 chr7D 82.110 218 35 4 169 384 508896879 508897094 5.440000e-42 183
40 TraesCS2B01G285800 chr3B 84.264 197 20 4 419 605 703031443 703031248 1.960000e-41 182
41 TraesCS2B01G285800 chr7B 80.269 223 34 2 387 599 490891667 490891889 9.170000e-35 159
42 TraesCS2B01G285800 chr7B 81.609 174 32 0 173 346 629579233 629579060 2.570000e-30 145
43 TraesCS2B01G285800 chr6D 79.343 213 40 2 170 381 400551036 400550827 7.140000e-31 147
44 TraesCS2B01G285800 chr6D 78.771 179 33 5 169 344 9974546 9974722 2.010000e-21 115
45 TraesCS2B01G285800 chr6A 78.365 208 42 3 179 384 554781868 554781662 2.000000e-26 132


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 TraesCS2B01G285800 chr2B 393466745 393475571 8826 True 16301.0 16301 100.00000 1 8827 1 chr2B.!!$R1 8826
1 TraesCS2B01G285800 chr2D 324596799 324605511 8712 True 7096.5 11099 96.55750 169 8827 2 chr2D.!!$R3 8658
2 TraesCS2B01G285800 chr2D 324598765 324600965 2200 True 244.0 335 93.99225 4709 6906 4 chr2D.!!$R4 2197
3 TraesCS2B01G285800 chr2A 394010418 394019135 8717 False 2501.0 11031 94.52450 175 8827 6 chr2A.!!$F2 8652

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
446 447 0.107654 CTGGTCCCTCGTCAATTCCC 60.108 60.000 0.00 0.0 0.00 3.97 F
1336 1366 0.323451 GGCGGGAACTTGGGATCTTT 60.323 55.000 0.00 0.0 0.00 2.52 F
2089 2119 0.178915 TATGGCGGCCCTATACCAGT 60.179 55.000 17.97 0.0 35.20 4.00 F
2821 2851 0.948816 TGGGTAGGGGAGATGATGGA 59.051 55.000 0.00 0.0 0.00 3.41 F
4573 4615 0.688749 ATGGGCCAATGGAGGAAAGC 60.689 55.000 11.89 0.0 0.00 3.51 F
5844 5892 0.179043 TTACGCTTGGGTGCTGTGAA 60.179 50.000 0.45 0.0 0.00 3.18 F
6457 6506 0.035820 TATTGTCCACAGGAACCGGC 60.036 55.000 0.00 0.0 31.38 6.13 F
6486 6535 0.390472 GAAGCAGGACGAGGGAACAG 60.390 60.000 0.00 0.0 0.00 3.16 F
7167 7246 1.001378 CAGTAAACACAGGTTGCCAGC 60.001 52.381 0.00 0.0 37.30 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2091 0.174845 GGGCCGCCATAAAAAGTTCC 59.825 55.000 12.58 0.00 0.00 3.62 R
2254 2284 1.687612 CCCAGGCACATCTTGGTCT 59.312 57.895 0.00 0.00 0.00 3.85 R
3669 3699 0.721718 CTCCTCATCGGCGACAAAAC 59.278 55.000 13.76 0.00 0.00 2.43 R
4700 4742 0.827507 TCTTTCTTGGCCAAGCACCC 60.828 55.000 36.24 0.00 38.28 4.61 R
6233 6282 1.079405 CTGCCTTGCCTGCAAATGG 60.079 57.895 6.00 5.96 38.46 3.16 R
7167 7246 0.815095 GGTCGGCCAAATTTACTGGG 59.185 55.000 0.00 0.00 34.25 4.45 R
7404 7483 1.148273 TCACCAACTCCAGTGCACC 59.852 57.895 14.63 0.00 33.90 5.01 R
7726 7806 4.507756 TCATGAGAGTCAACACAAACGAAG 59.492 41.667 0.00 0.00 0.00 3.79 R
8618 8714 0.668535 GTTGGACAGGCAGTTGTTCC 59.331 55.000 0.00 0.00 0.00 3.62 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
27 28 9.701355 GGTGCAAATATTTGTTATTTTATGTGC 57.299 29.630 25.15 10.62 38.23 4.57
30 31 9.919348 GCAAATATTTGTTATTTTATGTGCAGG 57.081 29.630 25.15 0.00 38.23 4.85
48 49 2.779506 AGGTACTGCTAAAGGTGTTGC 58.220 47.619 0.00 0.00 37.18 4.17
49 50 1.463444 GGTACTGCTAAAGGTGTTGCG 59.537 52.381 0.00 0.00 0.00 4.85
50 51 2.140717 GTACTGCTAAAGGTGTTGCGT 58.859 47.619 0.00 0.00 0.00 5.24
51 52 0.944386 ACTGCTAAAGGTGTTGCGTG 59.056 50.000 0.00 0.00 0.00 5.34
52 53 1.225855 CTGCTAAAGGTGTTGCGTGA 58.774 50.000 0.00 0.00 0.00 4.35
53 54 1.806542 CTGCTAAAGGTGTTGCGTGAT 59.193 47.619 0.00 0.00 0.00 3.06
54 55 2.226330 TGCTAAAGGTGTTGCGTGATT 58.774 42.857 0.00 0.00 0.00 2.57
55 56 2.225491 TGCTAAAGGTGTTGCGTGATTC 59.775 45.455 0.00 0.00 0.00 2.52
56 57 2.484264 GCTAAAGGTGTTGCGTGATTCT 59.516 45.455 0.00 0.00 0.00 2.40
57 58 3.424962 GCTAAAGGTGTTGCGTGATTCTC 60.425 47.826 0.00 0.00 0.00 2.87
58 59 1.523758 AAGGTGTTGCGTGATTCTCC 58.476 50.000 0.00 0.00 0.00 3.71
59 60 0.687354 AGGTGTTGCGTGATTCTCCT 59.313 50.000 0.00 0.00 0.00 3.69
60 61 1.899814 AGGTGTTGCGTGATTCTCCTA 59.100 47.619 0.00 0.00 0.00 2.94
61 62 2.000447 GGTGTTGCGTGATTCTCCTAC 59.000 52.381 0.00 0.00 0.00 3.18
62 63 2.353803 GGTGTTGCGTGATTCTCCTACT 60.354 50.000 0.00 0.00 0.00 2.57
63 64 2.668457 GTGTTGCGTGATTCTCCTACTG 59.332 50.000 0.00 0.00 0.00 2.74
64 65 2.271800 GTTGCGTGATTCTCCTACTGG 58.728 52.381 0.00 0.00 0.00 4.00
65 66 1.847328 TGCGTGATTCTCCTACTGGA 58.153 50.000 0.00 0.00 40.69 3.86
