Multiple sequence alignment - TraesCS7D01G027800

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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 TraesCS7D01G027800 chr7D 100.000 2354 0 0 776 3129 13607644 13609997 0.000000e+00 4348.0
1 TraesCS7D01G027800 chr7D 89.671 668 69 0 1402 2069 13680793 13680126 0.000000e+00 852.0
2 TraesCS7D01G027800 chr7D 100.000 457 0 0 1 457 13606869 13607325 0.000000e+00 845.0
3 TraesCS7D01G027800 chr7D 85.135 666 99 0 1402 2067 13697556 13696891 0.000000e+00 682.0
4 TraesCS7D01G027800 chr7D 79.891 368 55 5 1705 2067 13694908 13694555 5.180000e-63 252.0
5 TraesCS7D01G027800 chr7D 91.200 125 7 3 328 449 13720589 13720466 1.930000e-37 167.0
6 TraesCS7D01G027800 chr3D 94.283 997 10 11 2080 3065 585091112 585090152 0.000000e+00 1482.0
7 TraesCS7D01G027800 chr3D 97.106 622 18 0 1402 2023 585092653 585092032 0.000000e+00 1050.0
8 TraesCS7D01G027800 chr2D 90.348 632 55 5 777 1403 34428233 34427603 0.000000e+00 824.0
9 TraesCS7D01G027800 chr7A 88.329 694 51 19 2370 3041 13099722 13100407 0.000000e+00 806.0
10 TraesCS7D01G027800 chr7A 95.672 439 18 1 1501 1938 13098807 13099245 0.000000e+00 704.0
11 TraesCS7D01G027800 chr7A 86.069 524 69 4 839 1359 5701744 5702266 7.580000e-156 560.0
12 TraesCS7D01G027800 chr7A 93.443 244 15 1 2100 2342 13099486 13099729 8.250000e-96 361.0
13 TraesCS7D01G027800 chr7A 83.191 351 59 0 1717 2067 13185257 13184907 3.890000e-84 322.0
14 TraesCS7D01G027800 chr7A 85.417 96 7 2 2080 2175 13100344 13100432 3.320000e-15 93.5
15 TraesCS7D01G027800 chr7A 97.297 37 1 0 1425 1461 13098603 13098639 2.610000e-06 63.9
16 TraesCS7D01G027800 chr1D 89.474 627 59 5 776 1398 221106937 221106314 0.000000e+00 785.0
17 TraesCS7D01G027800 chr1D 84.561 570 79 8 830 1398 10985518 10984957 9.800000e-155 556.0
18 TraesCS7D01G027800 chr2B 89.050 621 65 2 782 1400 734280521 734279902 0.000000e+00 767.0
19 TraesCS7D01G027800 chr2B 82.617 512 85 4 892 1402 780985907 780986415 1.710000e-122 449.0
20 TraesCS7D01G027800 chr1A 88.062 578 63 4 824 1398 252659407 252658833 0.000000e+00 680.0
21 TraesCS7D01G027800 chr5D 82.231 529 88 6 879 1404 531251759 531251234 4.760000e-123 451.0
22 TraesCS7D01G027800 chr4B 81.648 534 93 5 872 1404 472142142 472142671 3.700000e-119 438.0


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 TraesCS7D01G027800 chr7D 13606869 13609997 3128 False 2596.50 4348 100.0000 1 3129 2 chr7D.!!$F1 3128
1 TraesCS7D01G027800 chr7D 13680126 13680793 667 True 852.00 852 89.6710 1402 2069 1 chr7D.!!$R1 667
2 TraesCS7D01G027800 chr7D 13694555 13697556 3001 True 467.00 682 82.5130 1402 2067 2 chr7D.!!$R3 665
3 TraesCS7D01G027800 chr3D 585090152 585092653 2501 True 1266.00 1482 95.6945 1402 3065 2 chr3D.!!$R1 1663
4 TraesCS7D01G027800 chr2D 34427603 34428233 630 True 824.00 824 90.3480 777 1403 1 chr2D.!!$R1 626
5 TraesCS7D01G027800 chr7A 5701744 5702266 522 False 560.00 560 86.0690 839 1359 1 chr7A.!!$F1 520
6 TraesCS7D01G027800 chr7A 13098603 13100432 1829 False 405.68 806 92.0316 1425 3041 5 chr7A.!!$F2 1616
7 TraesCS7D01G027800 chr1D 221106314 221106937 623 True 785.00 785 89.4740 776 1398 1 chr1D.!!$R2 622
8 TraesCS7D01G027800 chr1D 10984957 10985518 561 True 556.00 556 84.5610 830 1398 1 chr1D.!!$R1 568
9 TraesCS7D01G027800 chr2B 734279902 734280521 619 True 767.00 767 89.0500 782 1400 1 chr2B.!!$R1 618
10 TraesCS7D01G027800 chr2B 780985907 780986415 508 False 449.00 449 82.6170 892 1402 1 chr2B.!!$F1 510
11 TraesCS7D01G027800 chr1A 252658833 252659407 574 True 680.00 680 88.0620 824 1398 1 chr1A.!!$R1 574
12 TraesCS7D01G027800 chr5D 531251234 531251759 525 True 451.00 451 82.2310 879 1404 1 chr5D.!!$R1 525
13 TraesCS7D01G027800 chr4B 472142142 472142671 529 False 438.00 438 81.6480 872 1404 1 chr4B.!!$F1 532

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
357 358 0.040692 GGAACACGCGGACTTTTTCC 60.041 55.0 12.47 8.84 41.75 3.13 F
1247 1259 0.603707 ACACATGTGTCCGCCTCAAG 60.604 55.0 25.76 0.00 40.24 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2583 1.746220 TGTTGGTTTCAGTTGAACCCG 59.254 47.619 4.32 0.0 39.2 5.28 R
3075 5515 0.178767 AAAATACGGGGGTCTACGGC 59.821 55.000 0.00 0.0 0.0 5.68 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
20 21 1.931172 CTGTACCCGCAAATTCGTAGG 59.069 52.381 0.00 0.00 0.00 3.18
22 23 0.462403 TACCCGCAAATTCGTAGGGC 60.462 55.000 7.81 0.00 45.75 5.19
23 24 2.707039 CCGCAAATTCGTAGGGCG 59.293 61.111 0.00 0.00 46.61 6.13
24 25 2.022762 CGCAAATTCGTAGGGCGC 59.977 61.111 0.00 0.00 41.27 6.53
25 26 2.022762 GCAAATTCGTAGGGCGCG 59.977 61.111 0.00 0.00 41.07 6.86
26 27 2.707039 CAAATTCGTAGGGCGCGG 59.293 61.111 8.83 0.00 41.07 6.46
27 28 2.512974 AAATTCGTAGGGCGCGGG 60.513 61.111 8.83 0.00 41.07 6.13
43 44 3.372730 GGCATGCACCTGCGGAAA 61.373 61.111 21.36 0.00 45.83 3.13
44 45 2.126346 GCATGCACCTGCGGAAAC 60.126 61.111 14.21 0.00 45.83 2.78
