Multiple sequence alignment - TraesCS3A01G534100

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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 TraesCS3A01G534100 chr3A 100.000 2690 0 0 1 2690 746260414 746263103 0.000000e+00 4968.0
1 TraesCS3A01G534100 chr3A 79.904 209 35 4 2429 2630 746289884 746290092 2.160000e-31 147.0
2 TraesCS3A01G534100 chr3D 89.822 1631 103 18 1 1600 611406335 611407933 0.000000e+00 2034.0
3 TraesCS3A01G534100 chr3D 85.154 714 51 21 1613 2321 611407883 611408546 0.000000e+00 680.0
4 TraesCS3A01G534100 chr3D 95.181 249 9 2 2444 2690 611408595 611408842 9.030000e-105 390.0
5 TraesCS3A01G534100 chr3D 80.119 503 89 10 17 515 520284377 520284872 5.470000e-97 364.0
6 TraesCS3A01G534100 chr3D 79.918 488 93 5 1 488 436678451 436678933 1.180000e-93 353.0
7 TraesCS3A01G534100 chr3D 78.927 522 94 14 2 515 588473 588986 9.220000e-90 340.0
8 TraesCS3A01G534100 chr3D 94.444 54 3 0 2360 2413 611408543 611408596 1.720000e-12 84.2
9 TraesCS3A01G534100 chr3B 90.897 758 41 12 861 1598 829112868 829113617 0.000000e+00 992.0
10 TraesCS3A01G534100 chr3B 79.634 766 61 45 1566 2321 829113525 829114205 1.890000e-126 462.0
11 TraesCS3A01G534100 chr3B 93.333 225 12 1 2469 2690 829114257 829114481 2.000000e-86 329.0
12 TraesCS3A01G534100 chr3B 81.277 235 16 8 615 834 829112653 829112874 5.960000e-37 165.0
13 TraesCS3A01G534100 chr3B 92.593 54 4 0 2360 2413 829114202 829114255 7.980000e-11 78.7
14 TraesCS3A01G534100 chr6D 81.641 768 90 36 753 1489 16502652 16503399 8.290000e-165 590.0
15 TraesCS3A01G534100 chr6D 83.409 663 68 28 873 1513 24001443 24002085 6.460000e-161 577.0
16 TraesCS3A01G534100 chr6D 82.443 655 79 29 848 1489 16529661 16529030 8.470000e-150 540.0
17 TraesCS3A01G534100 chr6D 81.109 667 82 31 848 1489 16307397 16306750 6.690000e-136 494.0
18 TraesCS3A01G534100 chr6D 84.600 500 50 17 999 1489 16390085 16389604 3.130000e-129 472.0
19 TraesCS3A01G534100 chr6D 100.000 29 0 0 2662 2690 267129850 267129822 1.000000e-03 54.7
20 TraesCS3A01G534100 chr6B 82.712 671 78 27 842 1489 28925875 28926530 1.810000e-156 562.0
21 TraesCS3A01G534100 chr6B 86.590 522 49 15 999 1513 38877740 38878247 8.410000e-155 556.0
22 TraesCS3A01G534100 chr6B 81.887 657 83 29 848 1489 28256779 28256144 3.070000e-144 521.0
23 TraesCS3A01G534100 chr6B 82.464 633 75 26 875 1489 59232671 59233285 3.070000e-144 521.0
24 TraesCS3A01G534100 chr6B 80.237 759 95 40 755 1489 28517568 28516841 1.100000e-143 520.0
25 TraesCS3A01G534100 chr5D 80.603 763 99 26 757 1489 514924347 514923604 6.550000e-151 544.0
26 TraesCS3A01G534100 chr5D 81.973 527 91 4 1 527 59966567 59967089 6.830000e-121 444.0
27 TraesCS3A01G534100 chr5D 81.081 111 21 0 2495 2605 213079865 213079975 3.690000e-14 89.8
28 TraesCS3A01G534100 chr5D 100.000 29 0 0 2662 2690 213080067 213080095 1.000000e-03 54.7
29 TraesCS3A01G534100 chr1D 84.008 494 70 8 1 491 192915224 192914737 1.460000e-127 466.0
30 TraesCS3A01G534100 chr1A 84.362 486 53 19 1021 1499 21022856 21023325 3.160000e-124 455.0
31 TraesCS3A01G534100 chr1A 78.154 531 102 12 1 527 343633321 343632801 2.580000e-85 326.0
32 TraesCS3A01G534100 chr6A 81.132 530 88 12 2 527 59912651 59913172 5.360000e-112 414.0
33 TraesCS3A01G534100 chr4D 79.962 529 98 7 1 527 399224825 399225347 1.510000e-102 383.0
34 TraesCS3A01G534100 chr7D 82.883 111 19 0 2495 2605 52623761 52623871 1.700000e-17 100.0
35 TraesCS3A01G534100 chr2D 81.982 111 20 0 2498 2608 56184618 56184508 7.930000e-16 95.3


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 TraesCS3A01G534100 chr3A 746260414 746263103 2689 False 4968.00 4968 100.00000 1 2690 1 chr3A.!!$F1 2689
1 TraesCS3A01G534100 chr3D 611406335 611408842 2507 False 797.05 2034 91.15025 1 2690 4 chr3D.!!$F4 2689
2 TraesCS3A01G534100 chr3D 588473 588986 513 False 340.00 340 78.92700 2 515 1 chr3D.!!$F1 513
3 TraesCS3A01G534100 chr3B 829112653 829114481 1828 False 405.34 992 87.54680 615 2690 5 chr3B.!!$F1 2075
4 TraesCS3A01G534100 chr6D 16502652 16503399 747 False 590.00 590 81.64100 753 1489 1 chr6D.!!$F1 736
5 TraesCS3A01G534100 chr6D 24001443 24002085 642 False 577.00 577 83.40900 873 1513 1 chr6D.!!$F2 640
6 TraesCS3A01G534100 chr6D 16529030 16529661 631 True 540.00 540 82.44300 848 1489 1 chr6D.!!$R3 641
7 TraesCS3A01G534100 chr6D 16306750 16307397 647 True 494.00 494 81.10900 848 1489 1 chr6D.!!$R1 641
8 TraesCS3A01G534100 chr6B 28925875 28926530 655 False 562.00 562 82.71200 842 1489 1 chr6B.!!$F1 647
9 TraesCS3A01G534100 chr6B 38877740 38878247 507 False 556.00 556 86.59000 999 1513 1 chr6B.!!$F2 514
