Multiple sequence alignment - TraesCS2B01G245000

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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 TraesCS2B01G245000 chr2B 100.000 7389 0 0 1 7389 249214023 249206635 0.000000e+00 13646.0
1 TraesCS2B01G245000 chr2B 91.500 200 15 2 4637 4835 694263441 694263243 2.630000e-69 274.0
2 TraesCS2B01G245000 chr2B 91.279 172 11 3 6512 6680 31071589 31071759 1.600000e-56 231.0
3 TraesCS2B01G245000 chr2B 84.536 194 24 5 6515 6703 521915290 521915482 3.520000e-43 187.0
4 TraesCS2B01G245000 chr2B 80.751 213 34 7 6790 6998 464180597 464180388 7.670000e-35 159.0
5 TraesCS2B01G245000 chr2D 95.782 6567 193 46 1 6516 192999932 192993399 0.000000e+00 10515.0
6 TraesCS2B01G245000 chr2D 95.726 117 1 2 6675 6790 192993400 192993287 1.270000e-42 185.0
7 TraesCS2B01G245000 chr2A 96.662 3595 64 17 2968 6516 206856690 206853106 0.000000e+00 5923.0
8 TraesCS2B01G245000 chr2A 96.117 2395 77 13 382 2764 206859077 206856687 0.000000e+00 3893.0
9 TraesCS2B01G245000 chr2A 86.702 188 20 5 6515 6698 549968693 549968507 3.500000e-48 204.0
10 TraesCS2B01G245000 chr2A 89.796 147 14 1 243 388 206862941 206862795 3.520000e-43 187.0
11 TraesCS2B01G245000 chr2A 90.598 117 7 2 6675 6790 206853107 206852994 1.280000e-32 152.0
12 TraesCS2B01G245000 chr3B 85.644 613 62 12 6788 7389 40478904 40478307 8.140000e-174 621.0
13 TraesCS2B01G245000 chr3B 89.560 182 14 5 6515 6692 550322939 550322759 7.460000e-55 226.0
14 TraesCS2B01G245000 chr3B 87.302 189 18 6 6514 6699 709282561 709282376 2.090000e-50 211.0
15 TraesCS2B01G245000 chr3B 85.859 198 20 7 6512 6704 164331363 164331557 3.500000e-48 204.0
16 TraesCS2B01G245000 chr3B 78.099 242 43 7 4 240 780517733 780517497 2.150000e-30 145.0
17 TraesCS2B01G245000 chr7A 85.863 481 54 12 6788 7264 727123092 727122622 3.980000e-137 499.0
18 TraesCS2B01G245000 chr7A 88.889 135 15 0 6788 6922 647921307 647921441 4.590000e-37 167.0
19 TraesCS2B01G245000 chr7A 89.744 117 12 0 6788 6904 507427104 507426988 4.620000e-32 150.0
20 TraesCS2B01G245000 chr7A 91.781 73 5 1 7296 7368 727122629 727122558 4.720000e-17 100.0
21 TraesCS2B01G245000 chr7A 78.512 121 19 7 64 181 30155076 30154960 1.030000e-08 73.1
22 TraesCS2B01G245000 chr1D 91.545 343 28 1 7027 7368 476195144 476194802 8.680000e-129 472.0
23 TraesCS2B01G245000 chr1D 97.059 34 1 0 61 94 483371064 483371097 2.880000e-04 58.4
24 TraesCS2B01G245000 chr6A 95.556 180 6 1 4648 4825 153373069 153372890 3.370000e-73 287.0
25 TraesCS2B01G245000 chr4D 95.000 180 7 1 4648 4825 482703444 482703623 1.570000e-71 281.0
26 TraesCS2B01G245000 chr4D 89.560 182 14 5 6515 6692 129717408 129717588 7.460000e-55 226.0
27 TraesCS2B01G245000 chr3D 95.000 180 7 1 4648 4825 422517613 422517792 1.570000e-71 281.0
28 TraesCS2B01G245000 chr3D 90.805 174 13 3 6513 6683 272098432 272098605 5.770000e-56 230.0
29 TraesCS2B01G245000 chr4A 94.475 181 8 1 4647 4825 114586279 114586459 2.030000e-70 278.0
30 TraesCS2B01G245000 chr4A 85.417 192 21 6 6515 6704 652853258 652853444 7.570000e-45 193.0
31 TraesCS2B01G245000 chr4A 83.770 191 23 7 6515 6698 732302608 732302419 2.740000e-39 174.0
32 TraesCS2B01G245000 chr7B 93.085 188 11 1 4645 4830 252794266 252794453 2.630000e-69 274.0
33 TraesCS2B01G245000 chr7B 87.565 193 19 5 6492 6682 663256464 663256653 1.250000e-52 219.0
34 TraesCS2B01G245000 chr7B 86.096 187 23 3 6512 6696 593557090 593556905 1.630000e-46 198.0
35 TraesCS2B01G245000 chr5B 91.176 204 15 2 4644 4844 126245084 126245287 2.630000e-69 274.0
36 TraesCS2B01G245000 chr5B 80.508 118 20 3 64 181 541095086 541094972 3.670000e-13 87.9
37 TraesCS2B01G245000 chr5D 89.888 178 14 4 6506 6679 455740475 455740298 7.460000e-55 226.0
38 TraesCS2B01G245000 chr5D 89.714 175 14 3 6505 6676 420206034 420206207 3.470000e-53 220.0
39 TraesCS2B01G245000 chr1B 88.235 187 19 2 6508 6691 43457510 43457324 3.470000e-53 220.0
40 TraesCS2B01G245000 chr5A 89.143 175 15 4 6505 6676 533848151 533848324 1.610000e-51 215.0
41 TraesCS2B01G245000 chr5A 77.119 118 26 1 64 181 105413093 105412977 4.780000e-07 67.6
42 TraesCS2B01G245000 chr6B 89.051 137 13 2 6788 6924 35075194 35075328 1.270000e-37 169.0
43 TraesCS2B01G245000 chr7D 86.957 138 15 3 6788 6924 604590867 604590732 1.280000e-32 152.0
44 TraesCS2B01G245000 chr7D 80.159 126 18 7 59 181 154202426 154202547 3.670000e-13 87.9
45 TraesCS2B01G245000 chr6D 86.131 137 18 1 6788 6924 81153025 81153160 5.970000e-31 147.0
46 TraesCS2B01G245000 chrUn 80.808 198 25 6 6790 6974 347568466 347568269 7.730000e-30 143.0
47 TraesCS2B01G245000 chrUn 80.808 198 25 6 6790 6974 347606054 347605857 7.730000e-30 143.0
48 TraesCS2B01G245000 chr3A 85.401 137 20 0 6788 6924 93574375 93574511 7.730000e-30 143.0