58 59 2.670401 GGAAACGTCTTCAGCAGTTG 57.330 50.000 10.99 0.00 0.00 3.16
59 60 2.210116 GGAAACGTCTTCAGCAGTTGA 58.790 47.619 10.99 0.00 0.00 3.18
60 61 2.808543 GGAAACGTCTTCAGCAGTTGAT 59.191 45.455 10.99 0.00 35.27 2.57
61 62 3.120511 GGAAACGTCTTCAGCAGTTGATC 60.121 47.826 10.99 0.00 35.27 2.92
62 63 3.393089 AACGTCTTCAGCAGTTGATCT 57.607 42.857 0.00 0.00 35.27 2.75
63 64 2.681706 ACGTCTTCAGCAGTTGATCTG 58.318 47.619 0.00 0.00 46.12 2.90
71 72 3.107017 CAGTTGATCTGCGTCGTGA 57.893 52.632 0.00 0.00 37.36 4.35
72 73 1.633561 CAGTTGATCTGCGTCGTGAT 58.366 50.000 0.00 0.00 37.36 3.06
73 74 1.585668 CAGTTGATCTGCGTCGTGATC 59.414 52.381 17.45 17.45 39.43 2.92
74 75 0.924090 GTTGATCTGCGTCGTGATCC 59.076 55.000 19.81 8.39 38.53 3.36
75 76 0.525455 TTGATCTGCGTCGTGATCCG 60.525 55.000 19.81 0.00 38.53 4.18
76 77 1.355563 GATCTGCGTCGTGATCCGA 59.644 57.895 14.96 2.65 45.00 4.55
85 86 2.519377 TCGTGATCCGAACACAAGTT 57.481 45.000 9.23 0.00 44.03 2.66
86 87 2.131972 TCGTGATCCGAACACAAGTTG 58.868 47.619 9.23 0.00 44.03 3.16
87 88 1.194547 CGTGATCCGAACACAAGTTGG 59.805 52.381 7.96 0.00 38.30 3.77
88 89 1.069227 GTGATCCGAACACAAGTTGGC 60.069 52.381 7.96 0.00 38.30 4.52
89 90 1.234821 GATCCGAACACAAGTTGGCA 58.765 50.000 7.96 0.00 38.30 4.92
90 91 1.197721 GATCCGAACACAAGTTGGCAG 59.802 52.381 7.96 0.00 38.30 4.85
91 92 1.008538 CCGAACACAAGTTGGCAGC 60.009 57.895 7.96 0.00 38.30 5.25
92 93 1.369209 CGAACACAAGTTGGCAGCG 60.369 57.895 7.96 2.18 38.30 5.18
93 94 1.771073 CGAACACAAGTTGGCAGCGA 61.771 55.000 7.96 0.00 38.30 4.93
94 95 0.380378 GAACACAAGTTGGCAGCGAA 59.620 50.000 7.96 0.00 38.30 4.70
95 96 0.814457 AACACAAGTTGGCAGCGAAA 59.186 45.000 7.96 0.00 36.39 3.46
96 97 1.032014 ACACAAGTTGGCAGCGAAAT 58.968 45.000 7.96 0.00 0.00 2.17
97 98 1.408702 ACACAAGTTGGCAGCGAAATT 59.591 42.857 7.96 0.00 0.00 1.82
98 99 1.788308 CACAAGTTGGCAGCGAAATTG 59.212 47.619 23.56 23.56 34.43 2.32
99 100 1.269726 ACAAGTTGGCAGCGAAATTGG 60.270 47.619 27.05 13.80 33.04 3.16
100 101 1.039856 AAGTTGGCAGCGAAATTGGT 58.960 45.000 1.73 0.00 0.00 3.67
101 102 1.039856 AGTTGGCAGCGAAATTGGTT 58.960 45.000 0.00 0.00 0.00 3.67
102 103 1.000274 AGTTGGCAGCGAAATTGGTTC 60.000 47.619 0.00 0.00 0.00 3.62
103 104 1.035923 TTGGCAGCGAAATTGGTTCA 58.964 45.000 0.00 0.00 35.83 3.18
104 105 1.035923 TGGCAGCGAAATTGGTTCAA 58.964 45.000 0.00 0.00 35.83 2.69
105 106 1.410517 TGGCAGCGAAATTGGTTCAAA 59.589 42.857 0.00 0.00 35.83 2.69
106 107 2.036992 TGGCAGCGAAATTGGTTCAAAT 59.963 40.909 0.00 0.00 35.83 2.32
107 108 3.256879 TGGCAGCGAAATTGGTTCAAATA 59.743 39.130 0.00 0.00 35.83 1.40
108 109 4.081752 TGGCAGCGAAATTGGTTCAAATAT 60.082 37.500 0.00 0.00 35.83 1.28
109 110 4.869861 GGCAGCGAAATTGGTTCAAATATT 59.130 37.500 0.00 0.00 35.83 1.28
110 111 5.005682 GGCAGCGAAATTGGTTCAAATATTC 59.994 40.000 0.00 0.00 35.83 1.75
111 112 5.576384 GCAGCGAAATTGGTTCAAATATTCA 59.424 36.000 0.00 0.00 35.83 2.57
112 113 6.256321 GCAGCGAAATTGGTTCAAATATTCAT 59.744 34.615 0.00 0.00 35.83 2.57
113 114 7.614908 CAGCGAAATTGGTTCAAATATTCATG 58.385 34.615 0.00 0.00 35.83 3.07
114 115 7.488792 CAGCGAAATTGGTTCAAATATTCATGA 59.511 33.333 0.00 0.00 35.83 3.07
115 116 8.034215 AGCGAAATTGGTTCAAATATTCATGAA 58.966 29.630 11.26 11.26 35.83 2.57
116 117 8.819974 GCGAAATTGGTTCAAATATTCATGAAT 58.180 29.630 23.75 23.75 37.82 2.57
142 143 8.804688 ATTGTTATTCTGTAGAGATACTTCGC 57.195 34.615 0.00 0.00 0.00 4.70
143 144 7.569639 TGTTATTCTGTAGAGATACTTCGCT 57.430 36.000 0.00 0.00 35.96 4.93
144 145 7.997482 TGTTATTCTGTAGAGATACTTCGCTT 58.003 34.615 0.00 0.00 33.68 4.68
145 146 8.129840 TGTTATTCTGTAGAGATACTTCGCTTC 58.870 37.037 0.00 0.00 33.68 3.86
146 147 5.502153 TTCTGTAGAGATACTTCGCTTCC 57.498 43.478 0.00 0.00 33.68 3.46
147 148 3.560481 TCTGTAGAGATACTTCGCTTCCG 59.440 47.826 0.00 0.00 33.68 4.30
148 149 3.538591 TGTAGAGATACTTCGCTTCCGA 58.461 45.455 0.00 0.00 42.66 4.55
149 150 3.560481 TGTAGAGATACTTCGCTTCCGAG 59.440 47.826 0.00 0.00 45.35 4.63
150 151 1.335496 AGAGATACTTCGCTTCCGAGC 59.665 52.381 0.00 0.00 45.35 5.03
151 152 1.335496 GAGATACTTCGCTTCCGAGCT 59.665 52.381 0.00 0.00 46.96 4.09
152 153 1.066303 AGATACTTCGCTTCCGAGCTG 59.934 52.381 0.00 0.00 46.96 4.24
153 154 0.818296 ATACTTCGCTTCCGAGCTGT 59.182 50.000 0.00 0.00 46.96 4.40
154 155 0.601558 TACTTCGCTTCCGAGCTGTT 59.398 50.000 0.00 0.00 46.96 3.16
155 156 0.601558 ACTTCGCTTCCGAGCTGTTA 59.398 50.000 0.00 0.00 46.96 2.41
156 157 1.204941 ACTTCGCTTCCGAGCTGTTAT 59.795 47.619 0.00 0.00 46.96 1.89
157 158 2.426024 ACTTCGCTTCCGAGCTGTTATA 59.574 45.455 0.00 0.00 46.96 0.98
158 159 3.068307 ACTTCGCTTCCGAGCTGTTATAT 59.932 43.478 0.00 0.00 46.96 0.86
159 160 4.277672 ACTTCGCTTCCGAGCTGTTATATA 59.722 41.667 0.00 0.00 46.96 0.86
160 161 5.047943 ACTTCGCTTCCGAGCTGTTATATAT 60.048 40.000 0.00 0.00 46.96 0.86
161 162 4.733850 TCGCTTCCGAGCTGTTATATATG 58.266 43.478 0.00 0.00 46.96 1.78
