Multiple sequence alignment - TraesCS3A01G366700

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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 TraesCS3A01G366700 chr3A 100.000 2396 0 0 1 2396 615922277 615924672 0.000000e+00 4425
1 TraesCS3A01G366700 chr3A 81.589 516 46 23 57 526 613350104 613350616 4.830000e-102 381
2 TraesCS3A01G366700 chr3A 87.261 314 34 4 218 526 557654327 557654015 1.050000e-93 353
3 TraesCS3A01G366700 chr3A 85.976 164 22 1 588 751 144451345 144451183 8.800000e-40 174
4 TraesCS3A01G366700 chr3D 93.787 1014 54 6 524 1530 473468390 473469401 0.000000e+00 1515
5 TraesCS3A01G366700 chr3D 85.338 532 61 10 1535 2065 473469525 473470040 3.510000e-148 534
6 TraesCS3A01G366700 chr3D 90.449 178 15 2 2096 2272 473470114 473470290 1.430000e-57 233
7 TraesCS3A01G366700 chr3D 83.815 173 20 4 57 223 515082910 515083080 8.870000e-35 158
8 TraesCS3A01G366700 chr3D 92.754 69 4 1 3 71 79350771 79350704 5.450000e-17 99
9 TraesCS3A01G366700 chr3B 89.901 505 47 4 911 1413 628710520 628711022 0.000000e+00 647
10 TraesCS3A01G366700 chr3B 87.622 307 31 6 220 525 828818094 828818394 1.360000e-92 350
11 TraesCS3A01G366700 chr3B 87.879 132 13 3 60 191 512352182 512352054 4.130000e-33 152
12 TraesCS3A01G366700 chr3B 90.789 76 3 2 1 75 438152235 438152307 5.450000e-17 99
13 TraesCS3A01G366700 chr7A 82.724 492 57 12 60 526 110876008 110875520 1.710000e-111 412
14 TraesCS3A01G366700 chr7A 96.774 62 2 0 3 64 10047858 10047797 1.170000e-18 104
15 TraesCS3A01G366700 chrUn 82.046 479 58 17 60 523 48862510 48862045 1.340000e-102 383
16 TraesCS3A01G366700 chrUn 82.046 479 58 17 60 523 48871176 48870711 1.340000e-102 383
17 TraesCS3A01G366700 chrUn 82.046 479 58 17 60 523 48882874 48882409 1.340000e-102 383
18 TraesCS3A01G366700 chrUn 84.146 164 24 2 587 750 439522574 439522413 8.870000e-35 158
19 TraesCS3A01G366700 chr6A 81.568 472 58 19 74 527 32414192 32414652 1.750000e-96 363
20 TraesCS3A01G366700 chr6A 87.702 309 33 5 220 526 32446469 32446774 2.930000e-94 355
21 TraesCS3A01G366700 chr7B 85.366 164 22 2 588 751 730165978 730166139 4.100000e-38 169
22 TraesCS3A01G366700 chr1D 82.902 193 24 8 574 762 242825759 242825946 5.300000e-37 165
23 TraesCS3A01G366700 chr1D 95.455 66 3 0 3 68 371181572 371181637 3.260000e-19 106
24 TraesCS3A01G366700 chr5A 83.425 181 25 5 585 764 58490051 58490227 1.910000e-36 163
25 TraesCS3A01G366700 chr2B 84.146 164 24 2 587 750 14453717 14453556 8.870000e-35 158
26 TraesCS3A01G366700 chr2B 84.146 164 24 2 587 750 14482193 14482032 8.870000e-35 158
27 TraesCS3A01G366700 chr2B 84.146 164 24 2 587 750 14508774 14508613 8.870000e-35 158
28 TraesCS3A01G366700 chr6D 83.529 170 20 2 60 223 451669672 451669505 4.130000e-33 152
29 TraesCS3A01G366700 chr5D 86.667 135 15 2 57 191 27390075 27390206 1.920000e-31 147
30 TraesCS3A01G366700 chr2D 86.667 135 15 2 57 191 79904760 79904891 1.920000e-31 147
31 TraesCS3A01G366700 chr2D 98.276 58 1 0 3 60 372500431 372500488 4.210000e-18 102
32 TraesCS3A01G366700 chr2D 93.939 66 4 0 3 68 433133504 433133569 1.520000e-17 100
33 TraesCS3A01G366700 chr1A 85.333 150 12 4 60 202 150991325 150991179 1.920000e-31 147
34 TraesCS3A01G366700 chr2A 98.387 62 1 0 3 64 760098611 760098672 2.520000e-20 110
35 TraesCS3A01G366700 chr1B 96.923 65 1 1 1 65 417283788 417283725 9.060000e-20 108
36 TraesCS3A01G366700 chr1B 92.857 70 5 0 3 72 342136902 342136971 4.210000e-18 102


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 TraesCS3A01G366700 chr3A 615922277 615924672 2395 False 4425.000000 4425 100.000 1 2396 1 chr3A.!!$F2 2395
1 TraesCS3A01G366700 chr3A 613350104 613350616 512 False 381.000000 381 81.589 57 526 1 chr3A.!!$F1 469
2 TraesCS3A01G366700 chr3D 473468390 473470290 1900 False 760.666667 1515 89.858 524 2272 3 chr3D.!!$F2 1748
3 TraesCS3A01G366700 chr3B 628710520 628711022 502 False 647.000000 647 89.901 911 1413 1 chr3B.!!$F2 502

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