66 67 2.388735 TGCGTGATTCTCCTACTGGAT 58.611 47.619 0.00 0.00 42.29 3.41
67 68 2.766263 TGCGTGATTCTCCTACTGGATT 59.234 45.455 0.00 0.00 42.29 3.01
68 69 3.126831 GCGTGATTCTCCTACTGGATTG 58.873 50.000 0.00 0.00 42.29 2.67
69 70 3.181475 GCGTGATTCTCCTACTGGATTGA 60.181 47.826 0.00 0.00 42.29 2.57
70 71 4.502259 GCGTGATTCTCCTACTGGATTGAT 60.502 45.833 0.00 0.00 42.29 2.57
71 72 5.279006 GCGTGATTCTCCTACTGGATTGATA 60.279 44.000 0.00 0.00 42.29 2.15
72 73 6.738731 GCGTGATTCTCCTACTGGATTGATAA 60.739 42.308 0.00 0.00 42.29 1.75
73 74 6.642950 CGTGATTCTCCTACTGGATTGATAAC 59.357 42.308 0.00 0.00 42.29 1.89
74 75 6.931840 GTGATTCTCCTACTGGATTGATAACC 59.068 42.308 0.00 0.00 42.29 2.85
75 76 6.846505 TGATTCTCCTACTGGATTGATAACCT 59.153 38.462 0.00 0.00 42.29 3.50
76 77 7.348274 TGATTCTCCTACTGGATTGATAACCTT 59.652 37.037 0.00 0.00 42.29 3.50
77 78 6.485830 TCTCCTACTGGATTGATAACCTTG 57.514 41.667 0.00 0.00 42.29 3.61
78 79 6.202331 TCTCCTACTGGATTGATAACCTTGA 58.798 40.000 0.00 0.00 42.29 3.02
79 80 6.846505 TCTCCTACTGGATTGATAACCTTGAT 59.153 38.462 0.00 0.00 42.29 2.57
80 81 7.348274 TCTCCTACTGGATTGATAACCTTGATT 59.652 37.037 0.00 0.00 42.29 2.57
81 82 7.509546 TCCTACTGGATTGATAACCTTGATTC 58.490 38.462 0.00 0.00 37.46 2.52
82 83 7.348274 TCCTACTGGATTGATAACCTTGATTCT 59.652 37.037 0.00 0.00 37.46 2.40
83 84 7.995488 CCTACTGGATTGATAACCTTGATTCTT 59.005 37.037 0.00 0.00 34.57 2.52
86 87 9.178758 ACTGGATTGATAACCTTGATTCTTAAC 57.821 33.333 0.00 0.00 0.00 2.01
87 88 9.401058 CTGGATTGATAACCTTGATTCTTAACT 57.599 33.333 0.00 0.00 0.00 2.24
88 89 9.177608 TGGATTGATAACCTTGATTCTTAACTG 57.822 33.333 0.00 0.00 0.00 3.16
89 90 9.396022 GGATTGATAACCTTGATTCTTAACTGA 57.604 33.333 0.00 0.00 0.00 3.41
91 92 9.965902 ATTGATAACCTTGATTCTTAACTGAGT 57.034 29.630 0.00 0.00 0.00 3.41
92 93 8.777865 TGATAACCTTGATTCTTAACTGAGTG 57.222 34.615 0.00 0.00 0.00 3.51
93 94 8.593679 TGATAACCTTGATTCTTAACTGAGTGA 58.406 33.333 0.00 0.00 0.00 3.41
94 95 9.436957 GATAACCTTGATTCTTAACTGAGTGAA 57.563 33.333 0.00 0.00 0.00 3.18
95 96 9.793259 ATAACCTTGATTCTTAACTGAGTGAAA 57.207 29.630 0.00 0.00 0.00 2.69
96 97 8.697507 AACCTTGATTCTTAACTGAGTGAAAT 57.302 30.769 0.00 0.00 0.00 2.17
97 98 9.793259 AACCTTGATTCTTAACTGAGTGAAATA 57.207 29.630 0.00 0.00 0.00 1.40
98 99 9.220767 ACCTTGATTCTTAACTGAGTGAAATAC 57.779 33.333 0.00 0.00 0.00 1.89
99 100 9.442047 CCTTGATTCTTAACTGAGTGAAATACT 57.558 33.333 0.00 0.00 44.02 2.12
111 112 9.469097 ACTGAGTGAAATACTTATCTCTACTGT 57.531 33.333 0.00 0.00 40.53 3.55
123 124 9.509956 ACTTATCTCTACTGTACTACATCATCC 57.490 37.037 0.00 0.00 0.00 3.51
124 125 8.865420 TTATCTCTACTGTACTACATCATCCC 57.135 38.462 0.00 0.00 0.00 3.85
125 126 5.632118 TCTCTACTGTACTACATCATCCCC 58.368 45.833 0.00 0.00 0.00 4.81
126 127 5.372959 TCTCTACTGTACTACATCATCCCCT 59.627 44.000 0.00 0.00 0.00 4.79
127 128 5.632118 TCTACTGTACTACATCATCCCCTC 58.368 45.833 0.00 0.00 0.00 4.30
128 129 3.577919 ACTGTACTACATCATCCCCTCC 58.422 50.000 0.00 0.00 0.00 4.30
129 130 3.207777 ACTGTACTACATCATCCCCTCCT 59.792 47.826 0.00 0.00 0.00 3.69
130 131 3.829601 CTGTACTACATCATCCCCTCCTC 59.170 52.174 0.00 0.00 0.00 3.71
131 132 3.467483 TGTACTACATCATCCCCTCCTCT 59.533 47.826 0.00 0.00 0.00 3.69
132 133 3.715648 ACTACATCATCCCCTCCTCTT 57.284 47.619 0.00 0.00 0.00 2.85
133 134 3.582164 ACTACATCATCCCCTCCTCTTC 58.418 50.000 0.00 0.00 0.00 2.87
134 135 1.418334 ACATCATCCCCTCCTCTTCG 58.582 55.000 0.00 0.00 0.00 3.79
135 136 0.683973 CATCATCCCCTCCTCTTCGG 59.316 60.000 0.00 0.00 0.00 4.30
136 137 0.472734 ATCATCCCCTCCTCTTCGGG 60.473 60.000 0.00 0.00 40.29 5.14
140 141 4.147135 CCCTCCTCTTCGGGGAAA 57.853 61.111 0.00 0.00 42.58 3.13
141 142 2.621486 CCCTCCTCTTCGGGGAAAT 58.379 57.895 0.00 0.00 42.58 2.17
142 143 0.470341 CCCTCCTCTTCGGGGAAATC 59.530 60.000 0.00 0.00 42.58 2.17
143 144 0.470341 CCTCCTCTTCGGGGAAATCC 59.530 60.000 0.00 0.00 33.87 3.01
153 154 4.002797 GGAAATCCCAACGCAGCT 57.997 55.556 0.00 0.00 34.14 4.24
154 155 1.803289 GGAAATCCCAACGCAGCTC 59.197 57.895 0.00 0.00 34.14 4.09
155 156 1.425428 GAAATCCCAACGCAGCTCG 59.575 57.895 4.36 4.36 45.38 5.03
156 157 2.583685 GAAATCCCAACGCAGCTCGC 62.584 60.000 5.63 2.29 43.23 5.03
