Multiple sequence alignment - TraesCS3D01G431600

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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 TraesCS3D01G431600 chr3D 100.000 5442 0 0 1 5442 545262910 545257469 0.000000e+00 10050.0
1 TraesCS3D01G431600 chr4A 93.275 4610 238 37 879 5442 673956689 673961272 0.000000e+00 6730.0
2 TraesCS3D01G431600 chr4A 83.333 312 45 5 3019 3328 674620993 674621299 1.150000e-71 281.0
3 TraesCS3D01G431600 chr4A 90.000 60 6 0 3336 3395 674620948 674620889 1.630000e-10 78.7
4 TraesCS3D01G431600 chr4A 84.932 73 11 0 997 1069 674744525 674744453 2.100000e-09 75.0
5 TraesCS3D01G431600 chr7D 92.130 4714 243 39 813 5442 57094022 57089353 0.000000e+00 6532.0
6 TraesCS3D01G431600 chr7D 92.339 1214 76 6 2593 3794 57793943 57795151 0.000000e+00 1711.0
7 TraesCS3D01G431600 chr7D 89.333 675 31 10 879 1523 57777868 57778531 0.000000e+00 809.0
8 TraesCS3D01G431600 chr7D 94.588 388 20 1 1 388 57095209 57094823 2.810000e-167 599.0
9 TraesCS3D01G431600 chr7D 88.350 103 12 0 3898 4000 57536851 57536953 2.060000e-24 124.0
10 TraesCS3D01G431600 chr7A 94.770 3327 155 12 1664 4981 61819335 61816019 0.000000e+00 5162.0
11 TraesCS3D01G431600 chr7A 91.489 2914 172 28 879 3779 62083087 62085937 0.000000e+00 3938.0
12 TraesCS3D01G431600 chr7A 91.042 1295 105 3 3208 4499 61887265 61888551 0.000000e+00 1738.0
13 TraesCS3D01G431600 chr7A 88.796 839 71 15 1719 2541 61882612 61883443 0.000000e+00 1007.0
14 TraesCS3D01G431600 chr7A 87.153 685 70 9 2538 3212 61883601 61884277 0.000000e+00 761.0
15 TraesCS3D01G431600 chr7A 89.331 478 39 4 1 475 61822112 61821644 1.690000e-164 590.0
16 TraesCS3D01G431600 chr7A 93.280 372 17 3 1260 1624 61819703 61819333 4.790000e-150 542.0
17 TraesCS3D01G431600 chr7A 87.793 426 25 8 812 1210 61820437 61820012 1.770000e-129 473.0
18 TraesCS3D01G431600 chr7A 76.613 992 153 46 2114 3083 62743432 62742498 1.770000e-129 473.0
19 TraesCS3D01G431600 chr7A 80.426 516 77 14 3341 3852 62738862 62738367 6.660000e-99 372.0
20 TraesCS3D01G431600 chr7A 87.087 333 28 12 5123 5442 61815698 61815368 4.010000e-96 363.0
21 TraesCS3D01G431600 chr7A 99.153 118 1 0 4985 5102 61815923 61815806 4.270000e-51 213.0
22 TraesCS3D01G431600 chr7A 80.282 284 27 11 881 1147 61882290 61882561 2.590000e-43 187.0
23 TraesCS3D01G431600 chr7A 83.158 190 25 6 3136 3322 62739033 62738848 3.370000e-37 167.0
24 TraesCS3D01G431600 chrUn 77.643 908 140 35 2188 3081 91222796 91223654 1.360000e-135 494.0
25 TraesCS3D01G431600 chrUn 80.556 504 67 20 3342 3837 91224372 91224852 5.180000e-95 359.0
26 TraesCS3D01G431600 chrUn 88.060 134 16 0 3085 3218 91224068 91224201 5.640000e-35 159.0
27 TraesCS3D01G431600 chr5D 78.385 421 59 14 16 414 514209330 514208920 1.510000e-60 244.0
28 TraesCS3D01G431600 chr1A 87.283 173 17 5 157 328 152410280 152410112 5.560000e-45 193.0


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 TraesCS3D01G431600 chr3D 545257469 545262910 5441 True 10050.000000 10050 100.000000 1 5442 1 chr3D.!!$R1 5441
1 TraesCS3D01G431600 chr4A 673956689 673961272 4583 False 6730.000000 6730 93.275000 879 5442 1 chr4A.!!$F1 4563
2 TraesCS3D01G431600 chr7D 57089353 57095209 5856 True 3565.500000 6532 93.359000 1 5442 2 chr7D.!!$R1 5441
3 TraesCS3D01G431600 chr7D 57793943 57795151 1208 False 1711.000000 1711 92.339000 2593 3794 1 chr7D.!!$F3 1201
4 TraesCS3D01G431600 chr7D 57777868 57778531 663 False 809.000000 809 89.333000 879 1523 1 chr7D.!!$F2 644
5 TraesCS3D01G431600 chr7A 62083087 62085937 2850 False 3938.000000 3938 91.489000 879 3779 1 chr7A.!!$F1 2900
6 TraesCS3D01G431600 chr7A 61815368 61822112 6744 True 1223.833333 5162 91.902333 1 5442 6 chr7A.!!$R1 5441
7 TraesCS3D01G431600 chr7A 61882290 61888551 6261 False 923.250000 1738 86.818250 881 4499 4 chr7A.!!$F2 3618
8 TraesCS3D01G431600 chr7A 62738367 62743432 5065 True 337.333333 473 80.065667 2114 3852 3 chr7A.!!$R2 1738
9 TraesCS3D01G431600 chrUn 91222796 91224852 2056 False 337.333333 494 82.086333 2188 3837 3 chrUn.!!$F1 1649

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
563 1213 0.031857 TGCAATGCACGGGTTCTTTG 59.968 50.000 2.72 0.00 31.71 2.77 F
827 2395 0.036294 GCTTTAGGACTTCGGGCACT 60.036 55.000 0.00 0.00 0.00 4.40 F
1757 3655 0.886490 CTGCGGGGCATTCCTATGAC 60.886 60.000 0.00 0.00 38.13 3.06 F
2519 4437 2.285756 TGGTTTCTTGCGACGTAACTTG 59.714 45.455 0.00 0.00 0.00 3.16 F
4156 12817 1.080298 GGCTTTCAGTGGTGCATGC 60.080 57.895 11.82 11.82 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 4110 1.337728 TGACCACCTGATGTAAGCACG 60.338 52.381 0.0 0.0 0.0 5.34 R
2285 4203 2.288213 TGCCACACACAAACGAAAAACA 60.288 40.909 0.0 0.0 0.0 2.83 R
3024 5143 0.485099 ACCCATACCCCTGCAAACAA 59.515 50.000 0.0 0.0 0.0 2.83 R
4291 12952 0.178767 CATGACCCGCCTCATTCAGA 59.821 55.000 0.0 0.0 0.0 3.27 R
