Multiple sequence alignment - TraesCS2D01G409700

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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 TraesCS2D01G409700 chr2D 100.000 4422 0 0 3536 7957 524396480 524400901 0.000000e+00 8167.0
1 TraesCS2D01G409700 chr2D 100.000 3259 0 0 1 3259 524392945 524396203 0.000000e+00 6019.0
2 TraesCS2D01G409700 chr2D 87.151 1681 147 40 1000 2644 524466606 524468253 0.000000e+00 1844.0
3 TraesCS2D01G409700 chr2D 83.562 1819 162 69 1061 2830 524443128 524444858 0.000000e+00 1576.0
4 TraesCS2D01G409700 chr2D 92.878 674 38 7 7290 7957 532458363 532457694 0.000000e+00 970.0
5 TraesCS2D01G409700 chr2D 93.578 654 35 5 7310 7957 588227951 588228603 0.000000e+00 968.0
6 TraesCS2D01G409700 chr2D 93.425 654 34 6 7310 7957 382388753 382389403 0.000000e+00 961.0
7 TraesCS2D01G409700 chr2D 92.890 661 38 7 7301 7954 637943864 637944522 0.000000e+00 952.0
8 TraesCS2D01G409700 chr2D 86.623 755 58 15 5722 6440 524447108 524447855 0.000000e+00 795.0
9 TraesCS2D01G409700 chr2D 79.899 1184 139 44 3536 4665 524445100 524446238 0.000000e+00 776.0
10 TraesCS2D01G409700 chr2D 85.450 756 71 21 5722 6470 524516646 524517369 0.000000e+00 750.0
11 TraesCS2D01G409700 chr2D 82.750 829 80 22 6491 7300 524448503 524449287 0.000000e+00 680.0
12 TraesCS2D01G409700 chr2D 77.396 845 130 48 1000 1808 524320456 524321275 5.670000e-121 446.0
13 TraesCS2D01G409700 chr2D 84.091 484 43 20 1061 1528 524462145 524462610 3.410000e-118 436.0
14 TraesCS2D01G409700 chr2D 91.398 279 17 4 5282 5557 524516367 524516641 7.540000e-100 375.0
15 TraesCS2D01G409700 chr2D 91.336 277 19 3 5284 5557 524446829 524447103 2.710000e-99 374.0
16 TraesCS2D01G409700 chr2D 74.667 675 133 27 5781 6439 524153530 524154182 1.700000e-66 265.0
17 TraesCS2D01G409700 chr2D 86.512 215 22 4 4969 5179 524446380 524446591 6.210000e-56 230.0
18 TraesCS2D01G409700 chr2D 85.648 216 19 8 4969 5179 524515909 524516117 4.840000e-52 217.0
19 TraesCS2D01G409700 chr2D 88.068 176 21 0 3081 3256 524444854 524445029 8.090000e-50 209.0
20 TraesCS2D01G409700 chr2D 91.803 122 9 1 5178 5299 524516188 524516308 1.370000e-37 169.0
21 TraesCS2D01G409700 chr2D 85.600 125 11 2 1059 1177 524152160 524152283 3.010000e-24 124.0
22 TraesCS2D01G409700 chr2D 97.500 40 1 0 4266 4305 453625717 453625756 1.430000e-07 69.4
23 TraesCS2D01G409700 chr2D 95.349 43 1 1 4264 4305 13594434 13594392 5.150000e-07 67.6
24 TraesCS2D01G409700 chr2A 94.274 2026 81 15 3536 5558 670111541 670113534 0.000000e+00 3066.0
25 TraesCS2D01G409700 chr2A 91.698 1867 111 15 1284 3110 670109665 670111527 0.000000e+00 2549.0
26 TraesCS2D01G409700 chr2A 86.979 768 49 18 5722 6470 670113538 670114273 0.000000e+00 817.0
27 TraesCS2D01G409700 chr2A 86.179 492 57 9 6491 6981 670114376 670114857 9.150000e-144 521.0
28 TraesCS2D01G409700 chr2A 75.510 1029 194 42 5953 6956 669866980 669867975 1.220000e-122 451.0
29 TraesCS2D01G409700 chr2A 96.043 278 9 2 889 1166 670109305 670109580 1.220000e-122 451.0
30 TraesCS2D01G409700 chr2A 74.507 761 148 38 5926 6667 669885655 669886388 1.010000e-73 289.0
31 TraesCS2D01G409700 chr2A 95.122 82 3 1 1085 1166 669865444 669865524 2.330000e-25 128.0
32 TraesCS2D01G409700 chr2B 95.688 1229 39 6 5756 6970 620213615 620214843 0.000000e+00 1964.0
33 TraesCS2D01G409700 chr2B 94.444 756 31 4 1061 1813 620193857 620194604 0.000000e+00 1153.0
34 TraesCS2D01G409700 chr2B 86.481 1080 95 30 1829 2879 620194676 620195733 0.000000e+00 1138.0
35 TraesCS2D01G409700 chr2B 91.111 630 34 11 4955 5563 620212967 620213595 0.000000e+00 833.0
36 TraesCS2D01G409700 chr2B 83.111 900 98 32 1260 2122 620242077 620242959 0.000000e+00 771.0
37 TraesCS2D01G409700 chr2B 82.820 844 95 32 1000 1822 620023647 620024461 0.000000e+00 710.0
38 TraesCS2D01G409700 chr2B 86.057 667 70 16 4302 4955 620197245 620197901 0.000000e+00 695.0
39 TraesCS2D01G409700 chr2B 86.989 538 56 9 6471 7002 620275497 620276026 1.910000e-165 593.0
40 TraesCS2D01G409700 chr2B 94.857 350 16 2 6952 7299 620214855 620215204 5.430000e-151 545.0
41 TraesCS2D01G409700 chr2B 82.246 659 75 21 3564 4197 620196112 620196753 1.520000e-146 531.0
42 TraesCS2D01G409700 chr2B 89.008 373 28 7 6100 6470 620275041 620275402 4.380000e-122 449.0
43 TraesCS2D01G409700 chr2B 79.606 559 91 19 2153 2701 620268650 620269195 5.830000e-101 379.0
44 TraesCS2D01G409700 chr2B 75.762 755 126 40 1284 2010 619755268 619755993 2.140000e-85 327.0
45 TraesCS2D01G409700 chr2B 81.633 343 33 10 2927 3259 620195725 620196047 2.850000e-64 257.0
46 TraesCS2D01G409700 chr2B 90.000 180 14 3 5341 5518 620274486 620274663 6.210000e-56 230.0
47 TraesCS2D01G409700 chr2B 75.882 510 87 28 5953 6439 619756621 619757117 2.230000e-55 228.0
48 TraesCS2D01G409700 chr2B 85.906 149 17 4 1059 1206 619755084 619755229 1.070000e-33 156.0
49 TraesCS2D01G409700 chr2B 92.308 104 8 0 5194 5297 620274376 620274479 1.790000e-31 148.0
50 TraesCS2D01G409700 chr3A 91.584 903 67 5 1 898 7622936 7623834 0.000000e+00 1238.0
51 TraesCS2D01G409700 chr3A 74.906 267 51 11 6522 6781 574453345 574453602 3.040000e-19 108.0
52 TraesCS2D01G409700 chr5D 97.130 662 14 3 7301 7957 493821239 493821900 0.000000e+00 1112.0
