Multiple sequence alignment - TraesCS2D01G331600

Loading Multiple Alignment...

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 TraesCS2D01G331600 chr2D 100.000 9807 0 0 1 9807 424007875 423998069 0.000000e+00 18111.0
1 TraesCS2D01G331600 chr2D 98.550 5449 51 7 1851 7275 330748861 330743417 0.000000e+00 9600.0
2 TraesCS2D01G331600 chr2D 98.259 5456 62 8 1850 7275 608394740 608389288 0.000000e+00 9518.0
3 TraesCS2D01G331600 chr6D 98.532 5450 49 7 1851 7278 65404643 65399203 0.000000e+00 9592.0
4 TraesCS2D01G331600 chr6D 98.477 5450 53 11 1851 7275 202469389 202463945 0.000000e+00 9577.0
5 TraesCS2D01G331600 chr6D 98.264 3572 37 6 1850 5399 218401468 218397900 0.000000e+00 6229.0
6 TraesCS2D01G331600 chr4D 98.477 5451 53 7 1851 7276 395951942 395957387 0.000000e+00 9579.0
7 TraesCS2D01G331600 chr4D 98.330 5450 65 6 1848 7275 301744835 301739390 0.000000e+00 9537.0
8 TraesCS2D01G331600 chr4D 97.999 5397 61 12 1850 7214 61138754 61133373 0.000000e+00 9324.0
9 TraesCS2D01G331600 chr3D 98.294 5451 64 11 1851 7276 526474705 526480151 0.000000e+00 9524.0
10 TraesCS2D01G331600 chr3D 98.256 5447 61 11 1851 7275 538893483 538888049 0.000000e+00 9502.0
11 TraesCS2D01G331600 chr3D 98.023 4199 36 10 1851 6014 422546420 422542234 0.000000e+00 7251.0
12 TraesCS2D01G331600 chr3D 97.711 2446 22 9 1848 4271 540264058 540266491 0.000000e+00 4176.0
13 TraesCS2D01G331600 chr1D 98.224 5461 68 8 1846 7280 79103110 79097653 0.000000e+00 9520.0
14 TraesCS2D01G331600 chr1D 100.000 28 0 0 9780 9807 292178424 292178451 1.800000e-02 52.8
15 TraesCS2D01G331600 chr5D 98.242 5460 53 12 1847 7280 135063149 135068591 0.000000e+00 9511.0
16 TraesCS2D01G331600 chr5D 98.457 5186 53 6 1838 6998 443317048 443322231 0.000000e+00 9108.0
17 TraesCS2D01G331600 chr7D 98.186 5457 58 13 1847 7280 101514713 101520151 0.000000e+00 9491.0
18 TraesCS2D01G331600 chr7D 98.164 5447 64 7 1851 7275 444277279 444282711 0.000000e+00 9472.0
19 TraesCS2D01G331600 chr7D 98.018 5450 55 7 1851 7275 274871667 274866246 0.000000e+00 9417.0
20 TraesCS2D01G331600 chr2B 94.919 2027 64 22 7276 9273 497877586 497875570 0.000000e+00 3136.0
21 TraesCS2D01G331600 chr2B 88.226 1877 114 57 3 1857 497879366 497877575 0.000000e+00 2143.0
22 TraesCS2D01G331600 chr2B 86.082 388 38 10 9276 9649 497875535 497875150 4.270000e-108 403.0
23 TraesCS2D01G331600 chr2A 90.389 2414 155 34 7322 9663 564265091 564267499 0.000000e+00 3101.0
24 TraesCS2D01G331600 chr2A 94.032 620 22 10 87 703 564263298 564263905 0.000000e+00 926.0
25 TraesCS2D01G331600 chr2A 89.351 601 44 9 748 1333 564263906 564264501 0.000000e+00 737.0
26 TraesCS2D01G331600 chr2A 91.549 142 9 2 1643 1783 564264703 564264842 1.010000e-44 193.0
27 TraesCS2D01G331600 chr2A 83.636 220 14 7 1372 1585 564264501 564264704 4.680000e-43 187.0
28 TraesCS2D01G331600 chr2A 86.000 100 4 2 3 102 564262536 564262625 2.250000e-16 99.0
29 TraesCS2D01G331600 chr2A 97.500 40 0 1 1809 1848 564264907 564264945 6.360000e-07 67.6
30 TraesCS2D01G331600 chr2A 100.000 30 0 0 9778 9807 147994062 147994033 1.000000e-03 56.5
31 TraesCS2D01G331600 chr4A 100.000 28 0 0 9780 9807 631293744 631293717 1.800000e-02 52.8


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 TraesCS2D01G331600 chr2D 423998069 424007875 9806 True 18111.000000 18111 100.000000 1 9807 1 chr2D.!!$R2 9806
1 TraesCS2D01G331600 chr2D 330743417 330748861 5444 True 9600.000000 9600 98.550000 1851 7275 1 chr2D.!!$R1 5424
2 TraesCS2D01G331600 chr2D 608389288 608394740 5452 True 9518.000000 9518 98.259000 1850 7275 1 chr2D.!!$R3 5425
3 TraesCS2D01G331600 chr6D 65399203 65404643 5440 True 9592.000000 9592 98.532000 1851 7278 1 chr6D.!!$R1 5427
4 TraesCS2D01G331600 chr6D 202463945 202469389 5444 True 9577.000000 9577 98.477000 1851 7275 1 chr6D.!!$R2 5424
5 TraesCS2D01G331600 chr6D 218397900 218401468 3568 True 6229.000000 6229 98.264000 1850 5399 1 chr6D.!!$R3 3549
6 TraesCS2D01G331600 chr4D 395951942 395957387 5445 False 9579.000000 9579 98.477000 1851 7276 1 chr4D.!!$F1 5425
7 TraesCS2D01G331600 chr4D 301739390 301744835 5445 True 9537.000000 9537 98.330000 1848 7275 1 chr4D.!!$R2 5427
8 TraesCS2D01G331600 chr4D 61133373 61138754 5381 True 9324.000000 9324 97.999000 1850 7214 1 chr4D.!!$R1 5364
9 TraesCS2D01G331600 chr3D 526474705 526480151 5446 False 9524.000000 9524 98.294000 1851 7276 1 chr3D.!!$F1 5425
10 TraesCS2D01G331600 chr3D 538888049 538893483 5434 True 9502.000000 9502 98.256000 1851 7275 1 chr3D.!!$R2 5424
11 TraesCS2D01G331600 chr3D 422542234 422546420 4186 True 7251.000000 7251 98.023000 1851 6014 1 chr3D.!!$R1 4163
12 TraesCS2D01G331600 chr3D 540264058 540266491 2433 False 4176.000000 4176 97.711000 1848 4271 1 chr3D.!!$F2 2423
13 TraesCS2D01G331600 chr1D 79097653 79103110 5457 True 9520.000000 9520 98.224000 1846 7280 1 chr1D.!!$R1 5434
14 TraesCS2D01G331600 chr5D 135063149 135068591 5442 False 9511.000000 9511 98.242000 1847 7280 1 chr5D.!!$F1 5433
15 TraesCS2D01G331600 chr5D 443317048 443322231 5183 False 9108.000000 9108 98.457000 1838 6998 1 chr5D.!!$F2 5160