5170 14035 4.390297 GGCGAGAAGAATGTATATTGAGGC 59.610 45.833 0.0 0.0 0.0 4.70 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
85 87 2.239402 TGATGTGTGGAGCATGTATGGT 59.761 45.455 0.00 0.00 41.89 3.55
96 98 2.954318 GCATGTATGGTTGATTGGCTCT 59.046 45.455 0.00 0.00 0.00 4.09
145 149 7.888514 TTTATGGGATGGTATAGGTTGAGAT 57.111 36.000 0.00 0.00 0.00 2.75
282 286 4.277476 ACCTGCGGGATATTGAATCAAAA 58.723 39.130 21.41 0.00 36.25 2.44
358 362 3.173668 TGGATTACGTGTATGAGGTGC 57.826 47.619 0.00 0.00 0.00 5.01
367 371 0.246635 GTATGAGGTGCGTGTGAGGT 59.753 55.000 0.00 0.00 0.00 3.85
375 379 3.036084 CGTGTGAGGTGTGGCGTC 61.036 66.667 0.00 0.00 0.00 5.19
413 417 6.862711 ATAACAATCATGATGAGCAGTCAG 57.137 37.500 9.46 0.00 35.66 3.51
418 422 3.774616 TGATGAGCAGTCAGCATCC 57.225 52.632 0.00 0.00 44.18 3.51
424 428 2.401967 GCAGTCAGCATCCATCACC 58.598 57.895 0.00 0.00 44.79 4.02
431 435 0.036732 AGCATCCATCACCAACACGT 59.963 50.000 0.00 0.00 0.00 4.49
434 438 2.150390 CATCCATCACCAACACGTTCA 58.850 47.619 0.00 0.00 0.00 3.18
446 450 4.062293 CAACACGTTCAAATCCTAGGTGA 58.938 43.478 9.08 2.18 33.31 4.02
471 1121 1.139520 GTAAATGCCCGCCTTGCTG 59.860 57.895 0.00 0.00 0.00 4.41
499 1149 0.452784 GTCGTCTTTCGCCAATGCAC 60.453 55.000 0.00 0.00 39.67 4.57
526 1176 4.407365 AGGGTTCGGTCAGAATCAAAATT 58.593 39.130 0.00 0.00 41.70 1.82
533 1183 6.620678 TCGGTCAGAATCAAAATTGAAATCC 58.379 36.000 0.00 0.00 41.13 3.01
557 1207 0.244450 CTTCATTGCAATGCACGGGT 59.756 50.000 30.57 0.00 38.71 5.28
559 1209 0.243365 TCATTGCAATGCACGGGTTC 59.757 50.000 30.57 0.00 38.71 3.62
563 1213 0.031857 TGCAATGCACGGGTTCTTTG 59.968 50.000 2.72 0.00 31.71 2.77
564 1214 1.284297 GCAATGCACGGGTTCTTTGC 61.284 55.000 0.00 2.01 36.61 3.68
594 1603 8.919018 TTTTTGAGGTAAAACCCCCATATATT 57.081 30.769 0.00 0.00 39.75 1.28
598 1607 8.352808 TGAGGTAAAACCCCCATATATTAACT 57.647 34.615 0.00 0.00 39.75 2.24
599 1608 8.442374 TGAGGTAAAACCCCCATATATTAACTC 58.558 37.037 0.00 0.00 39.75 3.01
601 1610 8.966501 AGGTAAAACCCCCATATATTAACTCAT 58.033 33.333 0.00 0.00 39.75 2.90
606 1615 7.563724 ACCCCCATATATTAACTCATAACGT 57.436 36.000 0.00 0.00 0.00 3.99
607 1616 7.981142 ACCCCCATATATTAACTCATAACGTT 58.019 34.615 5.88 5.88 0.00 3.99
608 1617 8.098912 ACCCCCATATATTAACTCATAACGTTC 58.901 37.037 2.82 0.00 0.00 3.95
609 1618 8.098286 CCCCCATATATTAACTCATAACGTTCA 58.902 37.037 2.82 0.00 0.00 3.18
610 1619 9.667107 CCCCATATATTAACTCATAACGTTCAT 57.333 33.333 2.82 0.00 0.00 2.57
615 1624 3.992943 AACTCATAACGTTCATGGGGA 57.007 42.857 2.82 0.00 0.00 4.81
617 1626 5.623956 AACTCATAACGTTCATGGGGATA 57.376 39.130 2.82 0.00 0.00 2.59
618 1627 5.623956 ACTCATAACGTTCATGGGGATAA 57.376 39.130 2.82 0.00 0.00 1.75
621 1630 7.741785 ACTCATAACGTTCATGGGGATAATTA 58.258 34.615 2.82 0.00 0.00 1.40
624 1803 7.659799 TCATAACGTTCATGGGGATAATTACAG 59.340 37.037 2.82 0.00 0.00 2.74
627 1806 4.445735 CGTTCATGGGGATAATTACAGGGT 60.446 45.833 0.00 0.00 0.00 4.34
632 1811 2.490991 GGGATAATTACAGGGTCGTGC 58.509 52.381 0.00 0.00 0.00 5.34
633 1812 2.132762 GGATAATTACAGGGTCGTGCG 58.867 52.381 0.00 0.00 0.00 5.34
634 1813 2.132762 GATAATTACAGGGTCGTGCGG 58.867 52.381 0.00 0.00 0.00 5.69
635 1814 0.176219 TAATTACAGGGTCGTGCGGG 59.824 55.000 0.00 0.00 0.00 6.13
636 1815 2.530958 AATTACAGGGTCGTGCGGGG 62.531 60.000 0.00 0.00 0.00 5.73
654 1833 1.741525 GTGCCAAACCACACATGCT 59.258 52.632 0.00 0.00 36.77 3.79
655 1834 0.958091 GTGCCAAACCACACATGCTA 59.042 50.000 0.00 0.00 36.77 3.49
656 1835 1.339610 GTGCCAAACCACACATGCTAA 59.660 47.619 0.00 0.00 36.77 3.09
657 1836 2.034878 TGCCAAACCACACATGCTAAA 58.965 42.857 0.00 0.00 0.00 1.85
658 1837 2.035704 TGCCAAACCACACATGCTAAAG 59.964 45.455 0.00 0.00 0.00 1.85
659 1838 2.676076 CCAAACCACACATGCTAAAGC 58.324 47.619 0.00 0.00 42.50 3.51
669 1848 3.966215 GCTAAAGCACGTGCCTCA 58.034 55.556 35.51 19.66 43.38 3.86
670 1849 2.244000 GCTAAAGCACGTGCCTCAA 58.756 52.632 35.51 18.19 43.38 3.02
673 1852 2.351738 GCTAAAGCACGTGCCTCAAAAT 60.352 45.455 35.51 13.87 43.38 1.82
674 1853 2.888834 AAAGCACGTGCCTCAAAATT 57.111 40.000 35.51 19.18 43.38 1.82
675 1854 4.614993 GCTAAAGCACGTGCCTCAAAATTA 60.615 41.667 35.51 20.10 43.38 1.40
677 1856 2.504367 AGCACGTGCCTCAAAATTACT 58.496 42.857 35.51 10.89 43.38 2.24
679 1858 2.414161 GCACGTGCCTCAAAATTACTCC 60.414 50.000 30.12 0.00 34.31 3.85
680 1859 3.074412 CACGTGCCTCAAAATTACTCCT 58.926 45.455 0.82 0.00 0.00 3.69
682 1861 2.678336 CGTGCCTCAAAATTACTCCTCC 59.322 50.000 0.00 0.00 0.00 4.30
683 1862 3.619979 CGTGCCTCAAAATTACTCCTCCT 60.620 47.826 0.00 0.00 0.00 3.69
684 1863 4.382685 CGTGCCTCAAAATTACTCCTCCTA 60.383 45.833 0.00 0.00 0.00 2.94
686 1865 4.783227 TGCCTCAAAATTACTCCTCCTACT 59.217 41.667 0.00 0.00 0.00 2.57
687 1866 5.250774 TGCCTCAAAATTACTCCTCCTACTT 59.749 40.000 0.00 0.00 0.00 2.24
688 1867 6.181190 GCCTCAAAATTACTCCTCCTACTTT 58.819 40.000 0.00 0.00 0.00 2.66
689 1868 6.316640 GCCTCAAAATTACTCCTCCTACTTTC 59.683 42.308 0.00 0.00 0.00 2.62
