Multiple sequence alignment - TraesCS3A01G385400

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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 TraesCS3A01G385400 chr3A 100.000 3735 0 0 1 3735 634946442 634942708 0.000000e+00 6898
1 TraesCS3A01G385400 chr3A 89.630 135 7 5 2377 2506 332556292 332556160 8.300000e-37 165
2 TraesCS3A01G385400 chr3B 91.379 2981 155 33 778 3714 654434753 654431831 0.000000e+00 3988
3 TraesCS3A01G385400 chr3B 92.258 310 21 3 315 623 654435708 654435401 1.590000e-118 436
4 TraesCS3A01G385400 chr3B 90.323 186 7 5 1 182 654437074 654436896 2.240000e-57 233
5 TraesCS3A01G385400 chr3D 90.250 1559 111 25 780 2314 495494073 495492532 0.000000e+00 1999
6 TraesCS3A01G385400 chr3D 85.651 453 46 10 2506 2948 495492492 495492049 3.400000e-125 459
7 TraesCS3A01G385400 chr3D 96.154 182 6 1 1 182 495497081 495496901 2.820000e-76 296
8 TraesCS3A01G385400 chr3D 95.028 181 9 0 304 484 495496904 495496724 6.110000e-73 285
9 TraesCS3A01G385400 chr3D 91.083 157 11 2 3051 3207 315480425 315480578 3.780000e-50 209
10 TraesCS3A01G385400 chr3D 88.485 165 12 3 3051 3214 73853239 73853081 3.810000e-45 193
11 TraesCS3A01G385400 chr3D 87.805 164 13 3 3052 3214 76230994 76231151 6.370000e-43 185
12 TraesCS3A01G385400 chr3D 90.984 122 10 1 2378 2499 127342839 127342719 2.980000e-36 163
13 TraesCS3A01G385400 chr3D 89.394 132 7 5 2377 2503 251316012 251316141 3.860000e-35 159
14 TraesCS3A01G385400 chr3D 92.523 107 4 3 504 609 495496733 495496630 2.320000e-32 150
15 TraesCS3A01G385400 chr3D 83.206 131 18 2 2956 3086 495491977 495491851 2.360000e-22 117
16 TraesCS3A01G385400 chr4B 88.166 169 10 5 3050 3216 146469215 146469375 3.810000e-45 193
17 TraesCS3A01G385400 chr4B 87.574 169 9 8 3049 3214 438375179 438375338 6.370000e-43 185
18 TraesCS3A01G385400 chr4B 87.218 133 11 4 2375 2502 213084951 213085082 3.010000e-31 147
19 TraesCS3A01G385400 chr2D 87.006 177 13 6 3051 3224 79056167 79056336 1.370000e-44 191
20 TraesCS3A01G385400 chr2D 87.879 165 14 2 3051 3214 617101061 617101220 4.920000e-44 189
21 TraesCS3A01G385400 chr2A 86.441 177 14 5 3051 3224 79316005 79316174 6.370000e-43 185
22 TraesCS3A01G385400 chr7A 92.857 126 9 0 177 302 593450702 593450827 2.290000e-42 183
23 TraesCS3A01G385400 chr7A 90.625 128 8 2 2377 2500 498590259 498590386 2.310000e-37 167
24 TraesCS3A01G385400 chr5D 92.248 129 10 0 174 302 387621442 387621314 2.290000e-42 183
25 TraesCS3A01G385400 chr5A 92.857 126 9 0 177 302 676370180 676370305 2.290000e-42 183
26 TraesCS3A01G385400 chr5A 91.045 134 11 1 170 302 492896663 492896796 2.960000e-41 180
27 TraesCS3A01G385400 chr4D 92.857 126 9 0 177 302 36413235 36413360 2.290000e-42 183
28 TraesCS3A01G385400 chr4D 86.061 165 15 7 144 302 30403496 30403334 1.780000e-38 171
29 TraesCS3A01G385400 chr2B 92.248 129 10 0 174 302 199013855 199013727 2.290000e-42 183
30 TraesCS3A01G385400 chr1A 91.603 131 11 0 172 302 435066153 435066023 8.240000e-42 182
31 TraesCS3A01G385400 chr7D 89.437 142 12 3 164 302 567712438 567712579 3.830000e-40 176
32 TraesCS3A01G385400 chr7D 87.218 133 13 2 2376 2504 218490684 218490552 8.360000e-32 148
33 TraesCS3A01G385400 chr7B 87.218 133 11 4 2375 2502 336084342 336084473 3.010000e-31 147
34 TraesCS3A01G385400 chr4A 87.597 129 10 4 2376 2499 276912775 276912648 1.080000e-30 145


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 TraesCS3A01G385400 chr3A 634942708 634946442 3734 True 6898.000000 6898 100.000000 1 3735 1 chr3A.!!$R2 3734
1 TraesCS3A01G385400 chr3B 654431831 654437074 5243 True 1552.333333 3988 91.320000 1 3714 3 chr3B.!!$R1 3713
2 TraesCS3A01G385400 chr3D 495491851 495497081 5230 True 551.000000 1999 90.468667 1 3086 6 chr3D.!!$R3 3085

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
646 4118 0.249447 CACCGTGTCAAGAGTGAGCA 60.249 55.0 0.00 0.0 33.27 4.26 F
669 4141 0.454196 TGCGATTCGGATTGTCTCGA 59.546 50.0 8.34 0.0 0.00 4.04 F
860 4364 0.464554 GCCTAAGCCCACCACATCTC 60.465 60.0 0.00 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 5288 0.877743 GCTTGAAGTCCTTGTCAGGC 59.122 55.000 0.00 0.0 40.58 4.85 R
2380 5932 2.294284 CAAGTAATTTGGGCCGGAGGG 61.294 57.143 5.05 0.0 39.95 4.30 R
2801 6361 5.055144 CACTGATGATGGTCTGATGGTAAG 58.945 45.833 0.00 0.0 0.00 2.34 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
60 61 2.719739 ACGTTCAGGGTCGATCTTCTA 58.280 47.619 0.00 0.00 0.00 2.10