53 TraesCS2D01G409700 chr5D 87.925 911 89 10 1 899 564915637 564914736 0.000000e+00 1053.0
54 TraesCS2D01G409700 chr5D 100.000 37 0 0 4268 4304 8631024 8630988 1.430000e-07 69.4
55 TraesCS2D01G409700 chrUn 87.816 911 90 8 1 899 336119074 336118173 0.000000e+00 1048.0
56 TraesCS2D01G409700 chrUn 86.090 913 91 13 1 899 280213813 280214703 0.000000e+00 950.0
57 TraesCS2D01G409700 chr6D 94.037 654 32 5 7310 7957 444633201 444632549 0.000000e+00 985.0
58 TraesCS2D01G409700 chr6D 93.578 654 35 5 7310 7957 38471341 38470689 0.000000e+00 968.0
59 TraesCS2D01G409700 chr6D 92.922 664 39 6 7301 7957 448047844 448047182 0.000000e+00 959.0
60 TraesCS2D01G409700 chr1D 93.884 654 33 5 7310 7957 49745842 49745190 0.000000e+00 979.0
61 TraesCS2D01G409700 chr1D 90.854 164 15 0 5561 5724 319531315 319531152 3.740000e-53 220.0
62 TraesCS2D01G409700 chr1A 90.413 751 62 5 1 745 344495577 344496323 0.000000e+00 979.0
63 TraesCS2D01G409700 chr1A 95.833 168 7 0 732 899 344496340 344496507 1.020000e-68 272.0
64 TraesCS2D01G409700 chr6B 86.199 913 90 13 1 899 695263644 695262754 0.000000e+00 955.0
65 TraesCS2D01G409700 chr6B 92.121 165 12 1 5562 5726 487031928 487031765 1.730000e-56 231.0
66 TraesCS2D01G409700 chr6B 91.411 163 14 0 5562 5724 450843755 450843593 2.890000e-54 224.0
67 TraesCS2D01G409700 chr7D 86.004 543 48 10 101 631 9112917 9112391 2.510000e-154 556.0
68 TraesCS2D01G409700 chr7D 90.909 165 15 0 5560 5724 199085109 199085273 1.040000e-53 222.0
69 TraesCS2D01G409700 chr7D 100.000 37 0 0 4269 4305 575958221 575958257 1.430000e-07 69.4
70 TraesCS2D01G409700 chr7B 80.806 620 87 16 1 594 444440311 444440924 2.620000e-124 457.0
71 TraesCS2D01G409700 chr7B 80.291 619 92 13 1 594 474277515 474276902 2.640000e-119 440.0
72 TraesCS2D01G409700 chr3D 91.975 162 13 0 5562 5723 612268610 612268449 2.230000e-55 228.0
73 TraesCS2D01G409700 chr3D 90.854 164 15 0 5561 5724 211384844 211384681 3.740000e-53 220.0
74 TraesCS2D01G409700 chr3D 85.321 109 16 0 5404 5512 435646867 435646975 6.530000e-21 113.0
75 TraesCS2D01G409700 chr3D 100.000 30 0 0 1824 1853 458181882 458181853 1.000000e-03 56.5
76 TraesCS2D01G409700 chr7A 91.463 164 14 0 5560 5723 689378118 689378281 8.030000e-55 226.0
77 TraesCS2D01G409700 chr3B 91.463 164 14 0 5560 5723 26409577 26409414 8.030000e-55 226.0
78 TraesCS2D01G409700 chr3B 84.874 119 18 0 6522 6640 571753189 571753307 3.900000e-23 121.0
79 TraesCS2D01G409700 chr4D 91.411 163 14 0 5561 5723 23312056 23312218 2.890000e-54 224.0
80 TraesCS2D01G409700 chr4D 100.000 40 0 0 4266 4305 11871522 11871561 3.080000e-09 75.0
81 TraesCS2D01G409700 chr4A 81.579 114 14 5 248 360 597175718 597175825 3.960000e-13 87.9


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 TraesCS2D01G409700 chr2D 524392945 524400901 7956 False 7093.000000 8167 100.000000 1 7957 2 chr2D.!!$F7 7956
1 TraesCS2D01G409700 chr2D 524462145 524468253 6108 False 1140.000000 1844 85.621000 1000 2644 2 chr2D.!!$F9 1644
2 TraesCS2D01G409700 chr2D 532457694 532458363 669 True 970.000000 970 92.878000 7290 7957 1 chr2D.!!$R2 667
3 TraesCS2D01G409700 chr2D 588227951 588228603 652 False 968.000000 968 93.578000 7310 7957 1 chr2D.!!$F4 647
4 TraesCS2D01G409700 chr2D 382388753 382389403 650 False 961.000000 961 93.425000 7310 7957 1 chr2D.!!$F1 647
5 TraesCS2D01G409700 chr2D 637943864 637944522 658 False 952.000000 952 92.890000 7301 7954 1 chr2D.!!$F5 653
6 TraesCS2D01G409700 chr2D 524443128 524449287 6159 False 662.857143 1576 85.535714 1061 7300 7 chr2D.!!$F8 6239
7 TraesCS2D01G409700 chr2D 524320456 524321275 819 False 446.000000 446 77.396000 1000 1808 1 chr2D.!!$F3 808
8 TraesCS2D01G409700 chr2D 524515909 524517369 1460 False 377.750000 750 88.574750 4969 6470 4 chr2D.!!$F10 1501
9 TraesCS2D01G409700 chr2A 670109305 670114857 5552 False 1480.800000 3066 91.034600 889 6981 5 chr2A.!!$F3 6092
10 TraesCS2D01G409700 chr2A 669865444 669867975 2531 False 289.500000 451 85.316000 1085 6956 2 chr2A.!!$F2 5871
11 TraesCS2D01G409700 chr2A 669885655 669886388 733 False 289.000000 289 74.507000 5926 6667 1 chr2A.!!$F1 741
12 TraesCS2D01G409700 chr2B 620212967 620215204 2237 False 1114.000000 1964 93.885333 4955 7299 3 chr2B.!!$F6 2344
13 TraesCS2D01G409700 chr2B 620242077 620242959 882 False 771.000000 771 83.111000 1260 2122 1 chr2B.!!$F2 862
14 TraesCS2D01G409700 chr2B 620193857 620197901 4044 False 754.800000 1153 86.172200 1061 4955 5 chr2B.!!$F5 3894
15 TraesCS2D01G409700 chr2B 620023647 620024461 814 False 710.000000 710 82.820000 1000 1822 1 chr2B.!!$F1 822
16 TraesCS2D01G409700 chr2B 620268650 620269195 545 False 379.000000 379 79.606000 2153 2701 1 chr2B.!!$F3 548
17 TraesCS2D01G409700 chr2B 620274376 620276026 1650 False 355.000000 593 89.576250 5194 7002 4 chr2B.!!$F7 1808
18 TraesCS2D01G409700 chr2B 619755084 619757117 2033 False 237.000000 327 79.183333 1059 6439 3 chr2B.!!$F4 5380
19 TraesCS2D01G409700 chr3A 7622936 7623834 898 False 1238.000000 1238 91.584000 1 898 1 chr3A.!!$F1 897
20 TraesCS2D01G409700 chr5D 493821239 493821900 661 False 1112.000000 1112 97.130000 7301 7957 1 chr5D.!!$F1 656