23 24 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.0 15.81 0.0 43.2 4.57 F
444 489 0.180171 CCCACTCACACCACTCACAA 59.820 55.0 0.00 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1050 1104 0.539051 CCTTCTCGTGCCCTGATTCT 59.461 55.0 0.0 0.0 0.0 2.40 R
2272 2489 0.322187 GTGTGCGTAGTTCCCCCAAT 60.322 55.0 0.0 0.0 0.0 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.867055 GTATCACCATGATCTTGCGTG 57.133 47.619 17.02 17.02 38.26 5.34
21 22 2.408271 ATCACCATGATCTTGCGTGT 57.592 45.000 19.89 6.63 29.59 4.49
22 23 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
23 24 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
58 59 3.653539 AAAATTACTGCGTTCCCCAAC 57.346 42.857 0.00 0.00 0.00 3.77
65 66 2.637025 CGTTCCCCAACACTTGCG 59.363 61.111 0.00 0.00 32.14 4.85
71 72 3.582120 CCAACACTTGCGTGGCGT 61.582 61.111 0.00 0.00 45.50 5.68
72 73 2.407210 CAACACTTGCGTGGCGTT 59.593 55.556 0.00 0.00 45.50 4.84
91 92 3.688272 GTTGCAATGATCTGGAACGATG 58.312 45.455 0.59 0.00 37.80 3.84
95 96 1.959042 ATGATCTGGAACGATGGTGC 58.041 50.000 0.00 0.00 0.00 5.01
118 119 2.279186 CATACGATGTGGCGGCGA 60.279 61.111 12.98 0.00 35.12 5.54
130 131 2.117156 GCGGCGACTAGGGTAGACA 61.117 63.158 12.98 0.00 0.00 3.41
134 135 1.881324 GGCGACTAGGGTAGACATCTC 59.119 57.143 0.00 0.00 0.00 2.75
135 136 2.487625 GGCGACTAGGGTAGACATCTCT 60.488 54.545 0.00 0.00 0.00 3.10
149 150 7.612244 GGTAGACATCTCTGCCTGACTATATAA 59.388 40.741 0.00 0.00 44.09 0.98
151 152 8.065473 AGACATCTCTGCCTGACTATATAATG 57.935 38.462 0.00 0.00 0.00 1.90
155 156 4.086457 TCTGCCTGACTATATAATGCGGA 58.914 43.478 0.00 0.00 0.00 5.54
157 158 3.576550 TGCCTGACTATATAATGCGGACA 59.423 43.478 0.00 0.00 0.00 4.02
160 161 4.220821 CCTGACTATATAATGCGGACAGGT 59.779 45.833 0.00 0.00 37.95 4.00
179 180 2.564504 GGTTAGGTCGTGGGAGTAAACT 59.435 50.000 0.00 0.00 0.00 2.66
202 212 3.119849 CCAAGTCGCGATCCAAAAGAATT 60.120 43.478 14.06 0.00 0.00 2.17
203 213 4.475944 CAAGTCGCGATCCAAAAGAATTT 58.524 39.130 14.06 0.00 42.41 1.82
204 214 5.391523 CCAAGTCGCGATCCAAAAGAATTTA 60.392 40.000 14.06 0.00 37.28 1.40
205 215 5.873179 AGTCGCGATCCAAAAGAATTTAA 57.127 34.783 14.06 0.00 37.28 1.52
206 216 6.249035 AGTCGCGATCCAAAAGAATTTAAA 57.751 33.333 14.06 0.00 37.28 1.52
207 217 6.674066 AGTCGCGATCCAAAAGAATTTAAAA 58.326 32.000 14.06 0.00 37.28 1.52
208 218 6.581166 AGTCGCGATCCAAAAGAATTTAAAAC 59.419 34.615 14.06 0.00 37.28 2.43
259 298 7.696035 CAGCAAAAATATAGACAACGTGCATAA 59.304 33.333 0.00 0.00 31.95 1.90
266 305 3.728845 AGACAACGTGCATAACTCTGTT 58.271 40.909 0.00 0.00 0.00 3.16
281 320 2.290122 CTGTTCTCGGCTCGGCTCAT 62.290 60.000 0.00 0.00 0.00 2.90
285 324 2.759973 TCGGCTCGGCTCATTCCT 60.760 61.111 0.00 0.00 0.00 3.36
290 329 1.712977 GCTCGGCTCATTCCTGCAAG 61.713 60.000 0.00 0.00 0.00 4.01
293 332 4.007457 GCTCATTCCTGCAAGCCA 57.993 55.556 0.00 0.00 0.00 4.75
295 334 1.798735 CTCATTCCTGCAAGCCACG 59.201 57.895 0.00 0.00 0.00 4.94
317 362 2.185608 GCGAGCAAGGAGGAGGAC 59.814 66.667 0.00 0.00 0.00 3.85
321 366 3.706373 GCAAGGAGGAGGACCGCA 61.706 66.667 0.00 0.00 41.83 5.69
339 384 1.272769 GCACGTGTAGGTCTCCTCTTT 59.727 52.381 18.38 0.00 34.61 2.52
345 390 4.322049 CGTGTAGGTCTCCTCTTTTCATGT 60.322 45.833 0.00 0.00 34.61 3.21
366 411 6.665992 TGTTCATACAAGTGGTAGAAGAGT 57.334 37.500 0.00 0.00 34.92 3.24
371 416 3.978687 ACAAGTGGTAGAAGAGTTCACG 58.021 45.455 0.00 0.00 33.98 4.35
388 433 5.408604 AGTTCACGTTATAAAGAGGTGCAAG 59.591 40.000 5.36 0.00 34.01 4.01
393 438 5.168569 CGTTATAAAGAGGTGCAAGTCTCA 58.831 41.667 13.25 1.17 32.76 3.27
403 448 2.219674 GTGCAAGTCTCACTCAACTTCG 59.780 50.000 0.00 0.00 33.53 3.79
404 449 2.100749 TGCAAGTCTCACTCAACTTCGA 59.899 45.455 0.00 0.00 33.53 3.71
410 455 1.613925 CTCACTCAACTTCGAGGGTGA 59.386 52.381 15.13 15.13 37.69 4.02
426 471 5.621781 CGAGGGTGAGACTAAACTTTAGTCC 60.622 48.000 27.43 21.28 43.61 3.85
434 479 5.601313 AGACTAAACTTTAGTCCCACTCACA 59.399 40.000 27.43 0.00 43.61 3.58
444 489 0.180171 CCCACTCACACCACTCACAA 59.820 55.000 0.00 0.00 0.00 3.33
446 491 0.940126 CACTCACACCACTCACAAGC 59.060 55.000 0.00 0.00 0.00 4.01