693 1872 9.284968 TCAAAATTACTCCTCCTACTTTCAAAG 57.715 33.333 0.00 0.00 0.00 2.77
694 1873 7.689446 AAATTACTCCTCCTACTTTCAAAGC 57.311 36.000 0.00 0.00 0.00 3.51
695 1874 3.320673 ACTCCTCCTACTTTCAAAGCG 57.679 47.619 0.00 0.00 0.00 4.68
696 1875 2.028020 ACTCCTCCTACTTTCAAAGCGG 60.028 50.000 0.00 0.00 0.00 5.52
698 1877 2.635915 TCCTCCTACTTTCAAAGCGGAA 59.364 45.455 9.41 0.00 32.94 4.30
699 1878 2.742589 CCTCCTACTTTCAAAGCGGAAC 59.257 50.000 9.41 0.00 32.94 3.62
700 1879 3.399330 CTCCTACTTTCAAAGCGGAACA 58.601 45.455 9.41 0.00 32.94 3.18
702 1881 3.813166 TCCTACTTTCAAAGCGGAACAAG 59.187 43.478 6.35 0.00 31.06 3.16
703 1882 2.492019 ACTTTCAAAGCGGAACAAGC 57.508 45.000 0.00 0.00 0.00 4.01
705 1884 2.362077 ACTTTCAAAGCGGAACAAGCAT 59.638 40.909 0.00 0.00 37.01 3.79
706 1885 2.420628 TTCAAAGCGGAACAAGCATG 57.579 45.000 0.00 0.00 37.01 4.06
707 1886 1.317613 TCAAAGCGGAACAAGCATGT 58.682 45.000 0.00 0.00 43.14 3.21
708 1887 1.266718 TCAAAGCGGAACAAGCATGTC 59.733 47.619 0.00 0.00 39.40 3.06
709 1888 0.598065 AAAGCGGAACAAGCATGTCC 59.402 50.000 0.00 0.00 39.40 4.02
710 1889 1.244019 AAGCGGAACAAGCATGTCCC 61.244 55.000 0.00 0.00 39.40 4.46
711 1890 1.971167 GCGGAACAAGCATGTCCCA 60.971 57.895 0.00 0.00 39.40 4.37
712 1891 1.523154 GCGGAACAAGCATGTCCCAA 61.523 55.000 0.00 0.00 39.40 4.12
713 1892 0.958091 CGGAACAAGCATGTCCCAAA 59.042 50.000 0.00 0.00 39.40 3.28
714 1893 1.339610 CGGAACAAGCATGTCCCAAAA 59.660 47.619 0.00 0.00 39.40 2.44
717 1896 3.006752 GGAACAAGCATGTCCCAAAATCA 59.993 43.478 0.00 0.00 39.40 2.57
719 1898 2.028748 ACAAGCATGTCCCAAAATCAGC 60.029 45.455 0.00 0.00 33.41 4.26
722 1901 2.901839 AGCATGTCCCAAAATCAGCTTT 59.098 40.909 0.00 0.00 0.00 3.51
723 1902 3.325716 AGCATGTCCCAAAATCAGCTTTT 59.674 39.130 0.00 0.00 37.54 2.27
724 1903 3.681417 GCATGTCCCAAAATCAGCTTTTC 59.319 43.478 0.00 0.00 34.80 2.29
725 1904 3.641437 TGTCCCAAAATCAGCTTTTCG 57.359 42.857 0.00 0.00 34.80 3.46
727 1906 1.892474 TCCCAAAATCAGCTTTTCGGG 59.108 47.619 0.93 0.93 41.59 5.14
728 1907 1.672737 CCCAAAATCAGCTTTTCGGGC 60.673 52.381 0.00 0.00 37.85 6.13
729 1908 1.273327 CCAAAATCAGCTTTTCGGGCT 59.727 47.619 0.00 0.00 41.07 5.19
730 1909 2.491693 CCAAAATCAGCTTTTCGGGCTA 59.508 45.455 0.00 0.00 38.03 3.93
731 1910 3.131046 CCAAAATCAGCTTTTCGGGCTAT 59.869 43.478 0.00 0.00 38.03 2.97
733 1912 3.281727 AATCAGCTTTTCGGGCTATGA 57.718 42.857 0.00 0.00 38.03 2.15
734 1913 3.498774 ATCAGCTTTTCGGGCTATGAT 57.501 42.857 0.00 0.00 38.03 2.45
736 1915 2.435805 TCAGCTTTTCGGGCTATGATCT 59.564 45.455 0.00 0.00 38.03 2.75
737 1916 2.805099 CAGCTTTTCGGGCTATGATCTC 59.195 50.000 0.00 0.00 38.03 2.75
738 1917 2.147150 GCTTTTCGGGCTATGATCTCC 58.853 52.381 0.00 0.00 0.00 3.71
739 1918 2.224402 GCTTTTCGGGCTATGATCTCCT 60.224 50.000 0.00 0.00 0.00 3.69
740 1919 3.745797 GCTTTTCGGGCTATGATCTCCTT 60.746 47.826 0.00 0.00 0.00 3.36
741 1920 3.753294 TTTCGGGCTATGATCTCCTTC 57.247 47.619 0.00 0.00 0.00 3.46
742 1921 2.381752 TCGGGCTATGATCTCCTTCA 57.618 50.000 0.00 0.00 0.00 3.02
743 1922 1.964223 TCGGGCTATGATCTCCTTCAC 59.036 52.381 0.00 0.00 0.00 3.18
744 1923 1.967066 CGGGCTATGATCTCCTTCACT 59.033 52.381 0.00 0.00 0.00 3.41
745 1924 3.157881 CGGGCTATGATCTCCTTCACTA 58.842 50.000 0.00 0.00 0.00 2.74
746 1925 3.766591 CGGGCTATGATCTCCTTCACTAT 59.233 47.826 0.00 0.00 0.00 2.12
748 1927 4.081198 GGGCTATGATCTCCTTCACTATGG 60.081 50.000 0.00 0.00 0.00 2.74
749 1928 4.502962 GCTATGATCTCCTTCACTATGGC 58.497 47.826 0.00 0.00 0.00 4.40
750 1929 4.222588 GCTATGATCTCCTTCACTATGGCT 59.777 45.833 0.00 0.00 0.00 4.75
751 1930 5.279910 GCTATGATCTCCTTCACTATGGCTT 60.280 44.000 0.00 0.00 0.00 4.35
754 1933 4.657504 TGATCTCCTTCACTATGGCTTCAT 59.342 41.667 0.00 0.00 35.02 2.57
755 1934 5.131642 TGATCTCCTTCACTATGGCTTCATT 59.868 40.000 0.00 0.00 32.59 2.57
756 1935 5.441718 TCTCCTTCACTATGGCTTCATTT 57.558 39.130 0.00 0.00 32.59 2.32
757 1936 5.431765 TCTCCTTCACTATGGCTTCATTTC 58.568 41.667 0.00 0.00 32.59 2.17
758 1937 5.190528 TCTCCTTCACTATGGCTTCATTTCT 59.809 40.000 0.00 0.00 32.59 2.52
759 1938 5.819991 TCCTTCACTATGGCTTCATTTCTT 58.180 37.500 0.00 0.00 32.59 2.52
760 1939 5.882557 TCCTTCACTATGGCTTCATTTCTTC 59.117 40.000 0.00 0.00 32.59 2.87
761 1940 5.067023 CCTTCACTATGGCTTCATTTCTTCC 59.933 44.000 0.00 0.00 32.59 3.46
762 1941 5.441718 TCACTATGGCTTCATTTCTTCCT 57.558 39.130 0.00 0.00 32.59 3.36
764 1943 4.578105 CACTATGGCTTCATTTCTTCCTCC 59.422 45.833 0.00 0.00 32.59 4.30
766 1945 1.340017 TGGCTTCATTTCTTCCTCCCG 60.340 52.381 0.00 0.00 0.00 5.14
767 1946 1.340114 GGCTTCATTTCTTCCTCCCGT 60.340 52.381 0.00 0.00 0.00 5.28
770 1949 3.532542 CTTCATTTCTTCCTCCCGTACC 58.467 50.000 0.00 0.00 0.00 3.34
771 1950 2.829023 TCATTTCTTCCTCCCGTACCT 58.171 47.619 0.00 0.00 0.00 3.08
772 1951 3.178865 TCATTTCTTCCTCCCGTACCTT 58.821 45.455 0.00 0.00 0.00 3.50
773 1952 3.197116 TCATTTCTTCCTCCCGTACCTTC 59.803 47.826 0.00 0.00 0.00 3.46