21 TraesCS2D01G409700 chr5D 564914736 564915637 901 True 1053.000000 1053 87.925000 1 899 1 chr5D.!!$R2 898
22 TraesCS2D01G409700 chrUn 336118173 336119074 901 True 1048.000000 1048 87.816000 1 899 1 chrUn.!!$R1 898
23 TraesCS2D01G409700 chrUn 280213813 280214703 890 False 950.000000 950 86.090000 1 899 1 chrUn.!!$F1 898
24 TraesCS2D01G409700 chr6D 444632549 444633201 652 True 985.000000 985 94.037000 7310 7957 1 chr6D.!!$R2 647
25 TraesCS2D01G409700 chr6D 38470689 38471341 652 True 968.000000 968 93.578000 7310 7957 1 chr6D.!!$R1 647
26 TraesCS2D01G409700 chr6D 448047182 448047844 662 True 959.000000 959 92.922000 7301 7957 1 chr6D.!!$R3 656
27 TraesCS2D01G409700 chr1D 49745190 49745842 652 True 979.000000 979 93.884000 7310 7957 1 chr1D.!!$R1 647
28 TraesCS2D01G409700 chr1A 344495577 344496507 930 False 625.500000 979 93.123000 1 899 2 chr1A.!!$F1 898
29 TraesCS2D01G409700 chr6B 695262754 695263644 890 True 955.000000 955 86.199000 1 899 1 chr6B.!!$R3 898
30 TraesCS2D01G409700 chr7D 9112391 9112917 526 True 556.000000 556 86.004000 101 631 1 chr7D.!!$R1 530
31 TraesCS2D01G409700 chr7B 444440311 444440924 613 False 457.000000 457 80.806000 1 594 1 chr7B.!!$F1 593
32 TraesCS2D01G409700 chr7B 474276902 474277515 613 True 440.000000 440 80.291000 1 594 1 chr7B.!!$R1 593

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
954 1028 0.736053 AAACGGAGCAACTCGCAAAA 59.264 45.000 0.00 0.0 46.13 2.44 F
1641 5201 0.106894 AGCTAGCCAATTAGCCGTCC 59.893 55.000 12.13 0.0 45.69 4.79 F
1651 5211 0.317799 TTAGCCGTCCGTACTGCAAA 59.682 50.000 0.00 0.0 38.22 3.68 F
2522 6236 1.257750 CGAGGTCCCATGTGTCAGGA 61.258 60.000 0.00 0.0 0.00 3.86 F
3713 7494 0.179009 TGCAACTGCTTCCTGCTTCT 60.179 50.000 2.95 0.0 43.37 2.85 F
4496 8737 1.652563 ATGCGTACGAGCGAGCATA 59.347 52.632 21.65 0.0 46.93 3.14 F
4526 8767 0.037232 GTGAGTGGGAGGTGTGTAGC 60.037 60.000 0.00 0.0 0.00 3.58 F
4538 8781 0.541063 TGTGTAGCCGGGAGACAAGA 60.541 55.000 2.18 0.0 0.00 3.02 F
5471 9918 0.601046 GCTCCAAAGTGCCTTTTGCC 60.601 55.000 4.88 0.0 40.16 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 5707 1.526887 ACGCATGCTCAATATACGTGC 59.473 47.619 17.13 0.0 41.77 5.34 R
2975 6712 0.740149 CGGTAGTGGGTGCGTACATA 59.260 55.000 5.86 0.0 0.00 2.29 R
3218 6966 2.091885 ACACATGAAGGGACACCAAGTT 60.092 45.455 0.00 0.0 40.13 2.66 R
3960 7764 0.036010 CAACATTGACTCCGAGCCCT 60.036 55.000 0.00 0.0 0.00 5.19 R
4526 8767 2.028112 TCTTGTGATTCTTGTCTCCCGG 60.028 50.000 0.00 0.0 0.00 5.73 R
6205 10841 0.683179 ATGATCGGGTCAGTCCACGA 60.683 55.000 0.00 0.0 40.92 4.35 R
6382 11039 2.201732 CGTTCCGGTGATACTTGATGG 58.798 52.381 0.00 0.0 0.00 3.51 R
6641 11900 2.974489 GAAGGAGACGACGGCGACA 61.974 63.158 22.49 0.0 41.64 4.35 R
7305 12628 0.179081 GCCTACACCGATCCAAGGTC 60.179 60.000 0.00 0.0 40.59 3.85 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
25 26 6.293955 GCAAGTAGCATCTACAAAGGTTCAAA 60.294 38.462 6.74 0.00 44.79 2.69
39 40 7.768120 ACAAAGGTTCAAAATCAGCAAATTGTA 59.232 29.630 0.00 0.00 0.00 2.41
40 41 8.610896 CAAAGGTTCAAAATCAGCAAATTGTAA 58.389 29.630 0.00 0.00 0.00 2.41
41 42 7.713764 AGGTTCAAAATCAGCAAATTGTAAC 57.286 32.000 0.00 0.00 0.00 2.50
65 66 6.049149 CACTTACCAAGACGGATATGACAAT 58.951 40.000 0.00 0.00 38.63 2.71
147 159 9.474920 TTCACTTTAACTTGCTTGATATTTTGG 57.525 29.630 0.00 0.00 0.00 3.28
287 307 6.270463 TGTTGGTCCAATATATGTATACCCGT 59.730 38.462 7.77 0.00 0.00 5.28
452 487 4.887071 TGTGTTGCCTTCTAAGTTGACAAT 59.113 37.500 0.00 0.00 0.00 2.71
598 640 8.147058 ACAACTTGCCAAATGTTTATGTCATTA 58.853 29.630 0.00 0.00 34.92 1.90
599 641 8.649841 CAACTTGCCAAATGTTTATGTCATTAG 58.350 33.333 0.00 0.00 34.92 1.73
618 660 7.595502 GTCATTAGTATAGGGAAATCTGTCGTG 59.404 40.741 0.00 0.00 0.00 4.35
640 682 6.419710 CGTGTATATACGTGTTGGATGAATGT 59.580 38.462 13.29 0.00 39.13 2.71
701 744 6.098124 TGGACATGTTCTTTCTGTTCCAAAAT 59.902 34.615 5.55 0.00 0.00 1.82
741 814 8.431910 TTTTGAAGTTAGACTAGAGTATGGGT 57.568 34.615 0.00 0.00 0.00 4.51
918 992 1.136110 GAAGCAGTAGGTCTCAGCCTC 59.864 57.143 0.00 0.00 39.94 4.70
954 1028 0.736053 AAACGGAGCAACTCGCAAAA 59.264 45.000 0.00 0.00 46.13 2.44
1154 4618 3.760035 CCACCTCGAGACCGGGTG 61.760 72.222 15.71 13.85 46.81 4.61
1178 4642 5.473504 GCCCATTTTCTCACTCTGTTCTTTA 59.526 40.000 0.00 0.00 0.00 1.85
1201 4672 3.280295 TCAAGTTTTTCTACGCACCCAA 58.720 40.909 0.00 0.00 0.00 4.12
1454 4944 4.675114 GGTACATTTTGTTTGCGTTCTCAG 59.325 41.667 0.00 0.00 0.00 3.35
1457 4947 3.414549 TTTTGTTTGCGTTCTCAGGTC 57.585 42.857 0.00 0.00 0.00 3.85
1460 4950 2.571212 TGTTTGCGTTCTCAGGTCATT 58.429 42.857 0.00 0.00 0.00 2.57
1511 5026 2.248280 ACACATGTCAACCGCAACTA 57.752 45.000 0.00 0.00 0.00 2.24
1612 5161 1.582502 GTCGTCGATCGGTCATGTTTC 59.417 52.381 16.41 0.00 40.32 2.78
1640 5200 1.221414 CAGCTAGCCAATTAGCCGTC 58.779 55.000 12.13 0.00 45.69 4.79
1641 5201 0.106894 AGCTAGCCAATTAGCCGTCC 59.893 55.000 12.13 0.00 45.69 4.79
1642 5202 1.222115 GCTAGCCAATTAGCCGTCCG 61.222 60.000 2.29 0.00 40.10 4.79
1651 5211 0.317799 TTAGCCGTCCGTACTGCAAA 59.682 50.000 0.00 0.00 38.22 3.68
1673 5244 7.148755 GCAAATTCACGCTCAATTCTGTATTTT 60.149 33.333 0.00 0.00 0.00 1.82
1793 5375 1.836166 ACCTCACTGCAGCTACATGAT 59.164 47.619 15.27 0.00 0.00 2.45