158 163 4.327357 CGTCCAATACTTCAAGCTGTACAG 59.673 45.833 18.93 18.93 0.00 2.74
187 192 5.231702 TGTTTGTTTAATACTCCCTCCGT 57.768 39.130 0.00 0.00 0.00 4.69
188 193 5.240121 TGTTTGTTTAATACTCCCTCCGTC 58.760 41.667 0.00 0.00 0.00 4.79
189 194 4.476628 TTGTTTAATACTCCCTCCGTCC 57.523 45.455 0.00 0.00 0.00 4.79
190 195 3.716431 TGTTTAATACTCCCTCCGTCCT 58.284 45.455 0.00 0.00 0.00 3.85
191 196 4.870636 TGTTTAATACTCCCTCCGTCCTA 58.129 43.478 0.00 0.00 0.00 2.94
193 198 5.721000 TGTTTAATACTCCCTCCGTCCTAAA 59.279 40.000 0.00 0.00 0.00 1.85
194 199 6.213195 TGTTTAATACTCCCTCCGTCCTAAAA 59.787 38.462 0.00 0.00 0.00 1.52
195 200 7.092757 TGTTTAATACTCCCTCCGTCCTAAAAT 60.093 37.037 0.00 0.00 0.00 1.82
200 205 5.028131 ACTCCCTCCGTCCTAAAATTCTTA 58.972 41.667 0.00 0.00 0.00 2.10
201 206 5.666265 ACTCCCTCCGTCCTAAAATTCTTAT 59.334 40.000 0.00 0.00 0.00 1.73
202 207 6.170846 TCCCTCCGTCCTAAAATTCTTATC 57.829 41.667 0.00 0.00 0.00 1.75
203 208 4.989168 CCCTCCGTCCTAAAATTCTTATCG 59.011 45.833 0.00 0.00 0.00 2.92
204 209 5.452917 CCCTCCGTCCTAAAATTCTTATCGT 60.453 44.000 0.00 0.00 0.00 3.73
205 210 6.239120 CCCTCCGTCCTAAAATTCTTATCGTA 60.239 42.308 0.00 0.00 0.00 3.43
207 212 7.255381 CCTCCGTCCTAAAATTCTTATCGTAGA 60.255 40.741 0.00 0.00 45.75 2.59
208 213 8.174733 TCCGTCCTAAAATTCTTATCGTAGAT 57.825 34.615 0.00 0.00 45.12 1.98
209 214 8.636213 TCCGTCCTAAAATTCTTATCGTAGATT 58.364 33.333 0.00 0.00 45.12 2.40
210 215 9.257651 CCGTCCTAAAATTCTTATCGTAGATTT 57.742 33.333 0.00 0.00 45.12 2.17
222 227 9.368674 TCTTATCGTAGATTTCTCTAGATACGG 57.631 37.037 16.97 5.65 45.12 4.02
223 228 9.368674 CTTATCGTAGATTTCTCTAGATACGGA 57.631 37.037 16.97 8.01 45.12 4.69
224 229 9.887629 TTATCGTAGATTTCTCTAGATACGGAT 57.112 33.333 16.97 12.64 45.12 4.18
225 230 7.598189 TCGTAGATTTCTCTAGATACGGATG 57.402 40.000 16.97 0.00 34.63 3.51
226 231 7.160049 TCGTAGATTTCTCTAGATACGGATGT 58.840 38.462 16.97 0.00 34.63 3.06
228 233 9.100554 CGTAGATTTCTCTAGATACGGATGTAT 57.899 37.037 11.69 0.00 37.17 2.29
298 327 7.666063 AAGATAAGAATTTTGGAATGGAGGG 57.334 36.000 0.00 0.00 0.00 4.30
300 329 7.065504 AGATAAGAATTTTGGAATGGAGGGAG 58.934 38.462 0.00 0.00 0.00 4.30
301 330 4.682021 AGAATTTTGGAATGGAGGGAGT 57.318 40.909 0.00 0.00 0.00 3.85
302 331 4.347607 AGAATTTTGGAATGGAGGGAGTG 58.652 43.478 0.00 0.00 0.00 3.51
304 333 1.075601 TTTGGAATGGAGGGAGTGCT 58.924 50.000 0.00 0.00 0.00 4.40
305 334 0.620556 TTGGAATGGAGGGAGTGCTC 59.379 55.000 0.00 0.00 0.00 4.26
332 1392 2.094417 GCGAAAGAGAAGTCAATTCGGG 59.906 50.000 8.10 0.00 43.16 5.14
355 1415 2.678336 GAGGGGATGAAGCAAAGTAACG 59.322 50.000 0.00 0.00 0.00 3.18
359 1419 2.414161 GGATGAAGCAAAGTAACGTGCC 60.414 50.000 0.00 0.00 41.88 5.01
444 1505 3.702555 GCAAGCTCACGCGTCGTT 61.703 61.111 9.86 0.00 38.32 3.85
475 1536 1.372623 GTCGTTCTCACCACGGGAC 60.373 63.158 0.00 0.00 38.23 4.46
550 1611 2.148768 GTCGGGTTGAAGGAACGAATT 58.851 47.619 0.00 0.00 35.12 2.17
585 1646 3.264845 AATCGGCCCCCAGGTGTT 61.265 61.111 0.00 0.00 34.57 3.32
642 4114 2.502213 TACACACCGTGTCAAGAGTG 57.498 50.000 0.00 8.82 43.92 3.51
644 4116 1.202417 ACACACCGTGTCAAGAGTGAG 60.202 52.381 0.00 9.40 43.92 3.51
646 4118 0.249447 CACCGTGTCAAGAGTGAGCA 60.249 55.000 0.00 0.00 33.27 4.26
649 4121 1.462283 CCGTGTCAAGAGTGAGCATTG 59.538 52.381 0.00 0.00 33.27 2.82
668 4140 0.572590 GTGCGATTCGGATTGTCTCG 59.427 55.000 8.34 0.00 0.00 4.04
669 4141 0.454196 TGCGATTCGGATTGTCTCGA 59.546 50.000 8.34 0.00 0.00 4.04
672 4144 2.285084 GCGATTCGGATTGTCTCGAAAC 60.285 50.000 8.34 0.00 46.25 2.78
673 4145 2.921121 CGATTCGGATTGTCTCGAAACA 59.079 45.455 0.00 0.00 46.25 2.83
674 4146 3.241678 CGATTCGGATTGTCTCGAAACAC 60.242 47.826 0.00 0.00 46.25 3.32
675 4147 2.804697 TCGGATTGTCTCGAAACACA 57.195 45.000 0.00 0.00 32.11 3.72
677 4149 3.659786 TCGGATTGTCTCGAAACACATT 58.340 40.909 0.00 0.00 32.11 2.71
678 4150 4.811908 TCGGATTGTCTCGAAACACATTA 58.188 39.130 0.00 0.00 32.11 1.90
679 4151 5.416083 TCGGATTGTCTCGAAACACATTAT 58.584 37.500 0.00 0.00 32.11 1.28
680 4152 5.290885 TCGGATTGTCTCGAAACACATTATG 59.709 40.000 0.00 0.00 32.11 1.90
681 4153 5.290885 CGGATTGTCTCGAAACACATTATGA 59.709 40.000 0.00 0.00 0.00 2.15
682 4154 6.183360 CGGATTGTCTCGAAACACATTATGAA 60.183 38.462 0.00 0.00 0.00 2.57
683 4155 7.526608 GGATTGTCTCGAAACACATTATGAAA 58.473 34.615 0.00 0.00 0.00 2.69
684 4156 7.693951 GGATTGTCTCGAAACACATTATGAAAG 59.306 37.037 0.00 0.00 0.00 2.62
685 4157 7.490962 TTGTCTCGAAACACATTATGAAAGT 57.509 32.000 0.00 0.00 0.00 2.66
