Multiple sequence alignment - TraesCS5B01G303200

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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 TraesCS5B01G303200 chr5B 100.000 4563 0 0 1 4563 487609703 487605141 0.000000e+00 8427.0
1 TraesCS5B01G303200 chr5D 94.199 2982 102 29 237 3175 406596570 406593617 0.000000e+00 4482.0
2 TraesCS5B01G303200 chr5D 88.640 669 49 9 3748 4392 406593117 406592452 0.000000e+00 789.0
3 TraesCS5B01G303200 chr5D 93.584 452 17 7 3220 3662 406593618 406593170 0.000000e+00 664.0
4 TraesCS5B01G303200 chr5D 91.071 168 11 2 4 171 406596734 406596571 1.650000e-54 224.0
5 TraesCS5B01G303200 chr5A 89.273 1100 68 24 239 1309 512235690 512234612 0.000000e+00 1332.0
6 TraesCS5B01G303200 chr5A 91.043 815 51 11 2391 3184 512233470 512232657 0.000000e+00 1081.0
7 TraesCS5B01G303200 chr5A 96.939 588 13 3 1809 2392 512234161 512233575 0.000000e+00 981.0
8 TraesCS5B01G303200 chr5A 91.107 506 23 8 3177 3663 512232627 512232125 0.000000e+00 665.0
9 TraesCS5B01G303200 chr5A 89.916 476 35 10 3743 4213 512232093 512231626 6.530000e-168 601.0
10 TraesCS5B01G303200 chr5A 90.361 332 21 7 1445 1771 512234466 512234141 4.220000e-115 425.0
11 TraesCS5B01G303200 chr5A 94.737 171 8 1 1 171 512235866 512235697 9.730000e-67 265.0
12 TraesCS5B01G303200 chr5A 89.080 174 14 2 4223 4392 512231193 512231021 1.290000e-50 211.0
13 TraesCS5B01G303200 chr5A 92.857 84 6 0 3664 3747 669574298 669574215 6.200000e-24 122.0
14 TraesCS5B01G303200 chr6D 98.592 71 1 0 170 240 363038162 363038092 4.790000e-25 126.0
15 TraesCS5B01G303200 chr6D 90.000 90 7 1 151 240 91566709 91566796 1.040000e-21 115.0
16 TraesCS5B01G303200 chr1D 98.592 71 1 0 170 240 335585124 335585054 4.790000e-25 126.0
17 TraesCS5B01G303200 chr2D 97.260 73 2 0 168 240 53145725 53145797 1.720000e-24 124.0
18 TraesCS5B01G303200 chr7A 97.222 72 2 0 169 240 467851821 467851892 6.200000e-24 122.0
19 TraesCS5B01G303200 chr4B 97.222 72 2 0 169 240 82163463 82163392 6.200000e-24 122.0
20 TraesCS5B01G303200 chr7D 91.667 84 7 0 157 240 219834002 219833919 2.880000e-22 117.0
21 TraesCS5B01G303200 chr6B 91.667 84 7 0 157 240 290638546 290638463 2.880000e-22 117.0
22 TraesCS5B01G303200 chr6B 91.667 84 7 0 157 240 290666385 290666302 2.880000e-22 117.0
23 TraesCS5B01G303200 chr2A 91.667 84 7 0 3664 3747 683717006 683716923 2.880000e-22 117.0
24 TraesCS5B01G303200 chr2A 90.244 82 8 0 3666 3747 6327231 6327150 1.740000e-19 108.0
25 TraesCS5B01G303200 chr2A 93.750 64 3 1 3664 3727 403428012 403427950 1.350000e-15 95.3
26 TraesCS5B01G303200 chr2A 92.188 64 4 1 3664 3727 401431326 401431264 6.290000e-14 89.8
27 TraesCS5B01G303200 chr3A 91.026 78 7 0 3664 3741 9322166 9322243 6.240000e-19 106.0
28 TraesCS5B01G303200 chr1B 92.308 65 3 2 3664 3727 407127943 407128006 1.750000e-14 91.6
29 TraesCS5B01G303200 chr1B 92.308 65 3 2 3664 3727 631073120 631073057 1.750000e-14 91.6
30 TraesCS5B01G303200 chr1B 91.935 62 3 2 3664 3724 18577831 18577771 8.130000e-13 86.1


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 TraesCS5B01G303200 chr5B 487605141 487609703 4562 True 8427.000 8427 100.0000 1 4563 1 chr5B.!!$R1 4562
1 TraesCS5B01G303200 chr5D 406592452 406596734 4282 True 1539.750 4482 91.8735 4 4392 4 chr5D.!!$R1 4388
2 TraesCS5B01G303200 chr5A 512231021 512235866 4845 True 695.125 1332 91.5570 1 4392 8 chr5A.!!$R2 4391

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
519 521 0.035820 TCGTGTATGCAAAGACCCCC 60.036 55.0 0.00 0.0 0.00 5.40 F
1074 1097 0.802607 GTGTCCGGATCGCTCTCAAC 60.803 60.0 7.81 0.0 0.00 3.18 F
1123 1146 1.078709 TTGGAGCTTCAATCGCTTCG 58.921 50.0 2.32 0.0 37.96 3.79 F
2952 3120 0.625316 TCTGACCCCCATCAACCATG 59.375 55.0 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1449 0.614979 AGAAGAAGGTGCCGAGGCTA 60.615 55.000 15.75 0.00 42.51 3.93 R
2926 3094 0.543749 GATGGGGGTCAGAACTCAGG 59.456 60.000 0.00 0.00 0.00 3.86 R
3008 3176 1.717645 GCTTTTCGATTGCTGCAACAG 59.282 47.619 18.51 14.25 34.12 3.16 R
4471 5133 0.034186 GGGATGGTTCCATCACAGCA 60.034 55.000 26.50 0.00 44.00 4.41 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
70 71 8.814038 ATATATATTCTGGTCATTTTCAGGCC 57.186 34.615 0.00 0.00 0.00 5.19
135 136 5.048782 GCTTCCAAATCGATATGGTATGCAA 60.049 40.000 0.00 0.00 37.94 4.08
154 155 9.555727 GTATGCAAATGTTACCCTATTCTAAGA 57.444 33.333 0.00 0.00 0.00 2.10
171 172 6.443934 TCTAAGATCTCTGTTGCTGAGTAC 57.556 41.667 0.00 0.00 32.50 2.73
172 173 6.184068 TCTAAGATCTCTGTTGCTGAGTACT 58.816 40.000 0.00 0.00 32.50 2.73
173 174 4.981806 AGATCTCTGTTGCTGAGTACTC 57.018 45.455 16.32 16.32 32.50 2.59
174 175 3.699038 AGATCTCTGTTGCTGAGTACTCC 59.301 47.826 20.11 6.32 32.50 3.85
175 176 2.171840 TCTCTGTTGCTGAGTACTCCC 58.828 52.381 20.11 11.47 32.50 4.30
176 177 2.175202 CTCTGTTGCTGAGTACTCCCT 58.825 52.381 20.11 0.00 0.00 4.20
177 178 2.165437 CTCTGTTGCTGAGTACTCCCTC 59.835 54.545 20.11 9.40 0.00 4.30
178 179 1.205893 CTGTTGCTGAGTACTCCCTCC 59.794 57.143 20.11 6.36 0.00 4.30
179 180 1.267121 GTTGCTGAGTACTCCCTCCA 58.733 55.000 20.11 8.77 0.00 3.86
180 181 1.834263 GTTGCTGAGTACTCCCTCCAT 59.166 52.381 20.11 0.00 0.00 3.41
181 182 1.781786 TGCTGAGTACTCCCTCCATC 58.218 55.000 20.11 0.00 0.00 3.51
182 183 1.044611 GCTGAGTACTCCCTCCATCC 58.955 60.000 20.11 0.00 0.00 3.51
183 184 1.710816 CTGAGTACTCCCTCCATCCC 58.289 60.000 20.11 0.00 0.00 3.85