447 492 0.833287 ACTCACACCACTCACAAGCT 59.167 50.000 0.00 0.00 0.00 3.74
448 493 2.039418 ACTCACACCACTCACAAGCTA 58.961 47.619 0.00 0.00 0.00 3.32
451 496 2.079158 CACACCACTCACAAGCTATGG 58.921 52.381 0.00 0.00 36.46 2.74
462 507 1.538512 CAAGCTATGGATGAATGGGCG 59.461 52.381 0.00 0.00 0.00 6.13
469 514 1.139654 TGGATGAATGGGCGAAGAGAG 59.860 52.381 0.00 0.00 0.00 3.20
473 518 3.140325 TGAATGGGCGAAGAGAGTTTT 57.860 42.857 0.00 0.00 0.00 2.43
482 527 6.072673 TGGGCGAAGAGAGTTTTAGAATTTTC 60.073 38.462 0.00 0.00 0.00 2.29
489 535 6.771267 AGAGAGTTTTAGAATTTTCGTTGGGT 59.229 34.615 0.00 0.00 0.00 4.51
495 541 4.066646 AGAATTTTCGTTGGGTTTTGGG 57.933 40.909 0.00 0.00 0.00 4.12
502 548 0.833949 GTTGGGTTTTGGGCCAAAGA 59.166 50.000 28.89 18.19 34.72 2.52
538 585 5.782893 TCCAACAATCGAAAGGAAACATT 57.217 34.783 0.00 0.00 0.00 2.71
670 717 9.739276 TGGAGTAAAATGAGTGAATCTACATTT 57.261 29.630 0.00 0.00 42.25 2.32
800 848 1.442769 GAATCTGTTTGCTCGGCTGA 58.557 50.000 0.00 0.00 0.00 4.26
814 862 2.745100 CTGACGAGTCGGTCCCGA 60.745 66.667 18.30 3.90 46.87 5.14
829 877 2.606272 GTCCCGATGTTTAATGGACGAC 59.394 50.000 0.00 0.00 36.47 4.34
871 919 1.064654 ACGACTTAGTAATCGGCCGTC 59.935 52.381 27.15 10.91 42.67 4.79
999 1047 1.514443 CGAAGTCGAGCGGAGAACC 60.514 63.158 0.00 0.00 43.02 3.62
1003 1051 2.167861 GTCGAGCGGAGAACCATGC 61.168 63.158 0.00 0.00 35.59 4.06
1174 1228 1.593296 GGTAACGAGCCAGACCGTCT 61.593 60.000 0.00 0.00 38.13 4.18
1440 1494 8.129211 GCAGTTTAGTGTGTTCTTGAAAAGTAT 58.871 33.333 0.00 0.00 46.34 2.12
1458 1512 4.023291 AGTATTTGCAACATTGGGTAGGG 58.977 43.478 0.00 0.00 0.00 3.53
1530 1584 9.717942 ATCTATGAAGGTAGATTACTTGATTGC 57.282 33.333 0.00 0.00 38.02 3.56
1531 1585 8.150945 TCTATGAAGGTAGATTACTTGATTGCC 58.849 37.037 0.00 0.00 0.00 4.52
1532 1586 6.061022 TGAAGGTAGATTACTTGATTGCCA 57.939 37.500 0.00 0.00 0.00 4.92
1540 1713 6.479884 AGATTACTTGATTGCCAGAGAGTTT 58.520 36.000 0.00 0.00 0.00 2.66
1548 1721 1.072173 TGCCAGAGAGTTTGCTTAGCA 59.928 47.619 1.39 1.39 36.47 3.49
1550 1723 2.097142 GCCAGAGAGTTTGCTTAGCATG 59.903 50.000 8.05 0.85 38.76 4.06
1564 1737 5.337733 TGCTTAGCATGATTTGGCTTCAAAT 60.338 36.000 1.39 4.28 42.28 2.32
1580 1753 5.529060 GCTTCAAATCAAGTAGGTCCATAGG 59.471 44.000 0.00 0.00 0.00 2.57
1588 1761 0.469331 TAGGTCCATAGGTCGCCAGG 60.469 60.000 0.00 0.00 0.00 4.45
1595 1768 1.066143 CATAGGTCGCCAGGTCTTTGT 60.066 52.381 0.00 0.00 0.00 2.83
1602 1775 4.748600 GGTCGCCAGGTCTTTGTAATATAC 59.251 45.833 0.00 0.00 0.00 1.47
1663 1836 7.158099 AGTTGATTTGTTTTCTACTATGCCC 57.842 36.000 0.00 0.00 29.35 5.36
1668 1841 7.284489 TGATTTGTTTTCTACTATGCCCATACC 59.716 37.037 0.00 0.00 0.00 2.73
1674 1847 5.362105 TCTACTATGCCCATACCGTTTTT 57.638 39.130 0.00 0.00 0.00 1.94
1678 1851 1.996798 TGCCCATACCGTTTTTCCAA 58.003 45.000 0.00 0.00 0.00 3.53
1707 1880 1.200484 GAGTCTCGTTGTGGAGAGGAC 59.800 57.143 0.00 0.00 43.37 3.85
1715 1888 3.376234 CGTTGTGGAGAGGACGTTATCTA 59.624 47.826 3.70 0.00 0.00 1.98
1716 1889 4.670347 GTTGTGGAGAGGACGTTATCTAC 58.330 47.826 6.30 6.30 0.00 2.59
1717 1890 3.959293 TGTGGAGAGGACGTTATCTACA 58.041 45.455 10.86 10.86 33.91 2.74
1718 1891 4.533815 TGTGGAGAGGACGTTATCTACAT 58.466 43.478 16.28 0.00 38.62 2.29
1719 1892 4.954202 TGTGGAGAGGACGTTATCTACATT 59.046 41.667 16.28 0.00 38.62 2.71
1720 1893 5.163550 TGTGGAGAGGACGTTATCTACATTG 60.164 44.000 16.28 0.00 38.62 2.82
1731 1905 7.272244 ACGTTATCTACATTGAATGGACATCA 58.728 34.615 10.27 0.00 33.60 3.07
1733 1907 8.438513 CGTTATCTACATTGAATGGACATCATC 58.561 37.037 10.27 0.00 34.44 2.92
1754 1928 7.202526 TCATCGAAATGCCTGGAATAAATTTC 58.797 34.615 0.00 3.91 35.08 2.17
1781 1955 3.367992 TTTGAACACGCATGCAAATCT 57.632 38.095 19.57 0.00 0.00 2.40
1794 1968 5.585390 CATGCAAATCTATGACTTGAACCC 58.415 41.667 0.00 0.00 0.00 4.11
1802 1976 1.948104 TGACTTGAACCCGAGTTGTG 58.052 50.000 0.00 0.00 37.16 3.33
1805 1979 0.868406 CTTGAACCCGAGTTGTGCTC 59.132 55.000 0.00 0.00 40.77 4.26
1807 1981 0.531974 TGAACCCGAGTTGTGCTCAC 60.532 55.000 0.00 0.00 44.33 3.51