10 TraesCS3A01G534100 chr6B 28256144 28256779 635 True 521.00 521 81.88700 848 1489 1 chr6B.!!$R1 641
11 TraesCS3A01G534100 chr6B 59232671 59233285 614 False 521.00 521 82.46400 875 1489 1 chr6B.!!$F3 614
12 TraesCS3A01G534100 chr6B 28516841 28517568 727 True 520.00 520 80.23700 755 1489 1 chr6B.!!$R2 734
13 TraesCS3A01G534100 chr5D 514923604 514924347 743 True 544.00 544 80.60300 757 1489 1 chr5D.!!$R1 732
14 TraesCS3A01G534100 chr5D 59966567 59967089 522 False 444.00 444 81.97300 1 527 1 chr5D.!!$F1 526
15 TraesCS3A01G534100 chr1A 343632801 343633321 520 True 326.00 326 78.15400 1 527 1 chr1A.!!$R1 526
16 TraesCS3A01G534100 chr6A 59912651 59913172 521 False 414.00 414 81.13200 2 527 1 chr6A.!!$F1 525
17 TraesCS3A01G534100 chr4D 399224825 399225347 522 False 383.00 383 79.96200 1 527 1 chr4D.!!$F1 526

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
254 262 0.178882 AACCGGACCTAGGGTTTCCT 60.179 55.0 14.81 0.0 43.84 3.36 F
438 447 0.395686 GATCATAGGCCAGAGCAGCA 59.604 55.0 5.01 0.0 42.56 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1235 1342 0.171231 CGAGACAAGATCGGTCAGCA 59.829 55.0 18.66 0.0 37.74 4.41 R
2296 2580 0.030235 GGTCCAAGCACCGAACAAAC 59.970 55.0 0.00 0.0 0.00 2.93 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
43 48 1.675641 GAACATGGTGCCCGAAGCT 60.676 57.895 0.00 0.00 44.23 3.74
74 79 5.223449 AGAGATACTCGACCCAAAACAAA 57.777 39.130 0.00 0.00 35.36 2.83
96 101 8.241367 ACAAAAGAAGAACACAACTAAAATCGT 58.759 29.630 0.00 0.00 0.00 3.73
155 160 5.181245 ACCAAACATCTCCAAATCTAACACG 59.819 40.000 0.00 0.00 0.00 4.49
254 262 0.178882 AACCGGACCTAGGGTTTCCT 60.179 55.000 14.81 0.00 43.84 3.36
338 346 4.947147 GGGTGTCGCCACTGCCAA 62.947 66.667 4.48 0.00 41.53 4.52
344 353 1.528076 TCGCCACTGCCAACACAAT 60.528 52.632 0.00 0.00 0.00 2.71
415 424 1.329906 GCACAGATCAAAGATGAGGCG 59.670 52.381 0.00 0.00 39.39 5.52
438 447 0.395686 GATCATAGGCCAGAGCAGCA 59.604 55.000 5.01 0.00 42.56 4.41
439 448 1.003349 GATCATAGGCCAGAGCAGCAT 59.997 52.381 5.01 0.00 42.56 3.79
502 511 1.738830 GCGCTGCCAAACATGCAAT 60.739 52.632 0.00 0.00 38.46 3.56
555 564 5.086621 GCATATCCCAACCCCTATTTTGAT 58.913 41.667 0.00 0.00 0.00 2.57
559 568 3.535590 TCCCAACCCCTATTTTGATCCAT 59.464 43.478 0.00 0.00 0.00 3.41
562 571 3.686227 ACCCCTATTTTGATCCATGCA 57.314 42.857 0.00 0.00 0.00 3.96
566 575 6.325352 ACCCCTATTTTGATCCATGCATAAT 58.675 36.000 0.00 0.00 0.00 1.28
574 583 7.591421 TTTGATCCATGCATAATGATGAACT 57.409 32.000 0.00 0.00 38.72 3.01
579 588 6.363882 TCCATGCATAATGATGAACTTACCA 58.636 36.000 0.00 0.00 38.72 3.25
593 607 7.241663 TGAACTTACCACGATGTAATTATGC 57.758 36.000 0.00 0.00 30.75 3.14
596 610 5.461078 ACTTACCACGATGTAATTATGCGAC 59.539 40.000 10.27 0.00 30.75 5.19
598 612 3.802139 ACCACGATGTAATTATGCGACAG 59.198 43.478 10.27 3.35 0.00 3.51
608 622 6.597672 TGTAATTATGCGACAGAAATTCCACT 59.402 34.615 0.00 0.00 0.00 4.00
609 623 5.741388 ATTATGCGACAGAAATTCCACTC 57.259 39.130 0.00 0.00 0.00 3.51
610 624 2.542020 TGCGACAGAAATTCCACTCA 57.458 45.000 0.00 0.00 0.00 3.41
687 702 1.679898 CCCTCCGCCTGAAAAGAGT 59.320 57.895 0.00 0.00 0.00 3.24
824 852 2.893398 GAACCGATCCTGACCGCT 59.107 61.111 0.00 0.00 0.00 5.52
844 887 3.227276 CCCTCCCAGATCCGACGG 61.227 72.222 7.84 7.84 0.00 4.79
846 889 4.271816 CTCCCAGATCCGACGGCG 62.272 72.222 9.66 1.94 37.24 6.46
1196 1293 2.435938 CACCCAACCGATCCCGTG 60.436 66.667 0.00 0.00 0.00 4.94
1200 1297 2.579201 CAACCGATCCCGTGCTCT 59.421 61.111 0.00 0.00 0.00 4.09
1271 1390 4.224147 TGTCTCGGTTCTTTGGATGGATAA 59.776 41.667 0.00 0.00 0.00 1.75
1547 1809 2.553247 CCAAGAAGACCCCCAAGAAGAC 60.553 54.545 0.00 0.00 0.00 3.01
1548 1810 1.363246 AGAAGACCCCCAAGAAGACC 58.637 55.000 0.00 0.00 0.00 3.85
1549 1811 0.036294 GAAGACCCCCAAGAAGACCG 60.036 60.000 0.00 0.00 0.00 4.79
1550 1812 2.046217 GACCCCCAAGAAGACCGC 60.046 66.667 0.00 0.00 0.00 5.68
1551 1813 3.623703 GACCCCCAAGAAGACCGCC 62.624 68.421 0.00 0.00 0.00 6.13
1552 1814 4.778143 CCCCCAAGAAGACCGCCG 62.778 72.222 0.00 0.00 0.00 6.46
1556 1818 4.735132 CAAGAAGACCGCCGCCGA 62.735 66.667 0.00 0.00 36.29 5.54
1557 1819 4.736896 AAGAAGACCGCCGCCGAC 62.737 66.667 0.00 0.00 36.29 4.79
1564 1826 4.735132 CCGCCGCCGACAAGAAGA 62.735 66.667 0.00 0.00 36.29 2.87
1565 1827 3.479269 CGCCGCCGACAAGAAGAC 61.479 66.667 0.00 0.00 36.29 3.01
1566 1828 3.119096 GCCGCCGACAAGAAGACC 61.119 66.667 0.00 0.00 0.00 3.85
1567 1829 2.809601 CCGCCGACAAGAAGACCG 60.810 66.667 0.00 0.00 0.00 4.79
1568 1830 3.479269 CGCCGACAAGAAGACCGC 61.479 66.667 0.00 0.00 0.00 5.68
1569 1831 3.119096 GCCGACAAGAAGACCGCC 61.119 66.667 0.00 0.00 0.00 6.13