1871 5528 1.599667 CGCATTGATTGGCTGCATCTC 60.600 52.381 0.50 0.00 35.64 2.75
1872 5529 1.681793 GCATTGATTGGCTGCATCTCT 59.318 47.619 0.50 0.00 35.96 3.10
2030 5707 6.767902 AGGTATGGACAGTTGCTGTATATTTG 59.232 38.462 1.43 0.00 45.44 2.32
2185 5885 2.351418 TGGCGTCATCTTTATGCTTTCG 59.649 45.455 0.00 0.00 32.76 3.46
2301 6003 3.385193 ACATGTGGCTAAAAACTTGCC 57.615 42.857 0.00 0.00 46.26 4.52
2356 6064 5.515626 GTGAAGGTGATATATCGTTATCGGC 59.484 44.000 8.19 0.00 37.69 5.54
2465 6178 4.696479 ATTGTGTTTGTTTTATGGGGCA 57.304 36.364 0.00 0.00 0.00 5.36
2522 6236 1.257750 CGAGGTCCCATGTGTCAGGA 61.258 60.000 0.00 0.00 0.00 3.86
2588 6306 4.594970 ACACATCCCAACGATTTATCCAA 58.405 39.130 0.00 0.00 0.00 3.53
2650 6373 8.714179 CATCCTTACAAGTACGTCAACATAAAA 58.286 33.333 0.00 0.00 0.00 1.52
2679 6404 2.584608 GGATGGTGTCCCCTCACG 59.415 66.667 0.00 0.00 41.50 4.35
2900 6632 5.350914 GCATATCACTTGCTATCATCTCCAC 59.649 44.000 0.00 0.00 37.14 4.02
3018 6757 6.473397 GCTATGCCACATAATACTGTCTTC 57.527 41.667 0.00 0.00 0.00 2.87
3038 6777 7.279981 TGTCTTCAGTGTTATGCCACATAATAC 59.720 37.037 15.37 15.37 37.82 1.89
3078 6824 4.256920 CACCACTAGAGGAATGACAAAGG 58.743 47.826 13.71 0.00 0.00 3.11
3090 6836 9.525409 GAGGAATGACAAAGGAAAATATCATTG 57.475 33.333 2.21 0.00 37.02 2.82
3138 6884 9.463443 GTTTTAATTGTCTTGTTGCATAGAAGT 57.537 29.630 0.00 0.00 0.00 3.01
3145 6891 6.486320 TGTCTTGTTGCATAGAAGTGAAATCA 59.514 34.615 0.00 0.00 0.00 2.57
3152 6898 9.443283 GTTGCATAGAAGTGAAATCATTCATAC 57.557 33.333 0.00 0.00 46.67 2.39
3164 6910 9.904198 TGAAATCATTCATACTTTGGATACTCA 57.096 29.630 0.00 0.00 40.59 3.41
3198 6946 8.607459 AGCTATTGTATTCTGAATTTTCACTCG 58.393 33.333 8.38 0.00 32.90 4.18
3199 6947 8.604035 GCTATTGTATTCTGAATTTTCACTCGA 58.396 33.333 8.38 0.00 32.90 4.04
3203 6951 7.806690 TGTATTCTGAATTTTCACTCGAAAGG 58.193 34.615 8.38 0.00 42.00 3.11
3218 6966 5.163733 ACTCGAAAGGTACGCAAAAGAAAAA 60.164 36.000 0.00 0.00 0.00 1.94
3239 6987 1.494721 ACTTGGTGTCCCTTCATGTGT 59.505 47.619 0.00 0.00 0.00 3.72
3713 7494 0.179009 TGCAACTGCTTCCTGCTTCT 60.179 50.000 2.95 0.00 43.37 2.85
4159 7966 7.435488 GGATCTTCGATCTTTACAAATTCTCGA 59.565 37.037 4.10 0.00 32.45 4.04
4245 8457 3.514309 AGCGGTAGGTATGAAAACTGAGT 59.486 43.478 0.00 0.00 0.00 3.41
4247 8459 3.617263 CGGTAGGTATGAAAACTGAGTGC 59.383 47.826 0.00 0.00 0.00 4.40
4267 8480 6.282930 AGTGCAAATTATGAAGCAAGTGTTT 58.717 32.000 0.00 0.00 38.91 2.83
4296 8509 9.528018 TTTTTGCGAGAAAACTTTGAATCTATT 57.472 25.926 0.00 0.00 0.00 1.73
4297 8510 8.728088 TTTGCGAGAAAACTTTGAATCTATTC 57.272 30.769 0.00 0.00 37.31 1.75
4298 8511 7.433708 TGCGAGAAAACTTTGAATCTATTCA 57.566 32.000 1.23 1.23 44.42 2.57
4299 8512 8.044060 TGCGAGAAAACTTTGAATCTATTCAT 57.956 30.769 6.24 0.00 45.30 2.57
4300 8513 8.177663 TGCGAGAAAACTTTGAATCTATTCATC 58.822 33.333 6.24 0.92 45.30 2.92
4417 8630 8.098912 ACACCTATACGAAAATGAAAGGTTACT 58.901 33.333 0.00 0.00 33.67 2.24
4457 8671 7.340743 CCCACAACCATATAGAAAAATACACCA 59.659 37.037 0.00 0.00 0.00 4.17
4496 8737 1.652563 ATGCGTACGAGCGAGCATA 59.347 52.632 21.65 0.00 46.93 3.14
4526 8767 0.037232 GTGAGTGGGAGGTGTGTAGC 60.037 60.000 0.00 0.00 0.00 3.58
4538 8781 0.541063 TGTGTAGCCGGGAGACAAGA 60.541 55.000 2.18 0.00 0.00 3.02
4702 8956 5.379732 TTTGAAGTTTCACCAGAAAACGT 57.620 34.783 0.00 0.00 44.75 3.99
4703 8957 4.609691 TGAAGTTTCACCAGAAAACGTC 57.390 40.909 7.44 7.44 44.75 4.34
4759 9013 6.176975 TGTGCTTCTGTAATGTAAATTCCG 57.823 37.500 0.00 0.00 0.00 4.30
4772 9026 7.795482 ATGTAAATTCCGTTTCCGATTATGA 57.205 32.000 0.00 0.00 35.63 2.15
5053 9318 8.040132 TCCTTTAATTTGGTATGCCATCTTTTG 58.960 33.333 2.33 0.00 45.56 2.44
5471 9918 0.601046 GCTCCAAAGTGCCTTTTGCC 60.601 55.000 4.88 0.00 40.16 4.52
5558 10008 3.525537 CGTCAATCTGCTCATACAACCT 58.474 45.455 0.00 0.00 0.00 3.50
5563 10013 7.096023 CGTCAATCTGCTCATACAACCTTATAC 60.096 40.741 0.00 0.00 0.00 1.47
5564 10014 7.928706 GTCAATCTGCTCATACAACCTTATACT 59.071 37.037 0.00 0.00 0.00 2.12
5565 10015 8.144478 TCAATCTGCTCATACAACCTTATACTC 58.856 37.037 0.00 0.00 0.00 2.59
5566 10016 7.847711 ATCTGCTCATACAACCTTATACTCT 57.152 36.000 0.00 0.00 0.00 3.24
5567 10017 7.661536 TCTGCTCATACAACCTTATACTCTT 57.338 36.000 0.00 0.00 0.00 2.85
5568 10018 8.079211 TCTGCTCATACAACCTTATACTCTTT 57.921 34.615 0.00 0.00 0.00 2.52
5569 10019 8.198109 TCTGCTCATACAACCTTATACTCTTTC 58.802 37.037 0.00 0.00 0.00 2.62
5571 10021 7.981789 TGCTCATACAACCTTATACTCTTTCTG 59.018 37.037 0.00 0.00 0.00 3.02
5573 10023 9.877178 CTCATACAACCTTATACTCTTTCTGTT 57.123 33.333 0.00 0.00 0.00 3.16
5574 10024 9.871238 TCATACAACCTTATACTCTTTCTGTTC 57.129 33.333 0.00 0.00 0.00 3.18
5575 10025 9.099454 CATACAACCTTATACTCTTTCTGTTCC 57.901 37.037 0.00 0.00 0.00 3.62
5576 10026 7.317722 ACAACCTTATACTCTTTCTGTTCCT 57.682 36.000 0.00 0.00 0.00 3.36
5577 10027 8.431910 ACAACCTTATACTCTTTCTGTTCCTA 57.568 34.615 0.00 0.00 0.00 2.94
5578 10028 8.877195 ACAACCTTATACTCTTTCTGTTCCTAA 58.123 33.333 0.00 0.00 0.00 2.69
5579 10029 9.720769 CAACCTTATACTCTTTCTGTTCCTAAA 57.279 33.333 0.00 0.00 0.00 1.85
5603 10053 5.819825 ATAAGTCTTTTTGGAGATTCCGC 57.180 39.130 0.00 0.00 40.17 5.54
5604 10054 3.425162 AGTCTTTTTGGAGATTCCGCT 57.575 42.857 0.00 0.00 40.17 5.52
5605 10055 4.553330 AGTCTTTTTGGAGATTCCGCTA 57.447 40.909 0.00 0.00 40.17 4.26