157 158 3.899981 AATCCCAACGCAGCTCGCA 62.900 57.895 8.52 0.00 42.60 5.10
158 159 3.899981 ATCCCAACGCAGCTCGCAA 62.900 57.895 8.52 0.00 42.60 4.85
159 160 4.093952 CCCAACGCAGCTCGCAAG 62.094 66.667 8.52 0.00 42.60 4.01
160 161 3.349006 CCAACGCAGCTCGCAAGT 61.349 61.111 8.52 0.00 42.60 3.16
161 162 2.027073 CCAACGCAGCTCGCAAGTA 61.027 57.895 8.52 0.00 42.60 2.24
162 163 1.417592 CAACGCAGCTCGCAAGTAG 59.582 57.895 8.52 0.00 42.60 2.57
163 164 2.383527 AACGCAGCTCGCAAGTAGC 61.384 57.895 8.52 0.00 42.60 3.58
164 165 2.810887 CGCAGCTCGCAAGTAGCA 60.811 61.111 8.52 0.00 46.13 3.49
165 166 2.796425 CGCAGCTCGCAAGTAGCAG 61.796 63.158 8.52 0.00 46.13 4.24
166 167 1.739562 GCAGCTCGCAAGTAGCAGT 60.740 57.895 3.64 0.00 46.13 4.40
167 168 0.458543 GCAGCTCGCAAGTAGCAGTA 60.459 55.000 3.64 0.00 46.13 2.74
168 169 1.554392 CAGCTCGCAAGTAGCAGTAG 58.446 55.000 0.00 0.00 46.13 2.57
169 170 1.133216 CAGCTCGCAAGTAGCAGTAGA 59.867 52.381 0.00 0.00 46.13 2.59
170 171 2.028130 AGCTCGCAAGTAGCAGTAGAT 58.972 47.619 0.00 0.00 46.13 1.98
171 172 2.034053 AGCTCGCAAGTAGCAGTAGATC 59.966 50.000 0.00 0.00 46.13 2.75
172 173 2.645163 CTCGCAAGTAGCAGTAGATCG 58.355 52.381 0.00 0.00 46.13 3.69
173 174 1.333931 TCGCAAGTAGCAGTAGATCGG 59.666 52.381 0.00 0.00 46.13 4.18
178 179 0.599060 GTAGCAGTAGATCGGAGCCC 59.401 60.000 0.00 0.00 0.00 5.19
203 204 1.721926 GACCAACTCGAAGAAGAAGCG 59.278 52.381 0.00 0.00 34.09 4.68
259 260 6.072286 GGACTAAAAACCCTAACCTAAACTGC 60.072 42.308 0.00 0.00 0.00 4.40
290 291 1.988107 TGAGGCACTGGAATTCTCCTT 59.012 47.619 5.23 0.00 41.55 3.36
324 325 3.071206 GGAGCGGCAGACAGAGGA 61.071 66.667 1.45 0.00 0.00 3.71
330 331 1.806568 GGCAGACAGAGGAGAGACG 59.193 63.158 0.00 0.00 0.00 4.18
334 335 2.223479 GCAGACAGAGGAGAGACGAATC 60.223 54.545 0.00 0.00 0.00 2.52
338 339 2.095461 CAGAGGAGAGACGAATCCACA 58.905 52.381 0.00 0.00 38.12 4.17
339 340 2.096248 AGAGGAGAGACGAATCCACAC 58.904 52.381 0.00 0.00 38.12 3.82
383 384 2.983791 GTGTAACCCTAGCCGCCA 59.016 61.111 0.00 0.00 0.00 5.69
394 395 3.391049 CCTAGCCGCCACTAATCTTAAC 58.609 50.000 0.00 0.00 0.00 2.01
402 403 5.454187 CCGCCACTAATCTTAACCCTTCATA 60.454 44.000 0.00 0.00 0.00 2.15
428 429 6.426646 AACTTATGTTCACTTCTCTGGTCT 57.573 37.500 0.00 0.00 0.00 3.85
429 430 5.788450 ACTTATGTTCACTTCTCTGGTCTG 58.212 41.667 0.00 0.00 0.00 3.51
440 441 1.606601 CTGGTCTGGTCCCTCGTCA 60.607 63.158 0.00 0.00 0.00 4.35
441 442 1.152419 TGGTCTGGTCCCTCGTCAA 60.152 57.895 0.00 0.00 0.00 3.18
442 443 0.544357 TGGTCTGGTCCCTCGTCAAT 60.544 55.000 0.00 0.00 0.00 2.57
443 444 0.613777 GGTCTGGTCCCTCGTCAATT 59.386 55.000 0.00 0.00 0.00 2.32
444 445 1.405661 GGTCTGGTCCCTCGTCAATTC 60.406 57.143 0.00 0.00 0.00 2.17
445 446 0.902531 TCTGGTCCCTCGTCAATTCC 59.097 55.000 0.00 0.00 0.00 3.01
446 447 0.107654 CTGGTCCCTCGTCAATTCCC 60.108 60.000 0.00 0.00 0.00 3.97
447 448 0.838554 TGGTCCCTCGTCAATTCCCA 60.839 55.000 0.00 0.00 0.00 4.37
448 449 0.546598 GGTCCCTCGTCAATTCCCAT 59.453 55.000 0.00 0.00 0.00 4.00
449 450 1.668419 GTCCCTCGTCAATTCCCATG 58.332 55.000 0.00 0.00 0.00 3.66
452 453 2.509548 TCCCTCGTCAATTCCCATGAAT 59.490 45.455 0.00 0.00 43.08 2.57
467 468 6.736110 CCCATGAATCAAACAAGGGAATAT 57.264 37.500 0.00 0.00 45.62 1.28
479 491 9.573133 CAAACAAGGGAATATAAATTCTCACAC 57.427 33.333 1.16 0.00 43.96 3.82
502 514 7.416817 CACATAATTCCTATCATGTGCGAAAA 58.583 34.615 4.32 0.00 41.11 2.29
530 546 7.280205 GTGGATTGGTAATAAAACGACTCATCT 59.720 37.037 0.00 0.00 0.00 2.90
543 559 6.707440 ACGACTCATCTCATGTCTAATCTT 57.293 37.500 0.00 0.00 0.00 2.40
571 587 3.442076 ACTCCCTACACTAAACTCCCAG 58.558 50.000 0.00 0.00 0.00 4.45
596 612 3.262915 CCCTTCCCAAATATTGCCAAACA 59.737 43.478 0.00 0.00 0.00 2.83
611 627 5.035443 TGCCAAACACGTTGTTAATGTAAC 58.965 37.500 4.24 0.00 40.14 2.50
723 743 3.034721 AGGCACACATGAAAAGCATTG 57.965 42.857 0.00 0.00 34.15 2.82
724 744 1.461897 GGCACACATGAAAAGCATTGC 59.538 47.619 0.00 0.00 37.47 3.56
725 745 2.136728 GCACACATGAAAAGCATTGCA 58.863 42.857 11.91 0.00 37.89 4.08
726 746 2.739913 GCACACATGAAAAGCATTGCAT 59.260 40.909 11.91 0.00 37.89 3.96
727 747 3.187637 GCACACATGAAAAGCATTGCATT 59.812 39.130 11.91 1.75 37.89 3.56