1812 1986 1.609061 CCCGAGTTGTGCTCACTTCAT 60.609 52.381 1.47 0.00 44.33 2.57
1816 1990 3.434641 CGAGTTGTGCTCACTTCATGATT 59.565 43.478 0.00 0.00 44.33 2.57
1828 2002 8.268738 GCTCACTTCATGATTTGTTGTTTTAAC 58.731 33.333 0.00 0.00 36.48 2.01
1838 2012 7.642194 TGATTTGTTGTTTTAACTCGTTAGCTG 59.358 33.333 0.00 0.00 0.00 4.24
1851 2025 3.131396 CGTTAGCTGTATTAAGGCCCTG 58.869 50.000 0.00 0.00 0.00 4.45
1861 2035 6.786122 TGTATTAAGGCCCTGAAACTTACTT 58.214 36.000 0.00 0.00 0.00 2.24
1862 2036 7.920227 TGTATTAAGGCCCTGAAACTTACTTA 58.080 34.615 0.00 0.00 0.00 2.24
1863 2037 7.825761 TGTATTAAGGCCCTGAAACTTACTTAC 59.174 37.037 0.00 0.00 0.00 2.34
1864 2038 4.995624 AAGGCCCTGAAACTTACTTACT 57.004 40.909 0.00 0.00 0.00 2.24
1865 2039 4.995624 AGGCCCTGAAACTTACTTACTT 57.004 40.909 0.00 0.00 0.00 2.24
1866 2040 5.320488 AGGCCCTGAAACTTACTTACTTT 57.680 39.130 0.00 0.00 0.00 2.66
1872 2046 8.504815 GCCCTGAAACTTACTTACTTTCTAAAG 58.495 37.037 0.90 0.90 41.73 1.85
1888 2062 1.911057 AAAGAGAAAAGGAAGGGCGG 58.089 50.000 0.00 0.00 0.00 6.13
1901 2075 1.280457 AGGGCGGTTGATCTTCTTCT 58.720 50.000 0.00 0.00 0.00 2.85
1907 2081 5.416947 GGCGGTTGATCTTCTTCTTACTTA 58.583 41.667 0.00 0.00 0.00 2.24
1909 2083 6.018669 GGCGGTTGATCTTCTTCTTACTTATG 60.019 42.308 0.00 0.00 0.00 1.90
1911 2085 6.758886 CGGTTGATCTTCTTCTTACTTATGCT 59.241 38.462 0.00 0.00 0.00 3.79
1912 2086 7.278868 CGGTTGATCTTCTTCTTACTTATGCTT 59.721 37.037 0.00 0.00 0.00 3.91
1913 2087 8.951243 GGTTGATCTTCTTCTTACTTATGCTTT 58.049 33.333 0.00 0.00 0.00 3.51
1982 2156 1.528586 CGAGCATCCGCAAAATCTAGG 59.471 52.381 0.00 0.00 42.27 3.02
1983 2157 2.565841 GAGCATCCGCAAAATCTAGGT 58.434 47.619 0.00 0.00 42.27 3.08
2011 2185 2.635444 CTACTTCGTGCCACGTTTTTG 58.365 47.619 17.83 6.64 43.14 2.44
2023 2197 4.238514 CCACGTTTTTGTTCCTGTTTTGA 58.761 39.130 0.00 0.00 0.00 2.69
2027 2201 5.287513 ACGTTTTTGTTCCTGTTTTGATTCG 59.712 36.000 0.00 0.00 0.00 3.34
2032 2206 6.879188 TTGTTCCTGTTTTGATTCGTTTTC 57.121 33.333 0.00 0.00 0.00 2.29
2053 2227 5.918426 TCCCTTTGTTTTCCTTTTACGTT 57.082 34.783 0.00 0.00 0.00 3.99
2057 2231 6.196910 CCCTTTGTTTTCCTTTTACGTTTACG 59.803 38.462 0.00 0.00 46.33 3.18
2087 2268 9.519191 AGATAAAATTTTCTTCCCCCAAAAATG 57.481 29.630 6.72 0.00 33.95 2.32
2088 2269 9.295825 GATAAAATTTTCTTCCCCCAAAAATGT 57.704 29.630 6.72 0.00 33.95 2.71
2094 2275 5.966853 TCTTCCCCCAAAAATGTTTTCTT 57.033 34.783 0.00 0.00 0.00 2.52
2214 2431 9.912634 ACCATTAAACACTTCTTAAATCACATG 57.087 29.630 0.00 0.00 0.00 3.21
2222 2439 9.683069 ACACTTCTTAAATCACATGAACATTTC 57.317 29.630 0.00 0.00 0.00 2.17
2223 2440 9.903682 CACTTCTTAAATCACATGAACATTTCT 57.096 29.630 0.00 0.00 0.00 2.52
2279 2496 7.846066 TGAACATTGTTTATAGAAATTGGGGG 58.154 34.615 3.08 0.00 0.00 5.40
2280 2497 7.676043 TGAACATTGTTTATAGAAATTGGGGGA 59.324 33.333 3.08 0.00 0.00 4.81
2281 2498 8.442660 AACATTGTTTATAGAAATTGGGGGAA 57.557 30.769 0.00 0.00 0.00 3.97
2282 2499 7.847096 ACATTGTTTATAGAAATTGGGGGAAC 58.153 34.615 0.00 0.00 0.00 3.62
2283 2500 7.678171 ACATTGTTTATAGAAATTGGGGGAACT 59.322 33.333 0.00 0.00 0.00 3.01
2284 2501 9.196139 CATTGTTTATAGAAATTGGGGGAACTA 57.804 33.333 0.00 0.00 0.00 2.24
2285 2502 8.584063 TTGTTTATAGAAATTGGGGGAACTAC 57.416 34.615 0.00 0.00 0.00 2.73
2286 2503 6.824704 TGTTTATAGAAATTGGGGGAACTACG 59.175 38.462 0.00 0.00 0.00 3.51
2287 2504 2.124277 AGAAATTGGGGGAACTACGC 57.876 50.000 0.00 0.00 0.00 4.42
2288 2505 1.353022 AGAAATTGGGGGAACTACGCA 59.647 47.619 0.00 0.00 0.00 5.24
2289 2506 1.471287 GAAATTGGGGGAACTACGCAC 59.529 52.381 0.00 0.00 35.31 5.34
2290 2507 0.402504 AATTGGGGGAACTACGCACA 59.597 50.000 0.00 0.00 43.01 4.57
2291 2508 0.322187 ATTGGGGGAACTACGCACAC 60.322 55.000 0.00 0.00 44.34 3.82
2292 2509 1.697082 TTGGGGGAACTACGCACACA 61.697 55.000 0.00 0.00 44.34 3.72
2293 2510 1.298667 GGGGGAACTACGCACACAT 59.701 57.895 0.00 0.00 34.84 3.21
2294 2511 0.322187 GGGGGAACTACGCACACATT 60.322 55.000 0.00 0.00 34.84 2.71
2295 2512 1.530323 GGGGAACTACGCACACATTT 58.470 50.000 0.00 0.00 0.00 2.32
2296 2513 1.883926 GGGGAACTACGCACACATTTT 59.116 47.619 0.00 0.00 0.00 1.82