184 185 1.015609 TGAGTACTCCCTCCATCCCA 58.984 55.000 20.11 0.00 0.00 4.37
185 186 1.580658 TGAGTACTCCCTCCATCCCAT 59.419 52.381 20.11 0.00 0.00 4.00
186 187 2.795360 TGAGTACTCCCTCCATCCCATA 59.205 50.000 20.11 0.00 0.00 2.74
187 188 3.208922 TGAGTACTCCCTCCATCCCATAA 59.791 47.826 20.11 0.00 0.00 1.90
188 189 4.140447 TGAGTACTCCCTCCATCCCATAAT 60.140 45.833 20.11 0.00 0.00 1.28
189 190 5.077300 TGAGTACTCCCTCCATCCCATAATA 59.923 44.000 20.11 0.00 0.00 0.98
190 191 6.185677 AGTACTCCCTCCATCCCATAATAT 57.814 41.667 0.00 0.00 0.00 1.28
191 192 7.035394 TGAGTACTCCCTCCATCCCATAATATA 60.035 40.741 20.11 0.00 0.00 0.86
192 193 7.729350 AGTACTCCCTCCATCCCATAATATAA 58.271 38.462 0.00 0.00 0.00 0.98
193 194 7.846823 AGTACTCCCTCCATCCCATAATATAAG 59.153 40.741 0.00 0.00 0.00 1.73
194 195 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
195 196 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
196 197 5.667626 TCCCTCCATCCCATAATATAAGAGC 59.332 44.000 0.00 0.00 0.00 4.09
197 198 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
198 199 5.129485 CCTCCATCCCATAATATAAGAGCGT 59.871 44.000 0.00 0.00 0.00 5.07
199 200 6.352222 CCTCCATCCCATAATATAAGAGCGTT 60.352 42.308 0.00 0.00 0.00 4.84
200 201 7.016153 TCCATCCCATAATATAAGAGCGTTT 57.984 36.000 0.00 0.00 0.00 3.60
201 202 7.458397 TCCATCCCATAATATAAGAGCGTTTT 58.542 34.615 0.00 0.00 0.00 2.43
202 203 7.942341 TCCATCCCATAATATAAGAGCGTTTTT 59.058 33.333 0.00 0.00 0.00 1.94
333 335 4.081087 TCTGGCAGTCAAAGTACCCTATTC 60.081 45.833 15.27 0.00 0.00 1.75
351 353 3.719268 TTCTGGCAAGGCTTCAAGATA 57.281 42.857 0.00 0.00 0.00 1.98
502 504 6.525121 TGTAACTTCAAAGTCAGATGTTCG 57.475 37.500 0.00 0.00 38.57 3.95
507 509 6.223852 ACTTCAAAGTCAGATGTTCGTGTAT 58.776 36.000 0.00 0.00 32.86 2.29
519 521 0.035820 TCGTGTATGCAAAGACCCCC 60.036 55.000 0.00 0.00 0.00 5.40
588 590 9.715123 TTTATCATATGTGCTCGTGTAAAATTG 57.285 29.630 1.90 0.00 0.00 2.32
620 622 7.885399 TCAATAAAGAGAAGGAAAGAAAGGAGG 59.115 37.037 0.00 0.00 0.00 4.30
643 645 2.294233 GAGTCAAGCTCAAACATTGCCA 59.706 45.455 0.00 0.00 43.58 4.92
646 648 2.028839 TCAAGCTCAAACATTGCCATGG 60.029 45.455 7.63 7.63 34.27 3.66
652 654 3.164268 TCAAACATTGCCATGGTAAGCT 58.836 40.909 20.40 5.27 34.27 3.74
1074 1097 0.802607 GTGTCCGGATCGCTCTCAAC 60.803 60.000 7.81 0.00 0.00 3.18
1117 1140 4.037923 TGTTGAGGTTTTGGAGCTTCAATC 59.962 41.667 8.64 3.58 35.91 2.67
1123 1146 1.078709 TTGGAGCTTCAATCGCTTCG 58.921 50.000 2.32 0.00 37.96 3.79
1282 1308 3.191371 CCAGCTGTGTATTTTCTTGGTCC 59.809 47.826 13.81 0.00 0.00 4.46
1283 1309 3.191371 CAGCTGTGTATTTTCTTGGTCCC 59.809 47.826 5.25 0.00 0.00 4.46
1298 1324 2.167693 TGGTCCCGAACATGTAGATGAC 59.832 50.000 6.90 4.42 33.36 3.06
1371 1397 7.921786 TTTCTTCAGTTCTTCTCTGTTTTCA 57.078 32.000 0.00 0.00 34.86 2.69
1416 1449 2.425668 GTTTGGGCTGTAGTGTTTGTGT 59.574 45.455 0.00 0.00 0.00 3.72
1786 1829 8.337532 TGTGATGAATGAAATATGATCGTGTTC 58.662 33.333 0.00 2.27 0.00 3.18
1988 2031 8.361139 TGATCAATGATACAATTGCAATGCATA 58.639 29.630 13.82 6.37 38.76 3.14
2007 2050 5.311913 TGCATATTGTACCCATCTATTCCCA 59.688 40.000 0.00 0.00 0.00 4.37
2287 2332 2.222007 GCACTGAGCAGTATCTGGAG 57.778 55.000 2.36 0.00 44.79 3.86
2365 2410 2.891580 TCTTCAGGTATATGTCCGGCTC 59.108 50.000 0.00 0.00 0.00 4.70
2378 2423 3.513912 TGTCCGGCTCAAGATCTTCTTTA 59.486 43.478 4.57 0.00 33.78 1.85
2382 2427 5.421056 TCCGGCTCAAGATCTTCTTTAGTTA 59.579 40.000 4.57 0.00 33.78 2.24
2445 2596 8.676401 TGTATCTTGTTAATCACATGAACCATG 58.324 33.333 0.00 5.48 46.18 3.66
2464 2615 4.293415 CATGGTTGTTCAGCACTCTTTTC 58.707 43.478 0.00 0.00 35.09 2.29
2477 2629 4.933400 GCACTCTTTTCCGAACCATAGTTA 59.067 41.667 0.00 0.00 35.94 2.24
2509 2661 6.157211 CACTTATCGGTAACTCCATATGGAC 58.843 44.000 20.98 11.32 39.78 4.02
2638 2791 2.092838 CCGCTGACAAGATTTCGTCTTC 59.907 50.000 0.00 0.00 45.35 2.87
2643 2800 5.121454 GCTGACAAGATTTCGTCTTCTCAAT 59.879 40.000 0.00 0.00 45.35 2.57
2647 2804 7.063898 TGACAAGATTTCGTCTTCTCAATGATC 59.936 37.037 0.00 0.00 45.35 2.92
2650 2807 9.038803 CAAGATTTCGTCTTCTCAATGATCATA 57.961 33.333 9.04 0.00 45.35 2.15
2651 2808 8.586570 AGATTTCGTCTTCTCAATGATCATAC 57.413 34.615 9.04 0.40 31.47 2.39
2652 2809 6.812481 TTTCGTCTTCTCAATGATCATACG 57.188 37.500 9.04 13.02 0.00 3.06
2666 2823 6.373186 TGATCATACGAGTACGAGTTTGAT 57.627 37.500 20.32 20.32 42.66 2.57
2669 2826 5.745514 TCATACGAGTACGAGTTTGATAGC 58.254 41.667 10.82 0.00 42.66 2.97
2672 2829 2.776765 CGAGTACGAGTTTGATAGCGTG 59.223 50.000 0.00 0.00 42.66 5.34
2679 2836 1.531149 AGTTTGATAGCGTGTGTGTGC 59.469 47.619 0.00 0.00 0.00 4.57
2680 2837 1.262950 GTTTGATAGCGTGTGTGTGCA 59.737 47.619 0.00 0.00 0.00 4.57
2821 2986 3.055167 TCTGCACAGTTACATACCTGCAT 60.055 43.478 0.00 0.00 39.15 3.96
2830 2995 7.712639 ACAGTTACATACCTGCATATTTGAGAG 59.287 37.037 0.00 0.00 0.00 3.20
2833 2998 8.768955 GTTACATACCTGCATATTTGAGAGAAG 58.231 37.037 0.00 0.00 0.00 2.85
2834 2999 6.294473 ACATACCTGCATATTTGAGAGAAGG 58.706 40.000 0.00 0.00 0.00 3.46
2851 3018 5.730697 AGAGAAGGGGAATTCAGAATCTCTT 59.269 40.000 19.24 9.39 39.34 2.85
2878 3046 5.552178 TGTCTTCTAGGCTTTCCTTTTCTC 58.448 41.667 0.00 0.00 40.66 2.87
2890 3058 6.569418 GCTTTCCTTTTCTCAGACATTCTTCC 60.569 42.308 0.00 0.00 0.00 3.46
2899 3067 6.228995 TCTCAGACATTCTTCCATCATATGC 58.771 40.000 0.00 0.00 0.00 3.14
2926 3094 5.063186 CAGAGATATGTTCAGTTGTGCTGTC 59.937 44.000 0.00 0.00 45.23 3.51