1570 1832 2.809601 CCGACAAGAAGACCGCCG 60.810 66.667 0.00 0.00 0.00 6.46
1571 1833 3.479269 CGACAAGAAGACCGCCGC 61.479 66.667 0.00 0.00 0.00 6.53
1572 1834 3.119096 GACAAGAAGACCGCCGCC 61.119 66.667 0.00 0.00 0.00 6.13
1585 1847 4.735132 CCGCCGCCGACAAGAAGA 62.735 66.667 0.00 0.00 36.29 2.87
1586 1848 3.479269 CGCCGCCGACAAGAAGAC 61.479 66.667 0.00 0.00 36.29 3.01
1587 1849 3.119096 GCCGCCGACAAGAAGACC 61.119 66.667 0.00 0.00 0.00 3.85
1588 1850 2.809601 CCGCCGACAAGAAGACCG 60.810 66.667 0.00 0.00 0.00 4.79
1628 1890 2.383527 CCGCCGCTGACAAGAAGAC 61.384 63.158 0.00 0.00 0.00 3.01
1629 1891 2.383527 CGCCGCTGACAAGAAGACC 61.384 63.158 0.00 0.00 0.00 3.85
1633 1895 2.383527 GCTGACAAGAAGACCGCCG 61.384 63.158 0.00 0.00 0.00 6.46
1634 1896 2.357034 TGACAAGAAGACCGCCGC 60.357 61.111 0.00 0.00 0.00 6.53
1635 1897 3.119096 GACAAGAAGACCGCCGCC 61.119 66.667 0.00 0.00 0.00 6.13
1691 1953 4.883300 CGCCGCCGACGAGTAGAC 62.883 72.222 0.00 0.00 43.93 2.59
1697 1973 2.044555 CCGACGAGTAGACAGGGCA 61.045 63.158 0.00 0.00 0.00 5.36
1792 2069 0.038159 GTCTGGAGTCCGAACTGGTG 60.038 60.000 4.30 0.00 39.52 4.17
1797 2074 1.254954 GAGTCCGAACTGGTGGTAGT 58.745 55.000 0.00 0.00 39.52 2.73
1798 2075 1.201880 GAGTCCGAACTGGTGGTAGTC 59.798 57.143 0.00 0.00 39.52 2.59
1799 2076 1.203025 AGTCCGAACTGGTGGTAGTCT 60.203 52.381 0.00 0.00 39.52 3.24
1800 2077 1.067776 GTCCGAACTGGTGGTAGTCTG 60.068 57.143 0.00 0.00 39.52 3.51
1801 2078 0.966920 CCGAACTGGTGGTAGTCTGT 59.033 55.000 0.00 0.00 0.00 3.41
1802 2079 2.165167 CCGAACTGGTGGTAGTCTGTA 58.835 52.381 0.00 0.00 0.00 2.74
1803 2080 2.163815 CCGAACTGGTGGTAGTCTGTAG 59.836 54.545 0.00 0.00 0.00 2.74
1804 2081 2.415625 CGAACTGGTGGTAGTCTGTAGC 60.416 54.545 0.00 0.00 0.00 3.58
1805 2082 1.174783 ACTGGTGGTAGTCTGTAGCG 58.825 55.000 0.00 0.00 0.00 4.26
1806 2083 1.174783 CTGGTGGTAGTCTGTAGCGT 58.825 55.000 0.00 0.00 0.00 5.07
1807 2084 1.132643 CTGGTGGTAGTCTGTAGCGTC 59.867 57.143 0.00 0.00 0.00 5.19
1808 2085 0.098376 GGTGGTAGTCTGTAGCGTCG 59.902 60.000 0.00 0.00 0.00 5.12
1809 2086 1.081892 GTGGTAGTCTGTAGCGTCGA 58.918 55.000 0.00 0.00 0.00 4.20
1810 2087 1.669779 GTGGTAGTCTGTAGCGTCGAT 59.330 52.381 0.00 0.00 0.00 3.59
1811 2088 2.097142 GTGGTAGTCTGTAGCGTCGATT 59.903 50.000 0.00 0.00 0.00 3.34
1812 2089 2.096980 TGGTAGTCTGTAGCGTCGATTG 59.903 50.000 0.00 0.00 0.00 2.67
1813 2090 2.353889 GGTAGTCTGTAGCGTCGATTGA 59.646 50.000 0.00 0.00 0.00 2.57
1814 2091 3.003482 GGTAGTCTGTAGCGTCGATTGAT 59.997 47.826 0.00 0.00 0.00 2.57
1815 2092 3.341857 AGTCTGTAGCGTCGATTGATC 57.658 47.619 0.00 0.00 0.00 2.92
1816 2093 2.946329 AGTCTGTAGCGTCGATTGATCT 59.054 45.455 0.00 0.00 0.00 2.75
1817 2094 3.378742 AGTCTGTAGCGTCGATTGATCTT 59.621 43.478 0.00 0.00 0.00 2.40
1818 2095 3.483922 GTCTGTAGCGTCGATTGATCTTG 59.516 47.826 0.00 0.00 0.00 3.02
1819 2096 3.377172 TCTGTAGCGTCGATTGATCTTGA 59.623 43.478 0.00 0.00 0.00 3.02
1820 2097 4.104696 TGTAGCGTCGATTGATCTTGAA 57.895 40.909 0.00 0.00 0.00 2.69
1821 2098 4.682787 TGTAGCGTCGATTGATCTTGAAT 58.317 39.130 0.00 0.00 0.00 2.57
1822 2099 4.740205 TGTAGCGTCGATTGATCTTGAATC 59.260 41.667 0.00 0.00 0.00 2.52
1823 2100 3.785486 AGCGTCGATTGATCTTGAATCA 58.215 40.909 0.00 0.00 31.26 2.57
1824 2101 3.553511 AGCGTCGATTGATCTTGAATCAC 59.446 43.478 0.00 0.00 31.26 3.06
1825 2102 3.553511 GCGTCGATTGATCTTGAATCACT 59.446 43.478 0.00 0.00 31.26 3.41
1883 2160 2.807967 TGAAGCTGGAAACTTGATCGTG 59.192 45.455 0.00 0.00 0.00 4.35
1901 2178 4.331968 TCGTGTAGCCAATTCCAATCTTT 58.668 39.130 0.00 0.00 0.00 2.52
1913 2190 5.782893 TTCCAATCTTTTCCGTGTCAATT 57.217 34.783 0.00 0.00 0.00 2.32
1915 2192 6.155475 TCCAATCTTTTCCGTGTCAATTTT 57.845 33.333 0.00 0.00 0.00 1.82
1921 2198 3.422417 TTCCGTGTCAATTTTGCGAAA 57.578 38.095 0.53 0.53 0.00 3.46
1928 2205 4.670175 GTGTCAATTTTGCGAAATTTTGCC 59.330 37.500 24.46 9.40 42.14 4.52
1938 2215 1.798223 GAAATTTTGCCGGTTCTTGCC 59.202 47.619 1.90 0.00 0.00 4.52
1959 2242 1.348064 TGATCCCCTTGTTCGTCTGT 58.652 50.000 0.00 0.00 0.00 3.41
1970 2253 5.412526 TTGTTCGTCTGTACATTTGTTCC 57.587 39.130 0.00 0.00 0.00 3.62
1982 2265 4.702831 ACATTTGTTCCCACAATTTCACC 58.297 39.130 0.00 0.00 42.66 4.02
1983 2266 4.408596 ACATTTGTTCCCACAATTTCACCT 59.591 37.500 0.00 0.00 42.66 4.00
2029 2312 3.826524 TGGCAATAACTTGGTTCAGTGA 58.173 40.909 0.00 0.00 32.72 3.41
2034 2317 4.706842 ATAACTTGGTTCAGTGAGGTGT 57.293 40.909 0.00 0.00 0.00 4.16
2039 2322 1.283613 TGGTTCAGTGAGGTGTGGTTT 59.716 47.619 0.00 0.00 0.00 3.27
2052 2335 6.378564 TGAGGTGTGGTTTGTGAAATTTCTTA 59.621 34.615 18.64 5.43 0.00 2.10
2084 2367 2.628187 ATCTGCGGGGAAGGGGATCT 62.628 60.000 0.00 0.00 0.00 2.75