686 4158 7.490962 TGTCTCGAAACACATTATGAAAGTT 57.509 32.000 0.00 0.00 0.00 2.66
687 4159 7.925993 TGTCTCGAAACACATTATGAAAGTTT 58.074 30.769 0.00 7.00 35.33 2.66
688 4160 8.067784 TGTCTCGAAACACATTATGAAAGTTTC 58.932 33.333 20.67 20.67 42.63 2.78
689 4161 8.283291 GTCTCGAAACACATTATGAAAGTTTCT 58.717 33.333 24.07 5.22 43.41 2.52
690 4162 9.483916 TCTCGAAACACATTATGAAAGTTTCTA 57.516 29.630 24.07 18.27 43.41 2.10
691 4163 9.746711 CTCGAAACACATTATGAAAGTTTCTAG 57.253 33.333 24.07 21.19 43.41 2.43
692 4164 9.483916 TCGAAACACATTATGAAAGTTTCTAGA 57.516 29.630 24.07 17.78 43.41 2.43
693 4165 9.746711 CGAAACACATTATGAAAGTTTCTAGAG 57.253 33.333 24.07 14.16 43.41 2.43
751 4248 9.582431 TTCAGACCACTAGAAAAATATTACTCG 57.418 33.333 0.00 0.00 0.00 4.18
752 4249 7.705325 TCAGACCACTAGAAAAATATTACTCGC 59.295 37.037 0.00 0.00 0.00 5.03
753 4250 7.707035 CAGACCACTAGAAAAATATTACTCGCT 59.293 37.037 0.00 0.00 0.00 4.93
754 4251 7.921745 AGACCACTAGAAAAATATTACTCGCTC 59.078 37.037 0.00 0.00 0.00 5.03
755 4252 6.985059 ACCACTAGAAAAATATTACTCGCTCC 59.015 38.462 0.00 0.00 0.00 4.70
756 4253 6.984474 CCACTAGAAAAATATTACTCGCTCCA 59.016 38.462 0.00 0.00 0.00 3.86
757 4254 7.169982 CCACTAGAAAAATATTACTCGCTCCAG 59.830 40.741 0.00 0.00 0.00 3.86
758 4255 7.707035 CACTAGAAAAATATTACTCGCTCCAGT 59.293 37.037 0.00 0.00 0.00 4.00
759 4256 8.258708 ACTAGAAAAATATTACTCGCTCCAGTT 58.741 33.333 0.00 0.00 0.00 3.16
760 4257 7.923414 AGAAAAATATTACTCGCTCCAGTTT 57.077 32.000 0.00 0.00 0.00 2.66
761 4258 8.336801 AGAAAAATATTACTCGCTCCAGTTTT 57.663 30.769 0.00 0.00 0.00 2.43
762 4259 8.793592 AGAAAAATATTACTCGCTCCAGTTTTT 58.206 29.630 0.00 0.00 0.00 1.94
792 4289 3.849911 TGAGACAAATTACTCGCTCCAG 58.150 45.455 0.00 0.00 36.11 3.86
804 4301 1.081892 CGCTCCAGATGTCCACTTTG 58.918 55.000 0.00 0.00 0.00 2.77
809 4306 4.202151 GCTCCAGATGTCCACTTTGTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
812 4316 7.411486 TCCAGATGTCCACTTTGTTTTTAAA 57.589 32.000 0.00 0.00 0.00 1.52
858 4362 4.242602 GCCTAAGCCCACCACATC 57.757 61.111 0.00 0.00 0.00 3.06
860 4364 0.464554 GCCTAAGCCCACCACATCTC 60.465 60.000 0.00 0.00 0.00 2.75
866 4370 1.985159 AGCCCACCACATCTCAAACTA 59.015 47.619 0.00 0.00 0.00 2.24
867 4371 2.578021 AGCCCACCACATCTCAAACTAT 59.422 45.455 0.00 0.00 0.00 2.12
869 4373 4.130118 GCCCACCACATCTCAAACTATAG 58.870 47.826 0.00 0.00 0.00 1.31
873 4377 3.451178 ACCACATCTCAAACTATAGCGGT 59.549 43.478 0.00 0.00 0.00 5.68
889 4393 2.028876 GCGGTACCATTTTAGCCCATT 58.971 47.619 13.54 0.00 0.00 3.16
894 4399 5.048991 CGGTACCATTTTAGCCCATTATGTC 60.049 44.000 13.54 0.00 0.00 3.06
908 4413 3.904800 TTATGTCAGATGGGCTTTCGA 57.095 42.857 0.00 0.00 0.00 3.71
915 4420 4.156739 GTCAGATGGGCTTTCGAAAAATCT 59.843 41.667 12.41 13.73 0.00 2.40
918 4423 4.397417 AGATGGGCTTTCGAAAAATCTGAG 59.603 41.667 12.41 0.00 0.00 3.35
921 4426 3.237628 GGCTTTCGAAAAATCTGAGCAC 58.762 45.455 12.41 1.06 0.00 4.40
923 4428 3.057946 GCTTTCGAAAAATCTGAGCACCT 60.058 43.478 12.41 0.00 0.00 4.00
924 4429 4.470462 CTTTCGAAAAATCTGAGCACCTG 58.530 43.478 12.41 0.00 0.00 4.00
966 4471 2.270874 ATCCACATCCGCAACTCCCC 62.271 60.000 0.00 0.00 0.00 4.81
969 4474 2.438434 CATCCGCAACTCCCCCAC 60.438 66.667 0.00 0.00 0.00 4.61
970 4475 2.933287 ATCCGCAACTCCCCCACA 60.933 61.111 0.00 0.00 0.00 4.17
971 4476 3.268103 ATCCGCAACTCCCCCACAC 62.268 63.158 0.00 0.00 0.00 3.82
974 4479 4.678743 GCAACTCCCCCACACCCC 62.679 72.222 0.00 0.00 0.00 4.95
975 4480 3.979497 CAACTCCCCCACACCCCC 61.979 72.222 0.00 0.00 0.00 5.40
976 4481 4.217266 AACTCCCCCACACCCCCT 62.217 66.667 0.00 0.00 0.00 4.79
997 4505 2.203422 TTCCCACCAAACCCAGCG 60.203 61.111 0.00 0.00 0.00 5.18
1230 4747 4.658786 AGGCCCTCCAAGGACCGT 62.659 66.667 0.00 0.00 37.67 4.83
1233 4750 2.663196 CCCTCCAAGGACCGTGTC 59.337 66.667 6.67 0.00 37.67 3.67
1357 4874 3.345808 CCGTTGTGGCCGTGAGTG 61.346 66.667 0.00 0.00 0.00 3.51
1362 4879 0.531090 TTGTGGCCGTGAGTGTACAC 60.531 55.000 18.56 18.56 37.42 2.90
1373 4890 0.487772 AGTGTACACCCTCCCAGACT 59.512 55.000 22.28 0.00 0.00 3.24
1384 4901 3.379452 CCTCCCAGACTCTACAAAGGAT 58.621 50.000 0.00 0.00 0.00 3.24
1393 4910 6.475076 CAGACTCTACAAAGGATTCATCTTCG 59.525 42.308 0.00 0.00 0.00 3.79
1404 4932 5.525378 AGGATTCATCTTCGCAGTGAATTAC 59.475 40.000 11.67 9.27 41.30 1.89
1412 4940 7.525688 TCTTCGCAGTGAATTACTAATTCTG 57.474 36.000 18.31 12.19 45.85 3.02
1417 4945 6.754209 CGCAGTGAATTACTAATTCTGTCTCT 59.246 38.462 18.31 9.06 45.85 3.10