16 TraesCS2D01G331600 chr7D 101514713 101520151 5438 False 9491.000000 9491 98.186000 1847 7280 1 chr7D.!!$F1 5433
17 TraesCS2D01G331600 chr7D 444277279 444282711 5432 False 9472.000000 9472 98.164000 1851 7275 1 chr7D.!!$F2 5424
18 TraesCS2D01G331600 chr7D 274866246 274871667 5421 True 9417.000000 9417 98.018000 1851 7275 1 chr7D.!!$R1 5424
19 TraesCS2D01G331600 chr2B 497875150 497879366 4216 True 1894.000000 3136 89.742333 3 9649 3 chr2B.!!$R1 9646
20 TraesCS2D01G331600 chr2A 564262536 564267499 4963 False 758.657143 3101 90.351000 3 9663 7 chr2A.!!$F1 9660

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
213 902 0.160182 CGCACTTTAACGACCGTGAC 59.840 55.000 0.00 0.00 0.00 3.67 F
381 1071 1.228737 GGATCTCTCCTCCCTCCGG 60.229 68.421 0.00 0.00 38.65 5.14 F
1385 2109 1.415374 GCAGCTGCACTTGACAATTG 58.585 50.000 33.36 3.24 41.59 2.32 F
1650 2385 1.483415 TGCTCTGATGTGCTAGCATGA 59.517 47.619 22.51 11.37 39.92 3.07 F
1752 2488 2.342406 TGGGAGGACCTTGAGATGAA 57.658 50.000 0.00 0.00 41.11 2.57 F
2453 3232 2.991190 GGATGCTGCTGAACAACAAATG 59.009 45.455 0.00 0.00 0.00 2.32 F
2704 3504 3.425659 TCTATGCATATCGGAGAGCACT 58.574 45.455 6.92 0.00 43.63 4.40 F
4392 5230 1.084370 CCCTACTCGCGCCAAAGAAG 61.084 60.000 0.00 0.00 0.00 2.85 F
5893 6754 0.770499 TGTTCCTGTTGCTCCATGGA 59.230 50.000 15.27 15.27 0.00 3.41 F
7203 8065 1.934463 AGCACGTTGAAGCTGTTCG 59.066 52.632 0.00 0.00 40.13 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 2141 0.388907 ATTGCCAGATGCGTGCAAAC 60.389 50.000 6.28 0.0 46.82 2.93 R
1478 2212 1.541588 GCAGAACCATTTTCTCGCCTT 59.458 47.619 0.00 0.0 0.00 4.35 R
2687 3487 1.402787 TGAGTGCTCTCCGATATGCA 58.597 50.000 13.00 0.0 39.75 3.96 R
3335 4161 2.627699 GGATGGGCTGTTTTGTCTTTGA 59.372 45.455 0.00 0.0 0.00 2.69 R
3951 4788 6.777091 TGATCCTTCTCTTGTTCCAAATGAAA 59.223 34.615 0.00 0.0 33.94 2.69 R
4392 5230 0.820891 ACATGCGCCAAGATCCATCC 60.821 55.000 4.18 0.0 0.00 3.51 R
4578 5416 2.586425 CCTTCCTTTGTCTTGAAGGCA 58.414 47.619 0.00 0.0 46.13 4.75 R
6368 7229 2.358737 GCTTCACCAGGTCCACCG 60.359 66.667 0.00 0.0 42.08 4.94 R
7610 8576 0.685097 TCCTCTTTTGGGGAGTCACG 59.315 55.000 0.00 0.0 46.01 4.35 R
9357 10388 0.668401 GCCTGTTGGTTGCAATGAGC 60.668 55.000 0.59 0.0 38.72 4.26 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
56 57 3.822607 TTTTTGTGCACGGCAGTTT 57.177 42.105 13.13 0.00 40.08 2.66
57 58 2.086054 TTTTTGTGCACGGCAGTTTT 57.914 40.000 13.13 0.00 40.08 2.43
121 810 3.131396 GAGGAAAGAAGAAGCACGAACA 58.869 45.455 0.00 0.00 0.00 3.18
140 829 3.654201 TGCAAGGTAGCAAGCGTG 58.346 55.556 0.00 0.00 42.46 5.34
213 902 0.160182 CGCACTTTAACGACCGTGAC 59.840 55.000 0.00 0.00 0.00 3.67
245 934 6.070251 ACATTCCTTGGATAAATTTTGGTCCC 60.070 38.462 0.00 0.00 0.00 4.46
381 1071 1.228737 GGATCTCTCCTCCCTCCGG 60.229 68.421 0.00 0.00 38.65 5.14
420 1110 2.299297 TCGTTTCCCTCTCTTTCAGTCC 59.701 50.000 0.00 0.00 0.00 3.85
423 1113 3.838903 GTTTCCCTCTCTTTCAGTCCCTA 59.161 47.826 0.00 0.00 0.00 3.53
546 1238 2.985896 TGATTGGTTGAATCCCTCGTC 58.014 47.619 0.00 0.00 40.00 4.20
589 1282 4.295870 GTTATTCGACATAGATGCCGTGA 58.704 43.478 0.00 0.00 35.15 4.35
590 1283 2.951457 TTCGACATAGATGCCGTGAA 57.049 45.000 0.00 0.00 35.15 3.18
591 1284 2.951457 TCGACATAGATGCCGTGAAA 57.049 45.000 0.00 0.00 35.15 2.69
666 1366 5.615289 TGTGGTCAAATAATTTTTGTGGGG 58.385 37.500 10.72 0.00 0.00 4.96
806 1506 6.380846 AGCCATATATGCTTGTGGAAAAGAAA 59.619 34.615 7.24 0.00 34.87 2.52
838 1547 6.126565 GGTGGGGGTTAGATTTAAGTGACTAT 60.127 42.308 0.00 0.00 0.00 2.12
840 1549 7.832685 GTGGGGGTTAGATTTAAGTGACTATTT 59.167 37.037 0.00 0.00 0.00 1.40
841 1550 8.050930 TGGGGGTTAGATTTAAGTGACTATTTC 58.949 37.037 0.00 0.00 0.00 2.17
842 1551 8.050930 GGGGGTTAGATTTAAGTGACTATTTCA 58.949 37.037 0.00 0.00 0.00 2.69
843 1552 9.628500 GGGGTTAGATTTAAGTGACTATTTCAT 57.372 33.333 0.00 0.00 36.32 2.57
885 1594 2.224523 ACACATGTCCGGAACTCATTGT 60.225 45.455 5.23 10.03 0.00 2.71
1033 1750 4.498520 CGCAGCTCCGTGGATCGT 62.499 66.667 0.00 0.00 37.94 3.73
1058 1775 3.842923 CGCTCGGAGGCATGGAGT 61.843 66.667 7.20 0.00 0.00 3.85
1127 1844 4.850963 TGGTTCACTAAAGGTATTACCCCA 59.149 41.667 9.31 3.75 39.75 4.96
1142 1859 3.721087 ACCCCAATCCAGACAGTAAAG 57.279 47.619 0.00 0.00 0.00 1.85
1143 1860 2.290960 ACCCCAATCCAGACAGTAAAGC 60.291 50.000 0.00 0.00 0.00 3.51
1149 1866 4.965200 ATCCAGACAGTAAAGCCTATCC 57.035 45.455 0.00 0.00 0.00 2.59
1150 1867 3.719871 TCCAGACAGTAAAGCCTATCCA 58.280 45.455 0.00 0.00 0.00 3.41
1153 1870 4.101585 CCAGACAGTAAAGCCTATCCATGA 59.898 45.833 0.00 0.00 0.00 3.07
1346 2070 3.009033 AGTTTATGTACAGCCTGCCTGAA 59.991 43.478 0.33 0.00 44.64 3.02
1366 2090 3.325293 AGCACTATGAGACAACACTGG 57.675 47.619 0.00 0.00 0.00 4.00
1370 2094 2.005451 CTATGAGACAACACTGGCAGC 58.995 52.381 15.89 0.00 30.13 5.25
1385 2109 1.415374 GCAGCTGCACTTGACAATTG 58.585 50.000 33.36 3.24 41.59 2.32
1386 2110 1.933500 GCAGCTGCACTTGACAATTGG 60.934 52.381 33.36 0.00 41.59 3.16
1457 2191 4.682306 GTGTTGTGCACGTTGTCC 57.318 55.556 13.13 0.00 38.45 4.02
1502 2236 1.535462 CGAGAAAATGGTTCTGCGGTT 59.465 47.619 0.00 0.00 0.00 4.44