2943 3111 0.836400 GTCCTGAGTTCTGACCCCCA 60.836 60.000 0.00 0.00 0.00 4.96
2952 3120 0.625316 TCTGACCCCCATCAACCATG 59.375 55.000 0.00 0.00 0.00 3.66
2961 3129 5.075761 ACCCCCATCAACCATGCTTATTATA 59.924 40.000 0.00 0.00 0.00 0.98
3008 3176 8.634444 TCTTACTCTTGGTCTGCTCTTATTATC 58.366 37.037 0.00 0.00 0.00 1.75
3021 3189 6.141462 GCTCTTATTATCTGTTGCAGCAATC 58.859 40.000 11.96 5.96 0.00 2.67
3030 3198 2.223782 TGTTGCAGCAATCGAAAAGCTT 60.224 40.909 11.96 0.00 36.26 3.74
3100 3268 4.396790 TGGTTTGTGTTTCTGAACCTACAC 59.603 41.667 14.06 14.06 41.59 2.90
3174 3345 6.906157 AATGAACTTCCAAGTCAACATGAT 57.094 33.333 0.00 0.00 38.57 2.45
3195 3404 2.307392 TCAAATTGATTCCGGACTCCCA 59.693 45.455 18.26 6.33 0.00 4.37
3209 3418 5.531287 CCGGACTCCCAATTTCCTTAATTAG 59.469 44.000 0.00 0.00 34.69 1.73
3365 3584 7.437713 TCCAGATTGATATGGTACTCACTTT 57.562 36.000 4.70 0.00 40.04 2.66
3380 3599 8.349983 GGTACTCACTTTCTCTCTGATATTCTC 58.650 40.741 0.00 0.00 0.00 2.87
3417 3636 0.610174 CTGCTGCTCTCACCCTACAA 59.390 55.000 0.00 0.00 0.00 2.41
3418 3637 0.321671 TGCTGCTCTCACCCTACAAC 59.678 55.000 0.00 0.00 0.00 3.32
3426 3649 4.323104 GCTCTCACCCTACAACTCAGAAAT 60.323 45.833 0.00 0.00 0.00 2.17
3500 3723 2.526077 GACTTCACGACGCATACATGA 58.474 47.619 0.00 0.00 0.00 3.07
3520 3743 3.006752 TGAAAATTCCGGCATTTCAAGCT 59.993 39.130 19.95 4.07 39.40 3.74
3629 3852 8.023021 TGCAATAATGAGGAATGTAGTAGTCT 57.977 34.615 0.00 0.00 0.00 3.24
3630 3853 7.928167 TGCAATAATGAGGAATGTAGTAGTCTG 59.072 37.037 0.00 0.00 0.00 3.51
3631 3854 7.095439 GCAATAATGAGGAATGTAGTAGTCTGC 60.095 40.741 0.00 0.00 0.00 4.26
3632 3855 5.939764 AATGAGGAATGTAGTAGTCTGCA 57.060 39.130 0.00 0.00 40.26 4.41
3633 3856 5.939764 ATGAGGAATGTAGTAGTCTGCAA 57.060 39.130 0.00 0.00 39.49 4.08
3634 3857 5.939764 TGAGGAATGTAGTAGTCTGCAAT 57.060 39.130 0.00 0.00 39.49 3.56
3663 3887 7.044798 AGAACCTCTCATAAGTCATAACTTGC 58.955 38.462 0.00 0.00 45.37 4.01
3664 3888 6.552445 ACCTCTCATAAGTCATAACTTGCT 57.448 37.500 0.00 0.00 45.37 3.91
3665 3889 6.578023 ACCTCTCATAAGTCATAACTTGCTC 58.422 40.000 0.00 0.00 45.37 4.26
3666 3890 5.988561 CCTCTCATAAGTCATAACTTGCTCC 59.011 44.000 0.00 0.00 45.37 4.70
3667 3891 5.918608 TCTCATAAGTCATAACTTGCTCCC 58.081 41.667 0.00 0.00 45.37 4.30
3669 3893 5.918608 TCATAAGTCATAACTTGCTCCCTC 58.081 41.667 0.00 0.00 45.37 4.30
3670 3894 3.636153 AAGTCATAACTTGCTCCCTCC 57.364 47.619 0.00 0.00 44.13 4.30
3671 3895 1.482593 AGTCATAACTTGCTCCCTCCG 59.517 52.381 0.00 0.00 28.74 4.63
3672 3896 1.207329 GTCATAACTTGCTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
3673 3897 1.480954 TCATAACTTGCTCCCTCCGTC 59.519 52.381 0.00 0.00 0.00 4.79
3674 3898 0.831307 ATAACTTGCTCCCTCCGTCC 59.169 55.000 0.00 0.00 0.00 4.79
3677 3901 3.003173 TTGCTCCCTCCGTCCAGG 61.003 66.667 0.00 0.00 42.97 4.45
3678 3902 3.846405 TTGCTCCCTCCGTCCAGGT 62.846 63.158 0.00 0.00 41.99 4.00
3679 3903 3.775654 GCTCCCTCCGTCCAGGTG 61.776 72.222 0.00 0.00 41.99 4.00
3680 3904 3.775654 CTCCCTCCGTCCAGGTGC 61.776 72.222 0.00 0.00 41.99 5.01
3681 3905 4.631740 TCCCTCCGTCCAGGTGCA 62.632 66.667 0.00 0.00 41.99 4.57
3682 3906 3.402681 CCCTCCGTCCAGGTGCAT 61.403 66.667 0.00 0.00 41.99 3.96
3683 3907 2.063979 CCCTCCGTCCAGGTGCATA 61.064 63.158 0.00 0.00 41.99 3.14
3685 3909 1.443407 CTCCGTCCAGGTGCATAGG 59.557 63.158 0.00 0.00 41.99 2.57
3686 3910 2.032860 CTCCGTCCAGGTGCATAGGG 62.033 65.000 0.00 0.00 41.99 3.53
3687 3911 2.203070 CGTCCAGGTGCATAGGGC 60.203 66.667 0.00 0.00 45.13 5.19
3704 3928 8.976986 GCATAGGGCATCTAATGAAAATTTAG 57.023 34.615 0.00 0.00 43.97 1.85
3705 3929 8.579863 GCATAGGGCATCTAATGAAAATTTAGT 58.420 33.333 0.00 0.00 43.97 2.24
3710 3934 9.914131 GGGCATCTAATGAAAATTTAGTATTCC 57.086 33.333 0.00 0.00 0.00 3.01
3731 3955 7.433708 TTCCAAATATATAAGTCACCATGCG 57.566 36.000 0.00 0.00 0.00 4.73
3732 3956 6.530120 TCCAAATATATAAGTCACCATGCGT 58.470 36.000 0.00 0.00 0.00 5.24
3733 3957 6.426633 TCCAAATATATAAGTCACCATGCGTG 59.573 38.462 0.00 0.00 44.50 5.34
3744 3968 2.093216 CATGCGTGGAAGAAGCTCC 58.907 57.895 0.00 0.00 35.88 4.70
3745 3969 0.392193 CATGCGTGGAAGAAGCTCCT 60.392 55.000 0.00 0.00 36.35 3.69
3746 3970 0.107945 ATGCGTGGAAGAAGCTCCTC 60.108 55.000 0.00 0.00 36.35 3.71
3758 3982 0.108207 AGCTCCTCTACATGCCATGC 59.892 55.000 4.17 0.00 0.00 4.06
3800 4025 7.589958 TCCGGCACCATGTAAATTAATATTT 57.410 32.000 0.00 0.00 37.68 1.40
3863 4091 6.456988 GGTGATTTGACGAATTGACCTGTATC 60.457 42.308 9.09 0.00 32.05 2.24
3870 4098 7.431249 TGACGAATTGACCTGTATCTATAACC 58.569 38.462 0.00 0.00 0.00 2.85
3874 4102 7.813148 CGAATTGACCTGTATCTATAACCGATT 59.187 37.037 0.00 0.00 0.00 3.34
3928 4156 3.618690 TTTTTGCGGGGGATTTATTGG 57.381 42.857 0.00 0.00 0.00 3.16
3939 4167 5.011023 GGGGGATTTATTGGTGATGTTGATC 59.989 44.000 0.00 0.00 0.00 2.92
3956 4184 2.429250 TGATCGGGTAAATTCGCTCTGA 59.571 45.455 0.00 0.00 0.00 3.27
3963 4191 3.302740 GGTAAATTCGCTCTGATTCGCAG 60.303 47.826 0.00 0.00 46.31 5.18
4098 4326 4.000331 ACAAGTGATCTGTTGGAGAGTG 58.000 45.455 11.00 0.00 32.80 3.51
4099 4327 2.740981 CAAGTGATCTGTTGGAGAGTGC 59.259 50.000 0.00 0.00 32.80 4.40
4100 4328 1.067283 AGTGATCTGTTGGAGAGTGCG 60.067 52.381 0.00 0.00 32.80 5.34
4109 4337 2.930682 GTTGGAGAGTGCGGTAGAATTC 59.069 50.000 0.00 0.00 0.00 2.17
4172 4401 4.368315 GAATCGGTTTGCCTGTTTTTCTT 58.632 39.130 0.00 0.00 0.00 2.52