1444 4972 3.692406 GTCTTCGACGGGGCAGGT 61.692 66.667 0.00 0.00 0.00 4.00
1718 5247 3.580895 TGATGTAGTGGCTACCTTGACAA 59.419 43.478 0.00 0.00 36.24 3.18
1759 5288 4.508124 GGTTATAGAGTTGTCATTGCCTCG 59.492 45.833 0.00 0.00 0.00 4.63
1968 5520 6.831727 TTTTTGTTCATCAATTGCTGTCTG 57.168 33.333 9.00 0.00 35.84 3.51
1969 5521 4.508461 TTGTTCATCAATTGCTGTCTGG 57.492 40.909 9.00 0.00 0.00 3.86
1970 5522 3.489355 TGTTCATCAATTGCTGTCTGGT 58.511 40.909 9.00 0.00 0.00 4.00
1971 5523 3.890756 TGTTCATCAATTGCTGTCTGGTT 59.109 39.130 9.00 0.00 0.00 3.67
1972 5524 4.022935 TGTTCATCAATTGCTGTCTGGTTC 60.023 41.667 9.00 0.00 0.00 3.62
1973 5525 4.025040 TCATCAATTGCTGTCTGGTTCT 57.975 40.909 9.00 0.00 0.00 3.01
1974 5526 5.164620 TCATCAATTGCTGTCTGGTTCTA 57.835 39.130 9.00 0.00 0.00 2.10
1975 5527 5.748402 TCATCAATTGCTGTCTGGTTCTAT 58.252 37.500 9.00 0.00 0.00 1.98
1976 5528 5.819379 TCATCAATTGCTGTCTGGTTCTATC 59.181 40.000 9.00 0.00 0.00 2.08
1977 5529 5.426689 TCAATTGCTGTCTGGTTCTATCT 57.573 39.130 0.00 0.00 0.00 1.98
1978 5530 5.809001 TCAATTGCTGTCTGGTTCTATCTT 58.191 37.500 0.00 0.00 0.00 2.40
1979 5531 6.240894 TCAATTGCTGTCTGGTTCTATCTTT 58.759 36.000 0.00 0.00 0.00 2.52
1980 5532 6.716628 TCAATTGCTGTCTGGTTCTATCTTTT 59.283 34.615 0.00 0.00 0.00 2.27
1981 5533 6.749923 ATTGCTGTCTGGTTCTATCTTTTC 57.250 37.500 0.00 0.00 0.00 2.29
1982 5534 5.227569 TGCTGTCTGGTTCTATCTTTTCA 57.772 39.130 0.00 0.00 0.00 2.69
1983 5535 5.620206 TGCTGTCTGGTTCTATCTTTTCAA 58.380 37.500 0.00 0.00 0.00 2.69
1984 5536 5.470098 TGCTGTCTGGTTCTATCTTTTCAAC 59.530 40.000 0.00 0.00 0.00 3.18
1985 5537 5.703130 GCTGTCTGGTTCTATCTTTTCAACT 59.297 40.000 0.00 0.00 0.00 3.16
1990 5542 6.372659 TCTGGTTCTATCTTTTCAACTGATGC 59.627 38.462 0.00 0.00 0.00 3.91
2378 5930 5.447624 AAGGTACAAAACTTGCCATGTAC 57.552 39.130 6.41 6.41 44.56 2.90
2380 5932 4.760204 AGGTACAAAACTTGCCATGTACTC 59.240 41.667 12.86 5.51 44.64 2.59
2387 5939 1.622607 TTGCCATGTACTCCCTCCGG 61.623 60.000 0.00 0.00 0.00 5.14
2391 5943 3.326385 ATGTACTCCCTCCGGCCCA 62.326 63.158 0.00 0.00 0.00 5.36
2399 5951 0.033503 CCCTCCGGCCCAAATTACTT 60.034 55.000 0.00 0.00 0.00 2.24
2422 5974 9.030452 ACTTGTCTTAGATTTGTCTAGATCTGT 57.970 33.333 5.18 0.00 34.60 3.41
2500 6052 6.758806 ATAATTTGGGACGGAGGTAATACT 57.241 37.500 0.00 0.00 0.00 2.12
2501 6053 7.860649 ATAATTTGGGACGGAGGTAATACTA 57.139 36.000 0.00 0.00 0.00 1.82
2572 6132 7.553334 ACGTATGGTTACAGATATGTCTTTGT 58.447 34.615 0.00 0.00 30.42 2.83
2801 6361 7.964604 TTTGTTTCTTCCTCTTAAGCTCTAC 57.035 36.000 0.00 0.00 0.00 2.59
2901 6461 6.536941 GGTAAGAGAATTTCTGTCACAGATCC 59.463 42.308 8.74 0.00 40.39 3.36
2902 6462 6.371595 AAGAGAATTTCTGTCACAGATCCT 57.628 37.500 8.74 3.52 40.39 3.24
3024 6648 4.232091 AGTAGGAAGTTCTTGTTCTGGGA 58.768 43.478 2.25 0.00 0.00 4.37
3028 6652 5.458595 AGGAAGTTCTTGTTCTGGGAATTT 58.541 37.500 2.25 0.00 0.00 1.82
3031 6655 4.948847 AGTTCTTGTTCTGGGAATTTTGC 58.051 39.130 0.00 0.00 0.00 3.68
3032 6656 4.058124 GTTCTTGTTCTGGGAATTTTGCC 58.942 43.478 0.00 0.00 39.41 4.52
3117 6741 6.384178 TTGCGAATCGGATGTATATAAACG 57.616 37.500 4.35 0.00 0.00 3.60
3118 6742 5.463286 TGCGAATCGGATGTATATAAACGT 58.537 37.500 4.35 0.00 0.00 3.99
3119 6743 5.343860 TGCGAATCGGATGTATATAAACGTG 59.656 40.000 4.35 0.00 0.00 4.49
3120 6744 5.220154 GCGAATCGGATGTATATAAACGTGG 60.220 44.000 4.35 0.00 0.00 4.94
3124 6748 9.195411 GAATCGGATGTATATAAACGTGGTTTA 57.805 33.333 3.69 3.69 41.32 2.01
3132 6756 8.710551 TGTATATAAACGTGGTTTAGTGTGTTG 58.289 33.333 7.01 0.00 40.58 3.33
3171 6795 9.355215 CAGTCCGTATATAGTCCATATTGAAAC 57.645 37.037 0.00 0.00 31.96 2.78
3198 6822 6.256975 TCCGAAACATCCTATATTTGTGAACG 59.743 38.462 0.00 0.00 0.00 3.95
3276 6908 9.640963 CATAGGTATGCAAACTACTCCTATTAC 57.359 37.037 0.00 0.00 35.46 1.89
3278 6910 7.727181 AGGTATGCAAACTACTCCTATTACTG 58.273 38.462 0.00 0.00 0.00 2.74
3280 6912 7.985752 GGTATGCAAACTACTCCTATTACTGTT 59.014 37.037 0.00 0.00 0.00 3.16
3284 6916 8.591072 TGCAAACTACTCCTATTACTGTTAGTT 58.409 33.333 0.00 0.00 0.00 2.24
3285 6917 9.433153 GCAAACTACTCCTATTACTGTTAGTTT 57.567 33.333 4.87 4.87 36.16 2.66
3288 6920 8.303780 ACTACTCCTATTACTGTTAGTTTCCC 57.696 38.462 0.00 0.00 0.00 3.97
3289 6921 6.218108 ACTCCTATTACTGTTAGTTTCCCG 57.782 41.667 0.00 0.00 0.00 5.14
3310 6942 3.369147 CGAGTCATTCATGGTCTGAACAC 59.631 47.826 0.00 0.00 46.37 3.32
3329 6961 2.540101 CACGTCAGAAACAGTGTCCTTC 59.460 50.000 0.00 0.00 31.83 3.46