5606 10056 4.254492 AGTCTTTTTGGAGATTCCGCTAC 58.746 43.478 0.00 0.00 40.17 3.58
5607 10057 4.000988 GTCTTTTTGGAGATTCCGCTACA 58.999 43.478 0.00 0.00 40.17 2.74
5608 10058 4.454504 GTCTTTTTGGAGATTCCGCTACAA 59.545 41.667 0.00 0.00 40.17 2.41
5609 10059 5.048991 GTCTTTTTGGAGATTCCGCTACAAA 60.049 40.000 0.00 0.00 44.70 2.83
5610 10060 4.759516 TTTTGGAGATTCCGCTACAAAC 57.240 40.909 0.00 0.00 45.70 2.93
5611 10061 3.695830 TTGGAGATTCCGCTACAAACT 57.304 42.857 0.00 0.00 40.17 2.66
5612 10062 4.811969 TTGGAGATTCCGCTACAAACTA 57.188 40.909 0.00 0.00 40.17 2.24
5613 10063 4.119442 TGGAGATTCCGCTACAAACTAC 57.881 45.455 0.00 0.00 40.17 2.73
5614 10064 3.512329 TGGAGATTCCGCTACAAACTACA 59.488 43.478 0.00 0.00 40.17 2.74
5615 10065 4.161565 TGGAGATTCCGCTACAAACTACAT 59.838 41.667 0.00 0.00 40.17 2.29
5616 10066 5.361571 TGGAGATTCCGCTACAAACTACATA 59.638 40.000 0.00 0.00 40.17 2.29
5617 10067 5.690857 GGAGATTCCGCTACAAACTACATAC 59.309 44.000 0.00 0.00 0.00 2.39
5618 10068 6.216801 AGATTCCGCTACAAACTACATACA 57.783 37.500 0.00 0.00 0.00 2.29
5619 10069 6.273825 AGATTCCGCTACAAACTACATACAG 58.726 40.000 0.00 0.00 0.00 2.74
5620 10070 5.648178 TTCCGCTACAAACTACATACAGA 57.352 39.130 0.00 0.00 0.00 3.41
5621 10071 5.847111 TCCGCTACAAACTACATACAGAT 57.153 39.130 0.00 0.00 0.00 2.90
5622 10072 5.588240 TCCGCTACAAACTACATACAGATG 58.412 41.667 0.00 0.00 39.16 2.90
5623 10073 4.209288 CCGCTACAAACTACATACAGATGC 59.791 45.833 0.00 0.00 36.43 3.91
5624 10074 4.803613 CGCTACAAACTACATACAGATGCA 59.196 41.667 0.00 0.00 36.43 3.96
5625 10075 5.463392 CGCTACAAACTACATACAGATGCAT 59.537 40.000 0.00 0.00 36.43 3.96
5626 10076 6.640907 CGCTACAAACTACATACAGATGCATA 59.359 38.462 0.00 0.00 36.43 3.14
5627 10077 7.329471 CGCTACAAACTACATACAGATGCATAT 59.671 37.037 0.00 0.00 36.43 1.78
5628 10078 9.639601 GCTACAAACTACATACAGATGCATATA 57.360 33.333 0.00 0.00 36.43 0.86
5631 10081 9.698309 ACAAACTACATACAGATGCATATAGAC 57.302 33.333 0.00 0.00 36.43 2.59
5632 10082 9.696917 CAAACTACATACAGATGCATATAGACA 57.303 33.333 0.00 0.00 36.43 3.41
5666 10116 7.743104 AGTGTAGATTCACTTATTTTGCTTCG 58.257 34.615 0.00 0.00 44.92 3.79
5667 10117 7.387948 AGTGTAGATTCACTTATTTTGCTTCGT 59.612 33.333 0.00 0.00 44.92 3.85
5668 10118 8.653338 GTGTAGATTCACTTATTTTGCTTCGTA 58.347 33.333 0.00 0.00 35.68 3.43
5669 10119 9.378551 TGTAGATTCACTTATTTTGCTTCGTAT 57.621 29.630 0.00 0.00 0.00 3.06
5670 10120 9.638300 GTAGATTCACTTATTTTGCTTCGTATG 57.362 33.333 0.00 0.00 0.00 2.39
5671 10121 8.268850 AGATTCACTTATTTTGCTTCGTATGT 57.731 30.769 0.00 0.00 0.00 2.29
5672 10122 9.378551 AGATTCACTTATTTTGCTTCGTATGTA 57.621 29.630 0.00 0.00 0.00 2.29
5673 10123 9.638300 GATTCACTTATTTTGCTTCGTATGTAG 57.362 33.333 0.00 0.00 0.00 2.74
5674 10124 8.542497 TTCACTTATTTTGCTTCGTATGTAGT 57.458 30.769 0.00 0.00 0.00 2.73
5675 10125 8.181487 TCACTTATTTTGCTTCGTATGTAGTC 57.819 34.615 0.00 0.00 0.00 2.59
5676 10126 7.277098 TCACTTATTTTGCTTCGTATGTAGTCC 59.723 37.037 0.00 0.00 0.00 3.85
5677 10127 7.064134 CACTTATTTTGCTTCGTATGTAGTCCA 59.936 37.037 0.00 0.00 0.00 4.02
5678 10128 7.769044 ACTTATTTTGCTTCGTATGTAGTCCAT 59.231 33.333 0.00 0.00 37.58 3.41
5679 10129 9.256477 CTTATTTTGCTTCGTATGTAGTCCATA 57.744 33.333 0.00 0.00 34.86 2.74
5680 10130 7.715265 ATTTTGCTTCGTATGTAGTCCATAG 57.285 36.000 0.00 0.00 36.71 2.23
5681 10131 5.847111 TTGCTTCGTATGTAGTCCATAGT 57.153 39.130 0.00 0.00 36.71 2.12
5682 10132 5.183014 TGCTTCGTATGTAGTCCATAGTG 57.817 43.478 0.00 0.00 36.71 2.74
5683 10133 4.037565 TGCTTCGTATGTAGTCCATAGTGG 59.962 45.833 0.00 0.00 36.71 4.00
5684 10134 4.277672 GCTTCGTATGTAGTCCATAGTGGA 59.722 45.833 0.00 0.00 45.98 4.02
5700 10150 9.807921 TCCATAGTGGAATCTTTAAAAAGACTT 57.192 29.630 7.29 4.18 45.00 3.01
5718 10168 8.959705 AAAGACTTATATTTAGGAACGGAAGG 57.040 34.615 0.00 0.00 0.00 3.46
5719 10169 7.909485 AGACTTATATTTAGGAACGGAAGGA 57.091 36.000 0.00 0.00 0.00 3.36
5720 10170 7.953752 AGACTTATATTTAGGAACGGAAGGAG 58.046 38.462 0.00 0.00 0.00 3.69
5721 10171 7.564292 AGACTTATATTTAGGAACGGAAGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
5722 10172 8.773033 ACTTATATTTAGGAACGGAAGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
5723 10173 9.377238 ACTTATATTTAGGAACGGAAGGAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
5724 10174 9.640963 CTTATATTTAGGAACGGAAGGAGTATG 57.359 37.037 0.00 0.00 0.00 2.39
5725 10175 5.952347 ATTTAGGAACGGAAGGAGTATGT 57.048 39.130 0.00 0.00 0.00 2.29
5726 10176 4.996788 TTAGGAACGGAAGGAGTATGTC 57.003 45.455 0.00 0.00 0.00 3.06
5727 10177 2.816411 AGGAACGGAAGGAGTATGTCA 58.184 47.619 0.00 0.00 0.00 3.58
5728 10178 2.761208 AGGAACGGAAGGAGTATGTCAG 59.239 50.000 0.00 0.00 0.00 3.51
5729 10179 2.758979 GGAACGGAAGGAGTATGTCAGA 59.241 50.000 0.00 0.00 0.00 3.27
5730 10180 3.194968 GGAACGGAAGGAGTATGTCAGAA 59.805 47.826 0.00 0.00 0.00 3.02
5731 10181 3.870633 ACGGAAGGAGTATGTCAGAAC 57.129 47.619 0.00 0.00 0.00 3.01
5732 10182 3.432378 ACGGAAGGAGTATGTCAGAACT 58.568 45.455 0.00 0.00 0.00 3.01
5733 10183 4.597004 ACGGAAGGAGTATGTCAGAACTA 58.403 43.478 0.00 0.00 0.00 2.24
5793 10297 8.877864 TTTCTTTCATACAGACAATATTGGGT 57.122 30.769 19.37 15.36 0.00 4.51
5805 10309 4.711355 ACAATATTGGGTCATTGTCAAGGG 59.289 41.667 19.37 0.00 40.47 3.95