4190 4419 6.867662 TTTCTTCTGAGGAGTCAAAATGTC 57.132 37.500 0.00 0.00 30.14 3.06
4192 4421 5.928976 TCTTCTGAGGAGTCAAAATGTCAA 58.071 37.500 0.00 0.00 30.14 3.18
4194 4423 6.484643 TCTTCTGAGGAGTCAAAATGTCAAAG 59.515 38.462 0.00 0.00 30.14 2.77
4195 4424 5.065914 TCTGAGGAGTCAAAATGTCAAAGG 58.934 41.667 0.00 0.00 30.14 3.11
4196 4425 3.569701 TGAGGAGTCAAAATGTCAAAGGC 59.430 43.478 0.00 0.00 0.00 4.35
4197 4426 3.823304 GAGGAGTCAAAATGTCAAAGGCT 59.177 43.478 0.00 0.00 0.00 4.58
4198 4427 4.985538 AGGAGTCAAAATGTCAAAGGCTA 58.014 39.130 0.00 0.00 0.00 3.93
4199 4428 5.574188 AGGAGTCAAAATGTCAAAGGCTAT 58.426 37.500 0.00 0.00 0.00 2.97
4202 4839 6.071952 GGAGTCAAAATGTCAAAGGCTATTCA 60.072 38.462 0.00 0.00 0.00 2.57
4205 4842 6.803807 GTCAAAATGTCAAAGGCTATTCAGTC 59.196 38.462 0.00 0.00 0.00 3.51
4240 4890 3.509967 TGCTTCTCTTCTGGTCGTCATTA 59.490 43.478 0.00 0.00 0.00 1.90
4262 4920 1.548719 TGGGAGTCGTACAATGAGGTG 59.451 52.381 0.00 0.00 0.00 4.00
4263 4921 1.134788 GGGAGTCGTACAATGAGGTGG 60.135 57.143 0.00 0.00 0.00 4.61
4276 4934 0.600255 GAGGTGGACGTGTGAACCAG 60.600 60.000 0.00 0.00 35.01 4.00
4278 4936 1.597027 GTGGACGTGTGAACCAGGG 60.597 63.158 0.00 0.00 34.21 4.45
4325 4983 7.536895 CAAAAGATTGTTTGGAACATGACAA 57.463 32.000 0.00 0.00 44.50 3.18
4342 5000 6.698329 ACATGACAATGTGAGTTCATTTGTTG 59.302 34.615 0.00 10.37 45.51 3.33
4399 5061 4.824848 GCTTCGCGTCTATGGTATTATG 57.175 45.455 5.77 0.00 0.00 1.90
4400 5062 3.060895 GCTTCGCGTCTATGGTATTATGC 59.939 47.826 5.77 0.00 0.00 3.14
4401 5063 3.926821 TCGCGTCTATGGTATTATGCA 57.073 42.857 5.77 0.00 0.00 3.96
4402 5064 3.571571 TCGCGTCTATGGTATTATGCAC 58.428 45.455 5.77 0.00 0.00 4.57
4403 5065 3.004944 TCGCGTCTATGGTATTATGCACA 59.995 43.478 5.77 0.00 0.00 4.57
4404 5066 3.926527 CGCGTCTATGGTATTATGCACAT 59.073 43.478 0.00 0.00 0.00 3.21
4405 5067 4.388773 CGCGTCTATGGTATTATGCACATT 59.611 41.667 0.00 0.00 0.00 2.71
4406 5068 5.107104 CGCGTCTATGGTATTATGCACATTT 60.107 40.000 0.00 0.00 0.00 2.32
4407 5069 6.565811 CGCGTCTATGGTATTATGCACATTTT 60.566 38.462 0.00 0.00 0.00 1.82
4408 5070 7.138736 GCGTCTATGGTATTATGCACATTTTT 58.861 34.615 0.00 0.00 0.00 1.94
4424 5086 2.279582 TTTTTCGTTGCGCCTTTCAA 57.720 40.000 4.18 0.00 0.00 2.69
4425 5087 2.279582 TTTTCGTTGCGCCTTTCAAA 57.720 40.000 4.18 0.00 0.00 2.69
4426 5088 2.279582 TTTCGTTGCGCCTTTCAAAA 57.720 40.000 4.18 0.00 0.00 2.44
4427 5089 2.279582 TTCGTTGCGCCTTTCAAAAA 57.720 40.000 4.18 0.00 0.00 1.94
4466 5128 4.918653 GCGAATTGCGAACTAAGTTTTTG 58.081 39.130 0.00 0.00 44.57 2.44
4467 5129 4.439776 GCGAATTGCGAACTAAGTTTTTGT 59.560 37.500 0.00 0.00 44.57 2.83
4468 5130 5.051973 GCGAATTGCGAACTAAGTTTTTGTT 60.052 36.000 0.00 0.00 44.57 2.83
4469 5131 6.336392 CGAATTGCGAACTAAGTTTTTGTTG 58.664 36.000 0.00 0.00 44.57 3.33
4470 5132 6.020995 CGAATTGCGAACTAAGTTTTTGTTGT 60.021 34.615 0.00 0.00 44.57 3.32
4471 5133 7.462200 CGAATTGCGAACTAAGTTTTTGTTGTT 60.462 33.333 0.00 0.00 44.57 2.83
4472 5134 6.382821 TTGCGAACTAAGTTTTTGTTGTTG 57.617 33.333 0.00 0.00 0.00 3.33
4473 5135 4.324936 TGCGAACTAAGTTTTTGTTGTTGC 59.675 37.500 0.00 0.00 0.00 4.17
4474 5136 4.561213 GCGAACTAAGTTTTTGTTGTTGCT 59.439 37.500 0.00 0.00 0.00 3.91
4475 5137 5.498542 GCGAACTAAGTTTTTGTTGTTGCTG 60.499 40.000 0.00 0.00 0.00 4.41
4476 5138 5.571357 CGAACTAAGTTTTTGTTGTTGCTGT 59.429 36.000 0.00 0.00 0.00 4.40
4477 5139 6.452350 CGAACTAAGTTTTTGTTGTTGCTGTG 60.452 38.462 0.00 0.00 0.00 3.66
4478 5140 6.019779 ACTAAGTTTTTGTTGTTGCTGTGA 57.980 33.333 0.00 0.00 0.00 3.58
4479 5141 6.630071 ACTAAGTTTTTGTTGTTGCTGTGAT 58.370 32.000 0.00 0.00 0.00 3.06
4480 5142 5.783100 AAGTTTTTGTTGTTGCTGTGATG 57.217 34.783 0.00 0.00 0.00 3.07
4481 5143 4.183101 AGTTTTTGTTGTTGCTGTGATGG 58.817 39.130 0.00 0.00 0.00 3.51
4482 5144 4.081752 AGTTTTTGTTGTTGCTGTGATGGA 60.082 37.500 0.00 0.00 0.00 3.41
4483 5145 4.462508 TTTTGTTGTTGCTGTGATGGAA 57.537 36.364 0.00 0.00 0.00 3.53
4484 5146 3.435105 TTGTTGTTGCTGTGATGGAAC 57.565 42.857 0.00 0.00 38.49 3.62
4485 5147 1.680735 TGTTGTTGCTGTGATGGAACC 59.319 47.619 0.00 0.00 37.45 3.62
4486 5148 1.680735 GTTGTTGCTGTGATGGAACCA 59.319 47.619 0.00 0.00 37.45 3.67
4487 5149 2.291209 TGTTGCTGTGATGGAACCAT 57.709 45.000 6.00 6.00 37.45 3.55
4498 5160 1.140312 TGGAACCATCCCATCTAGGC 58.860 55.000 0.00 0.00 45.95 3.93
4499 5161 1.345422 TGGAACCATCCCATCTAGGCT 60.345 52.381 0.00 0.00 45.95 4.58
4500 5162 1.777272 GGAACCATCCCATCTAGGCTT 59.223 52.381 0.00 0.00 40.10 4.35
4501 5163 2.979678 GGAACCATCCCATCTAGGCTTA 59.020 50.000 0.00 0.00 40.10 3.09
4502 5164 3.394606 GGAACCATCCCATCTAGGCTTAA 59.605 47.826 0.00 0.00 40.10 1.85
4503 5165 4.141251 GGAACCATCCCATCTAGGCTTAAA 60.141 45.833 0.00 0.00 40.10 1.52
4504 5166 5.458215 GGAACCATCCCATCTAGGCTTAAAT 60.458 44.000 0.00 0.00 40.10 1.40
4505 5167 5.248380 ACCATCCCATCTAGGCTTAAATC 57.752 43.478 0.00 0.00 35.39 2.17
4506 5168 4.916424 ACCATCCCATCTAGGCTTAAATCT 59.084 41.667 0.00 0.00 35.39 2.40
4507 5169 5.013599 ACCATCCCATCTAGGCTTAAATCTC 59.986 44.000 0.00 0.00 35.39 2.75
4508 5170 5.013495 CCATCCCATCTAGGCTTAAATCTCA 59.987 44.000 0.00 0.00 35.39 3.27
4509 5171 6.296894 CCATCCCATCTAGGCTTAAATCTCAT 60.297 42.308 0.00 0.00 35.39 2.90
4510 5172 6.770286 TCCCATCTAGGCTTAAATCTCATT 57.230 37.500 0.00 0.00 35.39 2.57
4511 5173 6.773638 TCCCATCTAGGCTTAAATCTCATTC 58.226 40.000 0.00 0.00 35.39 2.67
4512 5174 6.560304 TCCCATCTAGGCTTAAATCTCATTCT 59.440 38.462 0.00 0.00 35.39 2.40