3333 6965 2.104792 TCAGAAACAGTGTCCTTCTGGG 59.895 50.000 26.41 11.23 44.04 4.45
3359 6991 2.679336 ACTGTTGTGTGGTTTCGGTTAC 59.321 45.455 0.00 0.00 0.00 2.50
3361 6993 2.678836 TGTTGTGTGGTTTCGGTTACAG 59.321 45.455 0.00 0.00 0.00 2.74
3366 6998 2.102757 TGTGGTTTCGGTTACAGTAGCA 59.897 45.455 0.00 0.00 0.00 3.49
3367 6999 3.244284 TGTGGTTTCGGTTACAGTAGCAT 60.244 43.478 0.00 0.00 0.00 3.79
3368 7000 3.370061 GTGGTTTCGGTTACAGTAGCATC 59.630 47.826 0.00 0.00 0.00 3.91
3374 7010 3.128764 TCGGTTACAGTAGCATCACTCAG 59.871 47.826 0.00 0.00 0.00 3.35
3377 7013 2.376808 ACAGTAGCATCACTCAGTGC 57.623 50.000 0.00 0.00 41.57 4.40
3426 7064 1.160329 GGAACGAACAGCAGCTGTGT 61.160 55.000 28.91 19.68 44.62 3.72
3434 7072 1.270518 ACAGCAGCTGTGTCTAACCAG 60.271 52.381 27.73 0.00 43.63 4.00
3459 7097 2.476619 ACGCTGTTTTCATCTCGTTGAG 59.523 45.455 0.00 0.00 30.55 3.02
3462 7100 2.476619 CTGTTTTCATCTCGTTGAGCGT 59.523 45.455 0.00 0.00 42.13 5.07
3483 7121 1.091771 CAGGTGATGCCGGCTACAAG 61.092 60.000 29.70 14.98 43.70 3.16
3493 7131 1.811679 GGCTACAAGACGCAGAGGC 60.812 63.158 0.00 0.00 0.00 4.70
3514 7152 0.178932 TGGTCCAGGAGCAGTGTAGT 60.179 55.000 17.89 0.00 35.04 2.73
3515 7153 1.076513 TGGTCCAGGAGCAGTGTAGTA 59.923 52.381 17.89 0.00 35.04 1.82
3516 7154 1.477295 GGTCCAGGAGCAGTGTAGTAC 59.523 57.143 14.20 0.00 0.00 2.73
3540 7178 2.931386 GTGCAGCGTCACAGTGAC 59.069 61.111 22.09 22.09 43.65 3.67
3553 7192 2.509336 GTGACGGAGCGACCCATG 60.509 66.667 0.00 0.00 34.64 3.66
3571 7215 2.182030 GTCTCGCCCGAAGACAGG 59.818 66.667 12.21 0.00 33.20 4.00
3606 7250 3.319137 TCTCAGCTATTTTGTCACGCT 57.681 42.857 0.00 0.00 0.00 5.07
3607 7251 4.450082 TCTCAGCTATTTTGTCACGCTA 57.550 40.909 0.00 0.00 0.00 4.26
3609 7253 4.082190 TCTCAGCTATTTTGTCACGCTAGT 60.082 41.667 0.00 0.00 0.00 2.57
3610 7254 5.124936 TCTCAGCTATTTTGTCACGCTAGTA 59.875 40.000 0.00 0.00 0.00 1.82
3654 7300 4.695396 ACACAGATTGCAGATCTGATCTC 58.305 43.478 29.49 16.84 46.25 2.75
3663 7309 4.995487 TGCAGATCTGATCTCATGTAATGC 59.005 41.667 27.04 15.20 46.21 3.56
3664 7310 4.091655 GCAGATCTGATCTCATGTAATGCG 59.908 45.833 27.04 3.92 46.21 4.73
3680 7326 0.528017 TGCGATCCTCGGATGCTATC 59.472 55.000 2.58 0.00 40.84 2.08
3699 7345 0.376152 CACTCGCTGCTGCTAATTGG 59.624 55.000 14.03 0.00 36.97 3.16
3714 7360 4.684485 GCTAATTGGATACTGTGCTGGTCT 60.684 45.833 0.00 0.00 37.61 3.85
3715 7361 3.550437 ATTGGATACTGTGCTGGTCTC 57.450 47.619 0.00 0.00 37.61 3.36
3716 7362 0.817654 TGGATACTGTGCTGGTCTCG 59.182 55.000 0.00 0.00 37.61 4.04
3717 7363 0.103208 GGATACTGTGCTGGTCTCGG 59.897 60.000 0.00 0.00 0.00 4.63
3718 7364 0.818296 GATACTGTGCTGGTCTCGGT 59.182 55.000 0.00 0.00 0.00 4.69
3719 7365 1.204941 GATACTGTGCTGGTCTCGGTT 59.795 52.381 0.00 0.00 0.00 4.44
3720 7366 0.601558 TACTGTGCTGGTCTCGGTTC 59.398 55.000 0.00 0.00 0.00 3.62
3721 7367 1.734477 CTGTGCTGGTCTCGGTTCG 60.734 63.158 0.00 0.00 0.00 3.95
3722 7368 2.338984 GTGCTGGTCTCGGTTCGT 59.661 61.111 0.00 0.00 0.00 3.85
3723 7369 2.022129 GTGCTGGTCTCGGTTCGTG 61.022 63.158 0.00 0.00 0.00 4.35
3724 7370 2.432628 GCTGGTCTCGGTTCGTGG 60.433 66.667 0.00 0.00 0.00 4.94
3725 7371 2.261671 CTGGTCTCGGTTCGTGGG 59.738 66.667 0.00 0.00 0.00 4.61
3726 7372 3.296709 CTGGTCTCGGTTCGTGGGG 62.297 68.421 0.00 0.00 0.00 4.96
3727 7373 4.754667 GGTCTCGGTTCGTGGGGC 62.755 72.222 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 0.522180 CGAGCCTACAACTCAGTCGT 59.478 55.000 0.00 0.00 33.58 4.34
166 171 4.633126 GGACGGAGGGAGTATTAAACAAAC 59.367 45.833 0.00 0.00 0.00 2.93
182 187 7.646314 TCTACGATAAGAATTTTAGGACGGAG 58.354 38.462 0.00 0.00 0.00 4.63
183 188 7.572523 TCTACGATAAGAATTTTAGGACGGA 57.427 36.000 0.00 0.00 0.00 4.69
184 189 8.813643 AATCTACGATAAGAATTTTAGGACGG 57.186 34.615 0.00 0.00 0.00 4.79
200 205 7.825270 ACATCCGTATCTAGAGAAATCTACGAT 59.175 37.037 18.34 9.92 33.57 3.73
201 206 7.160049 ACATCCGTATCTAGAGAAATCTACGA 58.840 38.462 18.34 8.51 33.57 3.43
202 207 7.367159 ACATCCGTATCTAGAGAAATCTACG 57.633 40.000 12.32 12.32 32.33 3.51
232 237 9.362539 CGGATGTATGTAGTTAAGTTTTAGTGT 57.637 33.333 0.00 0.00 0.00 3.55
233 238 9.362539 ACGGATGTATGTAGTTAAGTTTTAGTG 57.637 33.333 0.00 0.00 0.00 2.74
274 303 7.421684 TCCCTCCATTCCAAAATTCTTATCTT 58.578 34.615 0.00 0.00 0.00 2.40
276 305 6.836007 ACTCCCTCCATTCCAAAATTCTTATC 59.164 38.462 0.00 0.00 0.00 1.75
277 306 6.608808 CACTCCCTCCATTCCAAAATTCTTAT 59.391 38.462 0.00 0.00 0.00 1.73
278 307 5.951747 CACTCCCTCCATTCCAAAATTCTTA 59.048 40.000 0.00 0.00 0.00 2.10