2085 2368 3.089874 TGCGGGGAAGGGGATCTG 61.090 66.667 0.00 0.00 0.00 2.90
2089 2372 2.376842 GGGAAGGGGATCTGGGGA 59.623 66.667 0.00 0.00 0.00 4.81
2090 2373 1.072616 GGGAAGGGGATCTGGGGAT 60.073 63.158 0.00 0.00 34.45 3.85
2131 2415 2.236766 TCTAGGGTTCGTAGCATAGGC 58.763 52.381 11.98 0.00 36.92 3.93
2203 2487 2.753043 CGGGCAAGCTGCTGGATT 60.753 61.111 8.57 0.00 44.28 3.01
2227 2511 2.815647 CCGCTTTCTCGTCAGGCC 60.816 66.667 0.00 0.00 0.00 5.19
2296 2580 1.557832 TCCTGGTATTCGGTTTGGGAG 59.442 52.381 0.00 0.00 0.00 4.30
2303 2587 4.320714 GGTATTCGGTTTGGGAGTTTGTTC 60.321 45.833 0.00 0.00 0.00 3.18
2321 2605 2.046285 CGGTGCTTGGACCCCAATC 61.046 63.158 5.74 0.00 43.07 2.67
2323 2607 0.251787 GGTGCTTGGACCCCAATCTT 60.252 55.000 0.00 0.00 43.07 2.40
2324 2608 1.632589 GTGCTTGGACCCCAATCTTT 58.367 50.000 0.00 0.00 43.07 2.52
2325 2609 1.546029 GTGCTTGGACCCCAATCTTTC 59.454 52.381 0.00 0.00 43.07 2.62
2326 2610 1.186200 GCTTGGACCCCAATCTTTCC 58.814 55.000 0.00 0.00 43.07 3.13
2327 2611 1.272704 GCTTGGACCCCAATCTTTCCT 60.273 52.381 0.00 0.00 43.07 3.36
2328 2612 2.450476 CTTGGACCCCAATCTTTCCTG 58.550 52.381 0.00 0.00 43.07 3.86
2329 2613 1.455822 TGGACCCCAATCTTTCCTGT 58.544 50.000 0.00 0.00 0.00 4.00
2330 2614 1.075374 TGGACCCCAATCTTTCCTGTG 59.925 52.381 0.00 0.00 0.00 3.66
2331 2615 1.075536 GGACCCCAATCTTTCCTGTGT 59.924 52.381 0.00 0.00 0.00 3.72
2332 2616 2.490902 GGACCCCAATCTTTCCTGTGTT 60.491 50.000 0.00 0.00 0.00 3.32
2333 2617 2.820197 GACCCCAATCTTTCCTGTGTTC 59.180 50.000 0.00 0.00 0.00 3.18
2334 2618 1.812571 CCCCAATCTTTCCTGTGTTCG 59.187 52.381 0.00 0.00 0.00 3.95
2335 2619 2.552155 CCCCAATCTTTCCTGTGTTCGA 60.552 50.000 0.00 0.00 0.00 3.71
2336 2620 2.744202 CCCAATCTTTCCTGTGTTCGAG 59.256 50.000 0.00 0.00 0.00 4.04
2337 2621 3.557054 CCCAATCTTTCCTGTGTTCGAGA 60.557 47.826 0.00 0.00 0.00 4.04
2338 2622 4.256920 CCAATCTTTCCTGTGTTCGAGAT 58.743 43.478 0.00 0.00 0.00 2.75
2339 2623 4.331168 CCAATCTTTCCTGTGTTCGAGATC 59.669 45.833 0.00 0.00 0.00 2.75
2340 2624 5.174395 CAATCTTTCCTGTGTTCGAGATCT 58.826 41.667 0.00 0.00 0.00 2.75
2341 2625 4.179926 TCTTTCCTGTGTTCGAGATCTG 57.820 45.455 0.00 0.00 0.00 2.90
2342 2626 3.056536 TCTTTCCTGTGTTCGAGATCTGG 60.057 47.826 0.00 0.00 0.00 3.86
2343 2627 0.532573 TCCTGTGTTCGAGATCTGGC 59.467 55.000 0.00 0.00 0.00 4.85
2344 2628 0.803768 CCTGTGTTCGAGATCTGGCG 60.804 60.000 0.00 0.00 0.00 5.69
2345 2629 0.803768 CTGTGTTCGAGATCTGGCGG 60.804 60.000 0.00 0.00 0.00 6.13
2346 2630 1.519455 GTGTTCGAGATCTGGCGGG 60.519 63.158 0.00 0.00 0.00 6.13
2347 2631 1.982395 TGTTCGAGATCTGGCGGGT 60.982 57.895 0.00 0.00 0.00 5.28
2348 2632 1.519455 GTTCGAGATCTGGCGGGTG 60.519 63.158 0.00 0.00 0.00 4.61
2349 2633 1.982395 TTCGAGATCTGGCGGGTGT 60.982 57.895 0.00 0.00 0.00 4.16
2350 2634 1.945354 TTCGAGATCTGGCGGGTGTC 61.945 60.000 0.00 0.00 0.00 3.67
2351 2635 2.501610 GAGATCTGGCGGGTGTCC 59.498 66.667 0.00 0.00 0.00 4.02
2352 2636 2.039624 AGATCTGGCGGGTGTCCT 59.960 61.111 0.00 0.00 0.00 3.85
2353 2637 0.755698 GAGATCTGGCGGGTGTCCTA 60.756 60.000 0.00 0.00 0.00 2.94
2354 2638 0.105453 AGATCTGGCGGGTGTCCTAT 60.105 55.000 0.00 0.00 0.00 2.57
2355 2639 1.147191 AGATCTGGCGGGTGTCCTATA 59.853 52.381 0.00 0.00 0.00 1.31
2356 2640 2.180276 GATCTGGCGGGTGTCCTATAT 58.820 52.381 0.00 0.00 0.00 0.86
2357 2641 1.338107 TCTGGCGGGTGTCCTATATG 58.662 55.000 0.00 0.00 0.00 1.78
2358 2642 0.321671 CTGGCGGGTGTCCTATATGG 59.678 60.000 0.00 0.00 37.10 2.74
2359 2643 1.003718 GGCGGGTGTCCTATATGGC 60.004 63.158 0.00 0.00 35.26 4.40
2360 2644 1.752198 GCGGGTGTCCTATATGGCA 59.248 57.895 0.00 0.00 35.26 4.92
2361 2645 0.107831 GCGGGTGTCCTATATGGCAA 59.892 55.000 0.00 0.00 35.26 4.52
2362 2646 1.271379 GCGGGTGTCCTATATGGCAAT 60.271 52.381 0.00 0.00 35.26 3.56
2363 2647 2.814097 GCGGGTGTCCTATATGGCAATT 60.814 50.000 0.00 0.00 35.26 2.32
2364 2648 3.486383 CGGGTGTCCTATATGGCAATTT 58.514 45.455 0.00 0.00 35.26 1.82
2365 2649 3.253188 CGGGTGTCCTATATGGCAATTTG 59.747 47.826 0.00 0.00 35.26 2.32
2366 2650 3.005791 GGGTGTCCTATATGGCAATTTGC 59.994 47.826 13.04 13.04 44.08 3.68
2367 2651 3.891366 GGTGTCCTATATGGCAATTTGCT 59.109 43.478 20.06 4.94 44.28 3.91
2368 2652 5.070001 GGTGTCCTATATGGCAATTTGCTA 58.930 41.667 20.06 15.33 44.28 3.49
2369 2653 5.534654 GGTGTCCTATATGGCAATTTGCTAA 59.465 40.000 20.06 10.06 44.28 3.09
2370 2654 6.438763 GTGTCCTATATGGCAATTTGCTAAC 58.561 40.000 20.06 9.23 44.28 2.34
2371 2655 5.534654 TGTCCTATATGGCAATTTGCTAACC 59.465 40.000 20.06 5.02 44.28 2.85
2372 2656 4.759693 TCCTATATGGCAATTTGCTAACCG 59.240 41.667 20.06 5.73 44.28 4.44
2373 2657 4.082787 CCTATATGGCAATTTGCTAACCGG 60.083 45.833 20.06 0.00 44.28 5.28