4513 5175 7.072961 TCCCATCTAGGCTTAAATCTCATTCTT 59.927 37.037 0.00 0.00 35.39 2.52
4514 5176 7.723172 CCCATCTAGGCTTAAATCTCATTCTTT 59.277 37.037 0.00 0.00 35.39 2.52
4515 5177 8.566260 CCATCTAGGCTTAAATCTCATTCTTTG 58.434 37.037 0.00 0.00 0.00 2.77
4516 5178 8.566260 CATCTAGGCTTAAATCTCATTCTTTGG 58.434 37.037 0.00 0.00 0.00 3.28
4517 5179 5.588958 AGGCTTAAATCTCATTCTTTGGC 57.411 39.130 0.00 0.00 0.00 4.52
4518 5180 5.018809 AGGCTTAAATCTCATTCTTTGGCA 58.981 37.500 0.00 0.00 0.00 4.92
4519 5181 5.659971 AGGCTTAAATCTCATTCTTTGGCAT 59.340 36.000 0.00 0.00 0.00 4.40
4520 5182 5.751990 GGCTTAAATCTCATTCTTTGGCATG 59.248 40.000 0.00 0.00 0.00 4.06
4521 5183 6.335777 GCTTAAATCTCATTCTTTGGCATGT 58.664 36.000 0.00 0.00 0.00 3.21
4522 5184 6.255020 GCTTAAATCTCATTCTTTGGCATGTG 59.745 38.462 0.00 0.00 0.00 3.21
4523 5185 5.733620 AAATCTCATTCTTTGGCATGTGT 57.266 34.783 0.00 0.00 0.00 3.72
4524 5186 4.713824 ATCTCATTCTTTGGCATGTGTG 57.286 40.909 0.00 0.00 0.00 3.82
4540 5202 6.686130 CATGTGTGCTCATTTTTCTTCTTC 57.314 37.500 0.00 0.00 0.00 2.87
4541 5203 5.833406 TGTGTGCTCATTTTTCTTCTTCA 57.167 34.783 0.00 0.00 0.00 3.02
4542 5204 6.395426 TGTGTGCTCATTTTTCTTCTTCAT 57.605 33.333 0.00 0.00 0.00 2.57
4543 5205 6.808829 TGTGTGCTCATTTTTCTTCTTCATT 58.191 32.000 0.00 0.00 0.00 2.57
4544 5206 7.939782 TGTGTGCTCATTTTTCTTCTTCATTA 58.060 30.769 0.00 0.00 0.00 1.90
4545 5207 8.579006 TGTGTGCTCATTTTTCTTCTTCATTAT 58.421 29.630 0.00 0.00 0.00 1.28
4546 5208 9.415544 GTGTGCTCATTTTTCTTCTTCATTATT 57.584 29.630 0.00 0.00 0.00 1.40
4547 5209 9.985730 TGTGCTCATTTTTCTTCTTCATTATTT 57.014 25.926 0.00 0.00 0.00 1.40
4559 5221 8.390354 TCTTCTTCATTATTTTAGTGATGTGCG 58.610 33.333 0.00 0.00 0.00 5.34
4560 5222 7.609760 TCTTCATTATTTTAGTGATGTGCGT 57.390 32.000 0.00 0.00 0.00 5.24
4561 5223 8.039603 TCTTCATTATTTTAGTGATGTGCGTT 57.960 30.769 0.00 0.00 0.00 4.84
4562 5224 8.175069 TCTTCATTATTTTAGTGATGTGCGTTC 58.825 33.333 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.868622 AGAACCTACTTAGCTGATGTTACAG 58.131 40.000 0.00 0.00 40.43 2.74
54 55 1.402968 CATCGGCCTGAAAATGACCAG 59.597 52.381 0.00 0.00 0.00 4.00
58 59 2.198827 ACACATCGGCCTGAAAATGA 57.801 45.000 0.00 0.00 0.00 2.57
70 71 0.179174 GGGGCGCTAAAAACACATCG 60.179 55.000 7.64 0.00 0.00 3.84
135 136 9.440761 ACAGAGATCTTAGAATAGGGTAACATT 57.559 33.333 0.00 0.00 39.74 2.71
154 155 2.763448 GGGAGTACTCAGCAACAGAGAT 59.237 50.000 23.91 0.00 36.91 2.75
171 172 6.183361 GCTCTTATATTATGGGATGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
172 173 5.667626 GCTCTTATATTATGGGATGGAGGGA 59.332 44.000 0.00 0.00 0.00 4.20
173 174 5.453903 CGCTCTTATATTATGGGATGGAGGG 60.454 48.000 0.00 0.00 0.00 4.30
174 175 5.129485 ACGCTCTTATATTATGGGATGGAGG 59.871 44.000 0.00 0.00 0.00 4.30
175 176 6.227298 ACGCTCTTATATTATGGGATGGAG 57.773 41.667 0.00 0.00 0.00 3.86
176 177 6.620877 AACGCTCTTATATTATGGGATGGA 57.379 37.500 0.00 0.00 0.00 3.41
177 178 7.687941 AAAACGCTCTTATATTATGGGATGG 57.312 36.000 0.00 0.00 0.00 3.51
206 207 6.510536 AGAGCGTTTTTAACACTAGTGTAGT 58.489 36.000 28.13 16.41 44.13 2.73
207 208 7.404139 AAGAGCGTTTTTAACACTAGTGTAG 57.596 36.000 28.13 14.03 44.13 2.74
220 221 8.620416 TGCATGTCATAATATAAGAGCGTTTTT 58.380 29.630 0.00 0.00 0.00 1.94
221 222 8.153479 TGCATGTCATAATATAAGAGCGTTTT 57.847 30.769 0.00 0.00 0.00 2.43
222 223 7.728847 TGCATGTCATAATATAAGAGCGTTT 57.271 32.000 0.00 0.00 0.00 3.60
223 224 7.728847 TTGCATGTCATAATATAAGAGCGTT 57.271 32.000 0.00 0.00 0.00 4.84
224 225 7.728847 TTTGCATGTCATAATATAAGAGCGT 57.271 32.000 0.00 0.00 0.00 5.07
225 226 8.232513 ACATTTGCATGTCATAATATAAGAGCG 58.767 33.333 0.00 0.00 39.69 5.03
226 227 9.338291 CACATTTGCATGTCATAATATAAGAGC 57.662 33.333 0.00 0.00 42.14 4.09
233 234 9.518906 GACATTTCACATTTGCATGTCATAATA 57.481 29.630 14.46 0.00 42.14 0.98
234 235 8.255206 AGACATTTCACATTTGCATGTCATAAT 58.745 29.630 18.62 0.00 42.14 1.28
235 236 7.604549 AGACATTTCACATTTGCATGTCATAA 58.395 30.769 18.62 0.00 42.14 1.90
333 335 2.996631 AGTATCTTGAAGCCTTGCCAG 58.003 47.619 0.00 0.00 0.00 4.85
392 394 1.272147 GGAGGAGCATCTGGTTGGTTT 60.272 52.381 0.00 0.00 33.73 3.27
502 504 1.029947 CCGGGGGTCTTTGCATACAC 61.030 60.000 0.00 0.00 0.00 2.90
507 509 2.196997 CTCATCCGGGGGTCTTTGCA 62.197 60.000 0.00 0.00 0.00 4.08
519 521 1.325640 CAACATCGTCAAGCTCATCCG 59.674 52.381 0.00 0.00 0.00 4.18
643 645 5.426689 TGATGTCTCTTTCAGCTTACCAT 57.573 39.130 0.00 0.00 0.00 3.55
646 648 5.645497 ACCAATGATGTCTCTTTCAGCTTAC 59.355 40.000 0.00 0.00 0.00 2.34
652 654 9.685276 ATATGTTAACCAATGATGTCTCTTTCA 57.315 29.630 2.48 0.00 0.00 2.69
1117 1140 0.666577 AGAAGAACCGAACCGAAGCG 60.667 55.000 0.00 0.00 0.00 4.68
1123 1146 6.496338 AACATAATCAAGAAGAACCGAACC 57.504 37.500 0.00 0.00 0.00 3.62
1282 1308 9.645059 AATTATGATAGTCATCTACATGTTCGG 57.355 33.333 2.30 0.00 38.26 4.30
1371 1397 8.871629 ACTAAAACAAAGGGAAAACCAAAAAT 57.128 26.923 0.00 0.00 43.89 1.82
1416 1449 0.614979 AGAAGAAGGTGCCGAGGCTA 60.615 55.000 15.75 0.00 42.51 3.93
1462 1498 8.005662 TGCATTAATCATTTTTCTTGAACACG 57.994 30.769 0.00 0.00 0.00 4.49
1698 1739 4.150451 GCAAACCGGAAATGAGATGTTTTG 59.850 41.667 9.46 4.82 0.00 2.44
1779 1822 7.853437 CACATTTTACATGTAAACTGAACACGA 59.147 33.333 36.07 19.86 37.68 4.35
1988 2031 5.079643 GCATTGGGAATAGATGGGTACAAT 58.920 41.667 0.00 0.00 0.00 2.71
2007 2050 5.647658 TCAACATTCCGTAGATTTCAGCATT 59.352 36.000 0.00 0.00 0.00 3.56