774 1953 2.617840 TTCTTCCTCCCGTACCTTCT 57.382 50.000 0.00 0.00 0.00 2.85
775 1954 1.848652 TCTTCCTCCCGTACCTTCTG 58.151 55.000 0.00 0.00 0.00 3.02
779 1958 2.829023 TCCTCCCGTACCTTCTGAAAT 58.171 47.619 0.00 0.00 0.00 2.17
780 1959 2.500098 TCCTCCCGTACCTTCTGAAATG 59.500 50.000 0.00 0.00 0.00 2.32
781 1960 2.236395 CCTCCCGTACCTTCTGAAATGT 59.764 50.000 0.00 0.00 0.00 2.71
782 1961 3.522553 CTCCCGTACCTTCTGAAATGTC 58.477 50.000 0.00 0.00 0.00 3.06
783 1962 2.235402 TCCCGTACCTTCTGAAATGTCC 59.765 50.000 0.00 0.00 0.00 4.02
784 1963 2.236395 CCCGTACCTTCTGAAATGTCCT 59.764 50.000 0.00 0.00 0.00 3.85
785 1964 3.307480 CCCGTACCTTCTGAAATGTCCTT 60.307 47.826 0.00 0.00 0.00 3.36
787 1966 4.562757 CCGTACCTTCTGAAATGTCCTTCA 60.563 45.833 0.00 0.00 34.22 3.02
790 1969 5.825593 ACCTTCTGAAATGTCCTTCACTA 57.174 39.130 0.00 0.00 32.00 2.74
791 1970 6.380079 ACCTTCTGAAATGTCCTTCACTAT 57.620 37.500 0.00 0.00 32.00 2.12
792 1971 6.176183 ACCTTCTGAAATGTCCTTCACTATG 58.824 40.000 0.00 0.00 32.00 2.23
794 1973 5.762179 TCTGAAATGTCCTTCACTATGGT 57.238 39.130 0.00 0.00 32.00 3.55
795 1974 5.491070 TCTGAAATGTCCTTCACTATGGTG 58.509 41.667 2.16 2.16 44.23 4.17
796 1975 4.009675 TGAAATGTCCTTCACTATGGTGC 58.990 43.478 3.97 0.00 42.72 5.01
797 1976 3.719268 AATGTCCTTCACTATGGTGCA 57.281 42.857 3.97 0.00 42.72 4.57
798 1977 2.472695 TGTCCTTCACTATGGTGCAC 57.527 50.000 8.80 8.80 42.72 4.57
799 1978 1.337728 TGTCCTTCACTATGGTGCACG 60.338 52.381 11.45 0.00 42.72 5.34
800 1979 0.249120 TCCTTCACTATGGTGCACGG 59.751 55.000 11.45 2.87 42.72 4.94
801 1980 0.744414 CCTTCACTATGGTGCACGGG 60.744 60.000 11.45 0.00 42.72 5.28
802 1981 1.369091 CTTCACTATGGTGCACGGGC 61.369 60.000 11.45 0.34 42.72 6.13
803 1982 1.836999 TTCACTATGGTGCACGGGCT 61.837 55.000 12.74 0.00 42.72 5.19
804 1983 1.815421 CACTATGGTGCACGGGCTC 60.815 63.158 12.74 7.35 41.91 4.70
805 1984 1.990060 ACTATGGTGCACGGGCTCT 60.990 57.895 12.74 0.00 41.91 4.09
806 1985 1.221840 CTATGGTGCACGGGCTCTT 59.778 57.895 12.74 4.18 41.91 2.85
807 1986 0.392998 CTATGGTGCACGGGCTCTTT 60.393 55.000 12.74 1.42 41.91 2.52
808 1987 0.676466 TATGGTGCACGGGCTCTTTG 60.676 55.000 12.74 0.00 41.91 2.77
809 1988 4.043200 GGTGCACGGGCTCTTTGC 62.043 66.667 12.74 0.00 41.91 3.68
810 1989 2.980233 GTGCACGGGCTCTTTGCT 60.980 61.111 12.74 0.00 42.39 3.91
826 2394 0.321298 TGCTTTAGGACTTCGGGCAC 60.321 55.000 0.00 0.00 0.00 5.01
827 2395 0.036294 GCTTTAGGACTTCGGGCACT 60.036 55.000 0.00 0.00 0.00 4.40
828 2396 2.007547 GCTTTAGGACTTCGGGCACTC 61.008 57.143 0.00 0.00 0.00 3.51
838 2406 1.089481 TCGGGCACTCGATGAATTGC 61.089 55.000 0.00 0.00 33.92 3.56
884 2453 3.440522 GGACAGTTGGGCTTGTAGATTTC 59.559 47.826 0.00 0.00 0.00 2.17
1361 3239 3.587933 GTCTCCGCGCTCTCCGAT 61.588 66.667 5.56 0.00 40.02 4.18
1518 3396 2.171659 GGTGAGATTTCTCCCCTTCCTC 59.828 54.545 5.17 0.00 42.20 3.71
1657 3555 1.069358 TGAAATTTTGTGTTCGCCCCC 59.931 47.619 0.00 0.00 0.00 5.40
1680 3578 1.205893 CACTTCCTCAGGCTGTAGGTC 59.794 57.143 23.46 0.00 34.30 3.85
1694 3592 5.006358 GGCTGTAGGTCAACAATATGTTACG 59.994 44.000 0.00 0.00 38.77 3.18
1729 3627 9.500785 TTGATGTTCATGTATTGTGACTTTCTA 57.499 29.630 0.00 0.00 0.00 2.10
1757 3655 0.886490 CTGCGGGGCATTCCTATGAC 60.886 60.000 0.00 0.00 38.13 3.06
1934 3832 4.162690 GGCTCAATCCCGCCGAGT 62.163 66.667 0.00 0.00 36.45 4.18
2152 4065 7.184106 TCAGAAAAATCGTACTGTTTTGTCAC 58.816 34.615 6.02 1.39 29.38 3.67
2519 4437 2.285756 TGGTTTCTTGCGACGTAACTTG 59.714 45.455 0.00 0.00 0.00 3.16
2520 4438 2.349155 GGTTTCTTGCGACGTAACTTGG 60.349 50.000 0.00 0.00 0.00 3.61
2606 4693 3.885724 TGTCAGTTGGCATCTCGAATA 57.114 42.857 0.00 0.00 0.00 1.75
2665 4761 6.714810 ACAATTAAAGGTGTATGTCTTGAGCA 59.285 34.615 0.00 0.00 0.00 4.26
2670 4766 2.353889 GGTGTATGTCTTGAGCATGCAG 59.646 50.000 21.98 8.96 39.05 4.41
2747 4843 7.040823 AGTGAACTCTTCAAAGCTTGGATTTAG 60.041 37.037 3.86 5.34 42.15 1.85
2856 4962 8.617290 TGGAAACTTTATTAACCAGAGAGTTC 57.383 34.615 0.00 0.00 0.00 3.01
2903 5010 5.425539 TCCTTCCTCCTGTTCTAAATGGTAG 59.574 44.000 0.00 0.00 0.00 3.18
3203 8856 6.368779 ACTTACTTGCCATACTAACTGGAA 57.631 37.500 0.00 0.00 35.70 3.53
3240 11886 7.113965 CAGACGATTTTTGGATCTTGTTTCTTG 59.886 37.037 0.00 0.00 0.00 3.02
3269 11915 6.434340 AGAAGCTATGGTTTTCTTGGGTAAAG 59.566 38.462 0.00 0.00 37.22 1.85
3291 11937 3.004106 GCAAGCAGTGACAACTCTTCATT 59.996 43.478 0.00 0.00 32.98 2.57
3295 11944 4.883585 AGCAGTGACAACTCTTCATTGAAA 59.116 37.500 0.01 0.00 33.66 2.69
3329 11978 4.918810 ACATCAAAAGGGTCACACTTTC 57.081 40.909 5.23 0.00 37.18 2.62
3333 11982 1.981256 AAAGGGTCACACTTTCGCAT 58.019 45.000 0.00 0.00 33.07 4.73
3379 12028 5.863935 GGTCAAATTCAAATACAGTTCTGCC 59.136 40.000 0.00 0.00 0.00 4.85
3446 12097 4.720090 CATGCTGTTCAACTCAAAGCTAG 58.280 43.478 0.00 0.00 34.92 3.42
3495 12146 5.702209 GGTTGACAATTACGAACTTCCCTAA 59.298 40.000 0.00 0.00 0.00 2.69