49 TraesCS2B01G245000 chr1A 82.517 143 23 2 6790 6932 489352099 489352239 2.800000e-24 124.0
50 TraesCS2B01G245000 chr4B 77.070 157 33 3 15 170 616570386 616570540 3.670000e-13 87.9


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 TraesCS2B01G245000 chr2B 249206635 249214023 7388 True 13646.00 13646 100.00000 1 7389 1 chr2B.!!$R1 7388
1 TraesCS2B01G245000 chr2D 192993287 192999932 6645 True 5350.00 10515 95.75400 1 6790 2 chr2D.!!$R1 6789
2 TraesCS2B01G245000 chr2A 206852994 206862941 9947 True 2538.75 5923 93.29325 243 6790 4 chr2A.!!$R2 6547
3 TraesCS2B01G245000 chr3B 40478307 40478904 597 True 621.00 621 85.64400 6788 7389 1 chr3B.!!$R1 601
4 TraesCS2B01G245000 chr7A 727122558 727123092 534 True 299.50 499 88.82200 6788 7368 2 chr7A.!!$R3 580

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
441 4204 0.032678 CACTCGCCGAAGCTATCCAT 59.967 55.000 0.00 0.00 36.60 3.41 F
444 4207 0.750249 TCGCCGAAGCTATCCATTCA 59.250 50.000 0.00 0.00 36.60 2.57 F
530 4293 1.079336 GACGGGGAAGAAGGGAACG 60.079 63.158 0.00 0.00 0.00 3.95 F
604 4367 1.344191 ATGAAGAGGAGAGGCAGCCC 61.344 60.000 8.22 0.00 0.00 5.19 F
679 4442 1.373435 CGCGGGGGCCAGATTATTA 59.627 57.895 4.39 0.00 0.00 0.98 F
1318 5091 2.087095 CGTACTACGAGGTCCGCTCG 62.087 65.000 2.17 9.04 46.05 5.03 F
2800 6577 0.746659 GCATATGGTTGCCCTGTTCC 59.253 55.000 4.56 0.00 36.60 3.62 F
3926 7705 0.249955 TCAACGATGAGGCAGATGCA 59.750 50.000 7.19 0.00 44.36 3.96 F
3973 7752 0.466189 AGATTGGTATGCCTTGCCCG 60.466 55.000 0.16 0.00 35.27 6.13 F
4675 8455 1.512156 CCTTGGCGCAACGGTAAAGT 61.512 55.000 10.83 0.00 0.00 2.66 F
4707 8487 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18 F
4767 8547 3.328050 GGCTGCCTACTATAGACCCAAAT 59.672 47.826 12.43 0.00 0.00 2.32 F
6218 10049 1.785041 TTGGCACAGAAACAGCGAGC 61.785 55.000 0.00 0.00 42.39 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 5709 0.668535 GTGCCAACTTCCTCGCTTTT 59.331 50.000 0.00 0.00 0.00 2.27 R
2179 5954 7.143340 CCTTAACACCATTGCAGATCATAATG 58.857 38.462 0.00 2.79 0.00 1.90 R
2496 6273 4.928601 GGTGAACACCCTAAAAGAACAAC 58.071 43.478 12.42 0.00 45.68 3.32 R
2688 6465 7.023197 TGTCAGATGCATGATTAAGATGTTG 57.977 36.000 2.46 0.00 0.00 3.33 R
2793 6570 2.337361 GGTTTTGGACCGGAACAGG 58.663 57.895 9.46 0.00 39.00 4.00 R
3177 6956 4.157656 GGCCACTGCATGATTAACAGTTAA 59.842 41.667 8.22 8.22 42.59 2.01 R
4675 8455 1.955778 CTCATGGTCACAAGGCAACAA 59.044 47.619 0.00 0.00 41.41 2.83 R
5179 8961 3.149196 CAAGAGGAAGCAAGCCACTAAA 58.851 45.455 0.00 0.00 0.00 1.85 R
5542 9325 5.333581 TCAGTTTCCTCAGAGACATCCTTA 58.666 41.667 0.00 0.00 29.47 2.69 R
6197 10028 0.380378 TCGCTGTTTCTGTGCCAAAC 59.620 50.000 0.00 0.00 34.79 2.93 R
6218 10049 0.816421 ACCACCCGTGAAAACCTTCG 60.816 55.000 0.00 0.00 33.94 3.79 R
6226 10057 1.134640 CCGATTATGACCACCCGTGAA 60.135 52.381 0.00 0.00 0.00 3.18 R
7275 11137 0.460311 AGCATCAGTAGTACCACGGC 59.540 55.000 0.00 0.00 0.00 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
46 47 5.008331 TGTCGTTGTACAACTATCTCTCCT 58.992 41.667 30.47 0.00 39.08 3.69
78 79 5.284864 TCTCATCGATAGTTTGCATCTCAC 58.715 41.667 0.00 0.00 37.40 3.51
95 96 0.179056 CACCACCGAAGTCAACCACT 60.179 55.000 0.00 0.00 36.64 4.00
109 110 8.641498 AAGTCAACCACTGAATCTGAAAATAT 57.359 30.769 0.00 0.00 35.22 1.28
120 121 7.056635 TGAATCTGAAAATATGAACCCTCTCC 58.943 38.462 0.00 0.00 0.00 3.71
157 158 1.143183 ACCGTTGTCGTGAAGCTGT 59.857 52.632 0.00 0.00 35.01 4.40
161 162 1.335597 CGTTGTCGTGAAGCTGTAGGA 60.336 52.381 0.00 0.00 0.00 2.94
162 163 2.329379 GTTGTCGTGAAGCTGTAGGAG 58.671 52.381 0.00 0.00 0.00 3.69
163 164 0.888619 TGTCGTGAAGCTGTAGGAGG 59.111 55.000 0.00 0.00 0.00 4.30
164 165 0.889306 GTCGTGAAGCTGTAGGAGGT 59.111 55.000 0.00 0.00 0.00 3.85
165 166 1.135344 GTCGTGAAGCTGTAGGAGGTC 60.135 57.143 0.00 0.00 0.00 3.85
166 167 0.179161 CGTGAAGCTGTAGGAGGTCG 60.179 60.000 0.00 0.00 0.00 4.79
167 168 0.458716 GTGAAGCTGTAGGAGGTCGC 60.459 60.000 0.00 0.00 0.00 5.19
168 169 0.612174 TGAAGCTGTAGGAGGTCGCT 60.612 55.000 0.00 0.00 0.00 4.93
169 170 0.179124 GAAGCTGTAGGAGGTCGCTG 60.179 60.000 0.00 0.00 0.00 5.18
170 171 0.900647 AAGCTGTAGGAGGTCGCTGT 60.901 55.000 0.00 0.00 0.00 4.40
171 172 0.034380 AGCTGTAGGAGGTCGCTGTA 60.034 55.000 0.00 0.00 0.00 2.74
172 173 0.382515 GCTGTAGGAGGTCGCTGTAG 59.617 60.000 0.00 0.00 0.00 2.74
173 174 0.382515 CTGTAGGAGGTCGCTGTAGC 59.617 60.000 0.00 0.00 37.78 3.58
174 175 0.323087 TGTAGGAGGTCGCTGTAGCA 60.323 55.000 4.59 0.00 42.21 3.49
175 176 1.033574 GTAGGAGGTCGCTGTAGCAT 58.966 55.000 4.59 0.00 42.21 3.79
176 177 2.228059 GTAGGAGGTCGCTGTAGCATA 58.772 52.381 4.59 0.00 42.21 3.14
177 178 1.323412 AGGAGGTCGCTGTAGCATAG 58.677 55.000 4.59 0.00 42.21 2.23