282 311 2.833943 GCACTCCCTCCATTCCAAAATT 59.166 45.455 0.00 0.00 0.00 1.82
283 312 2.043526 AGCACTCCCTCCATTCCAAAAT 59.956 45.455 0.00 0.00 0.00 1.82
284 313 1.428912 AGCACTCCCTCCATTCCAAAA 59.571 47.619 0.00 0.00 0.00 2.44
286 315 0.620556 GAGCACTCCCTCCATTCCAA 59.379 55.000 0.00 0.00 0.00 3.53
287 316 2.300996 GAGCACTCCCTCCATTCCA 58.699 57.895 0.00 0.00 0.00 3.53
298 327 1.005340 CTTTCGCATCTGGAGCACTC 58.995 55.000 0.00 0.00 0.00 3.51
300 329 1.005340 CTCTTTCGCATCTGGAGCAC 58.995 55.000 0.00 0.00 0.00 4.40
301 330 0.897621 TCTCTTTCGCATCTGGAGCA 59.102 50.000 0.00 0.00 0.00 4.26
302 331 1.932511 CTTCTCTTTCGCATCTGGAGC 59.067 52.381 0.00 0.00 0.00 4.70
304 333 2.562738 TGACTTCTCTTTCGCATCTGGA 59.437 45.455 0.00 0.00 0.00 3.86
305 334 2.964740 TGACTTCTCTTTCGCATCTGG 58.035 47.619 0.00 0.00 0.00 3.86
306 335 5.542616 AATTGACTTCTCTTTCGCATCTG 57.457 39.130 0.00 0.00 0.00 2.90
307 336 4.328440 CGAATTGACTTCTCTTTCGCATCT 59.672 41.667 0.00 0.00 33.70 2.90
308 337 4.493220 CCGAATTGACTTCTCTTTCGCATC 60.493 45.833 0.00 0.00 38.21 3.91
309 338 3.372206 CCGAATTGACTTCTCTTTCGCAT 59.628 43.478 0.00 0.00 38.21 4.73
310 339 2.736721 CCGAATTGACTTCTCTTTCGCA 59.263 45.455 0.00 0.00 38.21 5.10
313 342 2.094417 CGCCCGAATTGACTTCTCTTTC 59.906 50.000 0.00 0.00 0.00 2.62
332 1392 0.678048 ACTTTGCTTCATCCCCTCGC 60.678 55.000 0.00 0.00 0.00 5.03
355 1415 4.256090 GCCGGCGAATGATGGCAC 62.256 66.667 12.58 0.00 46.76 5.01
475 1536 1.981254 AAAGCATTCGCCAATTGTCG 58.019 45.000 1.72 1.72 39.83 4.35
550 1611 0.246910 TTCACCGCCGTGCTGTATAA 59.753 50.000 0.00 0.00 40.04 0.98
585 1646 4.100963 TCAGAAAGTGAAGCTCCACTACAA 59.899 41.667 5.84 0.00 45.82 2.41
642 4114 0.940126 ATCCGAATCGCACAATGCTC 59.060 50.000 0.00 0.00 42.25 4.26
644 4116 1.202177 ACAATCCGAATCGCACAATGC 60.202 47.619 0.00 0.00 40.69 3.56
646 4118 2.609459 GAGACAATCCGAATCGCACAAT 59.391 45.455 0.00 0.00 0.00 2.71
649 4121 0.572590 CGAGACAATCCGAATCGCAC 59.427 55.000 0.00 0.00 0.00 5.34
660 4132 8.099364 ACTTTCATAATGTGTTTCGAGACAAT 57.901 30.769 10.75 4.42 0.00 2.71
672 4144 9.817365 CACAACTCTAGAAACTTTCATAATGTG 57.183 33.333 4.34 7.29 0.00 3.21
673 4145 8.507249 GCACAACTCTAGAAACTTTCATAATGT 58.493 33.333 4.34 0.00 0.00 2.71
674 4146 8.725148 AGCACAACTCTAGAAACTTTCATAATG 58.275 33.333 4.34 0.00 0.00 1.90
675 4147 8.854614 AGCACAACTCTAGAAACTTTCATAAT 57.145 30.769 4.34 0.00 0.00 1.28
677 4149 7.931407 TGAAGCACAACTCTAGAAACTTTCATA 59.069 33.333 4.34 0.00 0.00 2.15
678 4150 6.767902 TGAAGCACAACTCTAGAAACTTTCAT 59.232 34.615 4.34 0.00 0.00 2.57
679 4151 6.112734 TGAAGCACAACTCTAGAAACTTTCA 58.887 36.000 4.34 0.00 0.00 2.69
680 4152 6.604735 TGAAGCACAACTCTAGAAACTTTC 57.395 37.500 0.00 0.00 0.00 2.62
681 4153 6.767902 TGATGAAGCACAACTCTAGAAACTTT 59.232 34.615 0.00 0.00 0.00 2.66
682 4154 6.291377 TGATGAAGCACAACTCTAGAAACTT 58.709 36.000 0.00 0.00 0.00 2.66
683 4155 5.858381 TGATGAAGCACAACTCTAGAAACT 58.142 37.500 0.00 0.00 0.00 2.66
684 4156 6.163159 CTGATGAAGCACAACTCTAGAAAC 57.837 41.667 0.00 0.00 0.00 2.78
731 4228 6.984474 TGGAGCGAGTAATATTTTTCTAGTGG 59.016 38.462 0.00 0.00 0.00 4.00
732 4229 7.707035 ACTGGAGCGAGTAATATTTTTCTAGTG 59.293 37.037 0.00 0.00 0.00 2.74
767 4264 5.529430 TGGAGCGAGTAATTTGTCTCAAAAA 59.471 36.000 0.00 0.00 0.00 1.94
768 4265 5.060506 TGGAGCGAGTAATTTGTCTCAAAA 58.939 37.500 0.00 0.00 0.00 2.44
769 4266 4.637276 TGGAGCGAGTAATTTGTCTCAAA 58.363 39.130 0.00 0.00 0.00 2.69
770 4267 4.021456 TCTGGAGCGAGTAATTTGTCTCAA 60.021 41.667 0.00 0.00 0.00 3.02
771 4268 3.509967 TCTGGAGCGAGTAATTTGTCTCA 59.490 43.478 0.00 0.00 0.00 3.27
772 4269 4.111375 TCTGGAGCGAGTAATTTGTCTC 57.889 45.455 0.00 0.00 0.00 3.36
773 4270 4.081420 ACATCTGGAGCGAGTAATTTGTCT 60.081 41.667 0.00 0.00 0.00 3.41
774 4271 4.184629 ACATCTGGAGCGAGTAATTTGTC 58.815 43.478 0.00 0.00 0.00 3.18
775 4272 4.184629 GACATCTGGAGCGAGTAATTTGT 58.815 43.478 0.00 0.00 0.00 2.83
776 4273 3.557595 GGACATCTGGAGCGAGTAATTTG 59.442 47.826 0.00 0.00 0.00 2.32
812 4316 4.722361 TCTTAACAAAGTGGGCGTTTTT 57.278 36.364 0.00 0.00 0.00 1.94
816 4320 2.159382 CCATCTTAACAAAGTGGGCGT 58.841 47.619 0.00 0.00 0.00 5.68
817 4321 1.472480 CCCATCTTAACAAAGTGGGCG 59.528 52.381 10.69 0.00 42.69 6.13
858 4362 6.920569 AAAATGGTACCGCTATAGTTTGAG 57.079 37.500 7.57 0.00 0.00 3.02
860 4364 6.293244 GGCTAAAATGGTACCGCTATAGTTTG 60.293 42.308 7.57 0.00 0.00 2.93
866 4370 2.440253 TGGGCTAAAATGGTACCGCTAT 59.560 45.455 7.57 0.00 0.00 2.97