3504 12155 3.326880 ACGAACTTCCCTAACTGGTTCAT 59.673 43.478 0.00 0.00 36.91 2.57
3615 12276 3.382865 AGCGATATCAGTCTTGCTCAGAA 59.617 43.478 3.12 0.00 31.28 3.02
3634 12295 4.022068 CAGAAGGCAGCATTTTACCTTTCA 60.022 41.667 0.00 0.00 42.54 2.69
3664 12325 6.543465 TGTTATGCCCTTCTAATGTTGATGAG 59.457 38.462 0.00 0.00 0.00 2.90
3839 12500 1.133792 CAACCAACCCTGTCAGTTCCT 60.134 52.381 0.00 0.00 0.00 3.36
3969 12630 3.101437 TGCATTTACGGGTTCCTCTAGA 58.899 45.455 0.00 0.00 0.00 2.43
4137 12798 5.120363 GTCGTGGAGGTTTTACTGAAAGATC 59.880 44.000 0.00 0.00 37.43 2.75
4156 12817 1.080298 GGCTTTCAGTGGTGCATGC 60.080 57.895 11.82 11.82 0.00 4.06
4291 12952 7.951591 ACCTGCTGAAGTGTGTAAATTTATTT 58.048 30.769 0.31 0.00 0.00 1.40
4349 13010 5.332707 TCGATCTTCGTGACAGATTGTTAG 58.667 41.667 0.00 0.00 41.35 2.34
4356 13017 4.462834 TCGTGACAGATTGTTAGACTGGAT 59.537 41.667 0.00 0.00 36.17 3.41
4361 13022 8.607459 GTGACAGATTGTTAGACTGGATTAATG 58.393 37.037 0.00 0.00 36.17 1.90
4517 13181 1.552337 CTGGTGACTGTACTGCTGGAT 59.448 52.381 0.00 0.00 0.00 3.41
4729 13393 6.220726 TGATAGTGTAAAGTAGCATCTGCA 57.779 37.500 4.79 0.00 45.16 4.41
4799 13463 2.961526 TTAGCTGTCGACTCCATTCC 57.038 50.000 17.92 0.00 0.00 3.01
4838 13504 8.985315 TCATTTCTTCTGTCATGGCTAAATAT 57.015 30.769 0.00 0.00 0.00 1.28
4980 13646 4.236527 TCTAGACTGAGCCACTGATGTA 57.763 45.455 0.00 0.00 0.00 2.29
4981 13647 3.948473 TCTAGACTGAGCCACTGATGTAC 59.052 47.826 0.00 0.00 0.00 2.90
4982 13648 2.813907 AGACTGAGCCACTGATGTACT 58.186 47.619 0.00 0.00 0.00 2.73
5006 13775 8.077991 ACTATATTTTACATGACATGCACATGC 58.922 33.333 24.03 0.00 45.95 4.06
5230 14112 7.672239 TGGTCCTATAAAGCAATTTGTAACCTT 59.328 33.333 0.00 0.00 0.00 3.50
5293 14175 5.008118 CAGACCACTGAGAAGAAGGAAAAAC 59.992 44.000 0.00 0.00 46.03 2.43
5296 14178 5.126067 CCACTGAGAAGAAGGAAAAACTCA 58.874 41.667 0.00 0.00 34.13 3.41
5299 14181 6.969473 CACTGAGAAGAAGGAAAAACTCAAAC 59.031 38.462 0.00 0.00 34.71 2.93
5303 14185 8.028938 TGAGAAGAAGGAAAAACTCAAACAAAG 58.971 33.333 0.00 0.00 32.66 2.77
5304 14186 7.896811 AGAAGAAGGAAAAACTCAAACAAAGT 58.103 30.769 0.00 0.00 0.00 2.66
5350 14238 4.264253 TCAGACGCAAGAAATGGAATCAT 58.736 39.130 0.00 0.00 43.62 2.45
5356 14244 7.552687 AGACGCAAGAAATGGAATCATAGTTTA 59.447 33.333 0.00 0.00 43.62 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 8.397906 CACACATCATCCTGTTTTATCGTAATT 58.602 33.333 0.00 0.00 0.00 1.40
51 53 4.875536 TCCACACATCATCCTGTTTTATCG 59.124 41.667 0.00 0.00 0.00 2.92
85 87 3.378112 CCGCTTAAATCAGAGCCAATCAA 59.622 43.478 0.00 0.00 35.49 2.57
96 98 3.358111 TTCATGGTCCCGCTTAAATCA 57.642 42.857 0.00 0.00 0.00 2.57
139 143 8.296211 TCAGCCATGAAATATTTTGATCTCAA 57.704 30.769 1.43 0.00 30.61 3.02
145 149 6.050432 GCCAATCAGCCATGAAATATTTTGA 58.950 36.000 1.43 1.51 39.39 2.69
199 203 3.307762 GCCCAGCCTATTCTCCGAATATT 60.308 47.826 0.00 0.00 0.00 1.28
200 204 2.237392 GCCCAGCCTATTCTCCGAATAT 59.763 50.000 0.00 0.00 0.00 1.28
201 205 1.623811 GCCCAGCCTATTCTCCGAATA 59.376 52.381 0.00 0.00 0.00 1.75
202 206 0.398318 GCCCAGCCTATTCTCCGAAT 59.602 55.000 0.00 0.00 0.00 3.34
204 208 0.980754 TTGCCCAGCCTATTCTCCGA 60.981 55.000 0.00 0.00 0.00 4.55
206 210 1.064389 ACTTTGCCCAGCCTATTCTCC 60.064 52.381 0.00 0.00 0.00 3.71
207 211 2.424956 CAACTTTGCCCAGCCTATTCTC 59.575 50.000 0.00 0.00 0.00 2.87
358 362 3.036084 GACGCCACACCTCACACG 61.036 66.667 0.00 0.00 0.00 4.49
413 417 0.881118 AACGTGTTGGTGATGGATGC 59.119 50.000 0.00 0.00 0.00 3.91
416 420 2.333688 TTGAACGTGTTGGTGATGGA 57.666 45.000 0.00 0.00 0.00 3.41
418 422 3.253188 AGGATTTGAACGTGTTGGTGATG 59.747 43.478 0.00 0.00 0.00 3.07
424 428 4.062293 TCACCTAGGATTTGAACGTGTTG 58.938 43.478 17.98 0.00 0.00 3.33
446 450 2.186826 GCGGGCATTTACGAGGCAT 61.187 57.895 0.00 0.00 0.00 4.40
471 1121 1.070776 GCGAAAGACGACAACTTGTCC 60.071 52.381 14.98 3.68 44.20 4.02
490 1140 1.244019 AACCCTTCTCGTGCATTGGC 61.244 55.000 0.00 0.00 41.68 4.52
499 1149 0.601558 TTCTGACCGAACCCTTCTCG 59.398 55.000 0.00 0.00 36.06 4.04
526 1176 6.092944 GCATTGCAATGAAGAAATGGATTTCA 59.907 34.615 37.36 0.00 42.10 2.69
533 1183 3.061563 CCGTGCATTGCAATGAAGAAATG 59.938 43.478 37.36 21.45 41.47 2.32
538 1188 0.244450 ACCCGTGCATTGCAATGAAG 59.756 50.000 37.36 26.03 41.47 3.02
574 1583 8.442374 TGAGTTAATATATGGGGGTTTTACCTC 58.558 37.037 0.00 0.00 38.29 3.85
583 1592 8.098286 TGAACGTTATGAGTTAATATATGGGGG 58.902 37.037 0.00 0.00 31.14 5.40
584 1593 9.667107 ATGAACGTTATGAGTTAATATATGGGG 57.333 33.333 0.00 0.00 31.14 4.96
588 1597 9.667107 CCCCATGAACGTTATGAGTTAATATAT 57.333 33.333 0.00 0.00 31.14 0.86
589 1598 8.872134 TCCCCATGAACGTTATGAGTTAATATA 58.128 33.333 0.00 0.00 31.14 0.86
590 1599 7.741785 TCCCCATGAACGTTATGAGTTAATAT 58.258 34.615 0.00 0.00 31.14 1.28
591 1600 7.127012 TCCCCATGAACGTTATGAGTTAATA 57.873 36.000 0.00 0.00 31.14 0.98
593 1602 5.423704 TCCCCATGAACGTTATGAGTTAA 57.576 39.130 0.00 0.00 31.14 2.01