178 179 1.033574 GGAGGTCGCTGTAGCATAGT 58.966 55.000 4.59 0.00 42.21 2.12
179 180 1.001158 GGAGGTCGCTGTAGCATAGTC 60.001 57.143 4.59 0.00 42.21 2.59
180 181 1.950909 GAGGTCGCTGTAGCATAGTCT 59.049 52.381 4.59 0.00 42.21 3.24
181 182 3.139850 GAGGTCGCTGTAGCATAGTCTA 58.860 50.000 4.59 0.00 42.21 2.59
182 183 2.879646 AGGTCGCTGTAGCATAGTCTAC 59.120 50.000 4.59 0.00 42.21 2.59
183 184 2.349627 GGTCGCTGTAGCATAGTCTACG 60.350 54.545 4.59 0.00 41.29 3.51
184 185 2.543012 GTCGCTGTAGCATAGTCTACGA 59.457 50.000 4.59 0.00 41.29 3.43
185 186 2.543012 TCGCTGTAGCATAGTCTACGAC 59.457 50.000 4.59 0.00 41.29 4.34
186 187 2.349627 CGCTGTAGCATAGTCTACGACC 60.350 54.545 4.59 0.00 41.29 4.79
187 188 2.879646 GCTGTAGCATAGTCTACGACCT 59.120 50.000 0.00 0.00 41.29 3.85
188 189 3.058777 GCTGTAGCATAGTCTACGACCTC 60.059 52.174 0.00 0.00 41.29 3.85
189 190 3.474600 TGTAGCATAGTCTACGACCTCC 58.525 50.000 0.00 0.00 41.29 4.30
190 191 1.984066 AGCATAGTCTACGACCTCCC 58.016 55.000 0.00 0.00 32.18 4.30
191 192 1.495574 AGCATAGTCTACGACCTCCCT 59.504 52.381 0.00 0.00 32.18 4.20
192 193 1.609555 GCATAGTCTACGACCTCCCTG 59.390 57.143 0.00 0.00 32.18 4.45
193 194 1.609555 CATAGTCTACGACCTCCCTGC 59.390 57.143 0.00 0.00 32.18 4.85
194 195 0.106819 TAGTCTACGACCTCCCTGCC 60.107 60.000 0.00 0.00 32.18 4.85
195 196 2.439701 TCTACGACCTCCCTGCCG 60.440 66.667 0.00 0.00 0.00 5.69
196 197 2.439701 CTACGACCTCCCTGCCGA 60.440 66.667 0.00 0.00 0.00 5.54
197 198 2.753043 TACGACCTCCCTGCCGAC 60.753 66.667 0.00 0.00 0.00 4.79
198 199 3.278072 TACGACCTCCCTGCCGACT 62.278 63.158 0.00 0.00 0.00 4.18
226 227 7.192232 GTCTGAAGCACCATCAAATCTAAATC 58.808 38.462 0.00 0.00 0.00 2.17
234 235 7.098477 CACCATCAAATCTAAATCAAGGCAAA 58.902 34.615 0.00 0.00 0.00 3.68
239 240 5.705609 AATCTAAATCAAGGCAAACACGT 57.294 34.783 0.00 0.00 0.00 4.49
241 242 5.508200 TCTAAATCAAGGCAAACACGTTT 57.492 34.783 0.00 0.00 0.00 3.60
289 325 1.221466 ATCAACACACACCGTCGCTG 61.221 55.000 0.00 0.00 0.00 5.18
310 346 0.252012 CACCTGTCACCTCCTCCTCT 60.252 60.000 0.00 0.00 0.00 3.69
311 347 1.006043 CACCTGTCACCTCCTCCTCTA 59.994 57.143 0.00 0.00 0.00 2.43
313 349 1.686741 CCTGTCACCTCCTCCTCTACC 60.687 61.905 0.00 0.00 0.00 3.18
340 376 2.190578 GGACCTTGATCTGGCCGG 59.809 66.667 4.71 4.71 0.00 6.13
372 408 1.597989 CCGGTTGGATCGGTTACCA 59.402 57.895 1.13 0.00 42.33 3.25
376 412 0.252197 GTTGGATCGGTTACCAGGCT 59.748 55.000 1.13 0.00 37.48 4.58
408 4171 1.602327 ATCGCTGCTGCAGTCTCTCA 61.602 55.000 28.50 3.02 39.64 3.27
441 4204 0.032678 CACTCGCCGAAGCTATCCAT 59.967 55.000 0.00 0.00 36.60 3.41
444 4207 0.750249 TCGCCGAAGCTATCCATTCA 59.250 50.000 0.00 0.00 36.60 2.57
458 4221 1.309950 CATTCATGAGGGCAGAGCAG 58.690 55.000 0.00 0.00 0.00 4.24
506 4269 1.126488 ATGCAGACCGACATGAGGAT 58.874 50.000 16.59 4.45 0.00 3.24
530 4293 1.079336 GACGGGGAAGAAGGGAACG 60.079 63.158 0.00 0.00 0.00 3.95
568 4331 2.363406 GCATGGAGCTTTGCCCCT 60.363 61.111 6.08 0.00 41.15 4.79
604 4367 1.344191 ATGAAGAGGAGAGGCAGCCC 61.344 60.000 8.22 0.00 0.00 5.19
634 4397 1.653094 GGATTTTGGGTGATGCGCGA 61.653 55.000 12.10 0.00 0.00 5.87
664 4427 4.697756 TTGCTTGGAGGGGACGCG 62.698 66.667 3.53 3.53 0.00 6.01
677 4440 3.168528 ACGCGGGGGCCAGATTAT 61.169 61.111 12.47 0.00 0.00 1.28
679 4442 1.373435 CGCGGGGGCCAGATTATTA 59.627 57.895 4.39 0.00 0.00 0.98
684 4447 3.323691 GCGGGGGCCAGATTATTATTTTT 59.676 43.478 4.39 0.00 0.00 1.94
1112 4884 4.248174 TCCATTGCACTTGATCCCATTA 57.752 40.909 0.00 0.00 0.00 1.90
1117 4889 4.776435 TGCACTTGATCCCATTATCTCA 57.224 40.909 0.00 0.00 0.00 3.27
1166 4939 2.457598 TCGTGAGGTCAAATAGAGCCT 58.542 47.619 0.00 0.00 45.87 4.58
1243 5016 2.182842 CCGGCTGCTGCTACATTCC 61.183 63.158 15.64 0.00 39.59 3.01
1318 5091 2.087095 CGTACTACGAGGTCCGCTCG 62.087 65.000 2.17 9.04 46.05 5.03
1445 5218 5.163854 CGAAATGTACTGGTTCTAGGCAAAG 60.164 44.000 0.00 0.00 0.00 2.77
1495 5268 8.200364 TGTACAATGCAATATCGATGATATGG 57.800 34.615 8.54 0.00 35.67 2.74
1505 5278 9.447040 CAATATCGATGATATGGATGAAAATGC 57.553 33.333 8.54 0.00 35.67 3.56
1506 5279 8.975663 ATATCGATGATATGGATGAAAATGCT 57.024 30.769 8.54 0.00 34.40 3.79
1520 5293 5.240891 TGAAAATGCTGAAGAATCTCGAGT 58.759 37.500 13.13 0.00 0.00 4.18
1525 5298 6.900568 ATGCTGAAGAATCTCGAGTAAAAG 57.099 37.500 13.13 3.91 0.00 2.27
1608 5381 6.930731 AGGGTGTATCGTTGCAATAAAAATT 58.069 32.000 0.59 0.00 0.00 1.82
1609 5382 8.057536 AGGGTGTATCGTTGCAATAAAAATTA 57.942 30.769 0.59 0.00 0.00 1.40
1610 5383 8.524487 AGGGTGTATCGTTGCAATAAAAATTAA 58.476 29.630 0.59 0.00 0.00 1.40
2132 5907 3.592059 AGGCTGCAATGTGCTTTAAATG 58.408 40.909 0.50 0.00 45.31 2.32
2675 6452 3.243907 ACTGCACACTACCTTCAAGAGTC 60.244 47.826 0.00 0.00 0.00 3.36
2684 6461 4.897509 ACCTTCAAGAGTCATGTCATCA 57.102 40.909 0.00 0.00 0.00 3.07
2793 6570 6.707161 ACATATTTGATTTGCATATGGTTGCC 59.293 34.615 4.56 0.00 42.06 4.52