959 988 3.243805 ACGAAGATGCATCCTCTGATCTG 60.244 47.826 23.06 8.35 0.00 2.90
1003 1033 1.076014 CCCCCACACTAAACCCACC 59.924 63.158 0.00 0.00 0.00 4.61
1014 1044 4.459337 CACTAAACCCACCAATCTTCTTCC 59.541 45.833 0.00 0.00 0.00 3.46
1018 1048 2.716424 ACCCACCAATCTTCTTCCAAGA 59.284 45.455 0.00 0.00 0.00 3.02
1120 1150 2.261671 GACATGCACTCGGACGGT 59.738 61.111 0.00 0.00 0.00 4.83
1336 1366 0.323451 GGCGGGAACTTGGGATCTTT 60.323 55.000 0.00 0.00 0.00 2.52
1606 1636 2.282391 TGCAAGAAGGCGCACCAT 60.282 55.556 10.83 0.00 39.06 3.55
1894 1924 2.009681 TGCTGTCTCCCTTGTCAGTA 57.990 50.000 0.00 0.00 0.00 2.74
2061 2091 0.466124 GAGGTCCTCAATTCGGGGAG 59.534 60.000 14.46 0.00 0.00 4.30
2089 2119 0.178915 TATGGCGGCCCTATACCAGT 60.179 55.000 17.97 0.00 35.20 4.00
2254 2284 2.031245 CGTTGCAATGCAGTTTGGACTA 60.031 45.455 8.31 0.00 40.61 2.59
2336 2366 2.116238 CCTACGATTTGGAGGGGAAGA 58.884 52.381 0.00 0.00 0.00 2.87
2512 2542 1.078214 CATGGAAGCCGAGGCAGAA 60.078 57.895 17.18 0.00 44.88 3.02
2540 2570 2.349886 CGGAAAATGAAGAAGGCTCGAG 59.650 50.000 8.45 8.45 0.00 4.04
2776 2806 3.072211 GGTGCCAACTCCTACTGTAAAC 58.928 50.000 0.00 0.00 0.00 2.01
2821 2851 0.948816 TGGGTAGGGGAGATGATGGA 59.051 55.000 0.00 0.00 0.00 3.41
2845 2875 4.353777 ACTTCATGGCTAAGTCTCTGGTA 58.646 43.478 0.00 0.00 31.56 3.25
2961 2991 7.173218 GGTGTCAACTGAAATCTCTACATTCAA 59.827 37.037 0.00 0.00 33.08 2.69
3024 3054 2.228545 ACCAGTGAGCTGATCAGAGA 57.771 50.000 27.04 5.79 45.28 3.10
3124 3154 5.410746 TCTCTTGACTGATGTTGATTTCAGC 59.589 40.000 0.06 0.00 42.51 4.26
3345 3375 5.337554 CGAGTCTCGTGGTATGTCAAATAA 58.662 41.667 14.27 0.00 34.72 1.40
3441 3471 3.640029 ACCGTAGTTTCAGAAGGAGTTGA 59.360 43.478 0.00 0.00 0.00 3.18
3561 3591 3.509184 GCTTTGCCTGAGGAAATTCTTCT 59.491 43.478 0.65 0.00 0.00 2.85
3641 3671 2.031616 GTGCTGCTGCTGGAGTGA 59.968 61.111 17.00 0.00 40.48 3.41
3669 3699 5.567138 AATGATGAAGAAACCGCTTTAGG 57.433 39.130 0.00 0.00 37.30 2.69
3809 3839 8.048534 CATTGTAGAATGTGGAGAAGACATTT 57.951 34.615 4.45 0.00 42.74 2.32
3904 3934 8.292444 ACATTAATATGGCTGCAGTTCTTTTA 57.708 30.769 16.64 6.08 36.01 1.52
4012 4042 4.682859 GCAGAAGTAGAGGATGCAGAACAT 60.683 45.833 0.00 0.00 43.54 2.71
4043 4073 8.782137 AATTAATACTATGGCAAATGGAGGTT 57.218 30.769 0.00 0.00 0.00 3.50
4051 4081 3.645212 TGGCAAATGGAGGTTCAAATGAA 59.355 39.130 0.00 0.00 0.00 2.57
4171 4201 2.581246 AGGGCATGCAGATATGGATGAT 59.419 45.455 23.92 7.31 39.53 2.45
4394 4436 7.951530 ATACAAAGTGCAAAAATGAAAGGAG 57.048 32.000 0.00 0.00 0.00 3.69
4474 4516 2.916716 GCATGCAGAAACCAAACATACG 59.083 45.455 14.21 0.00 0.00 3.06
4573 4615 0.688749 ATGGGCCAATGGAGGAAAGC 60.689 55.000 11.89 0.00 0.00 3.51
4581 4623 2.426024 CAATGGAGGAAAGCACTGATGG 59.574 50.000 0.00 0.00 0.00 3.51
4697 4739 2.846371 CTTCCAGCAAGGGACGAAG 58.154 57.895 0.00 0.00 36.46 3.79
4700 4742 3.121030 CAGCAAGGGACGAAGCCG 61.121 66.667 0.00 0.00 42.50 5.52
4733 4775 7.616935 TGGCCAAGAAAGATATTGAAGAAGATT 59.383 33.333 0.61 0.00 29.05 2.40
4894 4936 2.417787 GGCACCAATTGAGAAAGATGCC 60.418 50.000 7.12 9.99 44.11 4.40
4986 5028 2.047830 AGTGAAACGAGAAGAAGGGGT 58.952 47.619 0.00 0.00 45.86 4.95
4989 5031 0.400594 AAACGAGAAGAAGGGGTGGG 59.599 55.000 0.00 0.00 0.00 4.61
5007 5049 0.250597 GGACGCAAGGTGTTAAGGGT 60.251 55.000 0.00 0.00 46.39 4.34
5182 5230 4.343814 GGTGTTGAGGAAAATCCCAAAGAA 59.656 41.667 0.00 0.00 37.19 2.52
5191 5239 6.210185 AGGAAAATCCCAAAGAAATCACTCAG 59.790 38.462 0.00 0.00 37.19 3.35
5200 5248 4.550076 AGAAATCACTCAGGAACAGGAG 57.450 45.455 0.00 0.00 37.89 3.69
5376 5424 5.447778 AATGAGAGGGAATCATTGTCTGT 57.552 39.130 0.62 0.00 43.87 3.41
5415 5463 4.808414 TTCAAGGAGTAGATGACCACAG 57.192 45.455 0.00 0.00 0.00 3.66
5526 5574 7.981789 TGCAGGAAGTGTCTATTAAACAGATAG 59.018 37.037 0.00 0.00 0.00 2.08
5603 5651 6.407525 GCCATATGGTAGGAGATGGATCTAAC 60.408 46.154 22.79 0.00 41.23 2.34
5643 5691 5.690865 AGGTTGATGAAACTTGGTCTACAA 58.309 37.500 0.00 0.00 38.92 2.41
5844 5892 0.179043 TTACGCTTGGGTGCTGTGAA 60.179 50.000 0.45 0.00 0.00 3.18
5988 6037 6.566079 TGGTGGAATCTGATCATACTCTTT 57.434 37.500 0.00 0.00 0.00 2.52