2297 2514 2.295070 GGGGAACTACGCACACATTTTT 59.705 45.455 0.00 0.00 0.00 1.94
2333 2550 8.633075 ATGAACATTGTTTATAGAAAATGCGG 57.367 30.769 3.08 0.00 34.13 5.69
2334 2551 7.032580 TGAACATTGTTTATAGAAAATGCGGG 58.967 34.615 3.08 0.00 34.13 6.13
2335 2552 6.767524 ACATTGTTTATAGAAAATGCGGGA 57.232 33.333 6.16 0.00 34.13 5.14
2336 2553 7.164230 ACATTGTTTATAGAAAATGCGGGAA 57.836 32.000 6.16 0.00 34.13 3.97
2337 2554 7.033185 ACATTGTTTATAGAAAATGCGGGAAC 58.967 34.615 6.16 0.00 34.13 3.62
2338 2555 6.827586 TTGTTTATAGAAAATGCGGGAACT 57.172 33.333 0.00 0.00 0.00 3.01
2339 2556 7.925043 TTGTTTATAGAAAATGCGGGAACTA 57.075 32.000 0.00 0.00 0.00 2.24
2340 2557 7.311364 TGTTTATAGAAAATGCGGGAACTAC 57.689 36.000 0.00 0.00 0.00 2.73
2341 2558 6.036300 TGTTTATAGAAAATGCGGGAACTACG 59.964 38.462 0.00 0.00 0.00 3.51
2350 2567 2.981400 CGGGAACTACGCACAAATTT 57.019 45.000 0.00 0.00 0.00 1.82
2351 2568 2.580589 CGGGAACTACGCACAAATTTG 58.419 47.619 16.67 16.67 0.00 2.32
2352 2569 2.031508 CGGGAACTACGCACAAATTTGT 60.032 45.455 18.13 18.13 43.36 2.83
2353 2570 3.186817 CGGGAACTACGCACAAATTTGTA 59.813 43.478 22.87 7.38 39.91 2.41
2354 2571 4.319622 CGGGAACTACGCACAAATTTGTAA 60.320 41.667 22.87 8.69 39.91 2.41
2355 2572 4.913345 GGGAACTACGCACAAATTTGTAAC 59.087 41.667 22.87 16.50 39.91 2.50
2356 2573 5.278120 GGGAACTACGCACAAATTTGTAACT 60.278 40.000 22.87 10.53 39.91 2.24
2357 2574 5.623673 GGAACTACGCACAAATTTGTAACTG 59.376 40.000 22.87 12.16 39.91 3.16
2358 2575 4.533222 ACTACGCACAAATTTGTAACTGC 58.467 39.130 22.87 19.62 39.91 4.40
2359 2576 3.428746 ACGCACAAATTTGTAACTGCA 57.571 38.095 22.87 0.00 39.91 4.41
2360 2577 3.976169 ACGCACAAATTTGTAACTGCAT 58.024 36.364 22.87 8.74 39.91 3.96
2361 2578 3.735240 ACGCACAAATTTGTAACTGCATG 59.265 39.130 22.87 12.51 39.91 4.06
2362 2579 3.980134 CGCACAAATTTGTAACTGCATGA 59.020 39.130 22.87 0.00 39.91 3.07
2363 2580 4.443725 CGCACAAATTTGTAACTGCATGAA 59.556 37.500 22.87 0.00 39.91 2.57
2364 2581 5.610124 CGCACAAATTTGTAACTGCATGAAC 60.610 40.000 22.87 1.79 39.91 3.18
2365 2582 5.233902 GCACAAATTTGTAACTGCATGAACA 59.766 36.000 22.87 0.00 39.91 3.18
2366 2583 6.238049 GCACAAATTTGTAACTGCATGAACAA 60.238 34.615 22.87 4.34 39.91 2.83
2367 2584 7.518689 GCACAAATTTGTAACTGCATGAACAAT 60.519 33.333 22.87 0.00 39.91 2.71
2368 2585 8.336806 CACAAATTTGTAACTGCATGAACAATT 58.663 29.630 22.87 3.77 39.91 2.32
2369 2586 8.891720 ACAAATTTGTAACTGCATGAACAATTT 58.108 25.926 22.10 8.32 40.16 1.82
2370 2587 9.719279 CAAATTTGTAACTGCATGAACAATTTT 57.281 25.926 10.15 15.20 36.56 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.001634 CACACGCAAGATCATGGTGATAC 59.998 47.826 19.56 0.00 37.20 2.24
1 2 3.197265 CACACGCAAGATCATGGTGATA 58.803 45.455 19.56 0.00 37.20 2.15
2 3 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
3 4 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
4 5 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
5 6 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
6 7 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
7 8 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
8 9 1.135112 TCTACGCACACGCAAGATCAT 60.135 47.619 0.00 0.00 45.53 2.45
9 10 0.242555 TCTACGCACACGCAAGATCA 59.757 50.000 0.00 0.00 45.53 2.92
10 11 1.346365 TTCTACGCACACGCAAGATC 58.654 50.000 0.00 0.00 45.53 2.75
11 12 2.010145 ATTCTACGCACACGCAAGAT 57.990 45.000 0.00 0.00 45.53 2.40
12 13 1.790755 AATTCTACGCACACGCAAGA 58.209 45.000 0.00 0.00 45.53 3.02
13 14 2.594529 AAATTCTACGCACACGCAAG 57.405 45.000 0.00 0.00 45.53 4.01
14 15 3.341857 AAAAATTCTACGCACACGCAA 57.658 38.095 0.00 0.00 45.53 4.85
47 48 2.335011 GCAAGTGTTGGGGAACGC 59.665 61.111 0.00 0.00 43.69 4.84
48 49 2.637025 CGCAAGTGTTGGGGAACG 59.363 61.111 0.00 0.00 39.66 3.95
65 66 0.179156 CCAGATCATTGCAACGCCAC 60.179 55.000 0.00 0.00 0.00 5.01
71 72 2.684374 CCATCGTTCCAGATCATTGCAA 59.316 45.455 0.00 0.00 0.00 4.08
72 73 2.291365 CCATCGTTCCAGATCATTGCA 58.709 47.619 0.00 0.00 0.00 4.08
95 96 0.300491 CGCCACATCGTATGGTTTCG 59.700 55.000 4.67 0.00 39.63 3.46