2800 6577 0.746659 GCATATGGTTGCCCTGTTCC 59.253 55.000 4.56 0.00 36.60 3.62
2828 6605 5.997129 CCAAAACCTTTGCCAAGATATTTGT 59.003 36.000 15.07 0.00 31.50 2.83
2941 6718 7.892778 TTAGTAATATTCGTTGCAACTGTCA 57.107 32.000 26.09 10.19 0.00 3.58
2957 6734 8.668353 TGCAACTGTCATTATTATTTCTCTCAC 58.332 33.333 0.00 0.00 0.00 3.51
3109 6888 3.575965 AGCGCCTTCCAAAAACAATAG 57.424 42.857 2.29 0.00 0.00 1.73
3177 6956 3.579586 TCAGGAGCATGCCAATTTTTCTT 59.420 39.130 15.66 0.00 0.00 2.52
3212 6991 2.877786 TGCAGTGGCCATTGTAATATCG 59.122 45.455 27.01 1.96 40.13 2.92
3222 7001 6.015504 GCCATTGTAATATCGAAGCATTACG 58.984 40.000 16.60 8.50 37.69 3.18
3926 7705 0.249955 TCAACGATGAGGCAGATGCA 59.750 50.000 7.19 0.00 44.36 3.96
3973 7752 0.466189 AGATTGGTATGCCTTGCCCG 60.466 55.000 0.16 0.00 35.27 6.13
4046 7825 9.278978 TGTGCATTTGTTCTACTAGAAATTACA 57.721 29.630 0.00 0.00 35.75 2.41
4230 8009 6.126594 CCACCTAGGTATAAATTTCTGGACCA 60.127 42.308 15.80 0.00 0.00 4.02
4463 8242 6.711277 TGAGTATTGCTAGAACCAGACAATT 58.289 36.000 0.00 0.00 33.31 2.32
4591 8370 3.573967 CACAAAATCCTGTTGGCTTAGGT 59.426 43.478 0.00 0.00 35.54 3.08
4663 8443 3.567579 TTGAAGGGGAGCCTTGGCG 62.568 63.158 5.95 0.00 0.00 5.69
4675 8455 1.512156 CCTTGGCGCAACGGTAAAGT 61.512 55.000 10.83 0.00 0.00 2.66
4707 8487 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
4767 8547 3.328050 GGCTGCCTACTATAGACCCAAAT 59.672 47.826 12.43 0.00 0.00 2.32
4999 8781 5.525745 TCGACATAGAGAGTTAGAGCTTCAG 59.474 44.000 0.00 0.00 0.00 3.02
5070 8852 7.141100 TGGTTTGGATTCTTCGACTTTTATC 57.859 36.000 0.00 0.00 0.00 1.75
5071 8853 6.712998 TGGTTTGGATTCTTCGACTTTTATCA 59.287 34.615 0.00 0.00 0.00 2.15
5094 8876 6.322712 TCATGTGCTTAAACTAAAGGGTTTGT 59.677 34.615 0.00 0.00 39.39 2.83
5179 8961 6.402766 CCATTATTTGTTACACGTGGACGAAT 60.403 38.462 27.98 27.98 43.02 3.34
5341 9124 9.116067 GGCAAATGTTAAGTGGTATTAGTATCA 57.884 33.333 0.00 0.00 0.00 2.15
5542 9325 3.459969 GGGATAAGGACAAGGACAAGGAT 59.540 47.826 0.00 0.00 0.00 3.24
5714 9515 8.891671 TCTTTCTTTTCAAAATTCCCAATCAG 57.108 30.769 0.00 0.00 0.00 2.90
5734 9535 4.081972 TCAGTTTTAAGCAAGTTGCCAACA 60.082 37.500 24.02 9.12 46.52 3.33
6047 9848 5.666474 AGTACTCCAATACCCTAGCTACT 57.334 43.478 0.00 0.00 0.00 2.57
6048 9849 6.776887 AGTACTCCAATACCCTAGCTACTA 57.223 41.667 0.00 0.00 0.00 1.82
6049 9850 6.541907 AGTACTCCAATACCCTAGCTACTAC 58.458 44.000 0.00 0.00 0.00 2.73
6050 9851 5.666474 ACTCCAATACCCTAGCTACTACT 57.334 43.478 0.00 0.00 0.00 2.57
6051 9852 6.776887 ACTCCAATACCCTAGCTACTACTA 57.223 41.667 0.00 0.00 0.00 1.82
6052 9853 6.781943 ACTCCAATACCCTAGCTACTACTAG 58.218 44.000 0.00 0.00 39.54 2.57
6093 9924 8.491331 ACAAAGAAAACCTACAAACGTAACTA 57.509 30.769 0.00 0.00 0.00 2.24
6197 10028 5.348164 TGAATCTACACATACACGACCATG 58.652 41.667 0.00 0.00 0.00 3.66
6218 10049 1.785041 TTGGCACAGAAACAGCGAGC 61.785 55.000 0.00 0.00 42.39 5.03
6226 10057 0.586802 GAAACAGCGAGCGAAGGTTT 59.413 50.000 0.00 8.87 39.88 3.27
6514 10345 8.324191 TCCCTTGTGTTCTGAATCTATTATCT 57.676 34.615 0.00 0.00 0.00 1.98
6515 10346 9.434275 TCCCTTGTGTTCTGAATCTATTATCTA 57.566 33.333 0.00 0.00 0.00 1.98
6516 10347 9.482627 CCCTTGTGTTCTGAATCTATTATCTAC 57.517 37.037 0.00 0.00 0.00 2.59
6520 10351 8.861086 TGTGTTCTGAATCTATTATCTACTCCC 58.139 37.037 0.00 0.00 0.00 4.30
6521 10352 9.084533 GTGTTCTGAATCTATTATCTACTCCCT 57.915 37.037 0.00 0.00 0.00 4.20
6522 10353 9.303116 TGTTCTGAATCTATTATCTACTCCCTC 57.697 37.037 0.00 0.00 0.00 4.30
6523 10354 8.745590 GTTCTGAATCTATTATCTACTCCCTCC 58.254 40.741 0.00 0.00 0.00 4.30
6524 10355 7.113437 TCTGAATCTATTATCTACTCCCTCCG 58.887 42.308 0.00 0.00 0.00 4.63
6525 10356 6.791371 TGAATCTATTATCTACTCCCTCCGT 58.209 40.000 0.00 0.00 0.00 4.69
6526 10357 7.239438 TGAATCTATTATCTACTCCCTCCGTT 58.761 38.462 0.00 0.00 0.00 4.44
6527 10358 7.393796 TGAATCTATTATCTACTCCCTCCGTTC 59.606 40.741 0.00 0.00 0.00 3.95
6528 10359 5.568392 TCTATTATCTACTCCCTCCGTTCC 58.432 45.833 0.00 0.00 0.00 3.62
6529 10360 3.967467 TTATCTACTCCCTCCGTTCCT 57.033 47.619 0.00 0.00 0.00 3.36
6530 10361 5.595814 ATTATCTACTCCCTCCGTTCCTA 57.404 43.478 0.00 0.00 0.00 2.94
6531 10362 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
6532 10363 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
6533 10364 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
6534 10365 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
6535 10366 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
6536 10367 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
6537 10368 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
6538 10369 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
6539 10370 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