6057 6106 2.492088 GGAAATGCAAGACCCTTGGTAC 59.508 50.000 8.55 0.00 35.25 3.34
6233 6282 4.836125 TCAATCTGACAAGGCTGTTTTC 57.164 40.909 0.00 0.00 35.30 2.29
6395 6444 2.045340 CTAACCCCACCCCTTGCG 60.045 66.667 0.00 0.00 0.00 4.85
6457 6506 0.035820 TATTGTCCACAGGAACCGGC 60.036 55.000 0.00 0.00 31.38 6.13
6486 6535 0.390472 GAAGCAGGACGAGGGAACAG 60.390 60.000 0.00 0.00 0.00 3.16
6842 6891 5.009631 ACACAAGCTGTTAATATGGCAGAA 58.990 37.500 0.00 0.00 32.39 3.02
6913 6962 7.884877 AGACCACAATAAATCAGATGTTGAAGA 59.115 33.333 9.33 0.00 39.77 2.87
6970 7019 1.134250 GGGGGCTCTTCAATCAGAGTC 60.134 57.143 0.00 0.00 43.76 3.36
6983 7032 6.571605 TCAATCAGAGTCTGAACATGAGATC 58.428 40.000 26.06 0.00 44.04 2.75
7120 7199 3.760580 AGGGGCTGAAGAATCGATAAG 57.239 47.619 0.00 0.00 0.00 1.73
7146 7225 6.252599 ACTATGGGAAGCATGTTTCTGATA 57.747 37.500 19.93 14.62 0.00 2.15
7167 7246 1.001378 CAGTAAACACAGGTTGCCAGC 60.001 52.381 0.00 0.00 37.30 4.85
7218 7297 6.322456 TGAAGAGGTCAGGAGAATACATAGTG 59.678 42.308 0.00 0.00 0.00 2.74
7296 7375 6.343703 TCTGATCCATCAAAGAGTACACATG 58.656 40.000 0.00 0.00 36.18 3.21
7379 7458 6.040166 AGGATATCAAAGTTCCATTGCATGAC 59.960 38.462 4.83 0.00 31.65 3.06
7381 7460 4.933505 TCAAAGTTCCATTGCATGACAA 57.066 36.364 0.00 0.33 44.01 3.18
7404 7483 2.619074 GGGAGGGTTTGTGGAAGAGATG 60.619 54.545 0.00 0.00 0.00 2.90
7726 7806 0.240945 ACCAATGCACGCTAGTTTGC 59.759 50.000 9.97 9.97 39.33 3.68
7791 7871 8.950007 TTTCTCTGGGGTGAAGTTTATTTAAT 57.050 30.769 0.00 0.00 0.00 1.40
7794 7874 9.374711 TCTCTGGGGTGAAGTTTATTTAATTTT 57.625 29.630 0.00 0.00 0.00 1.82
8081 8177 6.335471 TCTCATACTTTCCGTGAAACAGTA 57.665 37.500 0.00 0.00 35.74 2.74
8086 8182 8.339714 TCATACTTTCCGTGAAACAGTAAAAAG 58.660 33.333 0.00 0.00 35.74 2.27
8618 8714 4.037208 AGTTTGCATGAGACAAGAAACCTG 59.963 41.667 0.00 0.00 0.00 4.00
8654 8750 2.428171 CCAACTGAATGGAAATCGGCAT 59.572 45.455 0.00 0.00 43.54 4.40
8766 8862 0.806102 ATTCGTCATCGGAACCAGCG 60.806 55.000 0.00 0.00 37.69 5.18
8786 8882 1.207329 GTAGTGGTCGAAATCAGGCCT 59.793 52.381 0.00 0.00 33.78 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.701355 GCACATAAAATAACAAATATTTGCACC 57.299 29.630 24.82 0.00 42.15 5.01
27 28 2.484264 GCAACACCTTTAGCAGTACCTG 59.516 50.000 0.00 0.00 34.12 4.00
28 29 2.779506 GCAACACCTTTAGCAGTACCT 58.220 47.619 0.00 0.00 0.00 3.08
29 30 1.463444 CGCAACACCTTTAGCAGTACC 59.537 52.381 0.00 0.00 0.00 3.34
30 31 2.096417 CACGCAACACCTTTAGCAGTAC 60.096 50.000 0.00 0.00 0.00 2.73
31 32 2.139917 CACGCAACACCTTTAGCAGTA 58.860 47.619 0.00 0.00 0.00 2.74
32 33 0.944386 CACGCAACACCTTTAGCAGT 59.056 50.000 0.00 0.00 0.00 4.40
33 34 1.225855 TCACGCAACACCTTTAGCAG 58.774 50.000 0.00 0.00 0.00 4.24
34 35 1.890876 ATCACGCAACACCTTTAGCA 58.109 45.000 0.00 0.00 0.00 3.49
35 36 2.484264 AGAATCACGCAACACCTTTAGC 59.516 45.455 0.00 0.00 0.00 3.09
36 37 3.125316 GGAGAATCACGCAACACCTTTAG 59.875 47.826 0.00 0.00 36.25 1.85
37 38 3.071479 GGAGAATCACGCAACACCTTTA 58.929 45.455 0.00 0.00 36.25 1.85
38 39 1.880027 GGAGAATCACGCAACACCTTT 59.120 47.619 0.00 0.00 36.25 3.11
39 40 1.072331 AGGAGAATCACGCAACACCTT 59.928 47.619 0.00 0.00 36.25 3.50
40 41 0.687354 AGGAGAATCACGCAACACCT 59.313 50.000 0.00 0.00 36.25 4.00
41 42 2.000447 GTAGGAGAATCACGCAACACC 59.000 52.381 0.00 0.00 36.25 4.16
42 43 2.668457 CAGTAGGAGAATCACGCAACAC 59.332 50.000 0.00 0.00 36.25 3.32
43 44 2.353704 CCAGTAGGAGAATCACGCAACA 60.354 50.000 0.00 0.00 36.25 3.33
44 45 2.094182 TCCAGTAGGAGAATCACGCAAC 60.094 50.000 0.00 0.00 39.61 4.17
45 46 2.176045 TCCAGTAGGAGAATCACGCAA 58.824 47.619 0.00 0.00 39.61 4.85
46 47 1.847328 TCCAGTAGGAGAATCACGCA 58.153 50.000 0.00 0.00 39.61 5.24
57 58 7.512992 AGAATCAAGGTTATCAATCCAGTAGG 58.487 38.462 0.00 0.00 0.00 3.18
58 59 8.970859 AAGAATCAAGGTTATCAATCCAGTAG 57.029 34.615 0.00 0.00 0.00 2.57
60 61 9.178758 GTTAAGAATCAAGGTTATCAATCCAGT 57.821 33.333 0.00 0.00 0.00 4.00
61 62 9.401058 AGTTAAGAATCAAGGTTATCAATCCAG 57.599 33.333 0.00 0.00 0.00 3.86
62 63 9.177608 CAGTTAAGAATCAAGGTTATCAATCCA 57.822 33.333 0.00 0.00 0.00 3.41
63 64 9.396022 TCAGTTAAGAATCAAGGTTATCAATCC 57.604 33.333 0.00 0.00 0.00 3.01