6205 10841 1.271707 CCCTGTATGTGTTCCCCGTTT 60.272 52.381 0.00 0.00 0.00 3.60
6314 10971 4.821589 GCCCTCGGCGTCAAGGAG 62.822 72.222 14.10 6.08 39.62 3.69
6380 11037 0.832135 ACACCAGGGACATCGTGAGT 60.832 55.000 0.00 0.00 33.39 3.41
6382 11039 1.135083 CACCAGGGACATCGTGAGTAC 60.135 57.143 0.00 0.00 33.39 2.73
6641 11900 4.660938 GGCCAGTCTGCCGGGTTT 62.661 66.667 2.18 0.00 42.54 3.27
6670 11946 1.670087 CGTCTCCTTCTCGTTGCATGT 60.670 52.381 0.00 0.00 0.00 3.21
6704 11980 4.686091 TCACTCGCTAACAGTGATTTCTTG 59.314 41.667 0.00 0.00 44.33 3.02
6705 11981 3.433615 ACTCGCTAACAGTGATTTCTTGC 59.566 43.478 0.00 0.00 33.80 4.01
6706 11982 3.664107 TCGCTAACAGTGATTTCTTGCT 58.336 40.909 0.00 0.00 28.30 3.91
6708 11984 4.152402 TCGCTAACAGTGATTTCTTGCTTC 59.848 41.667 0.00 0.00 28.30 3.86
6709 11985 4.083855 CGCTAACAGTGATTTCTTGCTTCA 60.084 41.667 0.00 0.00 0.00 3.02
6712 11990 6.865205 GCTAACAGTGATTTCTTGCTTCATTT 59.135 34.615 0.00 0.00 0.00 2.32
6716 11994 7.144000 ACAGTGATTTCTTGCTTCATTTTCTC 58.856 34.615 0.00 0.00 0.00 2.87
7023 12342 1.271926 ACCTTGTGCATGTAGTTCCCC 60.272 52.381 0.00 0.00 0.00 4.81
7061 12380 5.847111 CATCCAGGATGTGTTGATGAAAT 57.153 39.130 20.30 0.00 35.89 2.17
7214 12537 4.340894 TCAGTCGTTTGATAAAGCATGC 57.659 40.909 10.51 10.51 0.00 4.06
7239 12562 2.942376 TGCCATTTTGCACCGTATAGAG 59.058 45.455 0.00 0.00 36.04 2.43
7318 12641 3.033659 ACTGATAGACCTTGGATCGGT 57.966 47.619 0.00 0.00 34.94 4.69
7354 12678 1.204941 CGGTGAACCTACCTTCTCCAG 59.795 57.143 0.00 0.00 38.62 3.86
7514 12840 1.904287 TTGTGGCAGCGATTAACCTT 58.096 45.000 0.00 0.00 0.00 3.50
7628 12955 4.011517 GTCAGGGGCCCGTTCGAA 62.012 66.667 16.16 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.283625 TGGTAAGTGTTACAATTTGCTGATT 57.716 32.000 2.78 0.00 37.88 2.57
39 40 5.046878 TGTCATATCCGTCTTGGTAAGTGTT 60.047 40.000 0.00 0.00 39.52 3.32
40 41 4.464951 TGTCATATCCGTCTTGGTAAGTGT 59.535 41.667 0.00 0.00 39.52 3.55
41 42 5.006153 TGTCATATCCGTCTTGGTAAGTG 57.994 43.478 0.00 0.00 39.52 3.16
147 159 2.629656 AATGGGTTGCGCTGTGCTC 61.630 57.895 14.92 7.48 46.63 4.26
211 231 6.455647 GTCCATATATCACATGAACGAAGGA 58.544 40.000 0.00 0.00 0.00 3.36
287 307 5.736951 ACAACCAAGGCATAGCAAATTAA 57.263 34.783 0.00 0.00 0.00 1.40
376 408 9.500864 CTCATAGTACGACATCAATATCATGAG 57.499 37.037 0.09 0.00 31.76 2.90
452 487 6.658849 ACAACATCAGCTATATTAACCACCA 58.341 36.000 0.00 0.00 0.00 4.17
598 640 8.880991 ATATACACGACAGATTTCCCTATACT 57.119 34.615 0.00 0.00 0.00 2.12
618 660 9.634163 TGATACATTCATCCAACACGTATATAC 57.366 33.333 2.53 2.53 0.00 1.47
701 744 0.597568 CAAAAGATGTGGCGCTCCAA 59.402 50.000 7.64 0.00 45.53 3.53
709 752 8.091449 ACTCTAGTCTAACTTCAAAAGATGTGG 58.909 37.037 0.00 0.00 0.00 4.17
918 992 6.598753 TCCGTTTTGTTGTTCTCTAGAAAG 57.401 37.500 0.00 0.00 35.58 2.62
1127 4591 3.083997 CGAGGTGGAAGGGGAGGG 61.084 72.222 0.00 0.00 0.00 4.30
1154 4618 3.416156 AGAACAGAGTGAGAAAATGGGC 58.584 45.455 0.00 0.00 0.00 5.36
1178 4642 2.876550 GGGTGCGTAGAAAAACTTGAGT 59.123 45.455 0.00 0.00 0.00 3.41
1201 4672 4.753662 TCGGCACCTCCTACCGCT 62.754 66.667 0.00 0.00 46.49 5.52
1454 4944 7.436430 TGATATGACGTAGAGAGTAATGACC 57.564 40.000 0.00 0.00 0.00 4.02
1460 4950 8.804204 TCTGAGTATGATATGACGTAGAGAGTA 58.196 37.037 0.00 0.00 0.00 2.59
1483 4995 3.242511 CGGTTGACATGTGTATGCATCTG 60.243 47.826 1.15 0.00 37.85 2.90
1511 5026 2.767505 GACGAACTTGAATGGACCTGT 58.232 47.619 0.00 0.00 0.00 4.00
1640 5200 0.796312 AGCGTGAATTTGCAGTACGG 59.204 50.000 10.62 0.00 35.49 4.02
1641 5201 1.459209 TGAGCGTGAATTTGCAGTACG 59.541 47.619 0.00 0.00 37.77 3.67
1642 5202 3.536158 TTGAGCGTGAATTTGCAGTAC 57.464 42.857 0.00 0.00 0.00 2.73
1651 5211 6.150976 TGGAAAATACAGAATTGAGCGTGAAT 59.849 34.615 0.00 0.00 0.00 2.57
1673 5244 0.254462 TATGCGCCACCTGAAATGGA 59.746 50.000 4.18 0.00 39.87 3.41
1871 5528 3.440522 TCACGTGGATCAGACAGTAAGAG 59.559 47.826 17.00 0.00 0.00 2.85
1872 5529 3.190744 GTCACGTGGATCAGACAGTAAGA 59.809 47.826 17.00 0.00 0.00 2.10
1928 5605 4.827835 CCCGATGTAGAGAGGACTTGATAA 59.172 45.833 0.00 0.00 0.00 1.75
2016 5693 8.279800 TCAATATACGTGCAAATATACAGCAAC 58.720 33.333 0.00 0.00 40.35 4.17
2030 5707 1.526887 ACGCATGCTCAATATACGTGC 59.473 47.619 17.13 0.00 41.77 5.34
2164 5864 2.351418 CGAAAGCATAAAGATGACGCCA 59.649 45.455 0.00 0.00 34.73 5.69
2185 5885 4.224370 TCCAACTTCATTACCTGTAGGGAC 59.776 45.833 2.53 0.00 40.27 4.46
2247 5947 6.656632 AGTCTCTTGTGTAGAATTGTGAGA 57.343 37.500 0.00 0.00 30.91 3.27
2321 6027 6.903883 ATATCACCTTCACGTACACATTTC 57.096 37.500 0.00 0.00 0.00 2.17
2465 6178 6.895756 TCCAGATTGGCCTATACTATAACGAT 59.104 38.462 3.32 0.00 37.47 3.73
2522 6236 6.408548 CCGGACCCATGATATAAGCTAATGAT 60.409 42.308 0.00 0.00 0.00 2.45
2650 6373 5.104259 GGACACCATCCTCTTATTTGTCT 57.896 43.478 0.00 0.00 45.22 3.41
2871 6603 4.129380 TGATAGCAAGTGATATGCCACAC 58.871 43.478 0.00 0.00 44.91 3.82
2900 6632 4.821589 GAAGCCCCGAGACGCCTG 62.822 72.222 0.00 0.00 0.00 4.85
2975 6712 0.740149 CGGTAGTGGGTGCGTACATA 59.260 55.000 5.86 0.00 0.00 2.29
3013 6752 6.683974 ATTATGTGGCATAACACTGAAGAC 57.316 37.500 4.00 0.00 41.84 3.01
3018 6757 6.763135 AGACAGTATTATGTGGCATAACACTG 59.237 38.462 25.87 25.87 41.93 3.66