6540 10371 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
6541 10372 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
6542 10373 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
6543 10374 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
6544 10375 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
6545 10376 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
6546 10377 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
6547 10378 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
6548 10379 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
6577 10408 8.710835 TTTGATAAATGTCTACATACGAAGCA 57.289 30.769 0.00 0.00 35.10 3.91
6578 10409 8.710835 TTGATAAATGTCTACATACGAAGCAA 57.289 30.769 0.00 0.00 35.10 3.91
6579 10410 8.710835 TGATAAATGTCTACATACGAAGCAAA 57.289 30.769 0.00 0.00 35.10 3.68
6580 10411 9.157104 TGATAAATGTCTACATACGAAGCAAAA 57.843 29.630 0.00 0.00 35.10 2.44
6584 10415 9.988350 AAATGTCTACATACGAAGCAAAATAAG 57.012 29.630 0.00 0.00 35.10 1.73
6585 10416 8.718102 ATGTCTACATACGAAGCAAAATAAGT 57.282 30.769 0.00 0.00 34.26 2.24
6586 10417 7.959733 TGTCTACATACGAAGCAAAATAAGTG 58.040 34.615 0.00 0.00 0.00 3.16
6587 10418 7.815549 TGTCTACATACGAAGCAAAATAAGTGA 59.184 33.333 0.00 0.00 0.00 3.41
6588 10419 8.653338 GTCTACATACGAAGCAAAATAAGTGAA 58.347 33.333 0.00 0.00 0.00 3.18
6589 10420 9.378551 TCTACATACGAAGCAAAATAAGTGAAT 57.621 29.630 0.00 0.00 0.00 2.57
6590 10421 9.638300 CTACATACGAAGCAAAATAAGTGAATC 57.362 33.333 0.00 0.00 0.00 2.52
6591 10422 8.268850 ACATACGAAGCAAAATAAGTGAATCT 57.731 30.769 0.00 0.00 0.00 2.40
6592 10423 9.378551 ACATACGAAGCAAAATAAGTGAATCTA 57.621 29.630 0.00 0.00 0.00 1.98
6593 10424 9.638300 CATACGAAGCAAAATAAGTGAATCTAC 57.362 33.333 0.00 0.00 0.00 2.59
6594 10425 7.667043 ACGAAGCAAAATAAGTGAATCTACA 57.333 32.000 0.00 0.00 0.00 2.74
6595 10426 7.519002 ACGAAGCAAAATAAGTGAATCTACAC 58.481 34.615 0.00 0.00 40.60 2.90
6636 10467 9.760926 ATATACATCTGTATGTGATAGTCCACT 57.239 33.333 12.10 0.00 45.99 4.00
6637 10468 6.798427 ACATCTGTATGTGATAGTCCACTT 57.202 37.500 0.00 0.00 44.79 3.16
6638 10469 6.577103 ACATCTGTATGTGATAGTCCACTTG 58.423 40.000 0.00 0.00 44.79 3.16
6639 10470 6.381133 ACATCTGTATGTGATAGTCCACTTGA 59.619 38.462 0.00 0.00 44.79 3.02
6640 10471 6.850752 TCTGTATGTGATAGTCCACTTGAA 57.149 37.500 0.00 0.00 37.89 2.69
6641 10472 7.239763 TCTGTATGTGATAGTCCACTTGAAA 57.760 36.000 0.00 0.00 37.89 2.69
6642 10473 7.851228 TCTGTATGTGATAGTCCACTTGAAAT 58.149 34.615 0.00 0.00 37.89 2.17
6643 10474 7.981789 TCTGTATGTGATAGTCCACTTGAAATC 59.018 37.037 0.00 0.00 37.89 2.17
6644 10475 7.851228 TGTATGTGATAGTCCACTTGAAATCT 58.149 34.615 0.00 0.00 37.89 2.40
6645 10476 8.977412 TGTATGTGATAGTCCACTTGAAATCTA 58.023 33.333 0.00 0.00 37.89 1.98
6646 10477 9.817809 GTATGTGATAGTCCACTTGAAATCTAA 57.182 33.333 0.00 0.00 37.89 2.10
6648 10479 9.739276 ATGTGATAGTCCACTTGAAATCTAAAA 57.261 29.630 0.00 0.00 37.89 1.52
6649 10480 9.567776 TGTGATAGTCCACTTGAAATCTAAAAA 57.432 29.630 0.00 0.00 37.89 1.94
6804 10636 7.480760 AAAAGAAGCATATTGTGTATTGGGT 57.519 32.000 0.00 0.00 0.00 4.51
6811 10644 2.754946 TTGTGTATTGGGTCCGTCTC 57.245 50.000 0.00 0.00 0.00 3.36
6822 10655 2.166050 GGGTCCGTCTCCTAGTTTCTTC 59.834 54.545 0.00 0.00 0.00 2.87
6840 10673 4.851843 TCTTCTATAGTTGAGGTCCGTGA 58.148 43.478 0.00 0.00 0.00 4.35
6853 10686 2.436911 GGTCCGTGACCCACCTTTATAT 59.563 50.000 10.92 0.00 46.19 0.86
6892 10727 7.139392 GTCTATACACGAAGAGCAATACATCA 58.861 38.462 0.00 0.00 0.00 3.07
6914 10749 7.862512 TCATGCAATTCTCACAACATACATA 57.137 32.000 0.00 0.00 0.00 2.29
6924 10759 9.803315 TTCTCACAACATACATAGTATCAGTTC 57.197 33.333 0.00 0.00 0.00 3.01
6932 10767 4.549668 ACATAGTATCAGTTCCCGGGTTA 58.450 43.478 22.86 7.24 0.00 2.85
6933 10768 4.587684 ACATAGTATCAGTTCCCGGGTTAG 59.412 45.833 22.86 9.52 0.00 2.34
6934 10769 1.761198 AGTATCAGTTCCCGGGTTAGC 59.239 52.381 22.86 3.73 0.00 3.09
6935 10770 1.761198 GTATCAGTTCCCGGGTTAGCT 59.239 52.381 22.86 6.55 0.00 3.32
6936 10771 1.286248 ATCAGTTCCCGGGTTAGCTT 58.714 50.000 22.86 0.00 0.00 3.74
6939 10774 1.449070 GTTCCCGGGTTAGCTTCCG 60.449 63.158 22.86 13.65 45.29 4.30
6940 10775 3.319441 TTCCCGGGTTAGCTTCCGC 62.319 63.158 22.86 3.86 44.45 5.54
6941 10776 4.851179 CCCGGGTTAGCTTCCGCC 62.851 72.222 14.18 2.91 44.45 6.13
6943 10778 4.851179 CGGGTTAGCTTCCGCCCC 62.851 72.222 9.34 3.50 39.78 5.80
6944 10779 4.501285 GGGTTAGCTTCCGCCCCC 62.501 72.222 0.00 0.00 36.60 5.40
6945 10780 4.851179 GGTTAGCTTCCGCCCCCG 62.851 72.222 0.00 0.00 36.60 5.73
7072 10933 1.959226 GCAGTTTCCGCCGAAGTCA 60.959 57.895 0.00 0.00 0.00 3.41
7073 10934 1.298859 GCAGTTTCCGCCGAAGTCAT 61.299 55.000 0.00 0.00 0.00 3.06
7094 10955 2.022902 CCGTGTCCGAGATCGACG 59.977 66.667 3.31 5.94 43.02 5.12