2413 2697 2.048444 TCCTCAATCATCCTGCTTGC 57.952 50.000 0.00 0.00 0.00 4.01
2414 2698 1.562942 TCCTCAATCATCCTGCTTGCT 59.437 47.619 0.00 0.00 0.00 3.91
2415 2699 1.676529 CCTCAATCATCCTGCTTGCTG 59.323 52.381 0.00 0.00 0.00 4.41
2416 2700 2.366533 CTCAATCATCCTGCTTGCTGT 58.633 47.619 0.00 0.00 0.00 4.40
2417 2701 2.753452 CTCAATCATCCTGCTTGCTGTT 59.247 45.455 0.00 0.00 0.00 3.16
2418 2702 3.159472 TCAATCATCCTGCTTGCTGTTT 58.841 40.909 0.00 0.00 0.00 2.83
2419 2703 3.057104 TCAATCATCCTGCTTGCTGTTTG 60.057 43.478 0.00 0.00 0.00 2.93
2420 2704 0.599558 TCATCCTGCTTGCTGTTTGC 59.400 50.000 0.00 0.00 43.25 3.68
2421 2705 0.601558 CATCCTGCTTGCTGTTTGCT 59.398 50.000 0.00 0.00 43.37 3.91
2422 2706 1.814394 CATCCTGCTTGCTGTTTGCTA 59.186 47.619 0.00 0.00 43.37 3.49
2423 2707 1.527034 TCCTGCTTGCTGTTTGCTAG 58.473 50.000 0.00 0.00 45.12 3.42
2434 2718 5.752098 GCTGTTTGCTAGCAAAAATAGTG 57.248 39.130 37.37 23.63 45.86 2.74
2435 2719 4.090498 GCTGTTTGCTAGCAAAAATAGTGC 59.910 41.667 37.37 28.09 45.86 4.40
2436 2720 5.193663 TGTTTGCTAGCAAAAATAGTGCA 57.806 34.783 37.37 27.04 45.86 4.57
2437 2721 5.782047 TGTTTGCTAGCAAAAATAGTGCAT 58.218 33.333 37.37 0.00 45.86 3.96
2438 2722 6.222389 TGTTTGCTAGCAAAAATAGTGCATT 58.778 32.000 37.37 0.00 45.86 3.56
2439 2723 7.374272 TGTTTGCTAGCAAAAATAGTGCATTA 58.626 30.769 37.37 14.09 45.86 1.90
2440 2724 8.034215 TGTTTGCTAGCAAAAATAGTGCATTAT 58.966 29.630 37.37 0.00 45.86 1.28
2441 2725 8.872845 GTTTGCTAGCAAAAATAGTGCATTATT 58.127 29.630 37.37 8.55 45.86 1.40
2442 2726 8.633075 TTGCTAGCAAAAATAGTGCATTATTC 57.367 30.769 27.50 3.18 44.74 1.75
2443 2727 7.999679 TGCTAGCAAAAATAGTGCATTATTCT 58.000 30.769 16.84 9.69 44.74 2.40
2444 2728 7.916977 TGCTAGCAAAAATAGTGCATTATTCTG 59.083 33.333 16.84 14.43 44.74 3.02
2445 2729 7.917505 GCTAGCAAAAATAGTGCATTATTCTGT 59.082 33.333 14.11 8.60 44.74 3.41
2446 2730 9.443283 CTAGCAAAAATAGTGCATTATTCTGTC 57.557 33.333 14.11 10.60 44.74 3.51
2474 2758 1.444119 TTGGTGCAAACGCTCTGTCC 61.444 55.000 0.00 0.00 0.00 4.02
2483 2767 2.839486 ACGCTCTGTCCAATCTGAAA 57.161 45.000 0.00 0.00 0.00 2.69
2515 2799 5.486526 AGTGCTAGGAGAAATCTGTTTGAG 58.513 41.667 0.00 0.00 0.00 3.02
2522 2806 3.829948 AGAAATCTGTTTGAGCATTGCG 58.170 40.909 2.38 0.00 0.00 4.85
2656 2942 7.432148 TTTATCCAGGTCATGCTAGTTTCTA 57.568 36.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 48 5.071923 TGGGTCGAGTATCTCTTATCTCTCA 59.928 44.000 0.00 0.00 0.00 3.27
74 79 6.477688 TCGACGATTTTAGTTGTGTTCTTCTT 59.522 34.615 0.00 0.00 0.00 2.52
92 97 1.671845 GTAGCTTCTCTGGTCGACGAT 59.328 52.381 9.92 0.00 0.00 3.73
96 101 0.039180 TGGGTAGCTTCTCTGGTCGA 59.961 55.000 0.00 0.00 0.00 4.20
167 172 4.021544 TGAAGGTGTTGTCTTGTTTTGCTT 60.022 37.500 0.00 0.00 0.00 3.91
216 221 1.970092 TTTCCGGACCAAACAACGAT 58.030 45.000 1.83 0.00 0.00 3.73
254 262 0.392998 GCCCCTCTTCGAGCATCAAA 60.393 55.000 0.00 0.00 33.17 2.69
338 346 2.358898 GCGAAATCCCTGCATATTGTGT 59.641 45.455 0.00 0.00 0.00 3.72
344 353 1.150536 GGGGCGAAATCCCTGCATA 59.849 57.895 0.00 0.00 45.80 3.14
438 447 2.381941 GGCTCCCCTTCCTGCAGAT 61.382 63.158 17.39 0.00 0.00 2.90
439 448 3.011517 GGCTCCCCTTCCTGCAGA 61.012 66.667 17.39 0.00 0.00 4.26
488 497 0.527113 CGGAGATTGCATGTTTGGCA 59.473 50.000 0.00 0.00 40.00 4.92
492 501 1.281867 TCCTCCGGAGATTGCATGTTT 59.718 47.619 33.39 0.00 0.00 2.83
493 502 0.911769 TCCTCCGGAGATTGCATGTT 59.088 50.000 33.39 0.00 0.00 2.71
549 558 8.014070 AGTTCATCATTATGCATGGATCAAAA 57.986 30.769 10.16 0.00 33.07 2.44
555 564 6.262944 GTGGTAAGTTCATCATTATGCATGGA 59.737 38.462 10.16 4.68 33.07 3.41
559 568 5.423886 TCGTGGTAAGTTCATCATTATGCA 58.576 37.500 0.00 0.00 32.76 3.96
562 571 9.778741 ATTACATCGTGGTAAGTTCATCATTAT 57.221 29.630 7.51 0.00 36.74 1.28
566 575 9.040939 CATAATTACATCGTGGTAAGTTCATCA 57.959 33.333 7.10 0.00 36.74 3.07
574 583 5.349809 TGTCGCATAATTACATCGTGGTAA 58.650 37.500 4.62 4.62 37.62 2.85
579 588 6.844696 ATTTCTGTCGCATAATTACATCGT 57.155 33.333 0.00 0.00 0.00 3.73
593 607 5.808042 ATTGATGAGTGGAATTTCTGTCG 57.192 39.130 0.00 0.00 0.00 4.35
596 610 8.681486 TGGTATATTGATGAGTGGAATTTCTG 57.319 34.615 0.00 0.00 0.00 3.02
598 612 7.229306 TGCTGGTATATTGATGAGTGGAATTTC 59.771 37.037 0.00 0.00 0.00 2.17
608 622 7.417683 CCCATTTTGTTGCTGGTATATTGATGA 60.418 37.037 0.00 0.00 0.00 2.92
609 623 6.702723 CCCATTTTGTTGCTGGTATATTGATG 59.297 38.462 0.00 0.00 0.00 3.07
610 624 6.610830 TCCCATTTTGTTGCTGGTATATTGAT 59.389 34.615 0.00 0.00 0.00 2.57
653 668 3.159472 GGAGGGGTTTTCGGTTATGTTT 58.841 45.455 0.00 0.00 0.00 2.83
700 715 0.601057 AGTTCGAAAATTTGGGGGCG 59.399 50.000 0.00 0.00 0.00 6.13
824 852 4.137615 TCGGATCTGGGAGGGCGA 62.138 66.667 0.62 0.00 0.00 5.54