1597 2331 7.037438 GTGTTATTGTTCTTATACCAGTCGGA 58.963 38.462 0.00 0.00 35.59 4.55
1598 2332 7.546667 GTGTTATTGTTCTTATACCAGTCGGAA 59.453 37.037 0.00 0.00 35.59 4.30
1603 2338 4.054780 TCTTATACCAGTCGGAACATGC 57.945 45.455 0.00 0.00 35.59 4.06
1620 2355 2.330440 TGCAGAGTTGAAGCTGTTGA 57.670 45.000 0.00 0.00 34.66 3.18
1622 2357 1.942657 GCAGAGTTGAAGCTGTTGACA 59.057 47.619 0.00 0.00 34.66 3.58
1650 2385 1.483415 TGCTCTGATGTGCTAGCATGA 59.517 47.619 22.51 11.37 39.92 3.07
1701 2436 9.061435 AGCTATCCAATTTTTATAGAGTCAAGC 57.939 33.333 0.00 0.00 0.00 4.01
1752 2488 2.342406 TGGGAGGACCTTGAGATGAA 57.658 50.000 0.00 0.00 41.11 2.57
1766 2502 4.579869 TGAGATGAAAACCTAAGCTGGTC 58.420 43.478 0.00 0.00 39.83 4.02
1768 2504 4.583871 AGATGAAAACCTAAGCTGGTCTG 58.416 43.478 0.00 0.00 39.83 3.51
1777 2513 4.042187 ACCTAAGCTGGTCTGATTGTTCTT 59.958 41.667 0.00 0.00 34.86 2.52
1784 2520 5.915196 GCTGGTCTGATTGTTCTTTTGTAAC 59.085 40.000 0.00 0.00 0.00 2.50
2453 3232 2.991190 GGATGCTGCTGAACAACAAATG 59.009 45.455 0.00 0.00 0.00 2.32
2488 3267 7.439655 GCGTGAAGATCTTAATAGGAGATTTGT 59.560 37.037 8.25 0.00 34.13 2.83
2687 3487 4.688321 GCCCTTGAAGAGCCAAATCTCTAT 60.688 45.833 0.00 0.00 42.25 1.98
2704 3504 3.425659 TCTATGCATATCGGAGAGCACT 58.574 45.455 6.92 0.00 43.63 4.40
2920 3726 4.192000 CGTTCAAGAGGAGCGCAT 57.808 55.556 11.47 0.00 43.20 4.73
3065 3872 7.606456 GGAAATAGGACTGTTTCAGATTACACA 59.394 37.037 18.83 0.00 40.85 3.72
3282 4108 6.730038 GCTCCATATCCTCCATATCCTCATAT 59.270 42.308 0.00 0.00 0.00 1.78
3950 4787 5.645201 AGGGCAAGGAAAATTCTTACTCTT 58.355 37.500 0.00 0.00 0.00 2.85
3951 4788 6.077993 AGGGCAAGGAAAATTCTTACTCTTT 58.922 36.000 0.00 0.00 0.00 2.52
4392 5230 1.084370 CCCTACTCGCGCCAAAGAAG 61.084 60.000 0.00 0.00 0.00 2.85
4427 5265 2.163815 GCATGTGTACGGACAGTAGAGT 59.836 50.000 0.00 0.00 35.82 3.24
4578 5416 0.839946 CCGGGGATGAATGGAAGACT 59.160 55.000 0.00 0.00 0.00 3.24
4929 5786 2.355716 CCGAGAATGGCCAACTCCTAAA 60.356 50.000 26.63 0.00 0.00 1.85
5120 5977 3.459710 AGCTCCTGTCTTGGTACTACT 57.540 47.619 0.00 0.00 0.00 2.57
5731 6592 3.202818 TGATCTTAGTGGCCATGTTGGAT 59.797 43.478 9.72 9.73 40.96 3.41
5893 6754 0.770499 TGTTCCTGTTGCTCCATGGA 59.230 50.000 15.27 15.27 0.00 3.41
6046 6907 6.889177 TCATCATGTGGCAAACCTATTCTTTA 59.111 34.615 0.00 0.00 36.63 1.85
6368 7229 4.568152 ACACTAAAGTTCCAACACATGC 57.432 40.909 0.00 0.00 0.00 4.06
6439 7300 5.565509 TGTCCTTTGCTGATAATTACACCA 58.434 37.500 0.00 0.00 0.00 4.17
7203 8065 1.934463 AGCACGTTGAAGCTGTTCG 59.066 52.632 0.00 0.00 40.13 3.95
7278 8140 4.877251 ACAAATTTTGTGCTGCTTCAACAT 59.123 33.333 13.80 3.00 43.48 2.71
7279 8141 5.201910 CAAATTTTGTGCTGCTTCAACATG 58.798 37.500 0.00 0.00 0.00 3.21
7280 8142 3.523606 TTTTGTGCTGCTTCAACATGT 57.476 38.095 0.00 0.00 0.00 3.21
7302 8164 4.682860 GTCTTGAGATGCATTTTGGTGTTG 59.317 41.667 0.00 0.00 0.00 3.33
7391 8355 6.432162 GCTTGGGCATAATGATCAGAAGATTA 59.568 38.462 0.09 0.00 38.54 1.75
7610 8576 5.332656 CGAACTTGTAGAAGCAGTTGAAGAC 60.333 44.000 0.00 0.00 31.68 3.01
7637 8603 2.714250 TCCCCAAAAGAGGAGTGCTAAA 59.286 45.455 0.00 0.00 0.00 1.85
7702 8668 7.606073 ACTGTTTTTACAACAAAGGCAAAATCT 59.394 29.630 0.00 0.00 0.00 2.40
7938 8906 7.128234 ACCCAAACTTACTGTTAGAGTGTTA 57.872 36.000 0.19 0.00 38.03 2.41
8060 9030 3.758554 CCCAAACCAGTCGAAAATGAGAT 59.241 43.478 0.00 0.00 0.00 2.75
8136 9133 4.989277 TGGTATCCGGTAGATAGTAGCAA 58.011 43.478 0.00 0.00 38.16 3.91
8151 9148 8.414003 AGATAGTAGCAATGAAAACATCGACTA 58.586 33.333 0.00 0.00 0.00 2.59
8153 9150 7.849804 AGTAGCAATGAAAACATCGACTATT 57.150 32.000 0.00 0.00 0.00 1.73
8660 9659 5.445069 TGTTGATGTATAACCCCCTTCATG 58.555 41.667 0.00 0.00 0.00 3.07
8666 9665 6.147437 TGTATAACCCCCTTCATGTTTCTT 57.853 37.500 0.00 0.00 0.00 2.52
8874 9873 0.740149 TGCTCCATAAAATGCTGCGG 59.260 50.000 0.00 0.00 32.36 5.69
8893 9892 1.468395 GGCTACGAGCACAGAAGAGTC 60.468 57.143 8.71 0.00 44.75 3.36
9064 10064 7.200434 ACATGATGAAGGATAACCAGTTACT 57.800 36.000 0.00 0.00 38.94 2.24
9270 10270 5.303845 ACAGTTCGGGAGTAGAGTTTTAACT 59.696 40.000 0.00 0.00 43.16 2.24
9327 10358 3.857157 TGGCCATAGGGTTACAATCTC 57.143 47.619 0.00 0.00 36.17 2.75
9357 10388 7.128234 ACAAGATCATGAATTTAAATGGGGG 57.872 36.000 4.68 0.00 0.00 5.40
9420 10451 6.018425 AGCATAATTAGCGAGACAATGTGAAG 60.018 38.462 0.00 0.00 37.01 3.02
9421 10452 6.238211 GCATAATTAGCGAGACAATGTGAAGT 60.238 38.462 0.00 0.00 0.00 3.01
9457 10489 7.870445 GGATCTAGCTATCTCAACTGGTTTAAG 59.130 40.741 0.00 0.00 0.00 1.85
9459 10491 4.518249 AGCTATCTCAACTGGTTTAAGCC 58.482 43.478 0.54 0.54 0.00 4.35
9491 10523 8.742777 TCTACCATTTGATTCTTGATTTCCTTG 58.257 33.333 0.00 0.00 0.00 3.61
9503 10535 4.855340 TGATTTCCTTGACCAGATTACCC 58.145 43.478 0.00 0.00 0.00 3.69
9517 10549 8.559301 GACCAGATTACCCAATGGTGATTTGAT 61.559 40.741 0.00 0.00 45.92 2.57
9536 10568 3.580022 TGATGAGGGAAGCATCGACATAT 59.420 43.478 0.00 0.00 43.88 1.78
9541 10577 3.643320 AGGGAAGCATCGACATATGAGAA 59.357 43.478 10.38 0.00 0.00 2.87
9551 10587 7.201504 GCATCGACATATGAGAACTATCATTGG 60.202 40.741 10.38 0.00 40.40 3.16
9562 10609 2.242196 ACTATCATTGGGTCCAACAGGG 59.758 50.000 4.37 0.00 38.88 4.45