3038 6777 2.148916 TGTTGCTACACCGAAGACAG 57.851 50.000 0.00 0.00 0.00 3.51
3078 6824 9.090692 CACTCCACATTTTCCAATGATATTTTC 57.909 33.333 1.97 0.00 42.35 2.29
3090 6836 5.003804 ACTACACATCACTCCACATTTTCC 58.996 41.667 0.00 0.00 0.00 3.13
3094 6840 8.635765 ATTAAAACTACACATCACTCCACATT 57.364 30.769 0.00 0.00 0.00 2.71
3138 6884 9.904198 TGAGTATCCAAAGTATGAATGATTTCA 57.096 29.630 0.00 0.00 45.57 2.69
3145 6891 7.735917 TCGGAATGAGTATCCAAAGTATGAAT 58.264 34.615 0.00 0.00 36.74 2.57
3152 6898 4.878397 AGCTTTCGGAATGAGTATCCAAAG 59.122 41.667 7.72 0.00 37.70 2.77
3164 6910 8.682936 ATTCAGAATACAATAGCTTTCGGAAT 57.317 30.769 13.02 13.02 37.82 3.01
3165 6911 8.506168 AATTCAGAATACAATAGCTTTCGGAA 57.494 30.769 10.26 10.26 36.95 4.30
3218 6966 2.091885 ACACATGAAGGGACACCAAGTT 60.092 45.455 0.00 0.00 40.13 2.66
3239 6987 2.842208 CAAGCGTGTGTTCTTTTCCA 57.158 45.000 0.00 0.00 0.00 3.53
3659 7412 7.911727 ACCGGCGAATTAATACAAATTTTAGAC 59.088 33.333 9.30 0.00 0.00 2.59
3666 7419 3.378742 TGCACCGGCGAATTAATACAAAT 59.621 39.130 9.30 0.00 45.35 2.32
3713 7494 1.073125 TGGGAAGAAAGCACGATCCAA 59.927 47.619 0.00 0.00 31.63 3.53
3861 7647 4.523558 AGGTTGTCTCAGGTAGTTACACTC 59.476 45.833 0.00 0.00 0.00 3.51
3918 7721 7.871463 TGACTTACTCCTTTACTTTCTTAGTGC 59.129 37.037 0.00 0.00 37.73 4.40
3960 7764 0.036010 CAACATTGACTCCGAGCCCT 60.036 55.000 0.00 0.00 0.00 5.19
4159 7966 3.383825 GCATCAAAGATCTGGATTTGCCT 59.616 43.478 0.00 0.00 36.55 4.75
4245 8457 7.551035 AAAAACACTTGCTTCATAATTTGCA 57.449 28.000 0.00 0.00 0.00 4.08
4270 8483 9.528018 AATAGATTCAAAGTTTTCTCGCAAAAA 57.472 25.926 0.00 0.00 0.00 1.94
4271 8484 9.180678 GAATAGATTCAAAGTTTTCTCGCAAAA 57.819 29.630 0.00 0.00 36.80 2.44
4272 8485 8.349245 TGAATAGATTCAAAGTTTTCTCGCAAA 58.651 29.630 2.41 0.00 43.26 3.68
4289 8502 9.896645 TGCTTTCACTAAGAAGATGAATAGATT 57.103 29.630 0.00 0.00 37.57 2.40
4290 8503 9.896645 TTGCTTTCACTAAGAAGATGAATAGAT 57.103 29.630 0.00 0.00 37.57 1.98
4291 8504 9.725019 TTTGCTTTCACTAAGAAGATGAATAGA 57.275 29.630 0.00 0.00 37.57 1.98
4294 8507 8.632679 TGTTTTGCTTTCACTAAGAAGATGAAT 58.367 29.630 0.00 0.00 37.57 2.57
4295 8508 7.915397 GTGTTTTGCTTTCACTAAGAAGATGAA 59.085 33.333 0.00 0.00 37.57 2.57
4296 8509 7.066887 TGTGTTTTGCTTTCACTAAGAAGATGA 59.933 33.333 0.00 0.00 37.57 2.92
4297 8510 7.195646 TGTGTTTTGCTTTCACTAAGAAGATG 58.804 34.615 0.00 0.00 37.57 2.90
4298 8511 7.333528 TGTGTTTTGCTTTCACTAAGAAGAT 57.666 32.000 0.00 0.00 37.57 2.40
4299 8512 6.751514 TGTGTTTTGCTTTCACTAAGAAGA 57.248 33.333 0.00 0.00 37.57 2.87
4300 8513 7.810766 TTTGTGTTTTGCTTTCACTAAGAAG 57.189 32.000 0.00 0.00 37.57 2.85
4347 8560 9.362151 TGTATTCCTTTTTGGTAATGTCTCTTT 57.638 29.630 0.00 0.00 37.07 2.52
4352 8565 7.061789 CGCTTTGTATTCCTTTTTGGTAATGTC 59.938 37.037 0.00 0.00 37.07 3.06
4358 8571 5.286438 GTTCGCTTTGTATTCCTTTTTGGT 58.714 37.500 0.00 0.00 37.07 3.67
4417 8630 3.388350 GGTTGTGGGGGTTTTATGTTTCA 59.612 43.478 0.00 0.00 0.00 2.69
4457 8671 9.780413 ACGCATTTGAACATTTTTGTTATTTTT 57.220 22.222 0.00 0.00 31.35 1.94
4470 8684 1.060553 CGCTCGTACGCATTTGAACAT 59.939 47.619 11.24 0.00 0.00 2.71
4496 8737 1.646447 TCCCACTCACATCCTCTAGGT 59.354 52.381 0.00 0.00 36.34 3.08
4526 8767 2.028112 TCTTGTGATTCTTGTCTCCCGG 60.028 50.000 0.00 0.00 0.00 5.73
4538 8781 3.200825 CCCATCCCACTAGTCTTGTGATT 59.799 47.826 14.99 0.00 37.60 2.57
4575 8829 2.171870 GGGAACAACCGATTCCTATCCA 59.828 50.000 3.91 0.00 44.43 3.41
4576 8830 2.171870 TGGGAACAACCGATTCCTATCC 59.828 50.000 3.91 0.00 44.43 2.59
4737 8991 6.178239 ACGGAATTTACATTACAGAAGCAC 57.822 37.500 0.00 0.00 0.00 4.40
4759 9013 8.345565 ACAGAGCATAAATTCATAATCGGAAAC 58.654 33.333 0.00 0.00 0.00 2.78
4947 9211 9.964354 TCATGTGCCTTAATCTAATATATTGCT 57.036 29.630 8.28 0.00 0.00 3.91
4948 9212 9.994432 GTCATGTGCCTTAATCTAATATATTGC 57.006 33.333 8.28 1.18 0.00 3.56
4967 9231 7.657336 ACCTTTACCAGTTAAAATGTCATGTG 58.343 34.615 0.00 0.00 0.00 3.21
5053 9318 3.000322 CCGTTGTCTATGCTTCGTCAATC 60.000 47.826 0.00 0.00 0.00 2.67
5335 9778 2.943033 ACACTCACACACTACCAAAAGC 59.057 45.455 0.00 0.00 0.00 3.51
5471 9918 8.040727 TGATCTGATATTATACCAAATCCGTGG 58.959 37.037 0.00 0.00 44.92 4.94
5577 10027 8.406297 GCGGAATCTCCAAAAAGACTTATATTT 58.594 33.333 0.00 0.00 35.91 1.40
5578 10028 7.775561 AGCGGAATCTCCAAAAAGACTTATATT 59.224 33.333 0.00 0.00 35.91 1.28
5579 10029 7.283329 AGCGGAATCTCCAAAAAGACTTATAT 58.717 34.615 0.00 0.00 35.91 0.86
5580 10030 6.650120 AGCGGAATCTCCAAAAAGACTTATA 58.350 36.000 0.00 0.00 35.91 0.98
5581 10031 5.501156 AGCGGAATCTCCAAAAAGACTTAT 58.499 37.500 0.00 0.00 35.91 1.73
5582 10032 4.906618 AGCGGAATCTCCAAAAAGACTTA 58.093 39.130 0.00 0.00 35.91 2.24
5583 10033 3.756117 AGCGGAATCTCCAAAAAGACTT 58.244 40.909 0.00 0.00 35.91 3.01
5584 10034 3.425162 AGCGGAATCTCCAAAAAGACT 57.575 42.857 0.00 0.00 35.91 3.24
5585 10035 4.000988 TGTAGCGGAATCTCCAAAAAGAC 58.999 43.478 0.00 0.00 35.91 3.01
5586 10036 4.280436 TGTAGCGGAATCTCCAAAAAGA 57.720 40.909 0.00 0.00 35.91 2.52
5587 10037 5.048713 AGTTTGTAGCGGAATCTCCAAAAAG 60.049 40.000 0.00 0.00 35.91 2.27
5588 10038 4.825085 AGTTTGTAGCGGAATCTCCAAAAA 59.175 37.500 0.00 0.00 35.91 1.94
5589 10039 4.394729 AGTTTGTAGCGGAATCTCCAAAA 58.605 39.130 0.00 0.00 35.91 2.44