957 1007 2.125106 AACCTCTCGGAATGCGGC 60.125 61.111 0.00 0.00 0.00 6.53
960 1010 1.092345 GCTGGAACCTCTCGGAATGC 61.092 60.000 0.00 0.00 0.00 3.56
963 1016 1.595993 CGAGCTGGAACCTCTCGGAA 61.596 60.000 19.60 0.00 44.06 4.30
1196 1293 0.539518 GAAGAGGGGAGGAACAGAGC 59.460 60.000 0.00 0.00 0.00 4.09
1200 1297 2.907042 GAGAAAGAAGAGGGGAGGAACA 59.093 50.000 0.00 0.00 0.00 3.18
1235 1342 0.171231 CGAGACAAGATCGGTCAGCA 59.829 55.000 18.66 0.00 37.74 4.41
1518 1780 4.699522 GTCTTCTTGGCGGCGGGT 62.700 66.667 9.78 0.00 0.00 5.28
1547 1809 4.735132 TCTTCTTGTCGGCGGCGG 62.735 66.667 31.73 15.35 0.00 6.13
1548 1810 3.479269 GTCTTCTTGTCGGCGGCG 61.479 66.667 27.15 27.15 0.00 6.46
1549 1811 3.119096 GGTCTTCTTGTCGGCGGC 61.119 66.667 3.62 3.62 0.00 6.53
1550 1812 2.809601 CGGTCTTCTTGTCGGCGG 60.810 66.667 7.21 0.00 0.00 6.13
1551 1813 3.479269 GCGGTCTTCTTGTCGGCG 61.479 66.667 0.00 0.00 0.00 6.46
1552 1814 3.119096 GGCGGTCTTCTTGTCGGC 61.119 66.667 0.00 0.00 40.61 5.54
1553 1815 2.809601 CGGCGGTCTTCTTGTCGG 60.810 66.667 0.00 0.00 0.00 4.79
1554 1816 3.479269 GCGGCGGTCTTCTTGTCG 61.479 66.667 9.78 0.00 0.00 4.35
1555 1817 3.119096 GGCGGCGGTCTTCTTGTC 61.119 66.667 9.78 0.00 0.00 3.18
1568 1830 4.735132 TCTTCTTGTCGGCGGCGG 62.735 66.667 31.73 15.35 0.00 6.13
1569 1831 3.479269 GTCTTCTTGTCGGCGGCG 61.479 66.667 27.15 27.15 0.00 6.46
1570 1832 3.119096 GGTCTTCTTGTCGGCGGC 61.119 66.667 3.62 3.62 0.00 6.53
1571 1833 2.809601 CGGTCTTCTTGTCGGCGG 60.810 66.667 7.21 0.00 0.00 6.13
1572 1834 3.479269 GCGGTCTTCTTGTCGGCG 61.479 66.667 0.00 0.00 0.00 6.46
1573 1835 3.119096 GGCGGTCTTCTTGTCGGC 61.119 66.667 0.00 0.00 40.61 5.54
1574 1836 2.809601 CGGCGGTCTTCTTGTCGG 60.810 66.667 0.00 0.00 0.00 4.79
1575 1837 3.479269 GCGGCGGTCTTCTTGTCG 61.479 66.667 9.78 0.00 0.00 4.35
1576 1838 3.119096 GGCGGCGGTCTTCTTGTC 61.119 66.667 9.78 0.00 0.00 3.18
1636 1898 3.435186 GGCAGCCTTCTTGTCGGC 61.435 66.667 3.29 0.00 46.65 5.54
1637 1899 3.121030 CGGCAGCCTTCTTGTCGG 61.121 66.667 10.54 0.00 0.00 4.79
1638 1900 3.793144 GCGGCAGCCTTCTTGTCG 61.793 66.667 10.54 0.00 37.42 4.35
1697 1973 0.505655 GAACTACGCGACGCAACTTT 59.494 50.000 21.35 7.04 0.00 2.66
1792 2069 2.353889 TCAATCGACGCTACAGACTACC 59.646 50.000 0.00 0.00 0.00 3.18
1797 2074 3.377172 TCAAGATCAATCGACGCTACAGA 59.623 43.478 0.00 0.00 0.00 3.41
1798 2075 3.695816 TCAAGATCAATCGACGCTACAG 58.304 45.455 0.00 0.00 0.00 2.74
1799 2076 3.775661 TCAAGATCAATCGACGCTACA 57.224 42.857 0.00 0.00 0.00 2.74
1800 2077 4.740205 TGATTCAAGATCAATCGACGCTAC 59.260 41.667 0.00 0.00 33.57 3.58
1801 2078 4.740205 GTGATTCAAGATCAATCGACGCTA 59.260 41.667 0.00 0.00 33.57 4.26
1802 2079 3.553511 GTGATTCAAGATCAATCGACGCT 59.446 43.478 0.00 0.00 33.57 5.07
1803 2080 3.553511 AGTGATTCAAGATCAATCGACGC 59.446 43.478 0.00 0.00 33.57 5.19
1804 2081 5.518128 AGAAGTGATTCAAGATCAATCGACG 59.482 40.000 0.00 0.00 33.57 5.12
1805 2082 6.312426 ACAGAAGTGATTCAAGATCAATCGAC 59.688 38.462 0.00 0.00 33.57 4.20
1806 2083 6.401394 ACAGAAGTGATTCAAGATCAATCGA 58.599 36.000 0.00 0.00 33.57 3.59
1807 2084 6.659361 ACAGAAGTGATTCAAGATCAATCG 57.341 37.500 0.00 0.00 33.57 3.34
1808 2085 7.516470 CGCTACAGAAGTGATTCAAGATCAATC 60.516 40.741 0.00 0.00 37.99 2.67
1809 2086 6.257411 CGCTACAGAAGTGATTCAAGATCAAT 59.743 38.462 0.00 0.00 37.99 2.57
1810 2087 5.578336 CGCTACAGAAGTGATTCAAGATCAA 59.422 40.000 0.00 0.00 37.99 2.57
1811 2088 5.105063 CGCTACAGAAGTGATTCAAGATCA 58.895 41.667 0.00 0.00 37.99 2.92
1812 2089 5.105752 ACGCTACAGAAGTGATTCAAGATC 58.894 41.667 0.00 0.00 39.15 2.75
1813 2090 5.078411 ACGCTACAGAAGTGATTCAAGAT 57.922 39.130 0.00 0.00 39.15 2.40
1814 2091 4.486090 GACGCTACAGAAGTGATTCAAGA 58.514 43.478 0.00 0.00 39.15 3.02
1815 2092 3.301906 CGACGCTACAGAAGTGATTCAAG 59.698 47.826 0.00 0.00 39.15 3.02
1816 2093 3.057806 TCGACGCTACAGAAGTGATTCAA 60.058 43.478 0.00 0.00 39.15 2.69
1817 2094 2.486592 TCGACGCTACAGAAGTGATTCA 59.513 45.455 0.00 0.00 39.15 2.57
1818 2095 3.132629 TCGACGCTACAGAAGTGATTC 57.867 47.619 0.00 0.00 39.15 2.52
1819 2096 3.784701 ATCGACGCTACAGAAGTGATT 57.215 42.857 0.00 0.00 39.15 2.57
1820 2097 3.128764 TCAATCGACGCTACAGAAGTGAT 59.871 43.478 0.00 0.00 39.15 3.06
1821 2098 2.486592 TCAATCGACGCTACAGAAGTGA 59.513 45.455 0.00 0.00 39.15 3.41
1822 2099 2.863739 TCAATCGACGCTACAGAAGTG 58.136 47.619 0.00 0.00 41.76 3.16
1823 2100 3.378742 AGATCAATCGACGCTACAGAAGT 59.621 43.478 0.00 0.00 0.00 3.01
1824 2101 3.958704 AGATCAATCGACGCTACAGAAG 58.041 45.455 0.00 0.00 0.00 2.85
1825 2102 4.105486 CAAGATCAATCGACGCTACAGAA 58.895 43.478 0.00 0.00 0.00 3.02
1883 2160 4.157840 ACGGAAAAGATTGGAATTGGCTAC 59.842 41.667 0.00 0.00 0.00 3.58