9587 10634 3.612955 GCTAGACTATTGAAGGGCTAGCG 60.613 52.174 16.18 0.00 43.84 4.26
9588 10635 2.667470 AGACTATTGAAGGGCTAGCGA 58.333 47.619 9.00 0.00 0.00 4.93
9589 10636 2.362717 AGACTATTGAAGGGCTAGCGAC 59.637 50.000 9.00 4.13 0.00 5.19
9590 10637 2.100916 GACTATTGAAGGGCTAGCGACA 59.899 50.000 9.00 3.26 0.00 4.35
9591 10638 2.700897 ACTATTGAAGGGCTAGCGACAT 59.299 45.455 9.00 0.00 0.00 3.06
9592 10639 3.895656 ACTATTGAAGGGCTAGCGACATA 59.104 43.478 9.00 0.00 0.00 2.29
9593 10640 3.838244 ATTGAAGGGCTAGCGACATAA 57.162 42.857 9.00 1.77 0.00 1.90
9594 10641 2.596904 TGAAGGGCTAGCGACATAAC 57.403 50.000 9.00 0.00 0.00 1.89
9595 10642 2.108168 TGAAGGGCTAGCGACATAACT 58.892 47.619 9.00 0.00 0.00 2.24
9596 10643 2.500098 TGAAGGGCTAGCGACATAACTT 59.500 45.455 9.00 4.22 0.00 2.66
9597 10644 3.055385 TGAAGGGCTAGCGACATAACTTT 60.055 43.478 9.00 0.00 0.00 2.66
9598 10645 3.180891 AGGGCTAGCGACATAACTTTC 57.819 47.619 9.00 0.00 0.00 2.62
9599 10646 2.500098 AGGGCTAGCGACATAACTTTCA 59.500 45.455 9.00 0.00 0.00 2.69
9600 10647 3.134804 AGGGCTAGCGACATAACTTTCAT 59.865 43.478 9.00 0.00 0.00 2.57
9601 10648 3.877508 GGGCTAGCGACATAACTTTCATT 59.122 43.478 9.00 0.00 0.00 2.57
9602 10649 5.054477 GGGCTAGCGACATAACTTTCATTA 58.946 41.667 9.00 0.00 0.00 1.90
9603 10650 5.701290 GGGCTAGCGACATAACTTTCATTAT 59.299 40.000 9.00 0.00 0.00 1.28
9604 10651 6.204882 GGGCTAGCGACATAACTTTCATTATT 59.795 38.462 9.00 0.00 0.00 1.40
9605 10652 7.072030 GGCTAGCGACATAACTTTCATTATTG 58.928 38.462 9.00 0.00 0.00 1.90
9606 10653 6.575201 GCTAGCGACATAACTTTCATTATTGC 59.425 38.462 0.00 0.00 0.00 3.56
9607 10654 6.683974 AGCGACATAACTTTCATTATTGCT 57.316 33.333 0.00 0.00 0.00 3.91
9608 10655 7.088589 AGCGACATAACTTTCATTATTGCTT 57.911 32.000 0.00 0.00 28.13 3.91
9609 10656 6.968904 AGCGACATAACTTTCATTATTGCTTG 59.031 34.615 0.00 0.00 28.13 4.01
9610 10657 6.966632 GCGACATAACTTTCATTATTGCTTGA 59.033 34.615 0.00 0.00 0.00 3.02
9611 10658 7.484641 GCGACATAACTTTCATTATTGCTTGAA 59.515 33.333 0.00 0.00 0.00 2.69
9612 10659 9.507280 CGACATAACTTTCATTATTGCTTGAAT 57.493 29.630 0.00 0.00 32.27 2.57
9618 10665 7.141363 ACTTTCATTATTGCTTGAATATCCGC 58.859 34.615 0.00 0.00 32.27 5.54
9619 10666 6.882610 TTCATTATTGCTTGAATATCCGCT 57.117 33.333 0.00 0.00 0.00 5.52
9620 10667 6.882610 TCATTATTGCTTGAATATCCGCTT 57.117 33.333 0.00 0.00 0.00 4.68
9621 10668 6.902341 TCATTATTGCTTGAATATCCGCTTC 58.098 36.000 0.00 0.00 0.00 3.86
9622 10669 3.885484 ATTGCTTGAATATCCGCTTCG 57.115 42.857 0.00 0.00 0.00 3.79
9623 10670 2.595124 TGCTTGAATATCCGCTTCGA 57.405 45.000 0.00 0.00 0.00 3.71
9624 10671 3.111853 TGCTTGAATATCCGCTTCGAT 57.888 42.857 0.00 0.00 0.00 3.59
9625 10672 3.466836 TGCTTGAATATCCGCTTCGATT 58.533 40.909 0.00 0.00 0.00 3.34
9626 10673 3.248363 TGCTTGAATATCCGCTTCGATTG 59.752 43.478 0.00 0.00 0.00 2.67
9627 10674 3.803555 CTTGAATATCCGCTTCGATTGC 58.196 45.455 0.00 0.00 0.00 3.56
9628 10675 2.832563 TGAATATCCGCTTCGATTGCA 58.167 42.857 10.74 0.00 0.00 4.08
9629 10676 3.402110 TGAATATCCGCTTCGATTGCAT 58.598 40.909 10.74 1.72 0.00 3.96
9630 10677 3.814842 TGAATATCCGCTTCGATTGCATT 59.185 39.130 10.74 3.70 0.00 3.56
9631 10678 3.818961 ATATCCGCTTCGATTGCATTG 57.181 42.857 10.74 0.50 0.00 2.82
9632 10679 1.382522 ATCCGCTTCGATTGCATTGT 58.617 45.000 10.74 0.00 0.00 2.71
9633 10680 1.164411 TCCGCTTCGATTGCATTGTT 58.836 45.000 10.74 0.00 0.00 2.83
9634 10681 1.135717 TCCGCTTCGATTGCATTGTTG 60.136 47.619 10.74 0.00 0.00 3.33
9649 10696 2.849880 TGTTGCAACAGAACAGAAGC 57.150 45.000 27.96 0.00 34.30 3.86
9650 10697 2.368439 TGTTGCAACAGAACAGAAGCT 58.632 42.857 27.96 0.00 34.30 3.74
9651 10698 3.540617 TGTTGCAACAGAACAGAAGCTA 58.459 40.909 27.96 0.41 34.30 3.32
9652 10699 3.561310 TGTTGCAACAGAACAGAAGCTAG 59.439 43.478 27.96 0.00 34.30 3.42
9653 10700 3.751479 TGCAACAGAACAGAAGCTAGA 57.249 42.857 0.00 0.00 0.00 2.43
9654 10701 3.657634 TGCAACAGAACAGAAGCTAGAG 58.342 45.455 0.00 0.00 0.00 2.43
9655 10702 3.070159 TGCAACAGAACAGAAGCTAGAGT 59.930 43.478 0.00 0.00 0.00 3.24
9656 10703 4.280929 TGCAACAGAACAGAAGCTAGAGTA 59.719 41.667 0.00 0.00 0.00 2.59
9657 10704 5.047021 TGCAACAGAACAGAAGCTAGAGTAT 60.047 40.000 0.00 0.00 0.00 2.12
9658 10705 6.152831 TGCAACAGAACAGAAGCTAGAGTATA 59.847 38.462 0.00 0.00 0.00 1.47
9659 10706 6.695278 GCAACAGAACAGAAGCTAGAGTATAG 59.305 42.308 0.00 0.00 0.00 1.31
9660 10707 7.415765 GCAACAGAACAGAAGCTAGAGTATAGA 60.416 40.741 0.00 0.00 0.00 1.98
9661 10708 8.462811 CAACAGAACAGAAGCTAGAGTATAGAA 58.537 37.037 0.00 0.00 0.00 2.10
9662 10709 8.220755 ACAGAACAGAAGCTAGAGTATAGAAG 57.779 38.462 0.00 0.00 0.00 2.85
9663 10710 7.284489 ACAGAACAGAAGCTAGAGTATAGAAGG 59.716 40.741 0.00 0.00 0.00 3.46
9664 10711 6.775629 AGAACAGAAGCTAGAGTATAGAAGGG 59.224 42.308 0.00 0.00 0.00 3.95
9665 10712 4.830600 ACAGAAGCTAGAGTATAGAAGGGC 59.169 45.833 0.00 0.00 0.00 5.19
9666 10713 5.076873 CAGAAGCTAGAGTATAGAAGGGCT 58.923 45.833 0.00 0.00 0.00 5.19
9667 10714 6.183361 ACAGAAGCTAGAGTATAGAAGGGCTA 60.183 42.308 0.00 0.00 0.00 3.93
9668 10715 6.374333 CAGAAGCTAGAGTATAGAAGGGCTAG 59.626 46.154 0.00 0.00 31.33 3.42