2422 2573 6.664816 ACCATGGTTCATGTGATTAACAAGAT 59.335 34.615 13.00 0.00 43.61 2.40
2445 2596 2.287009 CGGAAAAGAGTGCTGAACAACC 60.287 50.000 0.00 0.00 0.00 3.77
2454 2605 3.335579 ACTATGGTTCGGAAAAGAGTGC 58.664 45.455 0.00 0.00 0.00 4.40
2455 2606 7.333423 TGAATAACTATGGTTCGGAAAAGAGTG 59.667 37.037 0.00 0.00 36.92 3.51
2464 2615 4.034048 GTGTGCTGAATAACTATGGTTCGG 59.966 45.833 0.00 0.00 36.92 4.30
2477 2629 5.086104 AGTTACCGATAAGTGTGCTGAAT 57.914 39.130 0.00 0.00 0.00 2.57
2638 2791 5.991568 ACTCGTACTCGTATGATCATTGAG 58.008 41.667 24.90 24.90 38.33 3.02
2643 2800 5.806366 TCAAACTCGTACTCGTATGATCA 57.194 39.130 0.00 0.00 38.33 2.92
2647 2804 4.607646 CGCTATCAAACTCGTACTCGTATG 59.392 45.833 0.00 0.00 38.33 2.39
2650 2807 2.417933 ACGCTATCAAACTCGTACTCGT 59.582 45.455 0.00 0.00 38.33 4.18
2651 2808 2.776765 CACGCTATCAAACTCGTACTCG 59.223 50.000 0.00 0.00 33.51 4.18
2652 2809 3.542704 CACACGCTATCAAACTCGTACTC 59.457 47.826 0.00 0.00 33.51 2.59
2666 2823 3.500299 ACAAATATTGCACACACACGCTA 59.500 39.130 0.00 0.00 0.00 4.26
2669 2826 5.912396 AGTAAACAAATATTGCACACACACG 59.088 36.000 0.00 0.00 0.00 4.49
2672 2829 7.062848 GCAAAGTAAACAAATATTGCACACAC 58.937 34.615 3.64 0.00 41.93 3.82
2679 2836 7.961325 AACCCTGCAAAGTAAACAAATATTG 57.039 32.000 0.00 0.00 0.00 1.90
2680 2837 9.483916 GTAAACCCTGCAAAGTAAACAAATATT 57.516 29.630 0.00 0.00 0.00 1.28
2811 2976 5.704515 CCCTTCTCTCAAATATGCAGGTATG 59.295 44.000 0.00 0.00 0.00 2.39
2821 2986 6.891306 TCTGAATTCCCCTTCTCTCAAATA 57.109 37.500 2.27 0.00 0.00 1.40
2830 2995 7.473735 AAAAAGAGATTCTGAATTCCCCTTC 57.526 36.000 4.11 0.00 0.00 3.46
2851 3018 7.342026 AGAAAAGGAAAGCCTAGAAGACAAAAA 59.658 33.333 0.00 0.00 46.28 1.94
2856 3023 5.552178 TGAGAAAAGGAAAGCCTAGAAGAC 58.448 41.667 0.00 0.00 46.28 3.01
2865 3032 5.956068 AGAATGTCTGAGAAAAGGAAAGC 57.044 39.130 0.00 0.00 0.00 3.51
2869 3036 5.567037 TGGAAGAATGTCTGAGAAAAGGA 57.433 39.130 0.00 0.00 0.00 3.36
2871 3038 7.627298 ATGATGGAAGAATGTCTGAGAAAAG 57.373 36.000 0.00 0.00 0.00 2.27
2878 3046 4.992951 TCGCATATGATGGAAGAATGTCTG 59.007 41.667 6.97 0.00 0.00 3.51
2890 3058 6.810182 TGAACATATCTCTGTCGCATATGATG 59.190 38.462 6.97 0.00 35.09 3.07
2899 3067 4.032217 GCACAACTGAACATATCTCTGTCG 59.968 45.833 0.00 0.00 0.00 4.35
2926 3094 0.543749 GATGGGGGTCAGAACTCAGG 59.456 60.000 0.00 0.00 0.00 3.86
2943 3111 9.578576 ACTGAACATATAATAAGCATGGTTGAT 57.421 29.630 20.13 12.33 0.00 2.57
3008 3176 1.717645 GCTTTTCGATTGCTGCAACAG 59.282 47.619 18.51 14.25 34.12 3.16
3021 3189 3.922240 CACATCCATCCAAAAGCTTTTCG 59.078 43.478 21.45 15.53 0.00 3.46
3030 3198 2.583024 TGCTGTCACATCCATCCAAA 57.417 45.000 0.00 0.00 0.00 3.28
3100 3268 7.425577 TCAAACATGTATCAGTGAAGAAGTG 57.574 36.000 0.00 0.00 0.00 3.16
3174 3345 2.307392 TGGGAGTCCGGAATCAATTTGA 59.693 45.455 30.98 6.91 35.24 2.69
3209 3418 9.599322 GCACATTTAGTAATAATAGTGACATGC 57.401 33.333 15.23 5.00 0.00 4.06
3365 3584 6.535963 TTTGCACAGAGAATATCAGAGAGA 57.464 37.500 0.00 0.00 0.00 3.10
3380 3599 5.061808 GCAGCAGAAATCTTAATTTGCACAG 59.938 40.000 0.00 0.00 35.21 3.66
3417 3636 3.554934 TGTTGCTGTTGGATTTCTGAGT 58.445 40.909 0.00 0.00 0.00 3.41
3418 3637 4.543692 CTTGTTGCTGTTGGATTTCTGAG 58.456 43.478 0.00 0.00 0.00 3.35
3454 3677 5.416271 ACAATATTGGGTACTTCGTCTGT 57.584 39.130 19.37 0.00 0.00 3.41
3493 3716 6.219417 TGAAATGCCGGAATTTTCATGTAT 57.781 33.333 21.68 0.00 35.16 2.29
3500 3723 3.328505 CAGCTTGAAATGCCGGAATTTT 58.671 40.909 21.68 9.01 37.80 1.82
3520 3743 1.001764 CTGATTCTGGGGCAGTGCA 60.002 57.895 18.61 0.00 32.61 4.57
3603 3826 8.654997 AGACTACTACATTCCTCATTATTGCAT 58.345 33.333 0.00 0.00 0.00 3.96
3604 3827 7.928167 CAGACTACTACATTCCTCATTATTGCA 59.072 37.037 0.00 0.00 0.00 4.08
3605 3828 7.095439 GCAGACTACTACATTCCTCATTATTGC 60.095 40.741 0.00 0.00 0.00 3.56
3625 3848 4.202398 TGAGAGGTTCTTCAATTGCAGACT 60.202 41.667 7.34 2.81 0.00 3.24
3626 3849 4.067896 TGAGAGGTTCTTCAATTGCAGAC 58.932 43.478 7.34 3.70 0.00 3.51
3627 3850 4.356405 TGAGAGGTTCTTCAATTGCAGA 57.644 40.909 3.48 3.48 0.00 4.26
3629 3852 6.240894 ACTTATGAGAGGTTCTTCAATTGCA 58.759 36.000 0.00 0.00 0.00 4.08
3630 3853 6.372659 TGACTTATGAGAGGTTCTTCAATTGC 59.627 38.462 0.00 0.00 0.00 3.56
3631 3854 7.912056 TGACTTATGAGAGGTTCTTCAATTG 57.088 36.000 0.00 0.00 0.00 2.32
3633 3856 9.606631 GTTATGACTTATGAGAGGTTCTTCAAT 57.393 33.333 0.00 0.00 0.00 2.57
3634 3857 8.816894 AGTTATGACTTATGAGAGGTTCTTCAA 58.183 33.333 0.00 0.00 29.87 2.69
3663 3887 3.775654 GCACCTGGACGGAGGGAG 61.776 72.222 0.00 0.00 37.45 4.30
3664 3888 2.523740 TATGCACCTGGACGGAGGGA 62.524 60.000 0.00 0.00 37.45 4.20
3665 3889 2.032860 CTATGCACCTGGACGGAGGG 62.033 65.000 0.00 0.00 37.45 4.30
3666 3890 1.443407 CTATGCACCTGGACGGAGG 59.557 63.158 0.00 0.00 39.28 4.30
3667 3891 1.443407 CCTATGCACCTGGACGGAG 59.557 63.158 0.00 0.00 36.31 4.63
3669 3893 2.505982 CCCTATGCACCTGGACGG 59.494 66.667 0.00 0.00 39.35 4.79
3670 3894 2.203070 GCCCTATGCACCTGGACG 60.203 66.667 0.00 0.00 40.77 4.79
3679 3903 8.579863 ACTAAATTTTCATTAGATGCCCTATGC 58.420 33.333 0.00 0.00 36.07 3.14
3705 3929 9.161629 CGCATGGTGACTTATATATTTGGAATA 57.838 33.333 0.00 0.00 0.00 1.75
3707 3931 6.995686 ACGCATGGTGACTTATATATTTGGAA 59.004 34.615 0.00 0.00 0.00 3.53
3708 3932 6.530120 ACGCATGGTGACTTATATATTTGGA 58.470 36.000 0.00 0.00 0.00 3.53
3726 3950 0.392193 AGGAGCTTCTTCCACGCATG 60.392 55.000 0.00 0.00 39.84 4.06