7155 11016 2.046023 CCGTTGCAGCCAGATCCA 60.046 61.111 0.00 0.00 0.00 3.41
7181 11042 1.079127 CCGCAGTCCCGAGACAATT 60.079 57.895 0.00 0.00 46.15 2.32
7253 11115 2.092211 GCTACATCTCCACGTGAAAACG 59.908 50.000 19.30 4.88 39.31 3.60
7272 11134 4.410492 ACGAAGTCAATCAATCACTTGC 57.590 40.909 0.00 0.00 29.74 4.01
7275 11137 2.086869 AGTCAATCAATCACTTGCCCG 58.913 47.619 0.00 0.00 32.11 6.13
7290 11152 2.048023 CCCGCCGTGGTACTACTGA 61.048 63.158 7.83 0.00 35.15 3.41
7293 11155 0.870307 CGCCGTGGTACTACTGATGC 60.870 60.000 7.83 4.28 0.00 3.91
7353 11215 1.202417 GCTGATCGCTAAGTACTGCCA 60.202 52.381 0.00 0.00 35.14 4.92
7381 11243 2.233654 CGCTACACGCTGCTGGATC 61.234 63.158 0.00 0.00 36.13 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.911250 TGACAAGGAGAGATAGTTGTACAA 57.089 37.500 3.59 3.59 33.30 2.41
46 47 6.128553 GCAAACTATCGATGAGAACTTGACAA 60.129 38.462 8.54 0.00 0.00 3.18
78 79 0.105964 TCAGTGGTTGACTTCGGTGG 59.894 55.000 0.00 0.00 29.75 4.61
95 96 7.056635 GGAGAGGGTTCATATTTTCAGATTCA 58.943 38.462 0.00 0.00 0.00 2.57
109 110 0.114560 AGGTCTTCGGAGAGGGTTCA 59.885 55.000 0.00 0.00 38.43 3.18
134 135 0.249322 CTTCACGACAACGGTGGTCT 60.249 55.000 13.51 0.00 44.46 3.85
142 143 2.329379 CTCCTACAGCTTCACGACAAC 58.671 52.381 0.00 0.00 0.00 3.32
143 144 1.272490 CCTCCTACAGCTTCACGACAA 59.728 52.381 0.00 0.00 0.00 3.18
157 158 2.158652 ACTATGCTACAGCGACCTCCTA 60.159 50.000 0.00 0.00 45.83 2.94
161 162 2.060050 AGACTATGCTACAGCGACCT 57.940 50.000 0.00 0.00 45.83 3.85
162 163 2.349627 CGTAGACTATGCTACAGCGACC 60.350 54.545 0.00 0.00 45.83 4.79
163 164 2.543012 TCGTAGACTATGCTACAGCGAC 59.457 50.000 0.00 0.00 45.83 5.19
164 165 2.830104 TCGTAGACTATGCTACAGCGA 58.170 47.619 0.00 0.00 45.83 4.93
178 179 2.439701 CGGCAGGGAGGTCGTAGA 60.440 66.667 0.00 0.00 0.00 2.59
179 180 2.439701 TCGGCAGGGAGGTCGTAG 60.440 66.667 0.00 0.00 37.15 3.51
180 181 1.913951 TAGTCGGCAGGGAGGTCGTA 61.914 60.000 0.00 0.00 37.15 3.43
181 182 3.278072 TAGTCGGCAGGGAGGTCGT 62.278 63.158 0.00 0.00 37.15 4.34
182 183 2.439701 TAGTCGGCAGGGAGGTCG 60.440 66.667 0.00 0.00 37.19 4.79
183 184 2.128507 CCTAGTCGGCAGGGAGGTC 61.129 68.421 0.00 0.00 0.00 3.85
184 185 2.042843 CCTAGTCGGCAGGGAGGT 60.043 66.667 0.00 0.00 0.00 3.85
185 186 2.042843 ACCTAGTCGGCAGGGAGG 60.043 66.667 9.76 3.57 37.51 4.30
186 187 1.076632 AGACCTAGTCGGCAGGGAG 60.077 63.158 9.76 0.00 37.67 4.30
187 188 1.379977 CAGACCTAGTCGGCAGGGA 60.380 63.158 9.76 0.00 37.67 4.20
188 189 0.970937 TTCAGACCTAGTCGGCAGGG 60.971 60.000 9.76 3.89 37.67 4.45
189 190 0.457851 CTTCAGACCTAGTCGGCAGG 59.542 60.000 4.26 4.26 37.67 4.85
190 191 0.179124 GCTTCAGACCTAGTCGGCAG 60.179 60.000 0.00 0.00 37.67 4.85
191 192 0.898326 TGCTTCAGACCTAGTCGGCA 60.898 55.000 0.00 0.00 37.67 5.69
192 193 0.458716 GTGCTTCAGACCTAGTCGGC 60.459 60.000 0.00 0.00 37.67 5.54
193 194 0.173708 GGTGCTTCAGACCTAGTCGG 59.826 60.000 0.00 0.00 37.67 4.79
194 195 0.888619 TGGTGCTTCAGACCTAGTCG 59.111 55.000 0.00 0.00 37.67 4.18
195 196 2.497675 TGATGGTGCTTCAGACCTAGTC 59.502 50.000 0.00 0.00 34.26 2.59
196 197 2.540383 TGATGGTGCTTCAGACCTAGT 58.460 47.619 0.00 0.00 34.26 2.57
197 198 3.616956 TTGATGGTGCTTCAGACCTAG 57.383 47.619 0.00 0.00 34.26 3.02
198 199 4.225942 AGATTTGATGGTGCTTCAGACCTA 59.774 41.667 0.00 0.00 34.26 3.08
226 227 2.600731 TGTCAAAACGTGTTTGCCTTG 58.399 42.857 14.46 0.00 32.36 3.61
234 235 5.499139 ACAAATCTGATGTCAAAACGTGT 57.501 34.783 0.00 0.00 0.00 4.49
289 325 2.665603 GAGGAGGTGACAGGTGGC 59.334 66.667 0.00 0.00 0.00 5.01
313 349 2.484287 ATCAAGGTCCAACCAGGCCG 62.484 60.000 0.00 0.00 41.95 6.13
340 376 2.590007 CCGGCATGGTCTAGCAGC 60.590 66.667 0.00 0.00 0.00 5.25
385 421 2.745100 ACTGCAGCAGCGATGTGG 60.745 61.111 23.05 0.00 46.23 4.17
390 426 1.602327 ATGAGAGACTGCAGCAGCGA 61.602 55.000 23.05 0.27 46.23 4.93
427 4190 2.740981 CTCATGAATGGATAGCTTCGGC 59.259 50.000 0.00 0.00 42.17 5.54
431 4194 2.444388 TGCCCTCATGAATGGATAGCTT 59.556 45.455 13.78 0.00 0.00 3.74
441 4204 1.077930 GCTGCTCTGCCCTCATGAA 60.078 57.895 0.00 0.00 0.00 2.57
480 4243 0.250252 TGTCGGTCTGCATTGCTTCA 60.250 50.000 10.49 0.00 0.00 3.02
490 4253 2.027385 TCTCATCCTCATGTCGGTCTG 58.973 52.381 0.00 0.00 0.00 3.51
506 4269 0.614979 CCTTCTTCCCCGTCCTCTCA 60.615 60.000 0.00 0.00 0.00 3.27
575 4338 0.679960 TCCTCTTCATCGTCGGCTGA 60.680 55.000 0.00 0.00 0.00 4.26
582 4345 1.110442 CTGCCTCTCCTCTTCATCGT 58.890 55.000 0.00 0.00 0.00 3.73
588 4351 3.080121 CGGGCTGCCTCTCCTCTT 61.080 66.667 19.68 0.00 0.00 2.85
604 4367 1.812571 CCCAAAATCCACTGACCTTCG 59.187 52.381 0.00 0.00 0.00 3.79
609 4372 2.094545 GCATCACCCAAAATCCACTGAC 60.095 50.000 0.00 0.00 0.00 3.51
610 4373 2.170166 GCATCACCCAAAATCCACTGA 58.830 47.619 0.00 0.00 0.00 3.41
614 4377 1.889454 GCGCATCACCCAAAATCCA 59.111 52.632 0.30 0.00 0.00 3.41