1901 2178 3.422417 TTTCGCAAAATTGACACGGAA 57.578 38.095 0.00 0.00 0.00 4.30
1913 2190 1.861575 GAACCGGCAAAATTTCGCAAA 59.138 42.857 0.00 0.00 0.00 3.68
1915 2192 0.671251 AGAACCGGCAAAATTTCGCA 59.329 45.000 0.00 0.00 0.00 5.10
1921 2198 1.047801 AAGGCAAGAACCGGCAAAAT 58.952 45.000 0.00 0.00 33.69 1.82
1928 2205 1.032114 GGGGATCAAGGCAAGAACCG 61.032 60.000 0.00 0.00 33.69 4.44
1938 2215 2.289694 ACAGACGAACAAGGGGATCAAG 60.290 50.000 0.00 0.00 0.00 3.02
1959 2242 5.600484 AGGTGAAATTGTGGGAACAAATGTA 59.400 36.000 0.00 0.00 46.06 2.29
1982 2265 1.271926 CCCCCAAGAACACCTAACCAG 60.272 57.143 0.00 0.00 0.00 4.00
1983 2266 0.774908 CCCCCAAGAACACCTAACCA 59.225 55.000 0.00 0.00 0.00 3.67
2019 2302 0.916086 AACCACACCTCACTGAACCA 59.084 50.000 0.00 0.00 0.00 3.67
2029 2312 5.675684 AAGAAATTTCACAAACCACACCT 57.324 34.783 19.99 0.00 0.00 4.00
2034 2317 4.591072 CCCCCTAAGAAATTTCACAAACCA 59.409 41.667 19.99 0.00 0.00 3.67
2039 2322 4.733077 TGACCCCCTAAGAAATTTCACA 57.267 40.909 19.99 6.30 0.00 3.58
2052 2335 2.670148 GCAGATCGGTTGACCCCCT 61.670 63.158 0.00 0.00 0.00 4.79
2084 2367 0.550914 CCCAAATCCTTCGATCCCCA 59.449 55.000 0.00 0.00 0.00 4.96
2085 2368 0.178990 CCCCAAATCCTTCGATCCCC 60.179 60.000 0.00 0.00 0.00 4.81
2089 2372 6.614657 AGAAATAATCCCCAAATCCTTCGAT 58.385 36.000 0.00 0.00 0.00 3.59
2090 2373 6.013554 AGAAATAATCCCCAAATCCTTCGA 57.986 37.500 0.00 0.00 0.00 3.71
2131 2415 1.532505 CCAATTCAGCATCGCCTTTCG 60.533 52.381 0.00 0.00 40.15 3.46
2132 2416 1.202336 CCCAATTCAGCATCGCCTTTC 60.202 52.381 0.00 0.00 0.00 2.62
2133 2417 0.819582 CCCAATTCAGCATCGCCTTT 59.180 50.000 0.00 0.00 0.00 3.11
2134 2418 1.039233 CCCCAATTCAGCATCGCCTT 61.039 55.000 0.00 0.00 0.00 4.35
2135 2419 1.454479 CCCCAATTCAGCATCGCCT 60.454 57.895 0.00 0.00 0.00 5.52
2136 2420 1.037030 TTCCCCAATTCAGCATCGCC 61.037 55.000 0.00 0.00 0.00 5.54
2137 2421 0.383231 CTTCCCCAATTCAGCATCGC 59.617 55.000 0.00 0.00 0.00 4.58
2145 2429 1.205655 GCAGCCTTTCTTCCCCAATTC 59.794 52.381 0.00 0.00 0.00 2.17
2213 2497 0.250727 TTTGGGGCCTGACGAGAAAG 60.251 55.000 0.84 0.00 0.00 2.62
2227 2511 0.949105 CCTCCGACGAACAGTTTGGG 60.949 60.000 5.48 0.00 31.80 4.12
2296 2580 0.030235 GGTCCAAGCACCGAACAAAC 59.970 55.000 0.00 0.00 0.00 2.93
2321 2605 3.257393 CCAGATCTCGAACACAGGAAAG 58.743 50.000 0.00 0.00 0.00 2.62
2323 2607 1.066858 GCCAGATCTCGAACACAGGAA 60.067 52.381 0.00 0.00 0.00 3.36
2324 2608 0.532573 GCCAGATCTCGAACACAGGA 59.467 55.000 0.00 0.00 0.00 3.86
2325 2609 0.803768 CGCCAGATCTCGAACACAGG 60.804 60.000 0.00 0.00 0.00 4.00
2326 2610 0.803768 CCGCCAGATCTCGAACACAG 60.804 60.000 5.45 0.00 0.00 3.66
2327 2611 1.215382 CCGCCAGATCTCGAACACA 59.785 57.895 5.45 0.00 0.00 3.72
2328 2612 1.519455 CCCGCCAGATCTCGAACAC 60.519 63.158 5.45 0.00 0.00 3.32
2329 2613 1.982395 ACCCGCCAGATCTCGAACA 60.982 57.895 5.45 0.00 0.00 3.18
2330 2614 1.519455 CACCCGCCAGATCTCGAAC 60.519 63.158 5.45 0.00 0.00 3.95
2331 2615 1.945354 GACACCCGCCAGATCTCGAA 61.945 60.000 5.45 0.00 0.00 3.71
2332 2616 2.362503 ACACCCGCCAGATCTCGA 60.363 61.111 5.45 0.00 0.00 4.04
2333 2617 2.105128 GACACCCGCCAGATCTCG 59.895 66.667 0.00 0.00 0.00 4.04
2334 2618 0.755698 TAGGACACCCGCCAGATCTC 60.756 60.000 0.00 0.00 37.58 2.75
2335 2619 0.105453 ATAGGACACCCGCCAGATCT 60.105 55.000 0.00 0.00 37.58 2.75
2336 2620 1.629043 TATAGGACACCCGCCAGATC 58.371 55.000 0.00 0.00 37.58 2.75
2337 2621 1.902508 CATATAGGACACCCGCCAGAT 59.097 52.381 0.00 0.00 37.58 2.90
2338 2622 1.338107 CATATAGGACACCCGCCAGA 58.662 55.000 0.00 0.00 37.58 3.86
2339 2623 0.321671 CCATATAGGACACCCGCCAG 59.678 60.000 0.00 0.00 41.22 4.85
2340 2624 1.764571 GCCATATAGGACACCCGCCA 61.765 60.000 0.00 0.00 41.22 5.69
2341 2625 1.003718 GCCATATAGGACACCCGCC 60.004 63.158 0.00 0.00 41.22 6.13
2342 2626 0.107831 TTGCCATATAGGACACCCGC 59.892 55.000 0.00 0.00 41.22 6.13
2343 2627 2.859165 ATTGCCATATAGGACACCCG 57.141 50.000 0.00 0.00 41.22 5.28
2344 2628 3.005791 GCAAATTGCCATATAGGACACCC 59.994 47.826 6.72 0.00 41.22 4.61
2345 2629 3.891366 AGCAAATTGCCATATAGGACACC 59.109 43.478 15.04 0.00 46.52 4.16
2346 2630 6.438763 GTTAGCAAATTGCCATATAGGACAC 58.561 40.000 15.04 0.00 46.52 3.67
2347 2631 5.534654 GGTTAGCAAATTGCCATATAGGACA 59.465 40.000 15.04 0.00 46.52 4.02
2348 2632 5.334879 CGGTTAGCAAATTGCCATATAGGAC 60.335 44.000 15.04 2.35 46.52 3.85
2349 2633 4.759693 CGGTTAGCAAATTGCCATATAGGA 59.240 41.667 15.04 0.00 46.52 2.94
2350 2634 4.082787 CCGGTTAGCAAATTGCCATATAGG 60.083 45.833 15.04 7.84 46.52 2.57
2351 2635 4.615912 GCCGGTTAGCAAATTGCCATATAG 60.616 45.833 15.04 1.44 46.52 1.31
2352 2636 3.254657 GCCGGTTAGCAAATTGCCATATA 59.745 43.478 15.04 0.00 46.52 0.86