162 163 4.217767 TCGCTTCCGAGCTGTTATATATGT 59.782 41.667 0.00 0.00 46.96 2.29
163 164 4.923871 CGCTTCCGAGCTGTTATATATGTT 59.076 41.667 0.00 0.00 46.96 2.71
164 165 5.405571 CGCTTCCGAGCTGTTATATATGTTT 59.594 40.000 0.00 0.00 46.96 2.83
165 166 6.073765 CGCTTCCGAGCTGTTATATATGTTTT 60.074 38.462 0.00 0.00 46.96 2.43
166 167 7.518370 CGCTTCCGAGCTGTTATATATGTTTTT 60.518 37.037 0.00 0.00 46.96 1.94
167 168 7.798982 GCTTCCGAGCTGTTATATATGTTTTTC 59.201 37.037 0.00 0.00 45.65 2.29
168 169 8.958119 TTCCGAGCTGTTATATATGTTTTTCT 57.042 30.769 0.00 0.00 0.00 2.52
170 171 9.472361 TCCGAGCTGTTATATATGTTTTTCTAC 57.528 33.333 0.00 0.00 0.00 2.59
171 172 8.709646 CCGAGCTGTTATATATGTTTTTCTACC 58.290 37.037 0.00 0.00 0.00 3.18
172 173 9.477484 CGAGCTGTTATATATGTTTTTCTACCT 57.523 33.333 0.00 0.00 0.00 3.08
183 184 6.509418 TGTTTTTCTACCTGTTCATATGCC 57.491 37.500 0.00 0.00 0.00 4.40
184 185 6.007076 TGTTTTTCTACCTGTTCATATGCCA 58.993 36.000 0.00 0.00 0.00 4.92
185 186 6.072175 TGTTTTTCTACCTGTTCATATGCCAC 60.072 38.462 0.00 0.00 0.00 5.01
186 187 3.838244 TCTACCTGTTCATATGCCACC 57.162 47.619 0.00 0.00 0.00 4.61
187 188 2.438021 TCTACCTGTTCATATGCCACCC 59.562 50.000 0.00 0.00 0.00 4.61
188 189 0.107214 ACCTGTTCATATGCCACCCG 60.107 55.000 0.00 0.00 0.00 5.28
189 190 0.819259 CCTGTTCATATGCCACCCGG 60.819 60.000 0.00 0.00 0.00 5.73
190 191 0.180171 CTGTTCATATGCCACCCGGA 59.820 55.000 0.73 0.00 0.00 5.14
191 192 0.180171 TGTTCATATGCCACCCGGAG 59.820 55.000 0.73 0.00 0.00 4.63
192 193 1.148273 TTCATATGCCACCCGGAGC 59.852 57.895 0.73 3.04 0.00 4.70
193 194 1.344953 TTCATATGCCACCCGGAGCT 61.345 55.000 0.73 0.00 0.00 4.09
194 195 1.598962 CATATGCCACCCGGAGCTG 60.599 63.158 0.73 0.00 0.00 4.24
195 196 2.072487 ATATGCCACCCGGAGCTGT 61.072 57.895 0.73 0.00 0.00 4.40
196 197 1.635817 ATATGCCACCCGGAGCTGTT 61.636 55.000 0.73 0.00 0.00 3.16
197 198 2.252072 TATGCCACCCGGAGCTGTTC 62.252 60.000 0.73 0.00 0.00 3.18
198 199 4.329545 GCCACCCGGAGCTGTTCA 62.330 66.667 0.73 0.00 0.00 3.18
199 200 2.429930 CCACCCGGAGCTGTTCAA 59.570 61.111 0.73 0.00 0.00 2.69
200 201 1.966451 CCACCCGGAGCTGTTCAAC 60.966 63.158 0.73 0.00 0.00 3.18
201 202 1.966451 CACCCGGAGCTGTTCAACC 60.966 63.158 0.73 0.00 0.00 3.77
202 203 2.742372 CCCGGAGCTGTTCAACCG 60.742 66.667 0.73 0.00 44.16 4.44
203 204 2.030562 CCGGAGCTGTTCAACCGT 59.969 61.111 0.00 0.00 43.22 4.83
204 205 2.027625 CCGGAGCTGTTCAACCGTC 61.028 63.158 0.00 0.00 43.22 4.79
205 206 1.006102 CGGAGCTGTTCAACCGTCT 60.006 57.895 0.00 0.00 40.42 4.18
206 207 0.600255 CGGAGCTGTTCAACCGTCTT 60.600 55.000 0.00 0.00 40.42 3.01
207 208 1.149148 GGAGCTGTTCAACCGTCTTC 58.851 55.000 0.00 0.00 0.00 2.87
208 209 1.540363 GGAGCTGTTCAACCGTCTTCA 60.540 52.381 0.00 0.00 0.00 3.02
209 210 2.210116 GAGCTGTTCAACCGTCTTCAA 58.790 47.619 0.00 0.00 0.00 2.69
210 211 2.808543 GAGCTGTTCAACCGTCTTCAAT 59.191 45.455 0.00 0.00 0.00 2.57
211 212 3.214328 AGCTGTTCAACCGTCTTCAATT 58.786 40.909 0.00 0.00 0.00 2.32
212 213 3.632145 AGCTGTTCAACCGTCTTCAATTT 59.368 39.130 0.00 0.00 0.00 1.82
213 214 4.097892 AGCTGTTCAACCGTCTTCAATTTT 59.902 37.500 0.00 0.00 0.00 1.82
214 215 4.441087 GCTGTTCAACCGTCTTCAATTTTC 59.559 41.667 0.00 0.00 0.00 2.29
215 216 5.568685 TGTTCAACCGTCTTCAATTTTCA 57.431 34.783 0.00 0.00 0.00 2.69
216 217 6.142818 TGTTCAACCGTCTTCAATTTTCAT 57.857 33.333 0.00 0.00 0.00 2.57
217 218 5.976534 TGTTCAACCGTCTTCAATTTTCATG 59.023 36.000 0.00 0.00 0.00 3.07
218 219 5.766150 TCAACCGTCTTCAATTTTCATGT 57.234 34.783 0.00 0.00 0.00 3.21
219 220 5.518812 TCAACCGTCTTCAATTTTCATGTG 58.481 37.500 0.00 0.00 0.00 3.21
220 221 3.900941 ACCGTCTTCAATTTTCATGTGC 58.099 40.909 0.00 0.00 0.00 4.57
221 222 3.317711 ACCGTCTTCAATTTTCATGTGCA 59.682 39.130 0.00 0.00 0.00 4.57
222 223 4.022068 ACCGTCTTCAATTTTCATGTGCAT 60.022 37.500 0.00 0.00 0.00 3.96
223 224 4.325204 CCGTCTTCAATTTTCATGTGCATG 59.675 41.667 5.86 5.86 40.09 4.06
224 225 5.155643 CGTCTTCAATTTTCATGTGCATGA 58.844 37.500 10.48 10.48 45.30 3.07
310 311 3.870723 TTGAACTCGTGAACCATTTCG 57.129 42.857 0.00 0.00 34.04 3.46
311 312 3.100658 TGAACTCGTGAACCATTTCGA 57.899 42.857 0.00 0.00 34.04 3.71
315 316 3.706994 CTCGTGAACCATTTCGAGTTC 57.293 47.619 8.01 8.01 42.83 3.01
316 317 2.055838 TCGTGAACCATTTCGAGTTCG 58.944 47.619 9.79 0.00 44.29 3.95
317 318 1.461888 CGTGAACCATTTCGAGTTCGC 60.462 52.381 15.18 15.18 44.29 4.70
318 319 1.872388 TGAACCATTTCGAGTTCGCA 58.128 45.000 9.79 0.00 44.29 5.10
319 320 2.214347 TGAACCATTTCGAGTTCGCAA 58.786 42.857 9.79 0.00 44.29 4.85
320 321 2.614520 TGAACCATTTCGAGTTCGCAAA 59.385 40.909 9.79 0.04 44.29 3.68
321 322 2.681152 ACCATTTCGAGTTCGCAAAC 57.319 45.000 0.00 0.00 39.60 2.93
322 323 1.070175 ACCATTTCGAGTTCGCAAACG 60.070 47.619 0.00 0.00 40.48 3.60
336 337 3.666334 TCGCAAACGATTTTTCAAATCCG 59.334 39.130 0.00 2.35 45.12 4.18
337 338 3.717749 CGCAAACGATTTTTCAAATCCGC 60.718 43.478 0.00 2.18 43.93 5.54