108 109 3.942377 TACCCTAGTCGCCGCCACA 62.942 63.158 0.00 0.00 0.00 4.17
110 111 2.831742 CTACCCTAGTCGCCGCCA 60.832 66.667 0.00 0.00 0.00 5.69
118 119 2.516277 AGGCAGAGATGTCTACCCTAGT 59.484 50.000 5.50 0.00 36.95 2.57
130 131 5.163468 CCGCATTATATAGTCAGGCAGAGAT 60.163 44.000 0.00 0.00 0.00 2.75
134 135 4.177026 GTCCGCATTATATAGTCAGGCAG 58.823 47.826 0.00 0.00 0.00 4.85
135 136 3.576550 TGTCCGCATTATATAGTCAGGCA 59.423 43.478 0.00 0.00 0.00 4.75
149 150 1.255667 ACGACCTAACCTGTCCGCAT 61.256 55.000 0.00 0.00 0.00 4.73
151 152 1.445582 CACGACCTAACCTGTCCGC 60.446 63.158 0.00 0.00 0.00 5.54
155 156 0.178941 ACTCCCACGACCTAACCTGT 60.179 55.000 0.00 0.00 0.00 4.00
157 158 2.564504 GTTTACTCCCACGACCTAACCT 59.435 50.000 0.00 0.00 0.00 3.50
179 180 1.001520 TCTTTTGGATCGCGACTTGGA 59.998 47.619 12.93 0.57 0.00 3.53
183 184 5.873179 TTAAATTCTTTTGGATCGCGACT 57.127 34.783 12.93 0.00 0.00 4.18
187 197 5.631929 ACCGTTTTAAATTCTTTTGGATCGC 59.368 36.000 0.00 0.00 0.00 4.58
224 248 7.589395 TGTCTATATTTTTGCTGCTCGAAAAA 58.411 30.769 10.31 10.31 40.41 1.94
225 249 7.139896 TGTCTATATTTTTGCTGCTCGAAAA 57.860 32.000 0.00 6.43 41.06 2.29
227 251 6.542852 GTTGTCTATATTTTTGCTGCTCGAA 58.457 36.000 0.00 0.00 0.00 3.71
228 252 5.220397 CGTTGTCTATATTTTTGCTGCTCGA 60.220 40.000 0.00 0.00 0.00 4.04
259 298 2.995872 GCCGAGCCGAGAACAGAGT 61.996 63.158 0.00 0.00 0.00 3.24
266 305 2.786495 GGAATGAGCCGAGCCGAGA 61.786 63.158 0.00 0.00 0.00 4.04
281 320 4.617520 TCGCGTGGCTTGCAGGAA 62.618 61.111 5.77 0.00 0.00 3.36
306 351 3.382832 CGTGCGGTCCTCCTCCTT 61.383 66.667 0.00 0.00 0.00 3.36
317 362 2.181021 GGAGACCTACACGTGCGG 59.819 66.667 17.22 18.64 0.00 5.69
321 366 3.228453 TGAAAAGAGGAGACCTACACGT 58.772 45.455 0.00 0.00 31.76 4.49
339 384 7.676004 TCTTCTACCACTTGTATGAACATGAA 58.324 34.615 0.00 0.00 34.97 2.57
345 390 7.152645 GTGAACTCTTCTACCACTTGTATGAA 58.847 38.462 0.00 0.00 0.00 2.57
366 411 5.302360 ACTTGCACCTCTTTATAACGTGAA 58.698 37.500 0.00 0.00 0.00 3.18
371 416 6.166982 AGTGAGACTTGCACCTCTTTATAAC 58.833 40.000 10.22 1.59 36.95 1.89
388 433 1.614413 ACCCTCGAAGTTGAGTGAGAC 59.386 52.381 0.00 0.00 34.04 3.36
393 438 1.614413 GTCTCACCCTCGAAGTTGAGT 59.386 52.381 8.26 0.00 34.04 3.41
403 448 5.337410 GGGACTAAAGTTTAGTCTCACCCTC 60.337 48.000 36.81 25.15 42.92 4.30
404 449 4.531339 GGGACTAAAGTTTAGTCTCACCCT 59.469 45.833 36.81 14.28 42.92 4.34
410 455 5.601313 TGTGAGTGGGACTAAAGTTTAGTCT 59.399 40.000 36.81 25.62 42.54 3.24
426 471 1.586422 CTTGTGAGTGGTGTGAGTGG 58.414 55.000 0.00 0.00 0.00 4.00
434 479 2.840038 TCATCCATAGCTTGTGAGTGGT 59.160 45.455 0.00 0.00 0.00 4.16
444 489 1.059098 TCGCCCATTCATCCATAGCT 58.941 50.000 0.00 0.00 0.00 3.32
446 491 3.007290 TCTCTTCGCCCATTCATCCATAG 59.993 47.826 0.00 0.00 0.00 2.23
447 492 2.972021 TCTCTTCGCCCATTCATCCATA 59.028 45.455 0.00 0.00 0.00 2.74
448 493 1.770658 TCTCTTCGCCCATTCATCCAT 59.229 47.619 0.00 0.00 0.00 3.41
451 496 2.611225 ACTCTCTTCGCCCATTCATC 57.389 50.000 0.00 0.00 0.00 2.92
462 507 7.803659 CCCAACGAAAATTCTAAAACTCTCTTC 59.196 37.037 0.00 0.00 0.00 2.87
469 514 7.403421 CCAAAACCCAACGAAAATTCTAAAAC 58.597 34.615 0.00 0.00 0.00 2.43
473 518 4.501743 GCCCAAAACCCAACGAAAATTCTA 60.502 41.667 0.00 0.00 0.00 2.10
482 527 0.531753 CTTTGGCCCAAAACCCAACG 60.532 55.000 10.66 0.00 40.60 4.10
489 535 3.812882 GCTAGTAGGTCTTTGGCCCAAAA 60.813 47.826 10.66 0.00 32.75 2.44
495 541 4.096532 GGAATTTGCTAGTAGGTCTTTGGC 59.903 45.833 0.00 0.00 0.00 4.52
502 548 5.354234 CGATTGTTGGAATTTGCTAGTAGGT 59.646 40.000 0.00 0.00 0.00 3.08
555 602 7.495135 AATAAAAGCAACTTTCAACCCAATG 57.505 32.000 0.00 0.00 31.99 2.82
774 822 3.243367 CCGAGCAAACAGATTCCAAACAA 60.243 43.478 0.00 0.00 0.00 2.83
814 862 6.963049 GACTACAAGTCGTCCATTAAACAT 57.037 37.500 0.00 0.00 35.28 2.71
829 877 2.060326 TCCGTTTGCTCGACTACAAG 57.940 50.000 0.00 0.00 0.00 3.16
846 894 3.370276 GCCGATTACTAAGTCGTCTTCC 58.630 50.000 0.00 0.00 36.17 3.46
856 904 1.298563 CGCGACGGCCGATTACTAA 60.299 57.895 35.90 0.00 41.76 2.24
871 919 3.739300 CAGGGATTTATAGGTTGTACGCG 59.261 47.826 3.53 3.53 0.00 6.01