867 4371 1.838715 TGGGCTAAAATGGTACCGCTA 59.161 47.619 7.57 0.00 0.00 4.26
869 4373 1.687563 ATGGGCTAAAATGGTACCGC 58.312 50.000 7.57 2.83 0.00 5.68
873 4377 6.905736 TCTGACATAATGGGCTAAAATGGTA 58.094 36.000 1.89 0.00 0.00 3.25
889 4393 3.904800 TTCGAAAGCCCATCTGACATA 57.095 42.857 0.00 0.00 0.00 2.29
894 4399 4.156556 TCAGATTTTTCGAAAGCCCATCTG 59.843 41.667 26.40 26.40 35.60 2.90
908 4413 4.646492 ACAGAAACAGGTGCTCAGATTTTT 59.354 37.500 0.00 0.00 0.00 1.94
915 4420 3.281727 AGAAACAGAAACAGGTGCTCA 57.718 42.857 0.00 0.00 0.00 4.26
918 4423 3.363178 CGAAAGAAACAGAAACAGGTGC 58.637 45.455 0.00 0.00 0.00 5.01
921 4426 2.287608 GGCCGAAAGAAACAGAAACAGG 60.288 50.000 0.00 0.00 0.00 4.00
923 4428 1.679153 GGGCCGAAAGAAACAGAAACA 59.321 47.619 0.00 0.00 0.00 2.83
924 4429 1.000607 GGGGCCGAAAGAAACAGAAAC 60.001 52.381 0.00 0.00 0.00 2.78
966 4471 3.339093 GGAAGGGAGGGGGTGTGG 61.339 72.222 0.00 0.00 0.00 4.17
969 4474 3.339093 GTGGGAAGGGAGGGGGTG 61.339 72.222 0.00 0.00 0.00 4.61
970 4475 4.695791 GGTGGGAAGGGAGGGGGT 62.696 72.222 0.00 0.00 0.00 4.95
971 4476 4.693915 TGGTGGGAAGGGAGGGGG 62.694 72.222 0.00 0.00 0.00 5.40
972 4477 2.167037 TTTGGTGGGAAGGGAGGGG 61.167 63.158 0.00 0.00 0.00 4.79
973 4478 1.076727 GTTTGGTGGGAAGGGAGGG 59.923 63.158 0.00 0.00 0.00 4.30
974 4479 1.076727 GGTTTGGTGGGAAGGGAGG 59.923 63.158 0.00 0.00 0.00 4.30
975 4480 1.076727 GGGTTTGGTGGGAAGGGAG 59.923 63.158 0.00 0.00 0.00 4.30
976 4481 1.701757 TGGGTTTGGTGGGAAGGGA 60.702 57.895 0.00 0.00 0.00 4.20
1065 4573 0.108756 GACGATATCTAAGGGGCGCC 60.109 60.000 21.18 21.18 0.00 6.53
1107 4624 1.824224 AAGGGGAGGAAACCGTCGAC 61.824 60.000 5.18 5.18 0.00 4.20
1221 4738 1.344763 AGGAAGAAGACACGGTCCTTG 59.655 52.381 0.00 0.00 35.06 3.61
1226 4743 0.597072 GTCGAGGAAGAAGACACGGT 59.403 55.000 0.00 0.00 35.19 4.83
1230 4747 1.601166 TGACGTCGAGGAAGAAGACA 58.399 50.000 12.85 0.00 34.80 3.41
1233 4750 1.669211 GGGTTGACGTCGAGGAAGAAG 60.669 57.143 12.85 0.00 0.00 2.85
1357 4874 2.291411 TGTAGAGTCTGGGAGGGTGTAC 60.291 54.545 1.86 0.00 0.00 2.90
1362 4879 1.834263 CCTTTGTAGAGTCTGGGAGGG 59.166 57.143 1.86 0.00 0.00 4.30
1373 4890 5.084818 TGCGAAGATGAATCCTTTGTAGA 57.915 39.130 0.00 0.00 0.00 2.59
1384 4901 8.492673 AATTAGTAATTCACTGCGAAGATGAA 57.507 30.769 0.00 4.06 38.24 2.57
1404 4932 8.527810 AGACCTAGAACAAAGAGACAGAATTAG 58.472 37.037 0.00 0.00 0.00 1.73
1412 4940 5.373981 TCGAAGACCTAGAACAAAGAGAC 57.626 43.478 0.00 0.00 0.00 3.36
1444 4972 1.679977 CCTCCGGTACTCGTTCCCA 60.680 63.158 0.00 0.00 37.11 4.37
1571 5099 1.141657 ACACACTGTGTCTGCCATCTT 59.858 47.619 11.12 0.00 43.92 2.40
1652 5181 5.826601 TGCACAATCTGAGTTTGTTGTTA 57.173 34.783 6.18 0.00 35.18 2.41
1656 5185 4.496341 CGACTTGCACAATCTGAGTTTGTT 60.496 41.667 6.18 0.00 35.18 2.83
1657 5186 3.002656 CGACTTGCACAATCTGAGTTTGT 59.997 43.478 3.18 3.18 37.79 2.83
1759 5288 0.877743 GCTTGAAGTCCTTGTCAGGC 59.122 55.000 0.00 0.00 40.58 4.85
1961 5513 5.703130 AGTTGAAAAGATAGAACCAGACAGC 59.297 40.000 0.00 0.00 0.00 4.40
1962 5514 6.931281 TCAGTTGAAAAGATAGAACCAGACAG 59.069 38.462 0.00 0.00 0.00 3.51
1963 5515 6.826668 TCAGTTGAAAAGATAGAACCAGACA 58.173 36.000 0.00 0.00 0.00 3.41
1964 5516 7.625185 GCATCAGTTGAAAAGATAGAACCAGAC 60.625 40.741 0.00 0.00 0.00 3.51
1965 5517 6.372659 GCATCAGTTGAAAAGATAGAACCAGA 59.627 38.462 0.00 0.00 0.00 3.86
1966 5518 6.149973 TGCATCAGTTGAAAAGATAGAACCAG 59.850 38.462 0.00 0.00 0.00 4.00
1967 5519 6.003326 TGCATCAGTTGAAAAGATAGAACCA 58.997 36.000 0.00 0.00 0.00 3.67
1968 5520 6.500684 TGCATCAGTTGAAAAGATAGAACC 57.499 37.500 0.00 0.00 0.00 3.62
1969 5521 9.713740 CTAATGCATCAGTTGAAAAGATAGAAC 57.286 33.333 0.00 0.00 0.00 3.01
1970 5522 9.671279 TCTAATGCATCAGTTGAAAAGATAGAA 57.329 29.630 0.00 0.00 0.00 2.10
1971 5523 9.671279 TTCTAATGCATCAGTTGAAAAGATAGA 57.329 29.630 0.00 0.00 0.00 1.98
1972 5524 9.932699 CTTCTAATGCATCAGTTGAAAAGATAG 57.067 33.333 0.00 0.00 0.00 2.08
1973 5525 9.453572 ACTTCTAATGCATCAGTTGAAAAGATA 57.546 29.630 0.00 0.00 0.00 1.98
1974 5526 8.345724 ACTTCTAATGCATCAGTTGAAAAGAT 57.654 30.769 0.00 0.00 0.00 2.40
1975 5527 7.750229 ACTTCTAATGCATCAGTTGAAAAGA 57.250 32.000 0.00 0.00 0.00 2.52
1977 5529 9.844790 CATAACTTCTAATGCATCAGTTGAAAA 57.155 29.630 17.46 4.69 0.00 2.29
1978 5530 7.970061 GCATAACTTCTAATGCATCAGTTGAAA 59.030 33.333 17.46 4.95 46.19 2.69
1979 5531 7.475015 GCATAACTTCTAATGCATCAGTTGAA 58.525 34.615 17.46 8.08 46.19 2.69