338 339 3.717749 GCAAACGATTTTTCAAATCCGCG 60.718 43.478 0.00 0.00 0.00 6.46
339 340 2.256445 ACGATTTTTCAAATCCGCGG 57.744 45.000 22.12 22.12 0.00 6.46
340 341 1.807742 ACGATTTTTCAAATCCGCGGA 59.192 42.857 33.12 33.12 0.00 5.54
341 342 2.226912 ACGATTTTTCAAATCCGCGGAA 59.773 40.909 34.66 13.56 0.00 4.30
342 343 2.592459 CGATTTTTCAAATCCGCGGAAC 59.408 45.455 34.66 11.64 0.00 3.62
343 344 3.570559 GATTTTTCAAATCCGCGGAACA 58.429 40.909 34.66 10.40 0.00 3.18
344 345 2.409152 TTTTCAAATCCGCGGAACAC 57.591 45.000 34.66 0.00 0.00 3.32
354 355 3.326109 CGGAACACGCGGACTTTT 58.674 55.556 12.47 0.00 34.82 2.27
355 356 1.644913 CGGAACACGCGGACTTTTT 59.355 52.632 12.47 0.00 34.82 1.94
356 357 0.383860 CGGAACACGCGGACTTTTTC 60.384 55.000 12.47 3.13 34.82 2.29
357 358 0.040692 GGAACACGCGGACTTTTTCC 60.041 55.000 12.47 8.84 41.75 3.13
358 359 0.658897 GAACACGCGGACTTTTTCCA 59.341 50.000 12.47 0.00 46.29 3.53
359 360 1.064357 GAACACGCGGACTTTTTCCAA 59.936 47.619 12.47 0.00 46.29 3.53
360 361 0.661020 ACACGCGGACTTTTTCCAAG 59.339 50.000 12.47 0.00 46.29 3.61
361 362 0.661020 CACGCGGACTTTTTCCAAGT 59.339 50.000 12.47 0.00 46.29 3.16
362 363 1.064952 CACGCGGACTTTTTCCAAGTT 59.935 47.619 12.47 0.00 46.29 2.66
363 364 1.746787 ACGCGGACTTTTTCCAAGTTT 59.253 42.857 12.47 0.00 46.29 2.66
364 365 2.164827 ACGCGGACTTTTTCCAAGTTTT 59.835 40.909 12.47 0.00 46.29 2.43
365 366 3.183754 CGCGGACTTTTTCCAAGTTTTT 58.816 40.909 0.00 0.00 46.29 1.94
366 367 3.000177 CGCGGACTTTTTCCAAGTTTTTG 60.000 43.478 0.00 0.00 46.29 2.44
367 368 4.177783 GCGGACTTTTTCCAAGTTTTTGA 58.822 39.130 0.00 0.00 46.29 2.69
368 369 4.808895 GCGGACTTTTTCCAAGTTTTTGAT 59.191 37.500 0.00 0.00 46.29 2.57
369 370 5.293324 GCGGACTTTTTCCAAGTTTTTGATT 59.707 36.000 0.00 0.00 46.29 2.57
370 371 6.183360 GCGGACTTTTTCCAAGTTTTTGATTT 60.183 34.615 0.00 0.00 46.29 2.17
371 372 7.625395 GCGGACTTTTTCCAAGTTTTTGATTTT 60.625 33.333 0.00 0.00 46.29 1.82
372 373 8.233868 CGGACTTTTTCCAAGTTTTTGATTTTT 58.766 29.630 0.00 0.00 46.29 1.94
430 431 9.638239 TGGTGAAATTTATTAAAACTCATGAGC 57.362 29.630 22.83 1.64 0.00 4.26
431 432 9.860898 GGTGAAATTTATTAAAACTCATGAGCT 57.139 29.630 22.83 7.86 0.00 4.09
456 457 7.743520 TTTTTAAAAAGGTGCAAGTCTTACG 57.256 32.000 9.31 0.00 0.00 3.18
804 805 7.220030 AGCCAAGTTATTACAGTCATCCATAG 58.780 38.462 0.00 0.00 0.00 2.23
843 844 2.806244 GACCAAGCTACGCAAAAGAGAA 59.194 45.455 0.00 0.00 0.00 2.87
923 930 2.042686 TTCTTCATCATTCCAGCCGG 57.957 50.000 0.00 0.00 0.00 6.13
934 941 1.890041 CCAGCCGGAACACGTTGAA 60.890 57.895 5.05 0.00 42.24 2.69
1055 1065 4.443978 AATAGACCAATCCACCATCCAG 57.556 45.455 0.00 0.00 0.00 3.86
1233 1245 1.882912 ACACTCGTGCATTGACACAT 58.117 45.000 0.00 0.00 40.73 3.21
1247 1259 0.603707 ACACATGTGTCCGCCTCAAG 60.604 55.000 25.76 0.00 40.24 3.02
1361 1376 4.244862 CACAATTTTTCCCCTTTCCATCG 58.755 43.478 0.00 0.00 0.00 3.84
1385 1400 6.529829 CGTCTCTTCAACAAAGAATCTCTAGG 59.470 42.308 0.00 0.00 43.39 3.02
1421 1436 0.690192 TGGTGGACGTGTTCATGGAT 59.310 50.000 0.00 0.00 0.00 3.41
1463 1478 0.685458 AGGTCCAGTACGGCCGTATT 60.685 55.000 38.22 32.07 36.41 1.89
1890 2034 1.815196 CAGGATCTCGAGCTGCTGT 59.185 57.895 24.50 0.00 0.00 4.40
1950 2094 2.113986 GGCTGAAGGTGGTGCACT 59.886 61.111 17.98 0.00 34.40 4.40
2069 2583 2.100216 CGCAAATACCCGCTGCAC 59.900 61.111 0.00 0.00 35.78 4.57
2265 4079 1.077429 CTGAAACCCCTGGGCTAGC 60.077 63.158 7.39 6.04 39.32 3.42
2281 4101 2.737039 GCTAGCTACAGAACAGAGCACC 60.737 54.545 7.70 0.00 38.73 5.01
2700 4680 6.981722 ACTGAATTTGATGTCCCAAAGTAAC 58.018 36.000 0.00 0.00 39.13 2.50
2702 4682 6.980593 TGAATTTGATGTCCCAAAGTAACTG 58.019 36.000 0.00 0.00 39.13 3.16
2723 4940 6.177610 ACTGAACTTGAACTTGAACTTGGTA 58.822 36.000 0.00 0.00 0.00 3.25
2826 5044 0.036577 GCAGCCATGTCTGTCTGTCT 60.037 55.000 5.53 0.00 36.49 3.41
2827 5045 1.723220 CAGCCATGTCTGTCTGTCTG 58.277 55.000 0.00 0.00 0.00 3.51
2828 5046 1.001746 CAGCCATGTCTGTCTGTCTGT 59.998 52.381 0.00 0.00 0.00 3.41
2829 5047 1.274728 AGCCATGTCTGTCTGTCTGTC 59.725 52.381 0.00 0.00 0.00 3.51
2830 5048 1.274728 GCCATGTCTGTCTGTCTGTCT 59.725 52.381 0.00 0.00 0.00 3.41
2831 5049 2.930023 GCCATGTCTGTCTGTCTGTCTG 60.930 54.545 0.00 0.00 0.00 3.51
2832 5050 2.298446 CCATGTCTGTCTGTCTGTCTGT 59.702 50.000 0.00 0.00 0.00 3.41
2833 5051 3.573598 CATGTCTGTCTGTCTGTCTGTC 58.426 50.000 0.00 0.00 0.00 3.51
3065 5505 1.135803 CGATTTTAACTGGTGCGGTGG 60.136 52.381 0.00 0.00 0.00 4.61
3066 5506 1.201414 GATTTTAACTGGTGCGGTGGG 59.799 52.381 0.00 0.00 0.00 4.61
3067 5507 1.457009 TTTTAACTGGTGCGGTGGGC 61.457 55.000 0.00 0.00 43.96 5.36
3083 5523 4.509737 GCGTCCAGGGCCGTAGAC 62.510 72.222 13.24 13.24 0.00 2.59
3084 5524 3.834799 CGTCCAGGGCCGTAGACC 61.835 72.222 16.72 1.83 0.00 3.85
3090 5530 4.839706 GGGCCGTAGACCCCCGTA 62.840 72.222 0.00 0.00 42.01 4.02
3091 5531 2.522680 GGCCGTAGACCCCCGTAT 60.523 66.667 0.00 0.00 0.00 3.06