941 989 1.590259 TTTTGAGTTTTGCGGCGCC 60.590 52.632 30.82 19.07 0.00 6.53
979 1027 0.793853 GTTCTCCGCTCGACTTCGAC 60.794 60.000 0.00 0.00 44.22 4.20
1050 1104 0.539051 CCTTCTCGTGCCCTGATTCT 59.461 55.000 0.00 0.00 0.00 2.40
1437 1491 4.020543 TCCCTACCCAATGTTGCAAATAC 58.979 43.478 0.00 0.00 0.00 1.89
1440 1494 2.685106 TCCCTACCCAATGTTGCAAA 57.315 45.000 0.00 0.00 0.00 3.68
1458 1512 1.212751 GGAAAGCCGCACCACAATC 59.787 57.895 0.00 0.00 0.00 2.67
1510 1564 6.349300 TCTGGCAATCAAGTAATCTACCTTC 58.651 40.000 0.00 0.00 0.00 3.46
1513 1567 5.918608 TCTCTGGCAATCAAGTAATCTACC 58.081 41.667 0.00 0.00 0.00 3.18
1521 1575 2.555757 GCAAACTCTCTGGCAATCAAGT 59.444 45.455 0.00 0.00 0.00 3.16
1530 1584 3.603532 TCATGCTAAGCAAACTCTCTGG 58.396 45.455 0.00 0.00 43.62 3.86
1531 1585 5.814764 AATCATGCTAAGCAAACTCTCTG 57.185 39.130 0.00 0.00 43.62 3.35
1532 1586 5.125097 CCAAATCATGCTAAGCAAACTCTCT 59.875 40.000 0.00 0.00 43.62 3.10
1540 1713 3.090790 TGAAGCCAAATCATGCTAAGCA 58.909 40.909 0.00 0.00 44.86 3.91
1564 1737 2.029623 GCGACCTATGGACCTACTTGA 58.970 52.381 0.00 0.00 0.00 3.02
1568 1741 0.674534 CTGGCGACCTATGGACCTAC 59.325 60.000 0.00 0.00 0.00 3.18
1580 1753 4.443394 CGTATATTACAAAGACCTGGCGAC 59.557 45.833 0.00 0.00 0.00 5.19
1646 1819 5.120399 CGGTATGGGCATAGTAGAAAACAA 58.880 41.667 0.00 0.00 0.00 2.83
1649 1822 5.362105 AACGGTATGGGCATAGTAGAAAA 57.638 39.130 0.00 0.00 0.00 2.29
1654 1827 4.080469 TGGAAAAACGGTATGGGCATAGTA 60.080 41.667 0.00 0.00 0.00 1.82
1656 1829 3.283751 TGGAAAAACGGTATGGGCATAG 58.716 45.455 0.00 0.00 0.00 2.23
1657 1830 3.367646 TGGAAAAACGGTATGGGCATA 57.632 42.857 0.00 0.00 0.00 3.14
1659 1832 1.996798 TTGGAAAAACGGTATGGGCA 58.003 45.000 0.00 0.00 0.00 5.36
1660 1833 2.559231 TCTTTGGAAAAACGGTATGGGC 59.441 45.455 0.00 0.00 0.00 5.36
1678 1851 3.815401 CCACAACGAGACTCCAATTTCTT 59.185 43.478 0.00 0.00 0.00 2.52
1687 1860 1.200484 GTCCTCTCCACAACGAGACTC 59.800 57.143 0.00 0.00 35.09 3.36
1694 1867 3.870633 AGATAACGTCCTCTCCACAAC 57.129 47.619 0.00 0.00 0.00 3.32
1696 1869 3.959293 TGTAGATAACGTCCTCTCCACA 58.041 45.455 3.34 2.02 0.00 4.17
1707 1880 7.713764 TGATGTCCATTCAATGTAGATAACG 57.286 36.000 0.00 0.00 0.00 3.18
1715 1888 6.500910 CATTTCGATGATGTCCATTCAATGT 58.499 36.000 0.00 0.00 35.17 2.71
1716 1889 5.401376 GCATTTCGATGATGTCCATTCAATG 59.599 40.000 10.02 0.00 35.17 2.82
1717 1890 5.508489 GGCATTTCGATGATGTCCATTCAAT 60.508 40.000 10.02 0.00 35.17 2.57
1718 1891 4.202040 GGCATTTCGATGATGTCCATTCAA 60.202 41.667 10.02 0.00 35.17 2.69
1719 1892 3.316029 GGCATTTCGATGATGTCCATTCA 59.684 43.478 10.02 0.00 35.17 2.57
1720 1893 3.567164 AGGCATTTCGATGATGTCCATTC 59.433 43.478 16.97 2.16 35.17 2.67
1733 1907 5.871531 CGAAATTTATTCCAGGCATTTCG 57.128 39.130 10.02 10.02 45.55 3.46
1754 1928 3.423536 TGCATGCGTGTTCAAATTTTACG 59.576 39.130 14.09 8.73 37.77 3.18
1755 1929 4.963237 TGCATGCGTGTTCAAATTTTAC 57.037 36.364 14.09 0.00 0.00 2.01
1763 1937 3.688673 TCATAGATTTGCATGCGTGTTCA 59.311 39.130 14.09 0.00 0.00 3.18
1764 1938 4.031028 GTCATAGATTTGCATGCGTGTTC 58.969 43.478 14.09 7.38 0.00 3.18
1765 1939 3.691118 AGTCATAGATTTGCATGCGTGTT 59.309 39.130 14.09 0.00 0.00 3.32
1770 1944 5.039333 GGTTCAAGTCATAGATTTGCATGC 58.961 41.667 11.82 11.82 30.94 4.06
1781 1955 3.659786 CACAACTCGGGTTCAAGTCATA 58.340 45.455 0.00 0.00 32.73 2.15
1802 1976 6.833342 AAAACAACAAATCATGAAGTGAGC 57.167 33.333 14.17 0.00 40.92 4.26
1805 1979 8.471457 CGAGTTAAAACAACAAATCATGAAGTG 58.529 33.333 0.00 3.27 0.00 3.16
1807 1981 8.560576 ACGAGTTAAAACAACAAATCATGAAG 57.439 30.769 0.00 0.00 0.00 3.02
1812 1986 7.642194 CAGCTAACGAGTTAAAACAACAAATCA 59.358 33.333 0.00 0.00 0.00 2.57
1816 1990 6.425577 ACAGCTAACGAGTTAAAACAACAA 57.574 33.333 0.00 0.00 0.00 2.83
1828 2002 3.069729 AGGGCCTTAATACAGCTAACGAG 59.930 47.826 0.00 0.00 0.00 4.18
1838 2012 8.045507 AGTAAGTAAGTTTCAGGGCCTTAATAC 58.954 37.037 1.32 2.29 0.00 1.89
1865 2039 4.324267 CGCCCTTCCTTTTCTCTTTAGAA 58.676 43.478 0.00 0.00 40.03 2.10
1866 2040 3.307480 CCGCCCTTCCTTTTCTCTTTAGA 60.307 47.826 0.00 0.00 0.00 2.10