9669 10716 4.595986 AGCTAGAGTATAGAAGGGCTAGC 58.404 47.826 6.04 6.04 46.74 3.42
9676 10723 4.589374 AGTATAGAAGGGCTAGCGACATTT 59.411 41.667 9.00 0.00 31.33 2.32
9679 10726 2.237392 AGAAGGGCTAGCGACATTTCTT 59.763 45.455 9.00 3.66 0.00 2.52
9697 10744 9.079833 ACATTTCTTTCATTATTGCTTGAATCG 57.920 29.630 0.00 0.00 32.27 3.34
9704 10751 4.678509 TTATTGCTTGAATCGTCGCTTT 57.321 36.364 0.00 0.00 0.00 3.51
9736 10783 2.086869 TGCAATAGAACAGAAGCTGGC 58.913 47.619 0.00 0.00 35.51 4.85
9743 10790 0.886563 AACAGAAGCTGGCATGAAGC 59.113 50.000 11.74 11.74 44.65 3.86
9757 10804 5.768333 GCATGAAGCAAAAATAACCTCAC 57.232 39.130 0.00 0.00 44.79 3.51
9758 10805 4.627035 GCATGAAGCAAAAATAACCTCACC 59.373 41.667 0.00 0.00 44.79 4.02
9759 10806 5.782047 CATGAAGCAAAAATAACCTCACCA 58.218 37.500 0.00 0.00 0.00 4.17
9760 10807 6.400568 CATGAAGCAAAAATAACCTCACCAT 58.599 36.000 0.00 0.00 0.00 3.55
9761 10808 6.418057 TGAAGCAAAAATAACCTCACCATT 57.582 33.333 0.00 0.00 0.00 3.16
9762 10809 6.222389 TGAAGCAAAAATAACCTCACCATTG 58.778 36.000 0.00 0.00 0.00 2.82
9763 10810 5.806654 AGCAAAAATAACCTCACCATTGT 57.193 34.783 0.00 0.00 0.00 2.71
9764 10811 6.173427 AGCAAAAATAACCTCACCATTGTT 57.827 33.333 0.00 0.00 0.00 2.83
9765 10812 5.990996 AGCAAAAATAACCTCACCATTGTTG 59.009 36.000 0.00 0.00 32.38 3.33
9766 10813 5.757808 GCAAAAATAACCTCACCATTGTTGT 59.242 36.000 0.00 0.00 32.02 3.32
9767 10814 6.259829 GCAAAAATAACCTCACCATTGTTGTT 59.740 34.615 0.00 0.00 32.02 2.83
9768 10815 7.518211 GCAAAAATAACCTCACCATTGTTGTTC 60.518 37.037 0.00 0.00 32.02 3.18
9769 10816 5.722021 AATAACCTCACCATTGTTGTTCC 57.278 39.130 0.00 0.00 0.00 3.62
9770 10817 3.312736 AACCTCACCATTGTTGTTCCT 57.687 42.857 0.00 0.00 0.00 3.36
9771 10818 3.312736 ACCTCACCATTGTTGTTCCTT 57.687 42.857 0.00 0.00 0.00 3.36
9772 10819 4.447138 ACCTCACCATTGTTGTTCCTTA 57.553 40.909 0.00 0.00 0.00 2.69
9773 10820 4.798882 ACCTCACCATTGTTGTTCCTTAA 58.201 39.130 0.00 0.00 0.00 1.85
9774 10821 4.827284 ACCTCACCATTGTTGTTCCTTAAG 59.173 41.667 0.00 0.00 0.00 1.85
9775 10822 5.070001 CCTCACCATTGTTGTTCCTTAAGA 58.930 41.667 3.36 0.00 0.00 2.10
9776 10823 5.711976 CCTCACCATTGTTGTTCCTTAAGAT 59.288 40.000 3.36 0.00 0.00 2.40
9777 10824 6.127897 CCTCACCATTGTTGTTCCTTAAGATC 60.128 42.308 3.36 0.00 0.00 2.75
9778 10825 6.303054 TCACCATTGTTGTTCCTTAAGATCA 58.697 36.000 3.36 0.00 0.00 2.92
9779 10826 6.947733 TCACCATTGTTGTTCCTTAAGATCAT 59.052 34.615 3.36 0.00 0.00 2.45
9780 10827 7.031372 CACCATTGTTGTTCCTTAAGATCATG 58.969 38.462 3.36 0.00 0.00 3.07
9781 10828 6.038356 CCATTGTTGTTCCTTAAGATCATGC 58.962 40.000 3.36 0.00 0.00 4.06
9782 10829 5.643379 TTGTTGTTCCTTAAGATCATGCC 57.357 39.130 3.36 0.00 0.00 4.40
9783 10830 4.922206 TGTTGTTCCTTAAGATCATGCCT 58.078 39.130 3.36 0.00 0.00 4.75
9784 10831 4.701651 TGTTGTTCCTTAAGATCATGCCTG 59.298 41.667 3.36 0.00 0.00 4.85
9785 10832 4.574674 TGTTCCTTAAGATCATGCCTGT 57.425 40.909 3.36 0.00 0.00 4.00
9786 10833 4.517285 TGTTCCTTAAGATCATGCCTGTC 58.483 43.478 3.36 0.00 0.00 3.51
9787 10834 3.459232 TCCTTAAGATCATGCCTGTCG 57.541 47.619 3.36 0.00 0.00 4.35
9788 10835 2.766263 TCCTTAAGATCATGCCTGTCGT 59.234 45.455 3.36 0.00 0.00 4.34
9789 10836 2.868583 CCTTAAGATCATGCCTGTCGTG 59.131 50.000 3.36 0.00 0.00 4.35
9790 10837 2.602257 TAAGATCATGCCTGTCGTGG 57.398 50.000 0.00 0.00 32.54 4.94
9791 10838 0.904649 AAGATCATGCCTGTCGTGGA 59.095 50.000 0.00 0.00 32.54 4.02
9792 10839 0.904649 AGATCATGCCTGTCGTGGAA 59.095 50.000 0.00 0.00 32.54 3.53
9793 10840 1.487976 AGATCATGCCTGTCGTGGAAT 59.512 47.619 0.00 0.00 32.54 3.01
9794 10841 2.092753 AGATCATGCCTGTCGTGGAATT 60.093 45.455 0.00 0.00 32.54 2.17
9795 10842 1.452110 TCATGCCTGTCGTGGAATTG 58.548 50.000 0.00 0.00 32.54 2.32
9796 10843 1.167851 CATGCCTGTCGTGGAATTGT 58.832 50.000 0.00 0.00 0.00 2.71
9797 10844 1.131126 CATGCCTGTCGTGGAATTGTC 59.869 52.381 0.00 0.00 0.00 3.18
9798 10845 0.107643 TGCCTGTCGTGGAATTGTCA 59.892 50.000 0.00 0.00 0.00 3.58
9799 10846 0.517316 GCCTGTCGTGGAATTGTCAC 59.483 55.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 810 1.071471 ACGCTTGCTACCTTGCACT 59.929 52.632 0.00 0.00 43.20 4.40
138 827 1.896660 TCTTCTTTGCCACGCCCAC 60.897 57.895 0.00 0.00 0.00 4.61
139 828 1.896660 GTCTTCTTTGCCACGCCCA 60.897 57.895 0.00 0.00 0.00 5.36
140 829 2.954611 GTCTTCTTTGCCACGCCC 59.045 61.111 0.00 0.00 0.00 6.13
180 869 2.447244 AGTGCGACTCTTCTTCCTTG 57.553 50.000 0.00 0.00 0.00 3.61
213 902 1.843368 ATCCAAGGAATGTGCCACAG 58.157 50.000 3.00 0.00 0.00 3.66
245 934 6.428385 AAAAAGTCTAGCAATTGATCCTCG 57.572 37.500 10.34 0.00 0.00 4.63
285 974 1.202722 AGGGGCGGTATGGTTATTTCG 60.203 52.381 0.00 0.00 0.00 3.46
381 1071 1.380650 AGAGACGAGGAAGGAGGGC 60.381 63.158 0.00 0.00 0.00 5.19
420 1110 4.835891 AGAGGGCGTCGGGGTAGG 62.836 72.222 0.96 0.00 0.00 3.18
546 1238 3.128938 ACGAGTTCTCATCTAGGGTTTCG 59.871 47.826 0.00 0.00 0.00 3.46
647 1347 8.341903 CAGTTTTCCCCACAAAAATTATTTGAC 58.658 33.333 15.45 5.39 33.83 3.18
806 1506 1.229853 CTAACCCCCACCCCTCTGT 60.230 63.158 0.00 0.00 0.00 3.41
849 1558 8.783093 CCGGACATGTGTTATACAAAATGATAT 58.217 33.333 1.15 0.00 43.77 1.63