1980 5532 7.019774 GCATAACTTCTAATGCATCAGTTGA 57.980 36.000 17.46 1.61 46.19 3.18
1990 5542 7.307632 GCATCCTACACAGCATAACTTCTAATG 60.308 40.741 0.00 0.00 0.00 1.90
2266 5818 6.740944 TGGATATGATCGAAGGGAAAGTTA 57.259 37.500 0.00 0.00 0.00 2.24
2380 5932 2.294284 CAAGTAATTTGGGCCGGAGGG 61.294 57.143 5.05 0.00 39.95 4.30
2387 5939 7.602753 ACAAATCTAAGACAAGTAATTTGGGC 58.397 34.615 9.60 0.00 41.25 5.36
2465 6017 9.689501 TCCGTCCCAAATTATTAGTCTTAAATT 57.310 29.630 0.00 0.00 0.00 1.82
2475 6027 8.266363 AGTATTACCTCCGTCCCAAATTATTA 57.734 34.615 0.00 0.00 0.00 0.98
2480 6032 6.758806 AATAGTATTACCTCCGTCCCAAAT 57.241 37.500 0.00 0.00 0.00 2.32
2572 6132 6.173339 CCAAGAATTCAGTTCAGCCTTACTA 58.827 40.000 8.44 0.00 39.39 1.82
2801 6361 5.055144 CACTGATGATGGTCTGATGGTAAG 58.945 45.833 0.00 0.00 0.00 2.34
2889 6449 6.618287 TTACAAACAAAGGATCTGTGACAG 57.382 37.500 6.18 6.18 0.00 3.51
2931 6491 4.326826 CCACACATGACCAGTCTAACAAT 58.673 43.478 0.00 0.00 0.00 2.71
3097 6721 5.860182 ACCACGTTTATATACATCCGATTCG 59.140 40.000 0.00 0.00 0.00 3.34
3102 6726 7.436080 ACACTAAACCACGTTTATATACATCCG 59.564 37.037 0.00 0.00 37.37 4.18
3107 6731 8.170553 CCAACACACTAAACCACGTTTATATAC 58.829 37.037 0.00 0.00 37.37 1.47
3117 6741 3.692593 AGTGAACCAACACACTAAACCAC 59.307 43.478 0.00 0.00 44.06 4.16
3118 6742 3.942748 GAGTGAACCAACACACTAAACCA 59.057 43.478 0.00 0.00 45.54 3.67
3119 6743 3.942748 TGAGTGAACCAACACACTAAACC 59.057 43.478 0.00 0.00 45.54 3.27
3120 6744 5.751243 ATGAGTGAACCAACACACTAAAC 57.249 39.130 0.00 0.00 45.54 2.01
3132 6756 2.767505 ACGGACTGAAATGAGTGAACC 58.232 47.619 0.00 0.00 0.00 3.62
3171 6795 7.728847 TCACAAATATAGGATGTTTCGGATG 57.271 36.000 0.00 0.00 0.00 3.51
3198 6822 6.292150 CCTTCTGTTAAATGATACTCCCTCC 58.708 44.000 0.00 0.00 0.00 4.30
3267 6899 6.096564 ACTCGGGAAACTAACAGTAATAGGAG 59.903 42.308 0.00 0.00 0.00 3.69
3269 6901 6.127535 TGACTCGGGAAACTAACAGTAATAGG 60.128 42.308 0.00 0.00 0.00 2.57
3271 6903 6.839124 TGACTCGGGAAACTAACAGTAATA 57.161 37.500 0.00 0.00 0.00 0.98
3272 6904 5.733620 TGACTCGGGAAACTAACAGTAAT 57.266 39.130 0.00 0.00 0.00 1.89
3276 6908 4.566004 TGAATGACTCGGGAAACTAACAG 58.434 43.478 0.00 0.00 0.00 3.16
3278 6910 4.332819 CCATGAATGACTCGGGAAACTAAC 59.667 45.833 0.00 0.00 0.00 2.34
3280 6912 3.517901 ACCATGAATGACTCGGGAAACTA 59.482 43.478 0.00 0.00 0.00 2.24
3281 6913 2.305927 ACCATGAATGACTCGGGAAACT 59.694 45.455 0.00 0.00 0.00 2.66
3284 6916 2.093500 CAGACCATGAATGACTCGGGAA 60.093 50.000 0.00 0.00 0.00 3.97
3285 6917 1.482182 CAGACCATGAATGACTCGGGA 59.518 52.381 0.00 0.00 0.00 5.14
3286 6918 1.482182 TCAGACCATGAATGACTCGGG 59.518 52.381 0.00 0.00 34.02 5.14
3287 6919 2.967599 TCAGACCATGAATGACTCGG 57.032 50.000 0.00 0.00 34.02 4.63
3310 6942 2.797156 CAGAAGGACACTGTTTCTGACG 59.203 50.000 14.69 0.00 46.71 4.35
3329 6961 0.937304 CACACAACAGTTCGTCCCAG 59.063 55.000 0.00 0.00 0.00 4.45
3333 6965 2.536130 CGAAACCACACAACAGTTCGTC 60.536 50.000 0.00 0.00 0.00 4.20
3359 6991 1.275505 CGCACTGAGTGATGCTACTG 58.724 55.000 18.18 0.00 39.79 2.74
3361 6993 0.994995 CACGCACTGAGTGATGCTAC 59.005 55.000 18.18 0.00 41.83 3.58
3366 6998 3.002791 CCATAAACACGCACTGAGTGAT 58.997 45.455 18.18 4.94 41.83 3.06
3367 6999 2.412870 CCATAAACACGCACTGAGTGA 58.587 47.619 18.18 0.00 41.83 3.41
3368 7000 1.135972 GCCATAAACACGCACTGAGTG 60.136 52.381 8.52 8.52 44.57 3.51
3374 7010 3.216147 AGAATTGCCATAAACACGCAC 57.784 42.857 0.00 0.00 30.84 5.34
3377 7013 5.123186 TGAACCTAGAATTGCCATAAACACG 59.877 40.000 0.00 0.00 0.00 4.49
3434 7072 0.169009 GAGATGAAAACAGCGTGGGC 59.831 55.000 0.00 0.00 40.37 5.36
3474 7112 1.517257 CCTCTGCGTCTTGTAGCCG 60.517 63.158 0.00 0.00 0.00 5.52
3493 7131 1.532604 TACACTGCTCCTGGACCACG 61.533 60.000 0.00 0.00 0.00 4.94
3553 7192 2.182030 CTGTCTTCGGGCGAGACC 59.818 66.667 10.48 0.00 37.93 3.85
3571 7215 0.104855 TGAGATAGCATGTCCGGTGC 59.895 55.000 7.42 7.42 42.81 5.01
3606 7250 7.419203 TGGCTCCCTTAAGATATGCTATACTA 58.581 38.462 3.36 0.00 0.00 1.82
3607 7251 6.264528 TGGCTCCCTTAAGATATGCTATACT 58.735 40.000 3.36 0.00 0.00 2.12
3609 7253 6.500400 TGTTGGCTCCCTTAAGATATGCTATA 59.500 38.462 3.36 0.00 0.00 1.31
3610 7254 5.310594 TGTTGGCTCCCTTAAGATATGCTAT 59.689 40.000 3.36 0.00 0.00 2.97
3624 7270 0.895100 TGCAATCTGTGTTGGCTCCC 60.895 55.000 0.00 0.00 0.00 4.30
3664 7310 2.159448 CGAGTGATAGCATCCGAGGATC 60.159 54.545 0.85 0.00 31.62 3.36
3699 7345 0.818296 ACCGAGACCAGCACAGTATC 59.182 55.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.