1872 2046 0.881796 CAACCGCCCTTCCTTTTCTC 59.118 55.000 0.00 0.00 0.00 2.87
1875 2049 1.075536 AGATCAACCGCCCTTCCTTTT 59.924 47.619 0.00 0.00 0.00 2.27
1876 2050 0.698818 AGATCAACCGCCCTTCCTTT 59.301 50.000 0.00 0.00 0.00 3.11
1937 2111 6.414890 CGTGAGTTTCTTTTTGAGAGAGAAC 58.585 40.000 0.00 0.00 35.37 3.01
1940 2114 4.607114 CGCGTGAGTTTCTTTTTGAGAGAG 60.607 45.833 0.00 0.00 35.37 3.20
1941 2115 3.245284 CGCGTGAGTTTCTTTTTGAGAGA 59.755 43.478 0.00 0.00 35.37 3.10
1942 2116 3.245284 TCGCGTGAGTTTCTTTTTGAGAG 59.755 43.478 5.77 0.00 35.37 3.20
1982 2156 1.956620 GCACGAAGTAGCGAAGGCAC 61.957 60.000 0.00 0.00 41.61 5.01
1983 2157 1.736645 GCACGAAGTAGCGAAGGCA 60.737 57.895 0.00 0.00 41.61 4.75
2011 2185 4.743151 GGGAAAACGAATCAAAACAGGAAC 59.257 41.667 0.00 0.00 0.00 3.62
2023 2197 5.607939 AGGAAAACAAAGGGAAAACGAAT 57.392 34.783 0.00 0.00 0.00 3.34
2027 2201 6.591062 ACGTAAAAGGAAAACAAAGGGAAAAC 59.409 34.615 0.00 0.00 0.00 2.43
2032 2206 6.196910 CGTAAACGTAAAAGGAAAACAAAGGG 59.803 38.462 0.00 0.00 34.11 3.95
2069 2250 6.726379 AGAAAACATTTTTGGGGGAAGAAAA 58.274 32.000 0.00 0.00 0.00 2.29
2070 2251 6.320434 AGAAAACATTTTTGGGGGAAGAAA 57.680 33.333 0.00 0.00 0.00 2.52
2185 2402 9.959749 GTGATTTAAGAAGTGTTTAATGGTCAA 57.040 29.630 0.00 0.00 0.00 3.18
2266 2483 3.201266 TGCGTAGTTCCCCCAATTTCTAT 59.799 43.478 0.00 0.00 0.00 1.98
2272 2489 0.322187 GTGTGCGTAGTTCCCCCAAT 60.322 55.000 0.00 0.00 0.00 3.16
2273 2490 1.071814 GTGTGCGTAGTTCCCCCAA 59.928 57.895 0.00 0.00 0.00 4.12
2274 2491 1.485294 ATGTGTGCGTAGTTCCCCCA 61.485 55.000 0.00 0.00 0.00 4.96
2275 2492 0.322187 AATGTGTGCGTAGTTCCCCC 60.322 55.000 0.00 0.00 0.00 5.40
2276 2493 1.530323 AAATGTGTGCGTAGTTCCCC 58.470 50.000 0.00 0.00 0.00 4.81
2277 2494 3.636282 AAAAATGTGTGCGTAGTTCCC 57.364 42.857 0.00 0.00 0.00 3.97
2307 2524 9.729023 CCGCATTTTCTATAAACAATGTTCATA 57.271 29.630 0.00 0.00 0.00 2.15
2308 2525 7.706179 CCCGCATTTTCTATAAACAATGTTCAT 59.294 33.333 0.00 0.00 0.00 2.57
2309 2526 7.032580 CCCGCATTTTCTATAAACAATGTTCA 58.967 34.615 0.00 0.00 0.00 3.18
2310 2527 7.254852 TCCCGCATTTTCTATAAACAATGTTC 58.745 34.615 0.00 0.00 0.00 3.18
2311 2528 7.164230 TCCCGCATTTTCTATAAACAATGTT 57.836 32.000 0.00 0.00 0.00 2.71
2312 2529 6.767524 TCCCGCATTTTCTATAAACAATGT 57.232 33.333 0.00 0.00 0.00 2.71
2313 2530 7.257722 AGTTCCCGCATTTTCTATAAACAATG 58.742 34.615 0.00 0.00 0.00 2.82
2314 2531 7.404671 AGTTCCCGCATTTTCTATAAACAAT 57.595 32.000 0.00 0.00 0.00 2.71
2315 2532 6.827586 AGTTCCCGCATTTTCTATAAACAA 57.172 33.333 0.00 0.00 0.00 2.83
2316 2533 6.036300 CGTAGTTCCCGCATTTTCTATAAACA 59.964 38.462 0.00 0.00 0.00 2.83
2317 2534 6.416514 CGTAGTTCCCGCATTTTCTATAAAC 58.583 40.000 0.00 0.00 0.00 2.01
2318 2535 6.592798 CGTAGTTCCCGCATTTTCTATAAA 57.407 37.500 0.00 0.00 0.00 1.40
2331 2548 2.031508 ACAAATTTGTGCGTAGTTCCCG 60.032 45.455 22.71 0.00 40.49 5.14
2332 2549 3.636282 ACAAATTTGTGCGTAGTTCCC 57.364 42.857 22.71 0.00 40.49 3.97
2333 2550 5.623673 CAGTTACAAATTTGTGCGTAGTTCC 59.376 40.000 29.72 9.49 42.31 3.62
2334 2551 5.115021 GCAGTTACAAATTTGTGCGTAGTTC 59.885 40.000 29.72 12.60 42.31 3.01
2335 2552 4.973663 GCAGTTACAAATTTGTGCGTAGTT 59.026 37.500 29.72 6.50 42.31 2.24
2336 2553 4.035792 TGCAGTTACAAATTTGTGCGTAGT 59.964 37.500 29.72 14.14 42.31 2.73
2337 2554 4.532276 TGCAGTTACAAATTTGTGCGTAG 58.468 39.130 29.72 17.46 42.31 3.51
2338 2555 4.553756 TGCAGTTACAAATTTGTGCGTA 57.446 36.364 29.72 10.45 42.31 4.42
2339 2556 3.428746 TGCAGTTACAAATTTGTGCGT 57.571 38.095 29.72 13.32 42.31 5.24
2340 2557 3.980134 TCATGCAGTTACAAATTTGTGCG 59.020 39.130 29.72 17.08 42.31 5.34
2341 2558 5.233902 TGTTCATGCAGTTACAAATTTGTGC 59.766 36.000 29.72 24.06 42.31 4.57
2342 2559 6.825284 TGTTCATGCAGTTACAAATTTGTG 57.175 33.333 29.72 16.23 42.31 3.33
2343 2560 8.436046 AATTGTTCATGCAGTTACAAATTTGT 57.564 26.923 25.99 25.99 44.86 2.83
2344 2561 9.719279 AAAATTGTTCATGCAGTTACAAATTTG 57.281 25.926 16.67 16.67 34.25 2.32


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

AutoCloner maintained by Alex Coulton.