3092 5532 2.136229 GGCCGTAGACCCCCGTATT 61.136 63.158 0.00 0.00 0.00 1.89
3093 5533 1.689243 GGCCGTAGACCCCCGTATTT 61.689 60.000 0.00 0.00 0.00 1.40
3094 5534 0.178767 GCCGTAGACCCCCGTATTTT 59.821 55.000 0.00 0.00 0.00 1.82
3095 5535 1.407299 GCCGTAGACCCCCGTATTTTT 60.407 52.381 0.00 0.00 0.00 1.94
3096 5536 2.554142 CCGTAGACCCCCGTATTTTTC 58.446 52.381 0.00 0.00 0.00 2.29
3097 5537 2.169144 CCGTAGACCCCCGTATTTTTCT 59.831 50.000 0.00 0.00 0.00 2.52
3098 5538 3.451526 CGTAGACCCCCGTATTTTTCTC 58.548 50.000 0.00 0.00 0.00 2.87
3099 5539 3.119029 CGTAGACCCCCGTATTTTTCTCA 60.119 47.826 0.00 0.00 0.00 3.27
3100 5540 4.442472 CGTAGACCCCCGTATTTTTCTCAT 60.442 45.833 0.00 0.00 0.00 2.90
3101 5541 3.886123 AGACCCCCGTATTTTTCTCATG 58.114 45.455 0.00 0.00 0.00 3.07
3102 5542 3.265995 AGACCCCCGTATTTTTCTCATGT 59.734 43.478 0.00 0.00 0.00 3.21
3103 5543 4.014406 GACCCCCGTATTTTTCTCATGTT 58.986 43.478 0.00 0.00 0.00 2.71
3104 5544 4.412843 ACCCCCGTATTTTTCTCATGTTT 58.587 39.130 0.00 0.00 0.00 2.83
3105 5545 4.836175 ACCCCCGTATTTTTCTCATGTTTT 59.164 37.500 0.00 0.00 0.00 2.43
3106 5546 5.167845 CCCCCGTATTTTTCTCATGTTTTG 58.832 41.667 0.00 0.00 0.00 2.44
3107 5547 4.625311 CCCCGTATTTTTCTCATGTTTTGC 59.375 41.667 0.00 0.00 0.00 3.68
3108 5548 5.469479 CCCGTATTTTTCTCATGTTTTGCT 58.531 37.500 0.00 0.00 0.00 3.91
3109 5549 5.925969 CCCGTATTTTTCTCATGTTTTGCTT 59.074 36.000 0.00 0.00 0.00 3.91
3110 5550 6.089417 CCCGTATTTTTCTCATGTTTTGCTTC 59.911 38.462 0.00 0.00 0.00 3.86
3111 5551 6.640499 CCGTATTTTTCTCATGTTTTGCTTCA 59.360 34.615 0.00 0.00 0.00 3.02
3112 5552 7.329226 CCGTATTTTTCTCATGTTTTGCTTCAT 59.671 33.333 0.00 0.00 0.00 2.57
3113 5553 8.368126 CGTATTTTTCTCATGTTTTGCTTCATC 58.632 33.333 0.00 0.00 0.00 2.92
3114 5554 9.195411 GTATTTTTCTCATGTTTTGCTTCATCA 57.805 29.630 0.00 0.00 0.00 3.07
3115 5555 8.665643 ATTTTTCTCATGTTTTGCTTCATCAA 57.334 26.923 0.00 0.00 0.00 2.57
3116 5556 7.703298 TTTTCTCATGTTTTGCTTCATCAAG 57.297 32.000 0.00 0.00 0.00 3.02
3117 5557 6.638096 TTCTCATGTTTTGCTTCATCAAGA 57.362 33.333 0.00 0.00 0.00 3.02
3118 5558 6.638096 TCTCATGTTTTGCTTCATCAAGAA 57.362 33.333 0.00 0.00 34.41 2.52
3119 5559 6.441274 TCTCATGTTTTGCTTCATCAAGAAC 58.559 36.000 0.00 0.00 31.61 3.01
3120 5560 6.039605 TCTCATGTTTTGCTTCATCAAGAACA 59.960 34.615 0.00 0.00 34.66 3.18
3121 5561 6.210796 TCATGTTTTGCTTCATCAAGAACAG 58.789 36.000 0.00 0.00 34.20 3.16
3122 5562 4.935702 TGTTTTGCTTCATCAAGAACAGG 58.064 39.130 0.00 0.00 30.86 4.00
3123 5563 4.402155 TGTTTTGCTTCATCAAGAACAGGT 59.598 37.500 0.00 0.00 30.86 4.00
3124 5564 4.572985 TTTGCTTCATCAAGAACAGGTG 57.427 40.909 0.00 0.00 31.61 4.00
3125 5565 3.490439 TGCTTCATCAAGAACAGGTGA 57.510 42.857 0.00 0.00 31.61 4.02
3126 5566 3.405831 TGCTTCATCAAGAACAGGTGAG 58.594 45.455 0.00 0.00 31.61 3.51
3127 5567 3.181451 TGCTTCATCAAGAACAGGTGAGT 60.181 43.478 0.00 0.00 31.61 3.41
3128 5568 3.817647 GCTTCATCAAGAACAGGTGAGTT 59.182 43.478 0.00 0.00 31.61 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.931172 CCTACGAATTTGCGGGTACAG 59.069 52.381 0.00 0.00 35.12 2.74
1 2 1.405797 CCCTACGAATTTGCGGGTACA 60.406 52.381 11.06 0.00 35.12 2.90
2 3 1.292992 CCCTACGAATTTGCGGGTAC 58.707 55.000 11.06 0.00 35.12 3.34
3 4 0.462403 GCCCTACGAATTTGCGGGTA 60.462 55.000 17.66 0.35 37.24 3.69
5 6 3.107447 GCCCTACGAATTTGCGGG 58.893 61.111 13.90 13.90 37.97 6.13
35 36 1.221466 TGCTGAAGACGTTTCCGCAG 61.221 55.000 18.19 10.51 34.53 5.18
36 37 1.221466 CTGCTGAAGACGTTTCCGCA 61.221 55.000 19.72 19.72 36.54 5.69
37 38 1.222115 ACTGCTGAAGACGTTTCCGC 61.222 55.000 14.90 14.90 37.70 5.54
38 39 1.070577 CAACTGCTGAAGACGTTTCCG 60.071 52.381 0.00 0.00 40.83 4.30
39 40 2.210116 TCAACTGCTGAAGACGTTTCC 58.790 47.619 0.00 0.00 0.00 3.13
40 41 3.743396 AGATCAACTGCTGAAGACGTTTC 59.257 43.478 0.00 0.00 37.67 2.78
41 42 3.496130 CAGATCAACTGCTGAAGACGTTT 59.504 43.478 0.00 0.00 39.86 3.60
42 43 3.062763 CAGATCAACTGCTGAAGACGTT 58.937 45.455 0.00 0.00 39.86 3.99
43 44 2.681706 CAGATCAACTGCTGAAGACGT 58.318 47.619 0.00 0.00 39.86 4.34
54 55 1.469940 GGATCACGACGCAGATCAACT 60.470 52.381 23.78 0.00 41.84 3.16
55 56 0.924090 GGATCACGACGCAGATCAAC 59.076 55.000 23.78 10.47 41.84 3.18
56 57 3.345737 GGATCACGACGCAGATCAA 57.654 52.632 23.78 0.00 41.84 2.57
67 68 1.194547 CCAACTTGTGTTCGGATCACG 59.805 52.381 12.99 0.00 46.11 4.35
68 69 1.069227 GCCAACTTGTGTTCGGATCAC 60.069 52.381 11.38 11.38 33.52 3.06
69 70 1.234821 GCCAACTTGTGTTCGGATCA 58.765 50.000 0.00 0.00 33.52 2.92
70 71 1.197721 CTGCCAACTTGTGTTCGGATC 59.802 52.381 0.00 0.00 33.52 3.36
71 72 1.238439 CTGCCAACTTGTGTTCGGAT 58.762 50.000 0.00 0.00 33.52 4.18
72 73 1.444119 GCTGCCAACTTGTGTTCGGA 61.444 55.000 0.00 0.00 33.52 4.55
73 74 1.008538 GCTGCCAACTTGTGTTCGG 60.009 57.895 0.00 0.00 33.52 4.30
74 75 1.369209 CGCTGCCAACTTGTGTTCG 60.369 57.895 0.00 0.00 33.52 3.95
75 76 0.380378 TTCGCTGCCAACTTGTGTTC 59.620 50.000 0.00 0.00 33.52 3.18