2353 2637 2.035832 GCCGGTTAGCAAATTGCCATAT 59.964 45.455 15.04 0.00 46.52 1.78
2354 2638 1.407258 GCCGGTTAGCAAATTGCCATA 59.593 47.619 15.04 0.00 46.52 2.74
2355 2639 0.175531 GCCGGTTAGCAAATTGCCAT 59.824 50.000 15.04 0.00 46.52 4.40
2356 2640 0.897863 AGCCGGTTAGCAAATTGCCA 60.898 50.000 15.04 0.00 46.52 4.92
2357 2641 0.246360 AAGCCGGTTAGCAAATTGCC 59.754 50.000 15.04 0.00 46.52 4.52
2358 2642 2.479560 CCTAAGCCGGTTAGCAAATTGC 60.480 50.000 10.41 10.41 45.46 3.56
2359 2643 3.013921 TCCTAAGCCGGTTAGCAAATTG 58.986 45.455 11.22 0.00 37.41 2.32
2360 2644 3.359695 TCCTAAGCCGGTTAGCAAATT 57.640 42.857 11.22 0.00 37.41 1.82
2361 2645 3.054655 TCTTCCTAAGCCGGTTAGCAAAT 60.055 43.478 11.22 0.00 37.41 2.32
2362 2646 2.303600 TCTTCCTAAGCCGGTTAGCAAA 59.696 45.455 11.22 7.31 37.41 3.68
2363 2647 1.903860 TCTTCCTAAGCCGGTTAGCAA 59.096 47.619 11.22 3.04 37.41 3.91
2364 2648 1.563924 TCTTCCTAAGCCGGTTAGCA 58.436 50.000 11.22 0.00 37.41 3.49
2365 2649 2.102588 TGATCTTCCTAAGCCGGTTAGC 59.897 50.000 11.22 0.00 37.41 3.09
2366 2650 4.310769 CATGATCTTCCTAAGCCGGTTAG 58.689 47.826 1.90 9.94 38.35 2.34
2367 2651 3.494398 GCATGATCTTCCTAAGCCGGTTA 60.494 47.826 1.90 0.00 0.00 2.85
2368 2652 2.746472 GCATGATCTTCCTAAGCCGGTT 60.746 50.000 1.90 0.00 0.00 4.44
2369 2653 1.202698 GCATGATCTTCCTAAGCCGGT 60.203 52.381 1.90 0.00 0.00 5.28
2370 2654 1.071385 AGCATGATCTTCCTAAGCCGG 59.929 52.381 0.00 0.00 0.00 6.13
2371 2655 2.540265 AGCATGATCTTCCTAAGCCG 57.460 50.000 0.00 0.00 0.00 5.52
2372 2656 4.615588 ACTAGCATGATCTTCCTAAGCC 57.384 45.455 0.00 0.00 0.00 4.35
2373 2657 4.994217 GGAACTAGCATGATCTTCCTAAGC 59.006 45.833 11.42 0.00 0.00 3.09
2413 2697 5.221880 TGCACTATTTTTGCTAGCAAACAG 58.778 37.500 36.23 31.25 44.39 3.16
2414 2698 5.193663 TGCACTATTTTTGCTAGCAAACA 57.806 34.783 36.23 31.24 44.39 2.83
2415 2699 6.710692 AATGCACTATTTTTGCTAGCAAAC 57.289 33.333 36.23 24.49 44.39 2.93
2416 2700 9.086336 GAATAATGCACTATTTTTGCTAGCAAA 57.914 29.630 33.58 33.58 43.23 3.68
2417 2701 8.469200 AGAATAATGCACTATTTTTGCTAGCAA 58.531 29.630 26.06 26.06 40.86 3.91
2418 2702 7.916977 CAGAATAATGCACTATTTTTGCTAGCA 59.083 33.333 14.93 14.93 40.86 3.49
2419 2703 7.917505 ACAGAATAATGCACTATTTTTGCTAGC 59.082 33.333 8.10 8.10 40.86 3.42
2420 2704 9.443283 GACAGAATAATGCACTATTTTTGCTAG 57.557 33.333 1.38 0.00 40.86 3.42
2421 2705 9.177608 AGACAGAATAATGCACTATTTTTGCTA 57.822 29.630 1.38 0.00 40.86 3.49
2422 2706 7.972277 CAGACAGAATAATGCACTATTTTTGCT 59.028 33.333 1.38 4.06 40.86 3.91
2423 2707 7.221452 CCAGACAGAATAATGCACTATTTTTGC 59.779 37.037 1.38 2.21 40.63 3.68
2424 2708 8.246180 ACCAGACAGAATAATGCACTATTTTTG 58.754 33.333 1.38 6.80 0.00 2.44
2425 2709 8.246180 CACCAGACAGAATAATGCACTATTTTT 58.754 33.333 1.38 0.00 0.00 1.94
2426 2710 7.611467 TCACCAGACAGAATAATGCACTATTTT 59.389 33.333 1.38 0.00 0.00 1.82
2427 2711 7.112122 TCACCAGACAGAATAATGCACTATTT 58.888 34.615 1.38 0.00 0.00 1.40
2428 2712 6.653020 TCACCAGACAGAATAATGCACTATT 58.347 36.000 0.00 0.00 0.00 1.73
2429 2713 6.239217 TCACCAGACAGAATAATGCACTAT 57.761 37.500 0.00 0.00 0.00 2.12
2430 2714 5.675684 TCACCAGACAGAATAATGCACTA 57.324 39.130 0.00 0.00 0.00 2.74
2431 2715 4.558226 TCACCAGACAGAATAATGCACT 57.442 40.909 0.00 0.00 0.00 4.40
2432 2716 5.824904 ATTCACCAGACAGAATAATGCAC 57.175 39.130 0.00 0.00 32.98 4.57
2433 2717 6.350361 CCAAATTCACCAGACAGAATAATGCA 60.350 38.462 0.00 0.00 33.58 3.96
2434 2718 6.038356 CCAAATTCACCAGACAGAATAATGC 58.962 40.000 0.00 0.00 33.58 3.56
2435 2719 7.031372 CACCAAATTCACCAGACAGAATAATG 58.969 38.462 0.00 0.00 33.58 1.90
2436 2720 6.350445 GCACCAAATTCACCAGACAGAATAAT 60.350 38.462 0.00 0.00 33.58 1.28
2437 2721 5.048083 GCACCAAATTCACCAGACAGAATAA 60.048 40.000 0.00 0.00 33.58 1.40
2438 2722 4.458989 GCACCAAATTCACCAGACAGAATA 59.541 41.667 0.00 0.00 33.58 1.75
2439 2723 3.256631 GCACCAAATTCACCAGACAGAAT 59.743 43.478 0.00 0.00 36.09 2.40
2440 2724 2.622942 GCACCAAATTCACCAGACAGAA 59.377 45.455 0.00 0.00 0.00 3.02
2441 2725 2.229792 GCACCAAATTCACCAGACAGA 58.770 47.619 0.00 0.00 0.00 3.41
2442 2726 1.955778 TGCACCAAATTCACCAGACAG 59.044 47.619 0.00 0.00 0.00 3.51
2443 2727 2.064434 TGCACCAAATTCACCAGACA 57.936 45.000 0.00 0.00 0.00 3.41
2444 2728 3.123050 GTTTGCACCAAATTCACCAGAC 58.877 45.455 0.00 0.00 35.74 3.51
2445 2729 2.223688 CGTTTGCACCAAATTCACCAGA 60.224 45.455 0.00 0.00 35.74 3.86
2446 2730 2.126467 CGTTTGCACCAAATTCACCAG 58.874 47.619 0.00 0.00 35.74 4.00
2483 2767 3.492102 TCTCCTAGCACTTGCAGTTTT 57.508 42.857 3.62 0.00 45.16 2.43


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

AutoCloner maintained by Alex Coulton.