850 1559 7.988028 TCCGGACATGTGTTATACAAAATGATA 59.012 33.333 1.15 0.00 43.77 2.15
851 1560 6.826231 TCCGGACATGTGTTATACAAAATGAT 59.174 34.615 1.15 0.00 43.77 2.45
885 1594 1.962807 CCCTGAAGTTGATGTGCCAAA 59.037 47.619 0.00 0.00 0.00 3.28
1099 1816 2.922740 ACCTTTAGTGAACCAGCGAA 57.077 45.000 0.00 0.00 0.00 4.70
1127 1844 4.721776 TGGATAGGCTTTACTGTCTGGATT 59.278 41.667 0.00 0.00 0.00 3.01
1142 1859 7.934855 ATGAATGAATTACTCATGGATAGGC 57.065 36.000 0.00 0.00 44.43 3.93
1143 1860 9.388506 GGTATGAATGAATTACTCATGGATAGG 57.611 37.037 0.00 0.00 44.43 2.57
1149 1866 8.455903 AACAGGGTATGAATGAATTACTCATG 57.544 34.615 6.64 0.00 44.43 3.07
1186 1903 7.054855 GATGAGTAGAGTGTCATCAAAACAC 57.945 40.000 7.32 0.00 45.71 3.32
1245 1967 8.055279 ACAAAATATTCTAGTGGTCAATGGTG 57.945 34.615 0.00 0.00 0.00 4.17
1346 2070 2.613977 GCCAGTGTTGTCTCATAGTGCT 60.614 50.000 0.00 0.00 0.00 4.40
1356 2080 2.188829 TGCAGCTGCCAGTGTTGTC 61.189 57.895 34.64 4.94 41.18 3.18
1366 2090 1.415374 CAATTGTCAAGTGCAGCTGC 58.585 50.000 31.89 31.89 42.50 5.25
1370 2094 3.149196 ACTACCCAATTGTCAAGTGCAG 58.851 45.455 7.50 6.71 0.00 4.41
1385 2109 3.960571 GGAAAACTTCCCCTTACTACCC 58.039 50.000 0.00 0.00 44.30 3.69
1407 2141 0.388907 ATTGCCAGATGCGTGCAAAC 60.389 50.000 6.28 0.00 46.82 2.93
1457 2191 8.594687 CGCCTTTTTGTGATATAATTTTCCTTG 58.405 33.333 0.00 0.00 0.00 3.61
1478 2212 1.541588 GCAGAACCATTTTCTCGCCTT 59.458 47.619 0.00 0.00 0.00 4.35
1502 2236 2.158623 ACAAGCAGATTCACCAACCAGA 60.159 45.455 0.00 0.00 0.00 3.86
1579 2313 5.416083 CATGTTCCGACTGGTATAAGAACA 58.584 41.667 5.92 5.92 45.26 3.18
1586 2320 1.831106 TCTGCATGTTCCGACTGGTAT 59.169 47.619 0.00 0.00 36.30 2.73
1597 2331 2.579873 ACAGCTTCAACTCTGCATGTT 58.420 42.857 0.00 0.00 33.80 2.71
1598 2332 2.267174 ACAGCTTCAACTCTGCATGT 57.733 45.000 0.00 0.00 33.80 3.21
1603 2338 3.624861 AGTTGTCAACAGCTTCAACTCTG 59.375 43.478 17.78 0.00 44.36 3.35
1620 2355 1.696336 ACATCAGAGCACAGGAGTTGT 59.304 47.619 0.00 0.00 41.94 3.32
1622 2357 1.610102 GCACATCAGAGCACAGGAGTT 60.610 52.381 0.00 0.00 0.00 3.01
1701 2436 6.195244 GCAGAAATACATGCACTGATTAAACG 59.805 38.462 2.66 0.00 42.11 3.60
1752 2488 4.373156 ACAATCAGACCAGCTTAGGTTT 57.627 40.909 0.00 0.00 43.38 3.27
2453 3232 2.615869 AGATCTTCACGCAGCTCTTTC 58.384 47.619 0.00 0.00 0.00 2.62
2488 3267 4.033009 TCTTATCATCTCAACCAGCTGGA 58.967 43.478 39.19 17.18 38.94 3.86
2687 3487 1.402787 TGAGTGCTCTCCGATATGCA 58.597 50.000 13.00 0.00 39.75 3.96
2704 3504 5.894298 ATCTCTTGCATATGTAGGGTTGA 57.106 39.130 4.29 1.42 0.00 3.18
3065 3872 5.046950 CACTTGTAGCCTTAGAAACTCCTCT 60.047 44.000 0.00 0.00 0.00 3.69
3103 3910 5.401550 CAACTTGTTGCTCTTCAGTTTCAA 58.598 37.500 0.31 0.00 0.00 2.69
3335 4161 2.627699 GGATGGGCTGTTTTGTCTTTGA 59.372 45.455 0.00 0.00 0.00 2.69
3950 4787 7.287466 TGATCCTTCTCTTGTTCCAAATGAAAA 59.713 33.333 0.00 0.00 33.94 2.29
3951 4788 6.777091 TGATCCTTCTCTTGTTCCAAATGAAA 59.223 34.615 0.00 0.00 33.94 2.69
4392 5230 0.820891 ACATGCGCCAAGATCCATCC 60.821 55.000 4.18 0.00 0.00 3.51
4427 5265 4.022068 ACCTTACGGTGATCTTGTTAACGA 60.022 41.667 0.26 0.00 43.51 3.85
4578 5416 2.586425 CCTTCCTTTGTCTTGAAGGCA 58.414 47.619 0.00 0.00 46.13 4.75
4929 5786 5.248380 AGCTTCTTACCTCAGAAATGGTT 57.752 39.130 0.00 0.00 37.74 3.67
5120 5977 7.545265 CCAACTCAAAAGTCTTGTTGAAATCAA 59.455 33.333 12.71 0.00 39.98 2.57
5731 6592 2.429610 GGTTAGCGATAGTCTTGTCCCA 59.570 50.000 0.00 0.00 39.35 4.37
5893 6754 5.422214 ACGAAGTCCATAGAAATGTCCTT 57.578 39.130 0.00 0.00 29.74 3.36
6210 7071 6.478129 ACGGATCAGATTACCCAAAAACTTA 58.522 36.000 0.00 0.00 0.00 2.24
6368 7229 2.358737 GCTTCACCAGGTCCACCG 60.359 66.667 0.00 0.00 42.08 4.94
6439 7300 4.201822 GCCGCGAATCTCTTCAAATAACTT 60.202 41.667 8.23 0.00 0.00 2.66
7278 8140 3.890756 ACACCAAAATGCATCTCAAGACA 59.109 39.130 0.00 0.00 0.00 3.41
7279 8141 4.510038 ACACCAAAATGCATCTCAAGAC 57.490 40.909 0.00 0.00 0.00 3.01
7280 8142 4.341806 ACAACACCAAAATGCATCTCAAGA 59.658 37.500 0.00 0.00 0.00 3.02
7610 8576 0.685097 TCCTCTTTTGGGGAGTCACG 59.315 55.000 0.00 0.00 46.01 4.35
7637 8603 7.394077 GGAATCCCAAAACAAAAATCATGGATT 59.606 33.333 0.00 0.00 41.45 3.01
7839 8807 7.166473 CAGCTTCACTTTCATTAACAAGTTGAC 59.834 37.037 10.54 0.00 30.48 3.18
7843 8811 6.699575 ACAGCTTCACTTTCATTAACAAGT 57.300 33.333 0.00 0.00 33.29 3.16
7938 8906 8.084684 GCTTTTCTGAAACTTGTAGGATCAATT 58.915 33.333 1.58 0.00 0.00 2.32
7996 8964 1.956636 GCAAGGGCAATCTGACATCCA 60.957 52.381 0.00 0.00 40.72 3.41
8060 9030 4.142204 TGCAAAAGAAAGCAGTCATGACAA 60.142 37.500 27.02 0.00 35.51 3.18
8136 9133 8.184192 CCAAGCTAAAATAGTCGATGTTTTCAT 58.816 33.333 8.13 0.00 43.99 2.57
8151 9148 4.081406 TGCAGACACATCCAAGCTAAAAT 58.919 39.130 0.00 0.00 0.00 1.82
8153 9150 3.138884 TGCAGACACATCCAAGCTAAA 57.861 42.857 0.00 0.00 0.00 1.85
8666 9665 5.139727 ACATCAAGGTCTTCAATTTCCACA 58.860 37.500 0.00 0.00 0.00 4.17
8773 9772 4.056125 GGCGCCAACTTCTTGGGC 62.056 66.667 24.80 0.00 46.58 5.36
8803 9802 4.309879 CCTGCTCCCTGGCTCTAT 57.690 61.111 0.00 0.00 0.00 1.98
8832 9831 7.123247 AGCACAAATGTCAAATTAAGCTAGGAT 59.877 33.333 0.00 0.00 0.00 3.24