76 77 0.814457 TTTCGCTGCCAACTTGTGTT 59.186 45.000 0.00 0.00 36.75 3.32
77 78 1.032014 ATTTCGCTGCCAACTTGTGT 58.968 45.000 0.00 0.00 0.00 3.72
78 79 1.788308 CAATTTCGCTGCCAACTTGTG 59.212 47.619 2.72 0.00 0.00 3.33
79 80 1.269726 CCAATTTCGCTGCCAACTTGT 60.270 47.619 8.68 0.00 0.00 3.16
80 81 1.269726 ACCAATTTCGCTGCCAACTTG 60.270 47.619 3.69 3.69 0.00 3.16
81 82 1.039856 ACCAATTTCGCTGCCAACTT 58.960 45.000 0.00 0.00 0.00 2.66
82 83 1.000274 GAACCAATTTCGCTGCCAACT 60.000 47.619 0.00 0.00 0.00 3.16
83 84 1.269517 TGAACCAATTTCGCTGCCAAC 60.270 47.619 0.00 0.00 36.97 3.77
84 85 1.035923 TGAACCAATTTCGCTGCCAA 58.964 45.000 0.00 0.00 36.97 4.52
85 86 1.035923 TTGAACCAATTTCGCTGCCA 58.964 45.000 0.00 0.00 36.97 4.92
86 87 2.147436 TTTGAACCAATTTCGCTGCC 57.853 45.000 0.00 0.00 36.97 4.85
87 88 5.576384 TGAATATTTGAACCAATTTCGCTGC 59.424 36.000 0.00 0.00 36.97 5.25
88 89 7.488792 TCATGAATATTTGAACCAATTTCGCTG 59.511 33.333 0.00 0.00 36.97 5.18
89 90 7.546358 TCATGAATATTTGAACCAATTTCGCT 58.454 30.769 0.00 0.00 36.97 4.93
90 91 7.754069 TCATGAATATTTGAACCAATTTCGC 57.246 32.000 0.00 0.00 36.97 4.70
116 117 9.894783 GCGAAGTATCTCTACAGAATAACAATA 57.105 33.333 0.00 0.00 30.24 1.90
117 118 8.634444 AGCGAAGTATCTCTACAGAATAACAAT 58.366 33.333 0.00 0.00 30.24 2.71
118 119 7.997482 AGCGAAGTATCTCTACAGAATAACAA 58.003 34.615 0.00 0.00 30.24 2.83
119 120 7.569639 AGCGAAGTATCTCTACAGAATAACA 57.430 36.000 0.00 0.00 30.24 2.41
120 121 7.592164 GGAAGCGAAGTATCTCTACAGAATAAC 59.408 40.741 0.00 0.00 30.24 1.89
121 122 7.520131 CGGAAGCGAAGTATCTCTACAGAATAA 60.520 40.741 0.00 0.00 30.24 1.40
122 123 6.073167 CGGAAGCGAAGTATCTCTACAGAATA 60.073 42.308 0.00 0.00 30.24 1.75
123 124 5.278071 CGGAAGCGAAGTATCTCTACAGAAT 60.278 44.000 0.00 0.00 30.24 2.40
124 125 4.035324 CGGAAGCGAAGTATCTCTACAGAA 59.965 45.833 0.00 0.00 30.24 3.02
125 126 3.560481 CGGAAGCGAAGTATCTCTACAGA 59.440 47.826 0.00 0.00 0.00 3.41
126 127 3.560481 TCGGAAGCGAAGTATCTCTACAG 59.440 47.826 0.00 0.00 0.00 2.74
127 128 3.538591 TCGGAAGCGAAGTATCTCTACA 58.461 45.455 0.00 0.00 0.00 2.74
128 129 3.607542 GCTCGGAAGCGAAGTATCTCTAC 60.608 52.174 0.00 0.00 39.10 2.59
129 130 2.548904 GCTCGGAAGCGAAGTATCTCTA 59.451 50.000 0.00 0.00 39.10 2.43
130 131 1.335496 GCTCGGAAGCGAAGTATCTCT 59.665 52.381 0.00 0.00 39.10 3.10
131 132 1.761206 GCTCGGAAGCGAAGTATCTC 58.239 55.000 0.00 0.00 39.10 2.75
132 133 3.949031 GCTCGGAAGCGAAGTATCT 57.051 52.632 0.00 0.00 39.10 1.98
142 143 9.046296 AGAAAAACATATATAACAGCTCGGAAG 57.954 33.333 0.00 0.00 0.00 3.46
143 144 8.958119 AGAAAAACATATATAACAGCTCGGAA 57.042 30.769 0.00 0.00 0.00 4.30
144 145 9.472361 GTAGAAAAACATATATAACAGCTCGGA 57.528 33.333 0.00 0.00 0.00 4.55
145 146 8.709646 GGTAGAAAAACATATATAACAGCTCGG 58.290 37.037 0.00 0.00 0.00 4.63
146 147 9.477484 AGGTAGAAAAACATATATAACAGCTCG 57.523 33.333 0.00 0.00 0.00 5.03
157 158 8.850156 GGCATATGAACAGGTAGAAAAACATAT 58.150 33.333 6.97 0.00 32.38 1.78
158 159 7.831690 TGGCATATGAACAGGTAGAAAAACATA 59.168 33.333 6.97 0.00 0.00 2.29
159 160 6.663093 TGGCATATGAACAGGTAGAAAAACAT 59.337 34.615 6.97 0.00 0.00 2.71
160 161 6.007076 TGGCATATGAACAGGTAGAAAAACA 58.993 36.000 6.97 0.00 0.00 2.83
161 162 6.322491 GTGGCATATGAACAGGTAGAAAAAC 58.678 40.000 6.97 0.00 0.00 2.43
162 163 5.417580 GGTGGCATATGAACAGGTAGAAAAA 59.582 40.000 6.97 0.00 0.00 1.94
163 164 4.947388 GGTGGCATATGAACAGGTAGAAAA 59.053 41.667 6.97 0.00 0.00 2.29
164 165 4.523083 GGTGGCATATGAACAGGTAGAAA 58.477 43.478 6.97 0.00 0.00 2.52
165 166 3.118038 GGGTGGCATATGAACAGGTAGAA 60.118 47.826 6.97 0.00 0.00 2.10
166 167 2.438021 GGGTGGCATATGAACAGGTAGA 59.562 50.000 6.97 0.00 0.00 2.59
167 168 2.806745 CGGGTGGCATATGAACAGGTAG 60.807 54.545 6.97 0.00 0.00 3.18
168 169 1.140052 CGGGTGGCATATGAACAGGTA 59.860 52.381 6.97 0.00 0.00 3.08
169 170 0.107214 CGGGTGGCATATGAACAGGT 60.107 55.000 6.97 0.00 0.00 4.00
170 171 0.819259 CCGGGTGGCATATGAACAGG 60.819 60.000 6.97 7.46 0.00 4.00
171 172 0.180171 TCCGGGTGGCATATGAACAG 59.820 55.000 6.97 2.44 34.14 3.16
172 173 0.180171 CTCCGGGTGGCATATGAACA 59.820 55.000 6.97 1.34 34.14 3.18
173 174 1.166531 GCTCCGGGTGGCATATGAAC 61.167 60.000 6.97 3.63 34.14 3.18
174 175 1.148273 GCTCCGGGTGGCATATGAA 59.852 57.895 6.97 0.00 34.14 2.57
175 176 1.766059 AGCTCCGGGTGGCATATGA 60.766 57.895 6.97 0.00 34.14 2.15
176 177 1.598962 CAGCTCCGGGTGGCATATG 60.599 63.158 0.00 0.00 37.31 1.78
177 178 1.635817 AACAGCTCCGGGTGGCATAT 61.636 55.000 0.00 0.00 44.34 1.78
178 179 2.252072 GAACAGCTCCGGGTGGCATA 62.252 60.000 0.00 0.00 44.34 3.14
179 180 3.628646 GAACAGCTCCGGGTGGCAT 62.629 63.158 0.00 0.00 44.34 4.40
180 181 4.329545 GAACAGCTCCGGGTGGCA 62.330 66.667 0.00 0.00 44.34 4.92
181 182 3.842925 TTGAACAGCTCCGGGTGGC 62.843 63.158 0.00 4.03 44.34 5.01
182 183 1.966451 GTTGAACAGCTCCGGGTGG 60.966 63.158 0.00 0.00 44.34 4.61
183 184 1.966451 GGTTGAACAGCTCCGGGTG 60.966 63.158 0.00 0.00 45.40 4.61