594 1603 5.623956 ATCCCCATGAACGTTATGAGTTA 57.376 39.130 0.00 0.00 31.14 2.24
598 1607 7.510407 TGTAATTATCCCCATGAACGTTATGA 58.490 34.615 0.00 0.00 0.00 2.15
599 1608 7.094805 CCTGTAATTATCCCCATGAACGTTATG 60.095 40.741 0.00 5.82 0.00 1.90
601 1610 6.292923 CCTGTAATTATCCCCATGAACGTTA 58.707 40.000 0.00 0.00 0.00 3.18
602 1611 5.130350 CCTGTAATTATCCCCATGAACGTT 58.870 41.667 0.00 0.00 0.00 3.99
603 1612 4.445735 CCCTGTAATTATCCCCATGAACGT 60.446 45.833 0.00 0.00 0.00 3.99
604 1613 4.072131 CCCTGTAATTATCCCCATGAACG 58.928 47.826 0.00 0.00 0.00 3.95
606 1615 4.202419 CGACCCTGTAATTATCCCCATGAA 60.202 45.833 0.00 0.00 0.00 2.57
607 1616 3.326588 CGACCCTGTAATTATCCCCATGA 59.673 47.826 0.00 0.00 0.00 3.07
608 1617 3.072476 ACGACCCTGTAATTATCCCCATG 59.928 47.826 0.00 0.00 0.00 3.66
609 1618 3.072476 CACGACCCTGTAATTATCCCCAT 59.928 47.826 0.00 0.00 0.00 4.00
610 1619 2.436542 CACGACCCTGTAATTATCCCCA 59.563 50.000 0.00 0.00 0.00 4.96
611 1620 2.809299 GCACGACCCTGTAATTATCCCC 60.809 54.545 0.00 0.00 0.00 4.81
612 1621 2.490991 GCACGACCCTGTAATTATCCC 58.509 52.381 0.00 0.00 0.00 3.85
613 1622 2.132762 CGCACGACCCTGTAATTATCC 58.867 52.381 0.00 0.00 0.00 2.59
615 1624 1.202604 CCCGCACGACCCTGTAATTAT 60.203 52.381 0.00 0.00 0.00 1.28
617 1626 1.078708 CCCGCACGACCCTGTAATT 60.079 57.895 0.00 0.00 0.00 1.40
618 1627 2.582436 CCCGCACGACCCTGTAAT 59.418 61.111 0.00 0.00 0.00 1.89
632 1811 3.601685 GTGTGGTTTGGCACCCCG 61.602 66.667 0.00 0.00 46.68 5.73
633 1812 1.836604 ATGTGTGGTTTGGCACCCC 60.837 57.895 0.00 0.00 46.68 4.95
634 1813 1.367102 CATGTGTGGTTTGGCACCC 59.633 57.895 0.00 0.00 46.68 4.61
636 1815 0.958091 TAGCATGTGTGGTTTGGCAC 59.042 50.000 0.00 0.00 37.28 5.01
652 1831 0.591170 TTTGAGGCACGTGCTTTAGC 59.409 50.000 36.84 21.55 41.70 3.09
654 1833 4.517453 AGTAATTTTGAGGCACGTGCTTTA 59.483 37.500 36.84 25.85 41.70 1.85
655 1834 2.888834 AATTTTGAGGCACGTGCTTT 57.111 40.000 36.84 26.12 41.70 3.51
656 1835 2.884639 AGTAATTTTGAGGCACGTGCTT 59.115 40.909 36.84 32.13 41.70 3.91
657 1836 2.484264 GAGTAATTTTGAGGCACGTGCT 59.516 45.455 36.84 24.00 41.70 4.40
658 1837 2.414161 GGAGTAATTTTGAGGCACGTGC 60.414 50.000 32.15 32.15 41.14 5.34
659 1838 3.074412 AGGAGTAATTTTGAGGCACGTG 58.926 45.455 12.28 12.28 0.00 4.49
660 1839 3.335579 GAGGAGTAATTTTGAGGCACGT 58.664 45.455 0.00 0.00 0.00 4.49
661 1840 2.678336 GGAGGAGTAATTTTGAGGCACG 59.322 50.000 0.00 0.00 0.00 5.34
662 1841 3.956744 AGGAGGAGTAATTTTGAGGCAC 58.043 45.455 0.00 0.00 0.00 5.01
663 1842 4.783227 AGTAGGAGGAGTAATTTTGAGGCA 59.217 41.667 0.00 0.00 0.00 4.75
664 1843 5.360649 AGTAGGAGGAGTAATTTTGAGGC 57.639 43.478 0.00 0.00 0.00 4.70
665 1844 7.394816 TGAAAGTAGGAGGAGTAATTTTGAGG 58.605 38.462 0.00 0.00 0.00 3.86
666 1845 8.848474 TTGAAAGTAGGAGGAGTAATTTTGAG 57.152 34.615 0.00 0.00 0.00 3.02
667 1846 9.284968 CTTTGAAAGTAGGAGGAGTAATTTTGA 57.715 33.333 0.00 0.00 0.00 2.69
668 1847 8.023706 GCTTTGAAAGTAGGAGGAGTAATTTTG 58.976 37.037 6.81 0.00 0.00 2.44
669 1848 7.094762 CGCTTTGAAAGTAGGAGGAGTAATTTT 60.095 37.037 6.81 0.00 0.00 1.82
670 1849 6.371825 CGCTTTGAAAGTAGGAGGAGTAATTT 59.628 38.462 6.81 0.00 0.00 1.82
673 1852 4.322499 CCGCTTTGAAAGTAGGAGGAGTAA 60.322 45.833 13.65 0.00 32.61 2.24
674 1853 3.194968 CCGCTTTGAAAGTAGGAGGAGTA 59.805 47.826 13.65 0.00 32.61 2.59
675 1854 2.028020 CCGCTTTGAAAGTAGGAGGAGT 60.028 50.000 13.65 0.00 32.61 3.85
677 1856 2.253610 TCCGCTTTGAAAGTAGGAGGA 58.746 47.619 16.31 10.49 34.29 3.71
679 1858 3.399330 TGTTCCGCTTTGAAAGTAGGAG 58.601 45.455 18.34 3.24 38.19 3.69
680 1859 3.478857 TGTTCCGCTTTGAAAGTAGGA 57.521 42.857 16.31 16.31 36.28 2.94
682 1861 3.003275 TGCTTGTTCCGCTTTGAAAGTAG 59.997 43.478 6.81 1.55 0.00 2.57
683 1862 2.946329 TGCTTGTTCCGCTTTGAAAGTA 59.054 40.909 6.81 0.00 0.00 2.24
684 1863 1.748493 TGCTTGTTCCGCTTTGAAAGT 59.252 42.857 6.81 0.00 0.00 2.66
686 1865 2.100584 ACATGCTTGTTCCGCTTTGAAA 59.899 40.909 0.00 0.00 29.55 2.69
687 1866 1.680735 ACATGCTTGTTCCGCTTTGAA 59.319 42.857 0.00 0.00 29.55 2.69
688 1867 1.266718 GACATGCTTGTTCCGCTTTGA 59.733 47.619 6.70 0.00 35.79 2.69
689 1868 1.666888 GGACATGCTTGTTCCGCTTTG 60.667 52.381 6.70 0.00 35.79 2.77
693 1872 2.877691 GGGACATGCTTGTTCCGC 59.122 61.111 13.97 3.86 41.75 5.54
696 1875 4.240096 CTGATTTTGGGACATGCTTGTTC 58.760 43.478 6.70 4.47 39.30 3.18
698 1877 2.028748 GCTGATTTTGGGACATGCTTGT 60.029 45.455 4.68 4.68 39.30 3.16
699 1878 2.232941 AGCTGATTTTGGGACATGCTTG 59.767 45.455 0.00 0.00 39.30 4.01
700 1879 2.532843 AGCTGATTTTGGGACATGCTT 58.467 42.857 0.00 0.00 39.30 3.91
702 1881 3.323751 AAAGCTGATTTTGGGACATGC 57.676 42.857 0.00 0.00 39.30 4.06
703 1882 3.922240 CGAAAAGCTGATTTTGGGACATG 59.078 43.478 8.52 0.00 41.24 3.21
705 1884 3.641437 CGAAAAGCTGATTTTGGGACA 57.359 42.857 8.52 0.00 41.24 4.02
709 1888 1.273327 AGCCCGAAAAGCTGATTTTGG 59.727 47.619 8.52 7.24 41.24 3.28