3727 3951 0.107945 GAGGAGCTTCTTCCACGCAT 60.108 55.000 0.00 0.00 39.84 4.73
3728 3952 1.188219 AGAGGAGCTTCTTCCACGCA 61.188 55.000 0.00 0.00 39.84 5.24
3729 3953 0.818296 TAGAGGAGCTTCTTCCACGC 59.182 55.000 0.00 0.00 39.84 5.34
3730 3954 1.819288 TGTAGAGGAGCTTCTTCCACG 59.181 52.381 0.00 0.00 39.84 4.94
3731 3955 3.791245 CATGTAGAGGAGCTTCTTCCAC 58.209 50.000 0.00 0.00 39.84 4.02
3732 3956 2.169352 GCATGTAGAGGAGCTTCTTCCA 59.831 50.000 0.00 0.00 39.84 3.53
3733 3957 2.484594 GGCATGTAGAGGAGCTTCTTCC 60.485 54.545 0.00 0.00 37.52 3.46
3734 3958 2.169352 TGGCATGTAGAGGAGCTTCTTC 59.831 50.000 0.00 0.00 0.00 2.87
3735 3959 2.191400 TGGCATGTAGAGGAGCTTCTT 58.809 47.619 0.00 0.00 0.00 2.52
3736 3960 1.871418 TGGCATGTAGAGGAGCTTCT 58.129 50.000 0.00 0.00 0.00 2.85
3737 3961 2.492012 CATGGCATGTAGAGGAGCTTC 58.508 52.381 19.32 0.00 0.00 3.86
3738 3962 1.476471 GCATGGCATGTAGAGGAGCTT 60.476 52.381 26.94 0.00 0.00 3.74
3739 3963 0.108207 GCATGGCATGTAGAGGAGCT 59.892 55.000 26.94 0.00 0.00 4.09
3740 3964 0.888285 GGCATGGCATGTAGAGGAGC 60.888 60.000 26.94 11.10 0.00 4.70
3741 3965 0.602106 CGGCATGGCATGTAGAGGAG 60.602 60.000 26.94 8.51 0.00 3.69
3742 3966 1.048160 TCGGCATGGCATGTAGAGGA 61.048 55.000 26.94 14.60 0.00 3.71
3743 3967 0.602106 CTCGGCATGGCATGTAGAGG 60.602 60.000 29.60 18.86 34.59 3.69
3744 3968 1.226686 GCTCGGCATGGCATGTAGAG 61.227 60.000 31.30 31.30 38.23 2.43
3745 3969 1.227645 GCTCGGCATGGCATGTAGA 60.228 57.895 26.94 22.99 0.00 2.59
3746 3970 1.227764 AGCTCGGCATGGCATGTAG 60.228 57.895 26.94 21.26 0.00 2.74
3863 4091 8.894768 AATCCAAGAGAGAAAATCGGTTATAG 57.105 34.615 0.00 0.00 0.00 1.31
3874 4102 8.730680 GCAGTAAATACAAATCCAAGAGAGAAA 58.269 33.333 0.00 0.00 0.00 2.52
3928 4156 4.785341 GCGAATTTACCCGATCAACATCAC 60.785 45.833 0.00 0.00 0.00 3.06
3939 4167 2.218759 CGAATCAGAGCGAATTTACCCG 59.781 50.000 0.00 0.00 0.00 5.28
4098 4326 2.222819 CGTTTCTGCAGAATTCTACCGC 60.223 50.000 28.89 8.45 33.54 5.68
4099 4327 3.250744 TCGTTTCTGCAGAATTCTACCG 58.749 45.455 28.89 21.14 33.54 4.02
4100 4328 5.607119 TTTCGTTTCTGCAGAATTCTACC 57.393 39.130 28.89 12.00 33.54 3.18
4109 4337 0.109132 GGGCCATTTCGTTTCTGCAG 60.109 55.000 7.63 7.63 0.00 4.41
4140 4369 2.223409 GCAAACCGATTCCCCGATTAAC 60.223 50.000 0.00 0.00 0.00 2.01
4172 4401 5.065914 CCTTTGACATTTTGACTCCTCAGA 58.934 41.667 0.00 0.00 0.00 3.27
4190 4419 2.691409 TCGGGACTGAATAGCCTTTG 57.309 50.000 0.00 0.00 0.00 2.77
4192 4421 1.202698 GCATCGGGACTGAATAGCCTT 60.203 52.381 0.00 0.00 0.00 4.35
4194 4423 0.106708 TGCATCGGGACTGAATAGCC 59.893 55.000 0.00 0.00 0.00 3.93
4195 4424 1.802960 CATGCATCGGGACTGAATAGC 59.197 52.381 0.00 0.00 0.00 2.97
4196 4425 3.117491 ACATGCATCGGGACTGAATAG 57.883 47.619 0.00 0.00 0.00 1.73
4197 4426 3.558931 AACATGCATCGGGACTGAATA 57.441 42.857 0.00 0.00 0.00 1.75
4198 4427 2.424601 CAAACATGCATCGGGACTGAAT 59.575 45.455 0.00 0.00 0.00 2.57
4199 4428 1.811965 CAAACATGCATCGGGACTGAA 59.188 47.619 0.00 0.00 0.00 3.02
4202 4839 0.322816 AGCAAACATGCATCGGGACT 60.323 50.000 0.00 0.00 37.25 3.85
4205 4842 0.813184 AGAAGCAAACATGCATCGGG 59.187 50.000 0.00 0.00 37.56 5.14
4240 4890 1.825474 CCTCATTGTACGACTCCCACT 59.175 52.381 0.00 0.00 0.00 4.00
4262 4920 2.032071 CCCCTGGTTCACACGTCC 59.968 66.667 0.00 0.00 0.00 4.79
4263 4921 2.668550 GCCCCTGGTTCACACGTC 60.669 66.667 0.00 0.00 0.00 4.34
4276 4934 1.673337 GTACGTTTCACCCAGCCCC 60.673 63.158 0.00 0.00 0.00 5.80
4278 4936 0.533308 TGTGTACGTTTCACCCAGCC 60.533 55.000 16.82 0.00 35.25 4.85
4289 4947 3.625764 ACAATCTTTTGTGCTGTGTACGT 59.374 39.130 0.00 0.00 44.36 3.57
4298 4956 5.523188 TCATGTTCCAAACAATCTTTTGTGC 59.477 36.000 0.00 0.00 45.30 4.57
4325 4983 5.532406 AGTGCTACAACAAATGAACTCACAT 59.468 36.000 0.00 0.00 0.00 3.21
4342 5000 5.302059 TCAGATATAACCAGTGGAGTGCTAC 59.698 44.000 18.40 1.65 0.00 3.58
4405 5067 2.279582 TTGAAAGGCGCAACGAAAAA 57.720 40.000 10.83 0.00 0.00 1.94
4406 5068 2.279582 TTTGAAAGGCGCAACGAAAA 57.720 40.000 10.83 0.77 0.00 2.29
4407 5069 2.279582 TTTTGAAAGGCGCAACGAAA 57.720 40.000 10.83 6.70 0.00 3.46
4408 5070 2.279582 TTTTTGAAAGGCGCAACGAA 57.720 40.000 10.83 0.17 0.00 3.85
4430 5092 4.550639 CGCAATTCGCTTTTGCTTCTTTTT 60.551 37.500 12.68 0.00 45.67 1.94
4431 5093 3.060339 CGCAATTCGCTTTTGCTTCTTTT 60.060 39.130 12.68 0.00 45.67 2.27
4432 5094 2.472488 CGCAATTCGCTTTTGCTTCTTT 59.528 40.909 12.68 0.00 45.67 2.52
4433 5095 2.053627 CGCAATTCGCTTTTGCTTCTT 58.946 42.857 12.68 0.00 45.67 2.52
4434 5096 1.266718 TCGCAATTCGCTTTTGCTTCT 59.733 42.857 12.68 0.00 45.67 2.85
4435 5097 1.685302 TCGCAATTCGCTTTTGCTTC 58.315 45.000 12.68 0.00 45.67 3.86
4436 5098 1.786579 GTTCGCAATTCGCTTTTGCTT 59.213 42.857 12.68 0.00 45.67 3.91
4437 5099 1.001378 AGTTCGCAATTCGCTTTTGCT 60.001 42.857 12.68 0.00 45.67 3.91
4438 5100 1.408422 AGTTCGCAATTCGCTTTTGC 58.592 45.000 6.70 6.70 44.68 3.68
4439 5101 4.219033 ACTTAGTTCGCAATTCGCTTTTG 58.781 39.130 0.00 0.00 39.08 2.44
4440 5102 4.483476 ACTTAGTTCGCAATTCGCTTTT 57.517 36.364 0.00 0.00 39.08 2.27
4441 5103 4.483476 AACTTAGTTCGCAATTCGCTTT 57.517 36.364 0.00 0.00 39.08 3.51
4442 5104 4.483476 AAACTTAGTTCGCAATTCGCTT 57.517 36.364 0.00 0.00 39.08 4.68
4443 5105 4.483476 AAAACTTAGTTCGCAATTCGCT 57.517 36.364 0.00 0.00 39.08 4.93
4444 5106 4.439776 ACAAAAACTTAGTTCGCAATTCGC 59.560 37.500 0.00 0.00 38.27 4.70