65 66 9.965902 ACTCAGTTAAGAATCAAGGTTATCAAT 57.034 29.630 0.00 0.00 0.00 2.57
66 67 9.219603 CACTCAGTTAAGAATCAAGGTTATCAA 57.780 33.333 0.00 0.00 0.00 2.57
67 68 8.593679 TCACTCAGTTAAGAATCAAGGTTATCA 58.406 33.333 0.00 0.00 0.00 2.15
68 69 9.436957 TTCACTCAGTTAAGAATCAAGGTTATC 57.563 33.333 0.00 0.00 0.00 1.75
69 70 9.793259 TTTCACTCAGTTAAGAATCAAGGTTAT 57.207 29.630 0.00 0.00 0.00 1.89
70 71 9.793259 ATTTCACTCAGTTAAGAATCAAGGTTA 57.207 29.630 0.00 0.00 0.00 2.85
71 72 8.697507 ATTTCACTCAGTTAAGAATCAAGGTT 57.302 30.769 0.00 0.00 0.00 3.50
72 73 9.220767 GTATTTCACTCAGTTAAGAATCAAGGT 57.779 33.333 0.00 0.00 0.00 3.50
73 74 9.442047 AGTATTTCACTCAGTTAAGAATCAAGG 57.558 33.333 0.00 0.00 28.33 3.61
85 86 9.469097 ACAGTAGAGATAAGTATTTCACTCAGT 57.531 33.333 0.00 0.00 36.04 3.41
97 98 9.509956 GGATGATGTAGTACAGTAGAGATAAGT 57.490 37.037 9.25 0.00 0.00 2.24
98 99 8.952278 GGGATGATGTAGTACAGTAGAGATAAG 58.048 40.741 9.25 0.00 0.00 1.73
99 100 7.889073 GGGGATGATGTAGTACAGTAGAGATAA 59.111 40.741 9.25 0.00 0.00 1.75
100 101 7.239984 AGGGGATGATGTAGTACAGTAGAGATA 59.760 40.741 9.25 0.00 0.00 1.98
101 102 6.046168 AGGGGATGATGTAGTACAGTAGAGAT 59.954 42.308 9.25 0.00 0.00 2.75
102 103 5.372959 AGGGGATGATGTAGTACAGTAGAGA 59.627 44.000 9.25 0.00 0.00 3.10
103 104 5.636123 AGGGGATGATGTAGTACAGTAGAG 58.364 45.833 9.25 0.00 0.00 2.43
104 105 5.457778 GGAGGGGATGATGTAGTACAGTAGA 60.458 48.000 9.25 0.00 0.00 2.59
105 106 4.767928 GGAGGGGATGATGTAGTACAGTAG 59.232 50.000 9.25 0.00 0.00 2.57
106 107 4.419200 AGGAGGGGATGATGTAGTACAGTA 59.581 45.833 9.25 0.57 0.00 2.74
107 108 3.207777 AGGAGGGGATGATGTAGTACAGT 59.792 47.826 9.25 0.00 0.00 3.55
108 109 3.829601 GAGGAGGGGATGATGTAGTACAG 59.170 52.174 9.25 0.00 0.00 2.74
109 110 3.467483 AGAGGAGGGGATGATGTAGTACA 59.533 47.826 5.24 5.24 0.00 2.90
110 111 4.120946 AGAGGAGGGGATGATGTAGTAC 57.879 50.000 0.00 0.00 0.00 2.73
111 112 4.742012 GAAGAGGAGGGGATGATGTAGTA 58.258 47.826 0.00 0.00 0.00 1.82
112 113 3.582164 GAAGAGGAGGGGATGATGTAGT 58.418 50.000 0.00 0.00 0.00 2.73
113 114 2.560542 CGAAGAGGAGGGGATGATGTAG 59.439 54.545 0.00 0.00 0.00 2.74
114 115 2.598565 CGAAGAGGAGGGGATGATGTA 58.401 52.381 0.00 0.00 0.00 2.29
115 116 1.418334 CGAAGAGGAGGGGATGATGT 58.582 55.000 0.00 0.00 0.00 3.06
116 117 0.683973 CCGAAGAGGAGGGGATGATG 59.316 60.000 0.00 0.00 45.00 3.07
117 118 0.472734 CCCGAAGAGGAGGGGATGAT 60.473 60.000 0.00 0.00 44.10 2.45
118 119 1.075226 CCCGAAGAGGAGGGGATGA 60.075 63.158 0.00 0.00 44.10 2.92
119 120 3.555967 CCCGAAGAGGAGGGGATG 58.444 66.667 0.00 0.00 44.10 3.51
124 125 0.470341 GGATTTCCCCGAAGAGGAGG 59.530 60.000 0.00 0.00 45.00 4.30
136 137 1.803289 GAGCTGCGTTGGGATTTCC 59.197 57.895 0.00 0.00 0.00 3.13
137 138 1.425428 CGAGCTGCGTTGGGATTTC 59.575 57.895 0.00 0.00 34.64 2.17
138 139 2.690778 GCGAGCTGCGTTGGGATTT 61.691 57.895 0.00 0.00 43.41 2.17
139 140 3.127533 GCGAGCTGCGTTGGGATT 61.128 61.111 0.00 0.00 43.41 3.01
148 149 0.458543 TACTGCTACTTGCGAGCTGC 60.459 55.000 0.00 6.35 46.63 5.25
149 150 1.133216 TCTACTGCTACTTGCGAGCTG 59.867 52.381 0.00 3.17 46.63 4.24
150 151 1.464734 TCTACTGCTACTTGCGAGCT 58.535 50.000 0.00 0.00 46.63 4.09
151 152 2.389998 GATCTACTGCTACTTGCGAGC 58.610 52.381 0.00 0.00 46.63 5.03
152 153 2.603412 CCGATCTACTGCTACTTGCGAG 60.603 54.545 0.00 0.00 46.63 5.03
153 154 1.333931 CCGATCTACTGCTACTTGCGA 59.666 52.381 0.00 0.00 46.63 5.10
154 155 1.333931 TCCGATCTACTGCTACTTGCG 59.666 52.381 0.00 0.00 46.63 4.85
155 156 2.860582 GCTCCGATCTACTGCTACTTGC 60.861 54.545 0.00 0.00 43.25 4.01
156 157 2.287909 GGCTCCGATCTACTGCTACTTG 60.288 54.545 0.00 0.00 0.00 3.16
157 158 1.957877 GGCTCCGATCTACTGCTACTT 59.042 52.381 0.00 0.00 0.00 2.24
158 159 1.611519 GGCTCCGATCTACTGCTACT 58.388 55.000 0.00 0.00 0.00 2.57
159 160 0.599060 GGGCTCCGATCTACTGCTAC 59.401 60.000 0.00 0.00 0.00 3.58
160 161 3.037941 GGGCTCCGATCTACTGCTA 57.962 57.895 0.00 0.00 0.00 3.49
161 162 3.863606 GGGCTCCGATCTACTGCT 58.136 61.111 0.00 0.00 0.00 4.24
172 173 2.046217 GTTGGTCTTCCGGGCTCC 60.046 66.667 0.00 0.00 36.30 4.70
173 174 1.079057 GAGTTGGTCTTCCGGGCTC 60.079 63.158 0.00 0.00 36.30 4.70