710 1889 2.730550 AGCCCGAAAAGCTGATTTTG 57.269 45.000 8.52 1.62 41.24 2.44
711 1890 4.016444 TCATAGCCCGAAAAGCTGATTTT 58.984 39.130 2.91 2.91 43.88 1.82
712 1891 3.620488 TCATAGCCCGAAAAGCTGATTT 58.380 40.909 0.00 0.00 41.71 2.17
713 1892 3.281727 TCATAGCCCGAAAAGCTGATT 57.718 42.857 0.00 0.00 41.71 2.57
714 1893 3.072184 AGATCATAGCCCGAAAAGCTGAT 59.928 43.478 0.00 0.00 41.71 2.90
717 1896 2.224402 GGAGATCATAGCCCGAAAAGCT 60.224 50.000 0.00 0.00 44.49 3.74
719 1898 3.760580 AGGAGATCATAGCCCGAAAAG 57.239 47.619 0.00 0.00 0.00 2.27
722 1901 2.365617 GTGAAGGAGATCATAGCCCGAA 59.634 50.000 0.00 0.00 0.00 4.30
723 1902 1.964223 GTGAAGGAGATCATAGCCCGA 59.036 52.381 0.00 0.00 0.00 5.14
724 1903 1.967066 AGTGAAGGAGATCATAGCCCG 59.033 52.381 0.00 0.00 0.00 6.13
725 1904 4.081198 CCATAGTGAAGGAGATCATAGCCC 60.081 50.000 0.00 0.00 0.00 5.19
727 1906 4.222588 AGCCATAGTGAAGGAGATCATAGC 59.777 45.833 0.00 0.00 0.00 2.97
728 1907 5.999205 AGCCATAGTGAAGGAGATCATAG 57.001 43.478 0.00 0.00 0.00 2.23
729 1908 5.840693 TGAAGCCATAGTGAAGGAGATCATA 59.159 40.000 0.00 0.00 0.00 2.15
730 1909 4.657504 TGAAGCCATAGTGAAGGAGATCAT 59.342 41.667 0.00 0.00 0.00 2.45
731 1910 4.033009 TGAAGCCATAGTGAAGGAGATCA 58.967 43.478 0.00 0.00 0.00 2.92
733 1912 5.643421 AATGAAGCCATAGTGAAGGAGAT 57.357 39.130 0.00 0.00 31.59 2.75
734 1913 5.190528 AGAAATGAAGCCATAGTGAAGGAGA 59.809 40.000 0.00 0.00 31.59 3.71
736 1915 5.441718 AGAAATGAAGCCATAGTGAAGGA 57.558 39.130 0.00 0.00 31.59 3.36
737 1916 5.067023 GGAAGAAATGAAGCCATAGTGAAGG 59.933 44.000 0.00 0.00 31.59 3.46
738 1917 5.884792 AGGAAGAAATGAAGCCATAGTGAAG 59.115 40.000 0.00 0.00 31.59 3.02
739 1918 5.819991 AGGAAGAAATGAAGCCATAGTGAA 58.180 37.500 0.00 0.00 31.59 3.18
740 1919 5.431765 GAGGAAGAAATGAAGCCATAGTGA 58.568 41.667 0.00 0.00 31.59 3.41
741 1920 4.578105 GGAGGAAGAAATGAAGCCATAGTG 59.422 45.833 0.00 0.00 31.59 2.74
742 1921 4.385754 GGGAGGAAGAAATGAAGCCATAGT 60.386 45.833 0.00 0.00 31.59 2.12
743 1922 4.140536 GGGAGGAAGAAATGAAGCCATAG 58.859 47.826 0.00 0.00 31.59 2.23
744 1923 3.433598 CGGGAGGAAGAAATGAAGCCATA 60.434 47.826 0.00 0.00 31.59 2.74
745 1924 2.684927 CGGGAGGAAGAAATGAAGCCAT 60.685 50.000 0.00 0.00 33.66 4.40
746 1925 1.340017 CGGGAGGAAGAAATGAAGCCA 60.340 52.381 0.00 0.00 0.00 4.75
748 1927 2.115343 ACGGGAGGAAGAAATGAAGC 57.885 50.000 0.00 0.00 0.00 3.86
749 1928 3.197983 AGGTACGGGAGGAAGAAATGAAG 59.802 47.826 0.00 0.00 0.00 3.02
750 1929 3.178865 AGGTACGGGAGGAAGAAATGAA 58.821 45.455 0.00 0.00 0.00 2.57
751 1930 2.829023 AGGTACGGGAGGAAGAAATGA 58.171 47.619 0.00 0.00 0.00 2.57
754 1933 2.565834 CAGAAGGTACGGGAGGAAGAAA 59.434 50.000 0.00 0.00 0.00 2.52
755 1934 2.176889 CAGAAGGTACGGGAGGAAGAA 58.823 52.381 0.00 0.00 0.00 2.52
756 1935 1.356738 TCAGAAGGTACGGGAGGAAGA 59.643 52.381 0.00 0.00 0.00 2.87
757 1936 1.848652 TCAGAAGGTACGGGAGGAAG 58.151 55.000 0.00 0.00 0.00 3.46
758 1937 2.314071 TTCAGAAGGTACGGGAGGAA 57.686 50.000 0.00 0.00 0.00 3.36
759 1938 2.314071 TTTCAGAAGGTACGGGAGGA 57.686 50.000 0.00 0.00 0.00 3.71
760 1939 2.236395 ACATTTCAGAAGGTACGGGAGG 59.764 50.000 0.00 0.00 0.00 4.30
761 1940 3.522553 GACATTTCAGAAGGTACGGGAG 58.477 50.000 0.00 0.00 28.45 4.30
762 1941 2.235402 GGACATTTCAGAAGGTACGGGA 59.765 50.000 0.00 0.00 28.45 5.14
764 1943 3.611766 AGGACATTTCAGAAGGTACGG 57.388 47.619 0.00 0.00 35.57 4.02
766 1945 5.552178 AGTGAAGGACATTTCAGAAGGTAC 58.448 41.667 0.00 0.00 37.72 3.34
767 1946 5.825593 AGTGAAGGACATTTCAGAAGGTA 57.174 39.130 0.00 0.00 37.72 3.08
770 1949 6.176183 ACCATAGTGAAGGACATTTCAGAAG 58.824 40.000 0.00 0.00 37.72 2.85
771 1950 6.126863 ACCATAGTGAAGGACATTTCAGAA 57.873 37.500 0.00 0.00 37.72 3.02
772 1951 5.762179 ACCATAGTGAAGGACATTTCAGA 57.238 39.130 0.00 0.00 37.72 3.27
787 1966 1.553690 AAGAGCCCGTGCACCATAGT 61.554 55.000 12.15 0.00 41.13 2.12
790 1969 1.973281 CAAAGAGCCCGTGCACCAT 60.973 57.895 12.15 0.00 41.13 3.55
791 1970 2.594303 CAAAGAGCCCGTGCACCA 60.594 61.111 12.15 0.00 41.13 4.17
792 1971 4.043200 GCAAAGAGCCCGTGCACC 62.043 66.667 12.15 0.00 41.13 5.01
801 1980 2.416893 CCGAAGTCCTAAAGCAAAGAGC 59.583 50.000 0.00 0.00 46.19 4.09
802 1981 3.003480 CCCGAAGTCCTAAAGCAAAGAG 58.997 50.000 0.00 0.00 0.00 2.85
803 1982 2.874457 GCCCGAAGTCCTAAAGCAAAGA 60.874 50.000 0.00 0.00 0.00 2.52
804 1983 1.468914 GCCCGAAGTCCTAAAGCAAAG 59.531 52.381 0.00 0.00 0.00 2.77
805 1984 1.202830 TGCCCGAAGTCCTAAAGCAAA 60.203 47.619 0.00 0.00 0.00 3.68
806 1985 0.398696 TGCCCGAAGTCCTAAAGCAA 59.601 50.000 0.00 0.00 0.00 3.91
807 1986 0.321298 GTGCCCGAAGTCCTAAAGCA 60.321 55.000 0.00 0.00 0.00 3.91
808 1987 0.036294 AGTGCCCGAAGTCCTAAAGC 60.036 55.000 0.00 0.00 0.00 3.51
809 1988 1.736032 CGAGTGCCCGAAGTCCTAAAG 60.736 57.143 0.00 0.00 0.00 1.85
810 1989 0.245539 CGAGTGCCCGAAGTCCTAAA 59.754 55.000 0.00 0.00 0.00 1.85
838 2406 4.292178 GCGGGCCATCTCTCGAGG 62.292 72.222 13.56 3.44 0.00 4.63
884 2453 1.529244 GGGATGGGCTTGGATTCGG 60.529 63.158 0.00 0.00 0.00 4.30