184 185 2.430367 GGTTGAACAGCTCCGGGT 59.570 61.111 0.00 0.00 0.00 5.28
185 186 2.742372 CGGTTGAACAGCTCCGGG 60.742 66.667 0.00 0.00 39.41 5.73
186 187 2.027625 GACGGTTGAACAGCTCCGG 61.028 63.158 13.18 0.00 46.06 5.14
187 188 0.600255 AAGACGGTTGAACAGCTCCG 60.600 55.000 7.66 7.66 46.98 4.63
188 189 1.149148 GAAGACGGTTGAACAGCTCC 58.851 55.000 0.00 0.00 0.00 4.70
189 190 1.865865 TGAAGACGGTTGAACAGCTC 58.134 50.000 0.00 0.00 0.00 4.09
190 191 2.325583 TTGAAGACGGTTGAACAGCT 57.674 45.000 0.00 0.00 0.00 4.24
191 192 3.626028 AATTGAAGACGGTTGAACAGC 57.374 42.857 0.00 0.00 0.00 4.40
192 193 5.577835 TGAAAATTGAAGACGGTTGAACAG 58.422 37.500 0.00 0.00 0.00 3.16
193 194 5.568685 TGAAAATTGAAGACGGTTGAACA 57.431 34.783 0.00 0.00 0.00 3.18
194 195 5.977129 ACATGAAAATTGAAGACGGTTGAAC 59.023 36.000 0.00 0.00 0.00 3.18
195 196 5.976534 CACATGAAAATTGAAGACGGTTGAA 59.023 36.000 0.00 0.00 0.00 2.69
196 197 5.518812 CACATGAAAATTGAAGACGGTTGA 58.481 37.500 0.00 0.00 0.00 3.18
197 198 4.148696 GCACATGAAAATTGAAGACGGTTG 59.851 41.667 0.00 0.00 0.00 3.77
198 199 4.202101 TGCACATGAAAATTGAAGACGGTT 60.202 37.500 0.00 0.00 0.00 4.44
199 200 3.317711 TGCACATGAAAATTGAAGACGGT 59.682 39.130 0.00 0.00 0.00 4.83
200 201 3.899734 TGCACATGAAAATTGAAGACGG 58.100 40.909 0.00 0.00 0.00 4.79
201 202 5.155643 TCATGCACATGAAAATTGAAGACG 58.844 37.500 10.82 0.00 44.14 4.18
287 288 5.031578 CGAAATGGTTCACGAGTTCAAAAA 58.968 37.500 0.00 0.00 32.89 1.94
288 289 4.333095 TCGAAATGGTTCACGAGTTCAAAA 59.667 37.500 0.00 0.00 32.89 2.44
289 290 3.872182 TCGAAATGGTTCACGAGTTCAAA 59.128 39.130 0.00 0.00 32.89 2.69
290 291 3.459145 TCGAAATGGTTCACGAGTTCAA 58.541 40.909 0.00 0.00 32.89 2.69
291 292 3.057019 CTCGAAATGGTTCACGAGTTCA 58.943 45.455 0.00 0.00 44.37 3.18
292 293 3.706994 CTCGAAATGGTTCACGAGTTC 57.293 47.619 0.00 0.00 44.37 3.01
296 297 2.055838 CGAACTCGAAATGGTTCACGA 58.944 47.619 13.64 0.00 41.05 4.35
297 298 1.461888 GCGAACTCGAAATGGTTCACG 60.462 52.381 13.64 4.66 41.05 4.35
298 299 1.529438 TGCGAACTCGAAATGGTTCAC 59.471 47.619 13.64 6.30 41.05 3.18
299 300 1.872388 TGCGAACTCGAAATGGTTCA 58.128 45.000 13.64 0.00 41.05 3.18
300 301 2.961522 TTGCGAACTCGAAATGGTTC 57.038 45.000 2.69 5.44 43.02 3.62
301 302 2.601266 CGTTTGCGAACTCGAAATGGTT 60.601 45.455 14.84 0.00 43.02 3.67
302 303 1.070175 CGTTTGCGAACTCGAAATGGT 60.070 47.619 14.84 0.00 43.02 3.55
303 304 1.193650 TCGTTTGCGAACTCGAAATGG 59.806 47.619 14.84 0.00 44.92 3.16
304 305 2.570468 TCGTTTGCGAACTCGAAATG 57.430 45.000 14.84 6.61 44.92 2.32
315 316 3.717749 GCGGATTTGAAAAATCGTTTGCG 60.718 43.478 6.63 5.64 39.92 4.85
316 317 3.717749 CGCGGATTTGAAAAATCGTTTGC 60.718 43.478 0.00 7.03 0.00 3.68
317 318 3.181545 CCGCGGATTTGAAAAATCGTTTG 60.182 43.478 24.07 0.00 0.00 2.93
318 319 2.983803 CCGCGGATTTGAAAAATCGTTT 59.016 40.909 24.07 0.00 0.00 3.60
319 320 2.226912 TCCGCGGATTTGAAAAATCGTT 59.773 40.909 27.28 0.00 0.00 3.85
320 321 1.807742 TCCGCGGATTTGAAAAATCGT 59.192 42.857 27.28 0.00 0.00 3.73
321 322 2.535934 TCCGCGGATTTGAAAAATCG 57.464 45.000 27.28 0.00 0.00 3.34
322 323 3.363724 GTGTTCCGCGGATTTGAAAAATC 59.636 43.478 31.56 3.63 0.00 2.17
323 324 3.313690 GTGTTCCGCGGATTTGAAAAAT 58.686 40.909 31.56 0.00 0.00 1.82
324 325 2.733517 GTGTTCCGCGGATTTGAAAAA 58.266 42.857 31.56 8.52 0.00 1.94
325 326 1.334239 CGTGTTCCGCGGATTTGAAAA 60.334 47.619 31.56 9.43 33.47 2.29
326 327 0.236187 CGTGTTCCGCGGATTTGAAA 59.764 50.000 31.56 10.33 33.47 2.69
327 328 1.863491 CGTGTTCCGCGGATTTGAA 59.137 52.632 31.56 11.24 33.47 2.69
328 329 3.556625 CGTGTTCCGCGGATTTGA 58.443 55.556 31.56 11.71 33.47 2.69
337 338 0.383860 GAAAAAGTCCGCGTGTTCCG 60.384 55.000 4.92 0.00 40.40 4.30
338 339 0.040692 GGAAAAAGTCCGCGTGTTCC 60.041 55.000 4.92 2.63 36.40 3.62
339 340 3.449789 GGAAAAAGTCCGCGTGTTC 57.550 52.632 4.92 0.00 36.40 3.18
404 405 9.638239 GCTCATGAGTTTTAATAAATTTCACCA 57.362 29.630 23.38 0.00 0.00 4.17
405 406 9.860898 AGCTCATGAGTTTTAATAAATTTCACC 57.139 29.630 23.38 0.79 0.00 4.02
432 433 7.743520 CGTAAGACTTGCACCTTTTTAAAAA 57.256 32.000 12.62 12.62 43.02 1.94
804 805 0.445436 TCCGTCGCTTAGTTCGAGAC 59.555 55.000 0.00 0.00 36.56 3.36
843 844 4.021981 GGTTCTCTGCATGTTTTAGCCTTT 60.022 41.667 0.00 0.00 0.00 3.11
923 930 1.804748 GGGTGGAGATTCAACGTGTTC 59.195 52.381 0.00 0.00 0.00 3.18
934 941 0.616111 AGCGTCTCAAGGGTGGAGAT 60.616 55.000 0.00 0.00 42.85 2.75
1055 1065 7.751732 TGTCTATAATCAAAGCAATGACACAC 58.248 34.615 0.00 0.00 30.82 3.82
1233 1245 2.616797 TTTGGCTTGAGGCGGACACA 62.617 55.000 0.00 0.00 44.42 3.72
1238 1250 2.282462 ACCTTTGGCTTGAGGCGG 60.282 61.111 0.00 0.00 44.42 6.13
1247 1259 3.524541 CCTAATCAAATGCACCTTTGGC 58.475 45.455 11.79 0.00 36.87 4.52
1361 1376 6.816140 CCCTAGAGATTCTTTGTTGAAGAGAC 59.184 42.308 0.00 0.00 44.80 3.36
1413 1428 2.353704 GGTCATCGGCGATATCCATGAA 60.354 50.000 23.53 0.00 30.89 2.57