178 179 2.030185 TCTTCTTCGAGTTGGTCTTCCG 60.030 50.000 0.00 0.00 36.30 4.30
233 234 6.432162 CAGTTTAGGTTAGGGTTTTTAGTCCC 59.568 42.308 0.00 0.00 43.71 4.46
244 245 2.483188 CGGCTAGCAGTTTAGGTTAGGG 60.483 54.545 18.24 0.00 0.00 3.53
259 260 1.153549 GTGCCTCAACTCCGGCTAG 60.154 63.158 0.00 0.00 46.42 3.42
270 271 1.661463 AGGAGAATTCCAGTGCCTCA 58.339 50.000 0.65 0.00 46.64 3.86
317 318 2.096248 GTGGATTCGTCTCTCCTCTGT 58.904 52.381 0.00 0.00 32.47 3.41
324 325 0.171455 GAGCGTGTGGATTCGTCTCT 59.829 55.000 0.00 0.00 32.31 3.10
330 331 2.456119 CCAGCGAGCGTGTGGATTC 61.456 63.158 7.40 0.00 32.60 2.52
334 335 3.865929 AACTCCAGCGAGCGTGTGG 62.866 63.158 6.98 6.98 40.03 4.17
338 339 1.227556 AAACAACTCCAGCGAGCGT 60.228 52.632 0.00 0.00 40.03 5.07
339 340 1.205064 CAAACAACTCCAGCGAGCG 59.795 57.895 0.00 0.00 40.03 5.03
402 403 8.598041 AGACCAGAGAAGTGAACATAAGTTATT 58.402 33.333 0.00 0.00 38.30 1.40
425 426 1.405661 GGAATTGACGAGGGACCAGAC 60.406 57.143 0.00 0.00 0.00 3.51
428 429 0.838554 TGGGAATTGACGAGGGACCA 60.839 55.000 0.00 0.00 0.00 4.02
429 430 0.546598 ATGGGAATTGACGAGGGACC 59.453 55.000 0.00 0.00 0.00 4.46
440 441 5.425196 CCCTTGTTTGATTCATGGGAATT 57.575 39.130 10.17 0.00 46.63 2.17
444 445 6.736110 ATATTCCCTTGTTTGATTCATGGG 57.264 37.500 9.63 9.63 45.71 4.00
452 453 9.527157 TGTGAGAATTTATATTCCCTTGTTTGA 57.473 29.630 2.66 0.00 40.91 2.69
479 491 8.131100 ACTTTTTCGCACATGATAGGAATTATG 58.869 33.333 0.00 0.00 35.68 1.90
493 505 2.028130 ACCAATCCACTTTTTCGCACA 58.972 42.857 0.00 0.00 0.00 4.57
498 510 8.908678 GTCGTTTTATTACCAATCCACTTTTTC 58.091 33.333 0.00 0.00 0.00 2.29
502 514 6.938030 TGAGTCGTTTTATTACCAATCCACTT 59.062 34.615 0.00 0.00 0.00 3.16
530 546 9.661954 AGGGAGTTCTATTAAGATTAGACATGA 57.338 33.333 0.00 0.00 0.00 3.07
543 559 7.562821 GGGAGTTTAGTGTAGGGAGTTCTATTA 59.437 40.741 0.00 0.00 0.00 0.98
571 587 2.039418 GGCAATATTTGGGAAGGGGAC 58.961 52.381 0.00 0.00 0.00 4.46
691 711 4.771577 TCATGTGTGCCTTTTCCATACAAT 59.228 37.500 0.00 0.00 37.74 2.71
724 744 7.642669 CATAGTTATTTGTCCCTGCACTAATG 58.357 38.462 0.00 0.00 0.00 1.90
725 745 6.263168 GCATAGTTATTTGTCCCTGCACTAAT 59.737 38.462 0.00 0.00 0.00 1.73
726 746 5.588648 GCATAGTTATTTGTCCCTGCACTAA 59.411 40.000 0.00 0.00 0.00 2.24
727 747 5.123227 GCATAGTTATTTGTCCCTGCACTA 58.877 41.667 0.00 0.00 0.00 2.74
959 988 4.521146 AGATCAGTGGATGAACAATGGAC 58.479 43.478 0.00 0.00 42.53 4.02
1003 1033 2.675348 GGCGTCTCTTGGAAGAAGATTG 59.325 50.000 0.00 0.00 34.03 2.67
1044 1074 2.994995 AGGACATGGTGACGGCGA 60.995 61.111 16.62 0.00 0.00 5.54
1052 1082 2.052690 CGTCGGAGGAGGACATGGT 61.053 63.158 0.00 0.00 34.04 3.55
1606 1636 4.032452 TGCTTCATCCAGGCGGCA 62.032 61.111 13.08 0.00 0.00 5.69
1894 1924 1.447643 GATGTAGAGGGGCGCATGT 59.552 57.895 10.83 0.00 0.00 3.21
1984 2014 2.673523 CAGCTAGCAGCCCTTGGT 59.326 61.111 18.83 0.00 43.77 3.67
2061 2091 0.174845 GGGCCGCCATAAAAAGTTCC 59.825 55.000 12.58 0.00 0.00 3.62
2254 2284 1.687612 CCCAGGCACATCTTGGTCT 59.312 57.895 0.00 0.00 0.00 3.85
2336 2366 2.193993 AGGGGTAAAGATGGCTACGTT 58.806 47.619 0.00 0.00 0.00 3.99
2512 2542 2.879103 TCTTCATTTTCCGCTCCCTT 57.121 45.000 0.00 0.00 0.00 3.95
2540 2570 7.660208 TCGCTTTTTATCATTATTAGGGGAGAC 59.340 37.037 0.00 0.00 0.00 3.36
2776 2806 4.952845 TCATATCCCTATCCTTCCTCAGG 58.047 47.826 0.00 0.00 45.64 3.86
2821 2851 4.042187 ACCAGAGACTTAGCCATGAAGTTT 59.958 41.667 0.00 0.00 37.27 2.66
2845 2875 3.053917 ACACACCTTTGTACTTTGTCCCT 60.054 43.478 0.00 0.00 33.30 4.20
2961 2991 3.895656 CCATTCATCCTTGGCATCTTCAT 59.104 43.478 0.00 0.00 0.00 2.57
3068 3098 6.892658 TTCTTCTCTCTCCATAGATACTGC 57.107 41.667 0.00 0.00 0.00 4.40
3124 3154 2.890311 AGCTTCCTCTATGACATCCTCG 59.110 50.000 0.00 0.00 0.00 4.63
3242 3272 3.447586 GGTCTACCTGTAGCATCAAGACA 59.552 47.826 0.00 0.00 34.86 3.41
3441 3471 1.002242 TGTTCCCTCCCCAACCCTTT 61.002 55.000 0.00 0.00 0.00 3.11
3556 3586 3.769739 TTTGCCTGCTGAACTAGAAGA 57.230 42.857 0.00 0.00 33.38 2.87
3561 3591 3.689347 ACATCATTTGCCTGCTGAACTA 58.311 40.909 0.00 0.00 0.00 2.24
3641 3671 4.037923 AGCGGTTTCTTCATCATTTGTTGT 59.962 37.500 0.00 0.00 0.00 3.32
3669 3699 0.721718 CTCCTCATCGGCGACAAAAC 59.278 55.000 13.76 0.00 0.00 2.43