1343 3221 4.779966 TCGGAGAGCGCGGAGACT 62.780 66.667 8.83 0.00 0.00 3.24
1518 3396 2.555199 CAAGCTATTCGGGGAGAACAG 58.445 52.381 0.00 0.00 42.39 3.16
1657 3555 1.480137 CTACAGCCTGAGGAAGTGAGG 59.520 57.143 0.65 0.00 0.00 3.86
1680 3578 5.753744 ACACCAACACGTAACATATTGTTG 58.246 37.500 8.20 8.20 45.52 3.33
1694 3592 4.305989 ACATGAACATCAACACCAACAC 57.694 40.909 0.00 0.00 0.00 3.32
1934 3832 7.713507 GTCCATGTATAACTGTACCAAGCATAA 59.286 37.037 0.00 0.00 0.00 1.90
1944 3842 8.313944 ACTATGTTGGTCCATGTATAACTGTA 57.686 34.615 0.00 0.00 0.00 2.74
2087 4000 4.080582 TCGGTGTACATTTCTGGGATTCAT 60.081 41.667 0.00 0.00 0.00 2.57
2088 4001 3.262151 TCGGTGTACATTTCTGGGATTCA 59.738 43.478 0.00 0.00 0.00 2.57
2152 4065 5.106197 TGCCAATAACTCAACATTGCACTAG 60.106 40.000 0.00 0.00 32.00 2.57
2194 4110 1.337728 TGACCACCTGATGTAAGCACG 60.338 52.381 0.00 0.00 0.00 5.34
2284 4202 2.731976 GCCACACACAAACGAAAAACAA 59.268 40.909 0.00 0.00 0.00 2.83
2285 4203 2.288213 TGCCACACACAAACGAAAAACA 60.288 40.909 0.00 0.00 0.00 2.83
2286 4204 2.329379 TGCCACACACAAACGAAAAAC 58.671 42.857 0.00 0.00 0.00 2.43
2396 4314 7.056635 ACCCGATCATGTAATTCTTTTCTCAT 58.943 34.615 0.00 0.00 0.00 2.90
2519 4437 7.014422 AGCTAGTACAAGTATTATGAGGTGTCC 59.986 40.741 0.00 0.00 0.00 4.02
2520 4438 7.942990 AGCTAGTACAAGTATTATGAGGTGTC 58.057 38.462 0.00 0.00 0.00 3.67
2637 4731 8.556213 TCAAGACATACACCTTTAATTGTACC 57.444 34.615 0.00 0.00 31.09 3.34
2670 4766 9.495754 CTAATAATGAACTTCAACTTTGCTAGC 57.504 33.333 8.10 8.10 0.00 3.42
2747 4843 6.874134 TCTGTTAATTCAGCTTTGAGGTAGTC 59.126 38.462 0.00 0.00 35.63 2.59
2856 4962 8.680903 AGGAATGCTACAGAAGATTAAACAATG 58.319 33.333 0.00 0.00 0.00 2.82
2903 5010 1.414919 TCCATAATAGTGCCGTGGGTC 59.585 52.381 0.00 0.00 0.00 4.46
2910 5017 3.067106 CGTGTGGATCCATAATAGTGCC 58.933 50.000 19.62 1.65 0.00 5.01
3010 5128 6.534793 CCCTGCAAACAAAAATGATATACACC 59.465 38.462 0.00 0.00 0.00 4.16
3024 5143 0.485099 ACCCATACCCCTGCAAACAA 59.515 50.000 0.00 0.00 0.00 2.83
3203 8856 5.221106 CCAAAAATCGTCTGCATGATATGGT 60.221 40.000 0.00 0.00 29.60 3.55
3240 11886 5.221126 CCCAAGAAAACCATAGCTTCTATGC 60.221 44.000 8.02 0.00 0.00 3.14
3269 11915 1.942657 TGAAGAGTTGTCACTGCTTGC 59.057 47.619 0.00 0.00 31.22 4.01
3295 11944 7.734942 ACCCTTTTGATGTTTGTGATTGTATT 58.265 30.769 0.00 0.00 0.00 1.89
3329 11978 2.988493 CCTTTGATGGTTGTTTCATGCG 59.012 45.455 0.00 0.00 0.00 4.73
3333 11982 4.040217 CCAATCCCTTTGATGGTTGTTTCA 59.960 41.667 0.00 0.00 37.53 2.69
3379 12028 7.257003 TGTTTGCATGTTAATAAGCATACCAG 58.743 34.615 16.05 0.00 37.89 4.00
3421 12071 3.562505 CTTTGAGTTGAACAGCATGCTC 58.437 45.455 19.68 7.97 42.53 4.26
3446 12097 1.072159 ACCACAGAGCAGGAGCAAC 59.928 57.895 0.00 0.00 45.49 4.17
3504 12155 5.767665 TGAAATAGTAGAGCACTGGCAAAAA 59.232 36.000 0.00 0.00 44.61 1.94
3513 12164 4.737855 TCCTGGTGAAATAGTAGAGCAC 57.262 45.455 0.00 0.00 0.00 4.40
3615 12276 3.196254 CCATGAAAGGTAAAATGCTGCCT 59.804 43.478 0.00 0.00 0.00 4.75
3839 12500 9.330063 ACAGCGATCATCAAAATCTCTAATAAA 57.670 29.630 0.00 0.00 0.00 1.40
3969 12630 1.071385 CAGAGGACACAAGCAGAACCT 59.929 52.381 0.00 0.00 0.00 3.50
3973 12634 0.761187 AAGCAGAGGACACAAGCAGA 59.239 50.000 0.00 0.00 0.00 4.26
3974 12635 0.873054 CAAGCAGAGGACACAAGCAG 59.127 55.000 0.00 0.00 0.00 4.24
4111 12772 3.380479 TCAGTAAAACCTCCACGACTG 57.620 47.619 0.00 0.00 36.48 3.51
4137 12798 1.210931 CATGCACCACTGAAAGCCG 59.789 57.895 0.00 0.00 37.60 5.52
4144 12805 0.393944 AGATGAGGCATGCACCACTG 60.394 55.000 21.36 0.00 0.00 3.66
4156 12817 0.815734 CAAGCCAGCCAAAGATGAGG 59.184 55.000 0.00 0.00 0.00 3.86
4291 12952 0.178767 CATGACCCGCCTCATTCAGA 59.821 55.000 0.00 0.00 0.00 3.27
4349 13010 4.133078 CTCTGCCCTTCATTAATCCAGTC 58.867 47.826 0.00 0.00 0.00 3.51
4356 13017 5.185635 CCATCAAAACTCTGCCCTTCATTAA 59.814 40.000 0.00 0.00 0.00 1.40
4361 13022 2.519013 ACCATCAAAACTCTGCCCTTC 58.481 47.619 0.00 0.00 0.00 3.46
4517 13181 7.174253 GGATATGTTTTAACTCCACAGTTCACA 59.826 37.037 0.00 0.00 42.27 3.58
4729 13393 2.641815 TGCCTGGCCCAATTTATGTTTT 59.358 40.909 17.53 0.00 0.00 2.43
4799 13463 5.182001 AGAAGAAATGAACTGGAAACATCCG 59.818 40.000 0.00 0.00 41.51 4.18
4925 13591 2.145397 ATCTCTTGCAGACGGGTAGA 57.855 50.000 0.00 0.00 32.26 2.59
4980 13646 8.077991 GCATGTGCATGTCATGTAAAATATAGT 58.922 33.333 23.38 0.00 42.94 2.12
4981 13647 8.294577 AGCATGTGCATGTCATGTAAAATATAG 58.705 33.333 23.38 0.00 45.16 1.31
4982 13648 8.168790 AGCATGTGCATGTCATGTAAAATATA 57.831 30.769 23.38 0.00 45.16 0.86
5170 14035 4.390297 GGCGAGAAGAATGTATATTGAGGC 59.610 45.833 0.00 0.00 0.00 4.70
5237 14119 7.169645 TGCACAGCAAAGAAAATGATAAAGTTC 59.830 33.333 0.00 0.00 34.76 3.01
5277 14159 7.461182 TTGTTTGAGTTTTTCCTTCTTCTCA 57.539 32.000 0.00 0.00 0.00 3.27
5356 14244 7.042119 GCACAAATAGCACTAACAAACCAAATT 60.042 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.