1421 1436 2.504274 GGTGGGGTCATCGGCGATA 61.504 63.158 23.53 8.45 0.00 2.92
1620 1763 2.553028 GGTTTGGCATGTCCTTCTCAGA 60.553 50.000 0.00 0.00 35.26 3.27
1890 2034 1.865788 CGTCTACCGGACCCAAACGA 61.866 60.000 9.46 0.00 41.64 3.85
1950 2094 2.260869 GCAGGTTCGCCAAGCTCAA 61.261 57.895 0.00 0.00 38.33 3.02
2069 2583 1.746220 TGTTGGTTTCAGTTGAACCCG 59.254 47.619 4.32 0.00 39.20 5.28
2071 2585 2.165437 TGCTGTTGGTTTCAGTTGAACC 59.835 45.455 0.00 0.00 35.60 3.62
2072 2586 3.502191 TGCTGTTGGTTTCAGTTGAAC 57.498 42.857 0.00 0.00 35.60 3.18
2073 2587 3.509575 ACTTGCTGTTGGTTTCAGTTGAA 59.490 39.130 0.00 0.00 35.60 2.69
2076 2590 3.066760 GCTACTTGCTGTTGGTTTCAGTT 59.933 43.478 0.00 0.00 38.95 3.16
2077 2591 2.618709 GCTACTTGCTGTTGGTTTCAGT 59.381 45.455 0.00 0.00 38.95 3.41
2141 3781 5.899299 AGGATTTCAGCTACATTTTGATGC 58.101 37.500 0.00 0.00 0.00 3.91
2265 4079 3.138205 CGTAGGTGCTCTGTTCTGTAG 57.862 52.381 0.00 0.00 0.00 2.74
2700 4680 5.567138 ACCAAGTTCAAGTTCAAGTTCAG 57.433 39.130 0.00 0.00 0.00 3.02
2702 4682 8.926715 ATTTTACCAAGTTCAAGTTCAAGTTC 57.073 30.769 0.00 0.00 0.00 3.01
2723 4940 6.425417 ACGCGAATTAATCCAAACCAAATTTT 59.575 30.769 15.93 0.00 0.00 1.82
2760 4977 5.296813 ACAATAACAACAGAAGGCGAATC 57.703 39.130 0.00 0.00 0.00 2.52
2826 5044 2.115427 TGAACAAGGGACAGACAGACA 58.885 47.619 0.00 0.00 0.00 3.41
2827 5045 2.872858 GTTGAACAAGGGACAGACAGAC 59.127 50.000 0.00 0.00 0.00 3.51
2828 5046 2.158813 GGTTGAACAAGGGACAGACAGA 60.159 50.000 0.00 0.00 0.00 3.41
2829 5047 2.158755 AGGTTGAACAAGGGACAGACAG 60.159 50.000 0.00 0.00 0.00 3.51
2830 5048 1.843851 AGGTTGAACAAGGGACAGACA 59.156 47.619 0.00 0.00 0.00 3.41
2831 5049 2.222027 CAGGTTGAACAAGGGACAGAC 58.778 52.381 0.00 0.00 0.00 3.51
2832 5050 1.476833 GCAGGTTGAACAAGGGACAGA 60.477 52.381 0.00 0.00 0.00 3.41
2833 5051 0.954452 GCAGGTTGAACAAGGGACAG 59.046 55.000 0.00 0.00 0.00 3.51
3041 5481 0.815095 GCACCAGTTAAAATCGGGGG 59.185 55.000 0.00 0.00 0.00 5.40
3068 5508 3.468140 GGGTCTACGGCCCTGGAC 61.468 72.222 9.34 9.34 42.81 4.02
3069 5509 4.791069 GGGGTCTACGGCCCTGGA 62.791 72.222 3.22 0.00 45.39 3.86
3073 5513 4.839706 TACGGGGGTCTACGGCCC 62.840 72.222 0.00 0.00 45.35 5.80
3074 5514 1.689243 AAATACGGGGGTCTACGGCC 61.689 60.000 0.00 0.00 0.00 6.13
3075 5515 0.178767 AAAATACGGGGGTCTACGGC 59.821 55.000 0.00 0.00 0.00 5.68
3076 5516 2.169144 AGAAAAATACGGGGGTCTACGG 59.831 50.000 0.00 0.00 0.00 4.02
3077 5517 3.119029 TGAGAAAAATACGGGGGTCTACG 60.119 47.826 0.00 0.00 0.00 3.51
3078 5518 4.476628 TGAGAAAAATACGGGGGTCTAC 57.523 45.455 0.00 0.00 0.00 2.59
3079 5519 4.472108 ACATGAGAAAAATACGGGGGTCTA 59.528 41.667 0.00 0.00 0.00 2.59
3080 5520 3.265995 ACATGAGAAAAATACGGGGGTCT 59.734 43.478 0.00 0.00 0.00 3.85
3081 5521 3.617284 ACATGAGAAAAATACGGGGGTC 58.383 45.455 0.00 0.00 0.00 4.46
3082 5522 3.732048 ACATGAGAAAAATACGGGGGT 57.268 42.857 0.00 0.00 0.00 4.95
3083 5523 5.167845 CAAAACATGAGAAAAATACGGGGG 58.832 41.667 0.00 0.00 0.00 5.40
3084 5524 4.625311 GCAAAACATGAGAAAAATACGGGG 59.375 41.667 0.00 0.00 0.00 5.73
3085 5525 5.469479 AGCAAAACATGAGAAAAATACGGG 58.531 37.500 0.00 0.00 0.00 5.28
3086 5526 6.640499 TGAAGCAAAACATGAGAAAAATACGG 59.360 34.615 0.00 0.00 0.00 4.02
3087 5527 7.621832 TGAAGCAAAACATGAGAAAAATACG 57.378 32.000 0.00 0.00 0.00 3.06
3088 5528 9.195411 TGATGAAGCAAAACATGAGAAAAATAC 57.805 29.630 0.00 0.00 0.00 1.89
3089 5529 9.761504 TTGATGAAGCAAAACATGAGAAAAATA 57.238 25.926 0.00 0.00 0.00 1.40
3090 5530 8.665643 TTGATGAAGCAAAACATGAGAAAAAT 57.334 26.923 0.00 0.00 0.00 1.82
3091 5531 7.980662 TCTTGATGAAGCAAAACATGAGAAAAA 59.019 29.630 0.00 0.00 0.00 1.94
3092 5532 7.490840 TCTTGATGAAGCAAAACATGAGAAAA 58.509 30.769 0.00 0.00 0.00 2.29
3093 5533 7.041635 TCTTGATGAAGCAAAACATGAGAAA 57.958 32.000 0.00 0.00 0.00 2.52
3094 5534 6.638096 TCTTGATGAAGCAAAACATGAGAA 57.362 33.333 0.00 0.00 0.00 2.87
3095 5535 6.039605 TGTTCTTGATGAAGCAAAACATGAGA 59.960 34.615 0.00 0.00 35.01 3.27
3096 5536 6.210796 TGTTCTTGATGAAGCAAAACATGAG 58.789 36.000 0.00 0.00 35.01 2.90
3097 5537 6.146601 TGTTCTTGATGAAGCAAAACATGA 57.853 33.333 0.00 0.00 35.01 3.07
3098 5538 5.404366 CCTGTTCTTGATGAAGCAAAACATG 59.596 40.000 0.00 0.00 35.01 3.21
3099 5539 5.069516 ACCTGTTCTTGATGAAGCAAAACAT 59.930 36.000 0.00 0.00 35.01 2.71
3100 5540 4.402155 ACCTGTTCTTGATGAAGCAAAACA 59.598 37.500 0.00 0.00 35.01 2.83
3101 5541 4.741676 CACCTGTTCTTGATGAAGCAAAAC 59.258 41.667 0.00 0.00 35.01 2.43
3102 5542 4.644234 TCACCTGTTCTTGATGAAGCAAAA 59.356 37.500 0.00 0.00 35.01 2.44
3103 5543 4.206375 TCACCTGTTCTTGATGAAGCAAA 58.794 39.130 0.00 0.00 35.01 3.68
3104 5544 3.817084 CTCACCTGTTCTTGATGAAGCAA 59.183 43.478 0.00 0.00 35.01 3.91
3105 5545 3.181451 ACTCACCTGTTCTTGATGAAGCA 60.181 43.478 0.00 0.00 35.01 3.91
3106 5546 3.406764 ACTCACCTGTTCTTGATGAAGC 58.593 45.455 0.00 0.00 35.01 3.86


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

AutoCloner maintained by Alex Coulton.