8874 9873 1.470890 AGACTCTTCTGTGCTCGTAGC 59.529 52.381 0.58 0.58 42.82 3.58
9173 10173 5.242393 CCCAAAAGAATCATCGCCTGAATAT 59.758 40.000 0.00 0.00 37.44 1.28
9283 10314 8.917088 CCATGGAATAAAACTTCATGATTACCT 58.083 33.333 5.56 0.00 0.00 3.08
9292 10323 5.598005 CCTATGGCCATGGAATAAAACTTCA 59.402 40.000 29.26 2.71 0.00 3.02
9347 10378 2.235898 GTTGCAATGAGCCCCCATTTAA 59.764 45.455 0.59 0.00 44.83 1.52
9348 10379 1.830477 GTTGCAATGAGCCCCCATTTA 59.170 47.619 0.59 0.00 44.83 1.40
9351 10382 1.686800 GGTTGCAATGAGCCCCCAT 60.687 57.895 0.59 0.00 44.83 4.00
9352 10383 2.283821 GGTTGCAATGAGCCCCCA 60.284 61.111 0.59 0.00 44.83 4.96
9357 10388 0.668401 GCCTGTTGGTTGCAATGAGC 60.668 55.000 0.59 0.00 38.72 4.26
9420 10451 8.001875 TGAGATAGCTAGATCCCATAATAGGAC 58.998 40.741 0.00 0.00 35.85 3.85
9421 10452 8.119062 TGAGATAGCTAGATCCCATAATAGGA 57.881 38.462 0.00 0.00 37.93 2.94
9457 10489 0.034863 TCAAATGGTAGAACGGGGGC 60.035 55.000 0.00 0.00 0.00 5.80
9459 10491 3.886123 AGAATCAAATGGTAGAACGGGG 58.114 45.455 0.00 0.00 0.00 5.73
9503 10535 4.441079 GCTTCCCTCATCAAATCACCATTG 60.441 45.833 0.00 0.00 0.00 2.82
9517 10549 2.965147 TCATATGTCGATGCTTCCCTCA 59.035 45.455 1.90 0.00 0.00 3.86
9536 10568 4.288366 TGTTGGACCCAATGATAGTTCTCA 59.712 41.667 4.63 0.00 38.28 3.27
9541 10577 2.242196 CCCTGTTGGACCCAATGATAGT 59.758 50.000 4.63 0.00 38.28 2.12
9551 10587 0.617820 TCTAGCCTCCCTGTTGGACC 60.618 60.000 0.00 0.00 38.61 4.46
9562 10609 2.969262 AGCCCTTCAATAGTCTAGCCTC 59.031 50.000 0.00 0.00 0.00 4.70
9592 10639 7.649306 GCGGATATTCAAGCAATAATGAAAGTT 59.351 33.333 0.00 0.00 30.39 2.66
9593 10640 7.013655 AGCGGATATTCAAGCAATAATGAAAGT 59.986 33.333 0.00 0.00 30.39 2.66
9594 10641 7.365741 AGCGGATATTCAAGCAATAATGAAAG 58.634 34.615 0.00 0.00 30.39 2.62
9595 10642 7.275888 AGCGGATATTCAAGCAATAATGAAA 57.724 32.000 0.00 0.00 30.39 2.69
9596 10643 6.882610 AGCGGATATTCAAGCAATAATGAA 57.117 33.333 0.00 0.00 30.39 2.57
9597 10644 6.347644 CGAAGCGGATATTCAAGCAATAATGA 60.348 38.462 0.00 0.00 30.39 2.57
9598 10645 5.791974 CGAAGCGGATATTCAAGCAATAATG 59.208 40.000 0.00 0.00 30.39 1.90
9599 10646 5.700832 TCGAAGCGGATATTCAAGCAATAAT 59.299 36.000 0.00 0.00 30.39 1.28
9600 10647 5.053811 TCGAAGCGGATATTCAAGCAATAA 58.946 37.500 0.00 0.00 30.39 1.40
9601 10648 4.627058 TCGAAGCGGATATTCAAGCAATA 58.373 39.130 0.00 0.00 0.00 1.90
9602 10649 3.466836 TCGAAGCGGATATTCAAGCAAT 58.533 40.909 0.00 0.00 0.00 3.56
9603 10650 2.899976 TCGAAGCGGATATTCAAGCAA 58.100 42.857 0.00 0.00 0.00 3.91
9604 10651 2.595124 TCGAAGCGGATATTCAAGCA 57.405 45.000 0.00 0.00 0.00 3.91
9605 10652 3.803555 CAATCGAAGCGGATATTCAAGC 58.196 45.455 0.00 0.00 0.00 4.01
9606 10653 3.248363 TGCAATCGAAGCGGATATTCAAG 59.752 43.478 8.43 0.00 33.85 3.02
9607 10654 3.202097 TGCAATCGAAGCGGATATTCAA 58.798 40.909 8.43 0.00 33.85 2.69
9608 10655 2.832563 TGCAATCGAAGCGGATATTCA 58.167 42.857 8.43 0.00 33.85 2.57
9609 10656 4.153986 CAATGCAATCGAAGCGGATATTC 58.846 43.478 8.43 0.00 33.85 1.75
9610 10657 3.565482 ACAATGCAATCGAAGCGGATATT 59.435 39.130 8.43 1.03 33.85 1.28
9611 10658 3.141398 ACAATGCAATCGAAGCGGATAT 58.859 40.909 8.43 0.00 33.85 1.63
9612 10659 2.560504 ACAATGCAATCGAAGCGGATA 58.439 42.857 8.43 0.00 33.85 2.59
9613 10660 1.382522 ACAATGCAATCGAAGCGGAT 58.617 45.000 8.43 0.00 33.85 4.18
9614 10661 1.135717 CAACAATGCAATCGAAGCGGA 60.136 47.619 8.43 0.00 33.85 5.54
9615 10662 1.261989 CAACAATGCAATCGAAGCGG 58.738 50.000 8.43 3.98 33.85 5.52
9627 10674 3.488310 GCTTCTGTTCTGTTGCAACAATG 59.512 43.478 30.62 20.85 38.66 2.82
9628 10675 3.382546 AGCTTCTGTTCTGTTGCAACAAT 59.617 39.130 30.62 6.28 38.66 2.71
9629 10676 2.754552 AGCTTCTGTTCTGTTGCAACAA 59.245 40.909 30.62 19.24 38.66 2.83
9630 10677 2.368439 AGCTTCTGTTCTGTTGCAACA 58.632 42.857 29.36 29.36 37.37 3.33
9631 10678 3.809832 TCTAGCTTCTGTTCTGTTGCAAC 59.190 43.478 22.83 22.83 0.00 4.17
9632 10679 4.060900 CTCTAGCTTCTGTTCTGTTGCAA 58.939 43.478 0.00 0.00 0.00 4.08
9633 10680 3.070159 ACTCTAGCTTCTGTTCTGTTGCA 59.930 43.478 0.00 0.00 0.00 4.08
9634 10681 3.658709 ACTCTAGCTTCTGTTCTGTTGC 58.341 45.455 0.00 0.00 0.00 4.17
9635 10682 7.990917 TCTATACTCTAGCTTCTGTTCTGTTG 58.009 38.462 0.00 0.00 0.00 3.33
9636 10683 8.582657 TTCTATACTCTAGCTTCTGTTCTGTT 57.417 34.615 0.00 0.00 0.00 3.16
9637 10684 7.284489 CCTTCTATACTCTAGCTTCTGTTCTGT 59.716 40.741 0.00 0.00 0.00 3.41
9638 10685 7.255451 CCCTTCTATACTCTAGCTTCTGTTCTG 60.255 44.444 0.00 0.00 0.00 3.02
9639 10686 6.775629 CCCTTCTATACTCTAGCTTCTGTTCT 59.224 42.308 0.00 0.00 0.00 3.01
9640 10687 6.516028 GCCCTTCTATACTCTAGCTTCTGTTC 60.516 46.154 0.00 0.00 0.00 3.18
9641 10688 5.303333 GCCCTTCTATACTCTAGCTTCTGTT 59.697 44.000 0.00 0.00 0.00 3.16
9642 10689 4.830600 GCCCTTCTATACTCTAGCTTCTGT 59.169 45.833 0.00 0.00 0.00 3.41
9643 10690 5.076873 AGCCCTTCTATACTCTAGCTTCTG 58.923 45.833 0.00 0.00 0.00 3.02
9644 10691 5.333566 AGCCCTTCTATACTCTAGCTTCT 57.666 43.478 0.00 0.00 0.00 2.85
9645 10692 5.124936 GCTAGCCCTTCTATACTCTAGCTTC 59.875 48.000 2.29 0.00 43.19 3.86
9646 10693 5.014202 GCTAGCCCTTCTATACTCTAGCTT 58.986 45.833 2.29 0.00 43.19 3.74
9647 10694 4.595986 GCTAGCCCTTCTATACTCTAGCT 58.404 47.826 2.29 0.00 43.19 3.32