615 4378 1.226660 CGCGCATCACCCAAAATCC 60.227 57.895 8.75 0.00 0.00 3.01
634 4397 3.612247 AAGCAACTCGGGCAGCGAT 62.612 57.895 0.00 0.00 0.00 4.58
639 4402 2.032528 CTCCAAGCAACTCGGGCA 59.967 61.111 0.00 0.00 0.00 5.36
664 4427 6.210784 GGTCTAAAAATAATAATCTGGCCCCC 59.789 42.308 0.00 0.00 0.00 5.40
684 4447 7.827236 ACTCATATTTTGAACGATTTGGGTCTA 59.173 33.333 0.00 0.00 32.78 2.59
700 4470 8.980832 ATACTCCCTCCATCTACTCATATTTT 57.019 34.615 0.00 0.00 0.00 1.82
1112 4884 3.056322 GCAAAAGCAAACCAGGATGAGAT 60.056 43.478 0.00 0.00 39.69 2.75
1117 4889 1.422531 TGGCAAAAGCAAACCAGGAT 58.577 45.000 0.00 0.00 0.00 3.24
1243 5016 7.600065 ACTTGATCATTTTCCAAGTGAATCAG 58.400 34.615 0.00 0.00 45.92 2.90
1445 5218 3.499338 TCCAATGCCATGAATATCCCAC 58.501 45.455 0.00 0.00 0.00 4.61
1495 5268 6.036953 ACTCGAGATTCTTCAGCATTTTCATC 59.963 38.462 21.68 0.00 0.00 2.92
1505 5278 6.900568 ATGCTTTTACTCGAGATTCTTCAG 57.099 37.500 21.68 6.40 0.00 3.02
1506 5279 7.817478 TGTAATGCTTTTACTCGAGATTCTTCA 59.183 33.333 21.68 10.20 0.00 3.02
1520 5293 9.767684 CATATTTTCACTCGTGTAATGCTTTTA 57.232 29.630 0.00 0.00 0.00 1.52
1525 5298 6.257849 TCTCCATATTTTCACTCGTGTAATGC 59.742 38.462 0.00 0.00 0.00 3.56
1610 5383 9.465985 CCAAAATTATTCTGCAAAAGCAAAAAT 57.534 25.926 0.00 0.00 0.00 1.82
1934 5709 0.668535 GTGCCAACTTCCTCGCTTTT 59.331 50.000 0.00 0.00 0.00 2.27
2132 5907 7.201617 CCCAAGAACTAAGATGGAAAATACGAC 60.202 40.741 0.00 0.00 34.82 4.34
2179 5954 7.143340 CCTTAACACCATTGCAGATCATAATG 58.857 38.462 0.00 2.79 0.00 1.90
2486 6263 7.812669 CACCCTAAAAGAACAACATAAACCATC 59.187 37.037 0.00 0.00 0.00 3.51
2496 6273 4.928601 GGTGAACACCCTAAAAGAACAAC 58.071 43.478 12.42 0.00 45.68 3.32
2684 6461 7.501225 TCAGATGCATGATTAAGATGTTGACAT 59.499 33.333 2.46 0.00 39.70 3.06
2688 6465 7.023197 TGTCAGATGCATGATTAAGATGTTG 57.977 36.000 2.46 0.00 0.00 3.33
2793 6570 2.337361 GGTTTTGGACCGGAACAGG 58.663 57.895 9.46 0.00 39.00 4.00
2957 6734 8.032952 TCAGACATAATTCAACTTGTAGCTTG 57.967 34.615 0.00 0.00 0.00 4.01
3052 6831 6.377712 GGGATAGAGTACATTAAGTAGGCGAT 59.622 42.308 0.00 0.00 32.19 4.58
3109 6888 9.638300 CTTTTTCTCATTATGTAAGCATACGTC 57.362 33.333 0.00 0.00 37.31 4.34
3177 6956 4.157656 GGCCACTGCATGATTAACAGTTAA 59.842 41.667 8.22 8.22 42.59 2.01
3212 6991 4.396790 TGGGAAACATAACCGTAATGCTTC 59.603 41.667 0.00 0.00 31.59 3.86
3222 7001 9.965902 ATTAGAGATATCATGGGAAACATAACC 57.034 33.333 5.32 0.00 37.84 2.85
3603 7382 8.203681 AGTAGAGAAACATAAGGGTTACACTT 57.796 34.615 4.88 4.88 0.00 3.16
3607 7386 8.933807 GTCAAAGTAGAGAAACATAAGGGTTAC 58.066 37.037 0.00 0.00 0.00 2.50
3926 7705 5.596836 TCAACTTCTCAAAGCACCAAAAT 57.403 34.783 0.00 0.00 35.81 1.82
4076 7855 7.856145 AGATCAAACATCAGATGGTTAGAAC 57.144 36.000 13.58 11.57 38.32 3.01
4463 8242 9.820725 AAACAGAAAAATGAGATGTCAAAATCA 57.179 25.926 0.00 0.00 35.88 2.57
4543 8322 3.562826 CCCCCTAAAGTAACTTTCCACCC 60.563 52.174 0.00 0.00 35.21 4.61
4591 8370 6.414732 AGGGAATCGTCATGTTGATCTTTTA 58.585 36.000 0.00 0.00 0.00 1.52
4622 8401 3.412386 AGACTCCACAAACTACATTGCC 58.588 45.455 0.00 0.00 33.52 4.52
4624 8403 7.026631 TCAAAAGACTCCACAAACTACATTG 57.973 36.000 0.00 0.00 36.37 2.82
4675 8455 1.955778 CTCATGGTCACAAGGCAACAA 59.044 47.619 0.00 0.00 41.41 2.83
4707 8487 3.555966 CAAGAGGTTGTTTCCAGGACTT 58.444 45.455 0.00 0.00 0.00 3.01
4999 8781 9.109393 TCAATTGACTTAGCCAATCTGTATTAC 57.891 33.333 3.38 0.00 33.51 1.89
5070 8852 6.512297 ACAAACCCTTTAGTTTAAGCACATG 58.488 36.000 0.00 0.00 37.87 3.21
5071 8853 6.724893 ACAAACCCTTTAGTTTAAGCACAT 57.275 33.333 0.00 0.00 37.87 3.21
5179 8961 3.149196 CAAGAGGAAGCAAGCCACTAAA 58.851 45.455 0.00 0.00 0.00 1.85
5428 9211 5.434408 TCACATGCTGCAAAGAAGATATCT 58.566 37.500 6.36 0.00 41.32 1.98
5542 9325 5.333581 TCAGTTTCCTCAGAGACATCCTTA 58.666 41.667 0.00 0.00 29.47 2.69
6048 9849 9.688091 TCTTTGTCTCATTGATAGTCTACTAGT 57.312 33.333 0.00 0.00 0.00 2.57
6093 9924 5.321102 TGCCTGTACCTGTAAAATGAACAT 58.679 37.500 0.00 0.00 0.00 2.71
6197 10028 0.380378 TCGCTGTTTCTGTGCCAAAC 59.620 50.000 0.00 0.00 34.79 2.93
6218 10049 0.816421 ACCACCCGTGAAAACCTTCG 60.816 55.000 0.00 0.00 33.94 3.79
6226 10057 1.134640 CCGATTATGACCACCCGTGAA 60.135 52.381 0.00 0.00 0.00 3.18
6376 10207 5.693104 ACATGCATGACATTTCAACTTGAAC 59.307 36.000 32.75 0.00 35.89 3.18
6514 10345 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
6515 10346 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
6516 10347 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
6517 10348 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
6518 10349 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
6519 10350 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
6520 10351 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