3809 3839 6.886459 CCCTCATTGTCTTTTTCCATAAGAGA 59.114 38.462 0.00 0.00 32.60 3.10
3879 3909 6.780457 AAAGAACTGCAGCCATATTAATGT 57.220 33.333 15.27 0.00 0.00 2.71
4043 4073 1.974265 TCGTTGTGCCCTTCATTTGA 58.026 45.000 0.00 0.00 0.00 2.69
4051 4081 1.152963 AGCAACTTCGTTGTGCCCT 60.153 52.632 8.34 0.00 44.40 5.19
4171 4201 5.838955 TCTCTCCCTGTTAATCTCTTACCA 58.161 41.667 0.00 0.00 0.00 3.25
4379 4421 5.290400 GCTTATGAGCTCCTTTCATTTTTGC 59.710 40.000 12.15 0.00 45.65 3.68
4474 4516 5.010617 TGCAACTCCCTTAATCAAAACCTTC 59.989 40.000 0.00 0.00 0.00 3.46
4573 4615 2.290260 TGCCTTGACCTTACCATCAGTG 60.290 50.000 0.00 0.00 0.00 3.66
4581 4623 1.405121 CGGGTACTGCCTTGACCTTAC 60.405 57.143 0.00 0.00 37.43 2.34
4700 4742 0.827507 TCTTTCTTGGCCAAGCACCC 60.828 55.000 36.24 0.00 38.28 4.61
4894 4936 1.153353 CTGCATTGGGCTTTTGCTTG 58.847 50.000 0.00 0.00 46.54 4.01
4986 5028 0.250553 CCTTAACACCTTGCGTCCCA 60.251 55.000 0.00 0.00 0.00 4.37
4989 5031 0.872388 CACCCTTAACACCTTGCGTC 59.128 55.000 0.00 0.00 0.00 5.19
5007 5049 7.230913 CCTTAGTATTCTCCTCGGTATCTTTCA 59.769 40.741 0.00 0.00 0.00 2.69
5182 5230 4.594920 TCTTTCTCCTGTTCCTGAGTGATT 59.405 41.667 0.00 0.00 0.00 2.57
5191 5239 6.209361 GTTGTCAAATTCTTTCTCCTGTTCC 58.791 40.000 0.00 0.00 0.00 3.62
5200 5248 6.797033 CCACTGTATCGTTGTCAAATTCTTTC 59.203 38.462 0.00 0.00 0.00 2.62
5376 5424 2.773661 TGAATCTCCATAGCAGCTCCAA 59.226 45.455 0.00 0.00 0.00 3.53
5415 5463 2.821969 ACCTCATGCATGTCCAAAGTTC 59.178 45.455 25.43 0.00 0.00 3.01
5603 5651 4.941263 TCAACCTCCATAAGAACCAAATCG 59.059 41.667 0.00 0.00 0.00 3.34
5643 5691 3.878778 CCTCCTGGTTCTGAATTTCGAT 58.121 45.455 0.00 0.00 0.00 3.59
5760 5808 5.548056 AGGTCCTAAATCTTGTCTTTCCTCA 59.452 40.000 0.00 0.00 0.00 3.86
5844 5892 4.699257 GTCTCAGGTGAATCAGCTTGAAAT 59.301 41.667 12.76 0.00 40.40 2.17
5988 6037 3.410631 TTCCGATGCTTGTTCCTGTAA 57.589 42.857 0.00 0.00 0.00 2.41
6057 6106 1.275291 ACCACCAAGTGTATCGACCAG 59.725 52.381 0.00 0.00 0.00 4.00
6163 6212 3.857157 AAGTTGTACTTGCCTCCTCAA 57.143 42.857 0.00 0.00 37.00 3.02
6233 6282 1.079405 CTGCCTTGCCTGCAAATGG 60.079 57.895 6.00 5.96 38.46 3.16
6320 6369 1.147376 CTGGTTCCGTGTTCCCACA 59.853 57.895 0.00 0.00 41.93 4.17
6395 6444 9.908747 AGTATATGTATATAGAGAGACCCACAC 57.091 37.037 0.00 0.00 0.00 3.82
6486 6535 1.552337 TCTCCCTGTGTTCTCATCTGC 59.448 52.381 0.00 0.00 0.00 4.26
6707 6756 5.163416 TGTGTTCTCATCTGTTGTTCTCTCA 60.163 40.000 0.00 0.00 0.00 3.27
6842 6891 6.239317 GCTGGTTTTGGGAAGAAACTTTATCT 60.239 38.462 0.00 0.00 37.22 1.98
6913 6962 2.683152 GCAGCTTGATTCCATCCAGAGT 60.683 50.000 0.00 0.00 0.00 3.24
6930 6979 2.030451 CCTTGGACTCTTTTCTTGCAGC 60.030 50.000 0.00 0.00 0.00 5.25
6970 7019 5.406477 TGTTTCACTTCGATCTCATGTTCAG 59.594 40.000 0.00 0.00 0.00 3.02
6983 7032 9.716507 TTCTCTAAAATTTCTTGTTTCACTTCG 57.283 29.630 0.00 0.00 0.00 3.79
7052 7131 3.529533 CATACCTGAAGGAGCAACTGAG 58.470 50.000 2.62 0.00 38.94 3.35
7056 7135 3.118261 TGATCCATACCTGAAGGAGCAAC 60.118 47.826 2.62 0.00 44.05 4.17
7120 7199 5.415701 TCAGAAACATGCTTCCCATAGTTTC 59.584 40.000 5.23 0.00 43.22 2.78
7146 7225 2.297701 CTGGCAACCTGTGTTTACTGT 58.702 47.619 0.00 0.00 30.42 3.55
7167 7246 0.815095 GGTCGGCCAAATTTACTGGG 59.185 55.000 0.00 0.00 34.25 4.45
7296 7375 7.225931 TCGAGAATAATACCCAGCATTGTTTAC 59.774 37.037 0.00 0.00 0.00 2.01
7379 7458 1.895131 CTTCCACAAACCCTCCCATTG 59.105 52.381 0.00 0.00 0.00 2.82
7381 7460 1.355720 CTCTTCCACAAACCCTCCCAT 59.644 52.381 0.00 0.00 0.00 4.00
7404 7483 1.148273 TCACCAACTCCAGTGCACC 59.852 57.895 14.63 0.00 33.90 5.01
7726 7806 4.507756 TCATGAGAGTCAACACAAACGAAG 59.492 41.667 0.00 0.00 0.00 3.79
7794 7874 4.648762 TCACCTTCATTCAGGAAAGCAAAA 59.351 37.500 0.00 0.00 37.39 2.44
8086 8182 8.803799 CCGTATTTAAATGCAAGGTTGTAATTC 58.196 33.333 15.33 0.00 0.00 2.17
8618 8714 0.668535 GTTGGACAGGCAGTTGTTCC 59.331 55.000 0.00 0.00 0.00 3.62
8766 8862 1.207329 AGGCCTGATTTCGACCACTAC 59.793 52.381 3.11 0.00 0.00 2.73
8786 8882 4.323028 CCAAGTCAGTAATGAGGCTCAAGA 60.323 45.833 22.84 9.53 0.00 3.02


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

AutoCloner maintained by Alex Coulton.