9648 10695 3.375922 CGCTAGCCCTTCTATACTCTAGC 59.624 52.174 9.66 8.53 43.12 3.42
9649 10696 4.632688 GTCGCTAGCCCTTCTATACTCTAG 59.367 50.000 9.66 0.00 0.00 2.43
9650 10697 4.041321 TGTCGCTAGCCCTTCTATACTCTA 59.959 45.833 9.66 0.00 0.00 2.43
9651 10698 3.181442 TGTCGCTAGCCCTTCTATACTCT 60.181 47.826 9.66 0.00 0.00 3.24
9652 10699 3.147629 TGTCGCTAGCCCTTCTATACTC 58.852 50.000 9.66 0.00 0.00 2.59
9653 10700 3.225177 TGTCGCTAGCCCTTCTATACT 57.775 47.619 9.66 0.00 0.00 2.12
9654 10701 4.522722 AATGTCGCTAGCCCTTCTATAC 57.477 45.455 9.66 0.00 0.00 1.47
9655 10702 4.833380 AGAAATGTCGCTAGCCCTTCTATA 59.167 41.667 9.66 0.00 0.00 1.31
9656 10703 3.643792 AGAAATGTCGCTAGCCCTTCTAT 59.356 43.478 9.66 0.00 0.00 1.98
9657 10704 3.031736 AGAAATGTCGCTAGCCCTTCTA 58.968 45.455 9.66 0.00 0.00 2.10
9658 10705 1.834263 AGAAATGTCGCTAGCCCTTCT 59.166 47.619 9.66 7.29 0.00 2.85
9659 10706 2.317530 AGAAATGTCGCTAGCCCTTC 57.682 50.000 9.66 5.12 0.00 3.46
9660 10707 2.789409 AAGAAATGTCGCTAGCCCTT 57.211 45.000 9.66 0.00 0.00 3.95
9661 10708 2.027192 TGAAAGAAATGTCGCTAGCCCT 60.027 45.455 9.66 0.00 0.00 5.19
9662 10709 2.356135 TGAAAGAAATGTCGCTAGCCC 58.644 47.619 9.66 0.04 0.00 5.19
9663 10710 4.622701 AATGAAAGAAATGTCGCTAGCC 57.377 40.909 9.66 0.00 0.00 3.93
9664 10711 6.141369 GCAATAATGAAAGAAATGTCGCTAGC 59.859 38.462 4.06 4.06 0.00 3.42
9665 10712 7.412853 AGCAATAATGAAAGAAATGTCGCTAG 58.587 34.615 0.00 0.00 0.00 3.42
9666 10713 7.320443 AGCAATAATGAAAGAAATGTCGCTA 57.680 32.000 0.00 0.00 0.00 4.26
9667 10714 6.199937 AGCAATAATGAAAGAAATGTCGCT 57.800 33.333 0.00 0.00 0.00 4.93
9668 10715 6.527722 TCAAGCAATAATGAAAGAAATGTCGC 59.472 34.615 0.00 0.00 0.00 5.19
9669 10716 8.451687 TTCAAGCAATAATGAAAGAAATGTCG 57.548 30.769 0.00 0.00 0.00 4.35
9676 10723 6.477742 CGACGATTCAAGCAATAATGAAAGA 58.522 36.000 0.00 0.00 0.00 2.52
9679 10726 4.332543 AGCGACGATTCAAGCAATAATGAA 59.667 37.500 0.00 0.00 0.00 2.57
9736 10783 5.782047 TGGTGAGGTTATTTTTGCTTCATG 58.218 37.500 0.00 0.00 0.00 3.07
9743 10790 7.042119 GGAACAACAATGGTGAGGTTATTTTTG 60.042 37.037 4.82 0.00 31.35 2.44
9744 10791 6.989759 GGAACAACAATGGTGAGGTTATTTTT 59.010 34.615 4.82 0.00 0.00 1.94
9745 10792 6.326323 AGGAACAACAATGGTGAGGTTATTTT 59.674 34.615 4.82 0.00 0.00 1.82
9746 10793 5.838521 AGGAACAACAATGGTGAGGTTATTT 59.161 36.000 4.82 0.00 0.00 1.40
9747 10794 5.393866 AGGAACAACAATGGTGAGGTTATT 58.606 37.500 4.82 0.00 0.00 1.40
9748 10795 4.998051 AGGAACAACAATGGTGAGGTTAT 58.002 39.130 4.82 0.00 0.00 1.89
9749 10796 4.447138 AGGAACAACAATGGTGAGGTTA 57.553 40.909 4.82 0.00 0.00 2.85
9750 10797 3.312736 AGGAACAACAATGGTGAGGTT 57.687 42.857 4.82 0.00 0.00 3.50
9751 10798 3.312736 AAGGAACAACAATGGTGAGGT 57.687 42.857 4.82 0.00 0.00 3.85
9752 10799 5.070001 TCTTAAGGAACAACAATGGTGAGG 58.930 41.667 4.82 0.00 0.00 3.86
9753 10800 6.430925 TGATCTTAAGGAACAACAATGGTGAG 59.569 38.462 4.82 0.00 0.00 3.51
9754 10801 6.303054 TGATCTTAAGGAACAACAATGGTGA 58.697 36.000 4.82 0.00 0.00 4.02
9755 10802 6.573664 TGATCTTAAGGAACAACAATGGTG 57.426 37.500 1.85 0.00 0.00 4.17
9756 10803 6.350445 GCATGATCTTAAGGAACAACAATGGT 60.350 38.462 1.85 0.00 30.71 3.55
9757 10804 6.038356 GCATGATCTTAAGGAACAACAATGG 58.962 40.000 1.85 0.00 30.71 3.16
9758 10805 6.038356 GGCATGATCTTAAGGAACAACAATG 58.962 40.000 1.85 0.00 30.71 2.82
9759 10806 5.954150 AGGCATGATCTTAAGGAACAACAAT 59.046 36.000 1.85 0.00 30.71 2.71
9760 10807 5.183713 CAGGCATGATCTTAAGGAACAACAA 59.816 40.000 1.85 0.00 30.71 2.83
9761 10808 4.701651 CAGGCATGATCTTAAGGAACAACA 59.298 41.667 1.85 0.00 30.71 3.33
9762 10809 4.702131 ACAGGCATGATCTTAAGGAACAAC 59.298 41.667 4.84 0.00 30.71 3.32
9763 10810 4.922206 ACAGGCATGATCTTAAGGAACAA 58.078 39.130 4.84 0.00 30.71 2.83
9764 10811 4.517285 GACAGGCATGATCTTAAGGAACA 58.483 43.478 4.84 1.48 0.00 3.18
9765 10812 3.557595 CGACAGGCATGATCTTAAGGAAC 59.442 47.826 4.84 0.00 0.00 3.62
9766 10813 3.197766 ACGACAGGCATGATCTTAAGGAA 59.802 43.478 4.84 0.00 0.00 3.36
9767 10814 2.766263 ACGACAGGCATGATCTTAAGGA 59.234 45.455 4.84 0.00 0.00 3.36
9768 10815 2.868583 CACGACAGGCATGATCTTAAGG 59.131 50.000 4.84 0.00 0.00 2.69
9769 10816 2.868583 CCACGACAGGCATGATCTTAAG 59.131 50.000 4.84 0.00 0.00 1.85
9770 10817 2.499693 TCCACGACAGGCATGATCTTAA 59.500 45.455 4.84 0.00 0.00 1.85
9771 10818 2.107366 TCCACGACAGGCATGATCTTA 58.893 47.619 4.84 0.00 0.00 2.10
9772 10819 0.904649 TCCACGACAGGCATGATCTT 59.095 50.000 4.84 0.00 0.00 2.40
9773 10820 0.904649 TTCCACGACAGGCATGATCT 59.095 50.000 4.84 0.00 0.00 2.75
9774 10821 1.959042 ATTCCACGACAGGCATGATC 58.041 50.000 4.84 0.00 0.00 2.92
9775 10822 2.019249 CAATTCCACGACAGGCATGAT 58.981 47.619 4.84 0.00 0.00 2.45
9776 10823 1.271325 ACAATTCCACGACAGGCATGA 60.271 47.619 4.84 0.00 0.00 3.07
9777 10824 1.131126 GACAATTCCACGACAGGCATG 59.869 52.381 0.00 0.00 0.00 4.06
9778 10825 1.271325 TGACAATTCCACGACAGGCAT 60.271 47.619 0.00 0.00 0.00 4.40
9779 10826 0.107643 TGACAATTCCACGACAGGCA 59.892 50.000 0.00 0.00 0.00 4.75
9780 10827 0.517316 GTGACAATTCCACGACAGGC 59.483 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.