6521 10352 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
6522 10353 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
6551 10382 9.157104 TGCTTCGTATGTAGACATTTATCAAAA 57.843 29.630 0.00 0.00 37.76 2.44
6552 10383 8.710835 TGCTTCGTATGTAGACATTTATCAAA 57.289 30.769 0.00 0.00 37.76 2.69
6553 10384 8.710835 TTGCTTCGTATGTAGACATTTATCAA 57.289 30.769 0.00 0.00 37.76 2.57
6554 10385 8.710835 TTTGCTTCGTATGTAGACATTTATCA 57.289 30.769 0.00 0.00 37.76 2.15
6558 10389 9.988350 CTTATTTTGCTTCGTATGTAGACATTT 57.012 29.630 0.00 0.00 37.76 2.32
6559 10390 9.162764 ACTTATTTTGCTTCGTATGTAGACATT 57.837 29.630 0.00 0.00 37.76 2.71
6560 10391 8.604035 CACTTATTTTGCTTCGTATGTAGACAT 58.396 33.333 0.08 0.08 40.22 3.06
6561 10392 7.815549 TCACTTATTTTGCTTCGTATGTAGACA 59.184 33.333 0.00 0.00 0.00 3.41
6562 10393 8.181487 TCACTTATTTTGCTTCGTATGTAGAC 57.819 34.615 0.00 0.00 0.00 2.59
6563 10394 8.766000 TTCACTTATTTTGCTTCGTATGTAGA 57.234 30.769 0.00 0.00 0.00 2.59
6564 10395 9.638300 GATTCACTTATTTTGCTTCGTATGTAG 57.362 33.333 0.00 0.00 0.00 2.74
6565 10396 9.378551 AGATTCACTTATTTTGCTTCGTATGTA 57.621 29.630 0.00 0.00 0.00 2.29
6566 10397 8.268850 AGATTCACTTATTTTGCTTCGTATGT 57.731 30.769 0.00 0.00 0.00 2.29
6567 10398 9.638300 GTAGATTCACTTATTTTGCTTCGTATG 57.362 33.333 0.00 0.00 0.00 2.39
6568 10399 9.378551 TGTAGATTCACTTATTTTGCTTCGTAT 57.621 29.630 0.00 0.00 0.00 3.06
6569 10400 8.653338 GTGTAGATTCACTTATTTTGCTTCGTA 58.347 33.333 0.00 0.00 35.68 3.43
6570 10401 7.387948 AGTGTAGATTCACTTATTTTGCTTCGT 59.612 33.333 0.00 0.00 44.92 3.85
6571 10402 7.743104 AGTGTAGATTCACTTATTTTGCTTCG 58.257 34.615 0.00 0.00 44.92 3.79
6572 10403 8.940952 AGAGTGTAGATTCACTTATTTTGCTTC 58.059 33.333 0.98 0.00 46.81 3.86
6573 10404 8.854614 AGAGTGTAGATTCACTTATTTTGCTT 57.145 30.769 0.98 0.00 46.81 3.91
6574 10405 9.944376 TTAGAGTGTAGATTCACTTATTTTGCT 57.056 29.630 0.98 0.00 46.81 3.91
6610 10441 9.760926 AGTGGACTATCACATACAGATGTATAT 57.239 33.333 5.21 0.00 44.82 0.86
6611 10442 9.588096 AAGTGGACTATCACATACAGATGTATA 57.412 33.333 5.21 0.00 44.82 1.47
6612 10443 8.363390 CAAGTGGACTATCACATACAGATGTAT 58.637 37.037 0.00 0.00 44.82 2.29
6613 10444 7.559897 TCAAGTGGACTATCACATACAGATGTA 59.440 37.037 0.00 0.00 44.82 2.29
6615 10446 6.809869 TCAAGTGGACTATCACATACAGATG 58.190 40.000 0.00 0.00 39.93 2.90
6616 10447 7.423844 TTCAAGTGGACTATCACATACAGAT 57.576 36.000 0.00 0.00 39.93 2.90
6617 10448 6.850752 TTCAAGTGGACTATCACATACAGA 57.149 37.500 0.00 0.00 39.93 3.41
6618 10449 7.984050 AGATTTCAAGTGGACTATCACATACAG 59.016 37.037 0.00 0.00 39.93 2.74
6619 10450 7.851228 AGATTTCAAGTGGACTATCACATACA 58.149 34.615 0.00 0.00 39.93 2.29
6620 10451 9.817809 TTAGATTTCAAGTGGACTATCACATAC 57.182 33.333 0.00 0.00 39.93 2.39
6622 10453 9.739276 TTTTAGATTTCAAGTGGACTATCACAT 57.261 29.630 0.00 0.00 39.93 3.21
6623 10454 9.567776 TTTTTAGATTTCAAGTGGACTATCACA 57.432 29.630 0.00 0.00 39.93 3.58
6697 10528 5.688176 GTGGCTTGTTTGCGTCTTATTTTAA 59.312 36.000 0.00 0.00 0.00 1.52
6698 10529 5.216648 GTGGCTTGTTTGCGTCTTATTTTA 58.783 37.500 0.00 0.00 0.00 1.52
6801 10633 1.849977 AGAAACTAGGAGACGGACCC 58.150 55.000 0.00 0.00 0.00 4.46
6804 10636 6.897986 ACTATAGAAGAAACTAGGAGACGGA 58.102 40.000 6.78 0.00 0.00 4.69
6811 10644 7.468906 CGGACCTCAACTATAGAAGAAACTAGG 60.469 44.444 6.78 3.85 0.00 3.02
6868 10703 7.272037 TGATGTATTGCTCTTCGTGTATAGA 57.728 36.000 0.00 0.00 0.00 1.98
6873 10708 3.310774 GCATGATGTATTGCTCTTCGTGT 59.689 43.478 0.00 0.00 32.36 4.49
6892 10727 7.870509 ACTATGTATGTTGTGAGAATTGCAT 57.129 32.000 0.00 0.00 0.00 3.96
6914 10749 1.761198 GCTAACCCGGGAACTGATACT 59.239 52.381 32.02 0.00 36.31 2.12
7072 10933 2.833582 ATCTCGGACACGGGCGAT 60.834 61.111 0.00 0.00 41.40 4.58
7073 10934 3.515286 GATCTCGGACACGGGCGA 61.515 66.667 0.00 0.00 41.40 5.54
7094 10955 2.288025 TACAACAGCCCGACTCCCC 61.288 63.158 0.00 0.00 0.00 4.81
7139 11000 2.743752 CGTGGATCTGGCTGCAACG 61.744 63.158 0.50 0.00 0.00 4.10
7155 11016 4.681978 GGGACTGCGGCAACTCGT 62.682 66.667 3.44 0.00 0.00 4.18
7178 11039 2.128035 GTGAGCTATGCGTCGCTAATT 58.872 47.619 19.50 3.43 36.45 1.40
7181 11042 1.010013 CGTGAGCTATGCGTCGCTA 60.010 57.895 19.50 5.27 36.45 4.26
7253 11115 3.426695 CGGGCAAGTGATTGATTGACTTC 60.427 47.826 0.00 0.00 34.70 3.01
7272 11134 1.389609 ATCAGTAGTACCACGGCGGG 61.390 60.000 13.24 7.16 40.22 6.13
7275 11137 0.460311 AGCATCAGTAGTACCACGGC 59.540 55.000 0.00 0.00 0.00 5.68
7290 11152 1.003476 TGCACGTGATGGACAGCAT 60.003 52.632 22.23 0.00 32.07 3.79
7293 11155 2.393768 GCCTGCACGTGATGGACAG 61.394 63.158 22.23 15.91 0.00 3.51
7353 11215 1.154205 GCGTGTAGCGATCCAGCAAT 61.154 55.000 0.00 0.00 44.77 3.56


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

AutoCloner maintained by Alex Coulton.