4445 5107 6.020995 ACAACAAAAACTTAGTTCGCAATTCG 60.021 34.615 0.00 0.00 40.15 3.34
4446 5108 7.216920 ACAACAAAAACTTAGTTCGCAATTC 57.783 32.000 0.00 0.00 0.00 2.17
4447 5109 7.452231 CAACAACAAAAACTTAGTTCGCAATT 58.548 30.769 0.00 0.00 0.00 2.32
4448 5110 6.454981 GCAACAACAAAAACTTAGTTCGCAAT 60.455 34.615 0.00 0.00 0.00 3.56
4449 5111 5.164041 GCAACAACAAAAACTTAGTTCGCAA 60.164 36.000 0.00 0.00 0.00 4.85
4450 5112 4.324936 GCAACAACAAAAACTTAGTTCGCA 59.675 37.500 0.00 0.00 0.00 5.10
4451 5113 4.561213 AGCAACAACAAAAACTTAGTTCGC 59.439 37.500 0.00 0.00 0.00 4.70
4452 5114 5.571357 ACAGCAACAACAAAAACTTAGTTCG 59.429 36.000 0.00 0.00 0.00 3.95
4453 5115 6.584563 TCACAGCAACAACAAAAACTTAGTTC 59.415 34.615 0.00 0.00 0.00 3.01
4454 5116 6.451393 TCACAGCAACAACAAAAACTTAGTT 58.549 32.000 0.00 0.00 0.00 2.24
4455 5117 6.019779 TCACAGCAACAACAAAAACTTAGT 57.980 33.333 0.00 0.00 0.00 2.24
4456 5118 6.019640 CCATCACAGCAACAACAAAAACTTAG 60.020 38.462 0.00 0.00 0.00 2.18
4457 5119 5.809562 CCATCACAGCAACAACAAAAACTTA 59.190 36.000 0.00 0.00 0.00 2.24
4458 5120 4.630940 CCATCACAGCAACAACAAAAACTT 59.369 37.500 0.00 0.00 0.00 2.66
4459 5121 4.081752 TCCATCACAGCAACAACAAAAACT 60.082 37.500 0.00 0.00 0.00 2.66
4460 5122 4.180057 TCCATCACAGCAACAACAAAAAC 58.820 39.130 0.00 0.00 0.00 2.43
4461 5123 4.462508 TCCATCACAGCAACAACAAAAA 57.537 36.364 0.00 0.00 0.00 1.94
4462 5124 4.180057 GTTCCATCACAGCAACAACAAAA 58.820 39.130 0.00 0.00 0.00 2.44
4463 5125 3.430098 GGTTCCATCACAGCAACAACAAA 60.430 43.478 0.00 0.00 0.00 2.83
4464 5126 2.100584 GGTTCCATCACAGCAACAACAA 59.899 45.455 0.00 0.00 0.00 2.83
4465 5127 1.680735 GGTTCCATCACAGCAACAACA 59.319 47.619 0.00 0.00 0.00 3.33
4466 5128 1.680735 TGGTTCCATCACAGCAACAAC 59.319 47.619 0.00 0.00 0.00 3.32
4467 5129 2.064434 TGGTTCCATCACAGCAACAA 57.936 45.000 0.00 0.00 0.00 2.83
4468 5130 2.161855 GATGGTTCCATCACAGCAACA 58.838 47.619 22.34 0.00 41.60 3.33
4469 5131 1.474077 GGATGGTTCCATCACAGCAAC 59.526 52.381 26.50 9.33 43.20 4.17
4470 5132 1.616725 GGGATGGTTCCATCACAGCAA 60.617 52.381 26.50 0.00 44.00 3.91
4471 5133 0.034186 GGGATGGTTCCATCACAGCA 60.034 55.000 26.50 0.00 44.00 4.41
4472 5134 2.799176 GGGATGGTTCCATCACAGC 58.201 57.895 26.50 13.29 44.00 4.40
4478 5140 1.707427 GCCTAGATGGGATGGTTCCAT 59.293 52.381 3.80 3.80 46.73 3.41
4479 5141 1.140312 GCCTAGATGGGATGGTTCCA 58.860 55.000 0.00 0.00 44.60 3.53
4480 5142 1.439543 AGCCTAGATGGGATGGTTCC 58.560 55.000 0.00 0.00 41.77 3.62
4481 5143 4.706842 TTAAGCCTAGATGGGATGGTTC 57.293 45.455 0.00 0.00 36.00 3.62
4482 5144 5.373854 AGATTTAAGCCTAGATGGGATGGTT 59.626 40.000 0.00 0.00 36.00 3.67
4483 5145 4.916424 AGATTTAAGCCTAGATGGGATGGT 59.084 41.667 0.00 0.00 36.00 3.55
4484 5146 5.013495 TGAGATTTAAGCCTAGATGGGATGG 59.987 44.000 0.00 0.00 36.00 3.51
4485 5147 6.119240 TGAGATTTAAGCCTAGATGGGATG 57.881 41.667 0.00 0.00 36.00 3.51
4486 5148 6.966637 ATGAGATTTAAGCCTAGATGGGAT 57.033 37.500 0.00 0.00 36.00 3.85
4487 5149 6.560304 AGAATGAGATTTAAGCCTAGATGGGA 59.440 38.462 0.00 0.00 36.00 4.37
4488 5150 6.777782 AGAATGAGATTTAAGCCTAGATGGG 58.222 40.000 0.00 0.00 36.00 4.00
4489 5151 8.566260 CAAAGAATGAGATTTAAGCCTAGATGG 58.434 37.037 0.00 0.00 39.35 3.51
4490 5152 8.566260 CCAAAGAATGAGATTTAAGCCTAGATG 58.434 37.037 0.00 0.00 0.00 2.90
4491 5153 7.230309 GCCAAAGAATGAGATTTAAGCCTAGAT 59.770 37.037 0.00 0.00 0.00 1.98
4492 5154 6.543831 GCCAAAGAATGAGATTTAAGCCTAGA 59.456 38.462 0.00 0.00 0.00 2.43
4493 5155 6.319658 TGCCAAAGAATGAGATTTAAGCCTAG 59.680 38.462 0.00 0.00 0.00 3.02
4494 5156 6.186957 TGCCAAAGAATGAGATTTAAGCCTA 58.813 36.000 0.00 0.00 0.00 3.93
4495 5157 5.018809 TGCCAAAGAATGAGATTTAAGCCT 58.981 37.500 0.00 0.00 0.00 4.58
4496 5158 5.329035 TGCCAAAGAATGAGATTTAAGCC 57.671 39.130 0.00 0.00 0.00 4.35
4497 5159 6.255020 CACATGCCAAAGAATGAGATTTAAGC 59.745 38.462 0.00 0.00 0.00 3.09
4498 5160 7.274904 CACACATGCCAAAGAATGAGATTTAAG 59.725 37.037 0.00 0.00 0.00 1.85
4499 5161 7.092079 CACACATGCCAAAGAATGAGATTTAA 58.908 34.615 0.00 0.00 0.00 1.52
4500 5162 6.623486 CACACATGCCAAAGAATGAGATTTA 58.377 36.000 0.00 0.00 0.00 1.40
4501 5163 5.475719 CACACATGCCAAAGAATGAGATTT 58.524 37.500 0.00 0.00 0.00 2.17
4502 5164 4.619863 GCACACATGCCAAAGAATGAGATT 60.620 41.667 0.00 0.00 46.97 2.40
4503 5165 3.119245 GCACACATGCCAAAGAATGAGAT 60.119 43.478 0.00 0.00 46.97 2.75
4504 5166 2.229543 GCACACATGCCAAAGAATGAGA 59.770 45.455 0.00 0.00 46.97 3.27
4505 5167 2.602878 GCACACATGCCAAAGAATGAG 58.397 47.619 0.00 0.00 46.97 2.90
4506 5168 2.728690 GCACACATGCCAAAGAATGA 57.271 45.000 0.00 0.00 46.97 2.57
4517 5179 6.210796 TGAAGAAGAAAAATGAGCACACATG 58.789 36.000 0.00 0.00 0.00 3.21
4518 5180 6.395426 TGAAGAAGAAAAATGAGCACACAT 57.605 33.333 0.00 0.00 0.00 3.21
4519 5181 5.833406 TGAAGAAGAAAAATGAGCACACA 57.167 34.783 0.00 0.00 0.00 3.72
4520 5182 8.976986 ATAATGAAGAAGAAAAATGAGCACAC 57.023 30.769 0.00 0.00 0.00 3.82
4521 5183 9.985730 AAATAATGAAGAAGAAAAATGAGCACA 57.014 25.926 0.00 0.00 0.00 4.57
4533 5195 8.390354 CGCACATCACTAAAATAATGAAGAAGA 58.610 33.333 0.00 0.00 0.00 2.87
4534 5196 8.177663 ACGCACATCACTAAAATAATGAAGAAG 58.822 33.333 0.00 0.00 0.00 2.85
4535 5197 8.039603 ACGCACATCACTAAAATAATGAAGAA 57.960 30.769 0.00 0.00 0.00 2.52
4536 5198 7.609760 ACGCACATCACTAAAATAATGAAGA 57.390 32.000 0.00 0.00 0.00 2.87
4537 5199 8.315554 GAACGCACATCACTAAAATAATGAAG 57.684 34.615 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.