5590 10040 4.015872 AGTTTGTAGCGGAATCTCCAAA 57.984 40.909 0.00 0.00 35.91 3.28
5591 10041 3.695830 AGTTTGTAGCGGAATCTCCAA 57.304 42.857 0.00 0.00 35.91 3.53
5592 10042 3.512329 TGTAGTTTGTAGCGGAATCTCCA 59.488 43.478 0.00 0.00 35.91 3.86
5593 10043 4.119442 TGTAGTTTGTAGCGGAATCTCC 57.881 45.455 0.00 0.00 0.00 3.71
5594 10044 6.270815 TGTATGTAGTTTGTAGCGGAATCTC 58.729 40.000 0.00 0.00 0.00 2.75
5595 10045 6.096423 TCTGTATGTAGTTTGTAGCGGAATCT 59.904 38.462 0.00 0.00 0.00 2.40
5596 10046 6.270815 TCTGTATGTAGTTTGTAGCGGAATC 58.729 40.000 0.00 0.00 0.00 2.52
5597 10047 6.216801 TCTGTATGTAGTTTGTAGCGGAAT 57.783 37.500 0.00 0.00 0.00 3.01
5598 10048 5.648178 TCTGTATGTAGTTTGTAGCGGAA 57.352 39.130 0.00 0.00 0.00 4.30
5599 10049 5.588240 CATCTGTATGTAGTTTGTAGCGGA 58.412 41.667 0.00 0.00 0.00 5.54
5600 10050 4.209288 GCATCTGTATGTAGTTTGTAGCGG 59.791 45.833 0.00 0.00 35.38 5.52
5601 10051 4.803613 TGCATCTGTATGTAGTTTGTAGCG 59.196 41.667 0.00 0.00 35.38 4.26
5602 10052 6.851222 ATGCATCTGTATGTAGTTTGTAGC 57.149 37.500 0.00 0.00 35.38 3.58
5605 10055 9.698309 GTCTATATGCATCTGTATGTAGTTTGT 57.302 33.333 0.19 0.00 34.91 2.83
5606 10056 9.696917 TGTCTATATGCATCTGTATGTAGTTTG 57.303 33.333 0.19 0.00 34.91 2.93
5642 10092 7.519002 ACGAAGCAAAATAAGTGAATCTACAC 58.481 34.615 0.00 0.00 40.60 2.90
5643 10093 7.667043 ACGAAGCAAAATAAGTGAATCTACA 57.333 32.000 0.00 0.00 0.00 2.74
5644 10094 9.638300 CATACGAAGCAAAATAAGTGAATCTAC 57.362 33.333 0.00 0.00 0.00 2.59
5645 10095 9.378551 ACATACGAAGCAAAATAAGTGAATCTA 57.621 29.630 0.00 0.00 0.00 1.98
5646 10096 8.268850 ACATACGAAGCAAAATAAGTGAATCT 57.731 30.769 0.00 0.00 0.00 2.40
5647 10097 9.638300 CTACATACGAAGCAAAATAAGTGAATC 57.362 33.333 0.00 0.00 0.00 2.52
5648 10098 9.162764 ACTACATACGAAGCAAAATAAGTGAAT 57.837 29.630 0.00 0.00 0.00 2.57
5649 10099 8.542497 ACTACATACGAAGCAAAATAAGTGAA 57.458 30.769 0.00 0.00 0.00 3.18
5650 10100 7.277098 GGACTACATACGAAGCAAAATAAGTGA 59.723 37.037 0.00 0.00 0.00 3.41
5651 10101 7.064134 TGGACTACATACGAAGCAAAATAAGTG 59.936 37.037 0.00 0.00 0.00 3.16
5652 10102 7.101054 TGGACTACATACGAAGCAAAATAAGT 58.899 34.615 0.00 0.00 0.00 2.24
5653 10103 7.534085 TGGACTACATACGAAGCAAAATAAG 57.466 36.000 0.00 0.00 0.00 1.73
5654 10104 9.256477 CTATGGACTACATACGAAGCAAAATAA 57.744 33.333 0.00 0.00 41.03 1.40
5655 10105 8.418662 ACTATGGACTACATACGAAGCAAAATA 58.581 33.333 0.00 0.00 41.03 1.40
5656 10106 7.224753 CACTATGGACTACATACGAAGCAAAAT 59.775 37.037 0.00 0.00 41.03 1.82
5657 10107 6.533723 CACTATGGACTACATACGAAGCAAAA 59.466 38.462 0.00 0.00 41.03 2.44
5658 10108 6.040247 CACTATGGACTACATACGAAGCAAA 58.960 40.000 0.00 0.00 41.03 3.68
5659 10109 5.451381 CCACTATGGACTACATACGAAGCAA 60.451 44.000 0.00 0.00 40.96 3.91
5660 10110 4.037565 CCACTATGGACTACATACGAAGCA 59.962 45.833 0.00 0.00 40.96 3.91
5661 10111 4.277672 TCCACTATGGACTACATACGAAGC 59.722 45.833 0.00 0.00 42.67 3.86
5672 10122 9.232473 GTCTTTTTAAAGATTCCACTATGGACT 57.768 33.333 8.07 0.00 43.23 3.85
5673 10123 9.232473 AGTCTTTTTAAAGATTCCACTATGGAC 57.768 33.333 8.07 0.00 43.23 4.02
5674 10124 9.807921 AAGTCTTTTTAAAGATTCCACTATGGA 57.192 29.630 8.07 0.00 44.55 3.41
5692 10142 9.392259 CCTTCCGTTCCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
5693 10143 8.765517 TCCTTCCGTTCCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
5694 10144 8.315220 TCCTTCCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
5695 10145 7.564292 ACTCCTTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
5696 10146 7.724287 ACTCCTTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
5697 10147 7.672122 ACTCCTTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
5698 10148 9.640963 CATACTCCTTCCGTTCCTAAATATAAG 57.359 37.037 0.00 0.00 0.00 1.73
5699 10149 9.151177 ACATACTCCTTCCGTTCCTAAATATAA 57.849 33.333 0.00 0.00 0.00 0.98
5700 10150 8.716674 ACATACTCCTTCCGTTCCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
5701 10151 7.289317 TGACATACTCCTTCCGTTCCTAAATAT 59.711 37.037 0.00 0.00 0.00 1.28
5702 10152 6.608405 TGACATACTCCTTCCGTTCCTAAATA 59.392 38.462 0.00 0.00 0.00 1.40
5703 10153 5.424252 TGACATACTCCTTCCGTTCCTAAAT 59.576 40.000 0.00 0.00 0.00 1.40
5704 10154 4.773674 TGACATACTCCTTCCGTTCCTAAA 59.226 41.667 0.00 0.00 0.00 1.85
5705 10155 4.346730 TGACATACTCCTTCCGTTCCTAA 58.653 43.478 0.00 0.00 0.00 2.69
5706 10156 3.952323 CTGACATACTCCTTCCGTTCCTA 59.048 47.826 0.00 0.00 0.00 2.94
5707 10157 2.761208 CTGACATACTCCTTCCGTTCCT 59.239 50.000 0.00 0.00 0.00 3.36
5708 10158 2.758979 TCTGACATACTCCTTCCGTTCC 59.241 50.000 0.00 0.00 0.00 3.62
5709 10159 4.082136 AGTTCTGACATACTCCTTCCGTTC 60.082 45.833 0.00 0.00 0.00 3.95
5710 10160 3.833070 AGTTCTGACATACTCCTTCCGTT 59.167 43.478 0.00 0.00 0.00 4.44
5711 10161 3.432378 AGTTCTGACATACTCCTTCCGT 58.568 45.455 0.00 0.00 0.00 4.69
5712 10162 5.067936 ACATAGTTCTGACATACTCCTTCCG 59.932 44.000 0.00 0.00 0.00 4.30
5713 10163 6.472686 ACATAGTTCTGACATACTCCTTCC 57.527 41.667 0.00 0.00 0.00 3.46
5714 10164 7.276658 CACAACATAGTTCTGACATACTCCTTC 59.723 40.741 0.00 0.00 0.00 3.46
5715 10165 7.039011 TCACAACATAGTTCTGACATACTCCTT 60.039 37.037 0.00 0.00 0.00 3.36
5716 10166 6.437477 TCACAACATAGTTCTGACATACTCCT 59.563 38.462 0.00 0.00 0.00 3.69
5717 10167 6.631016 TCACAACATAGTTCTGACATACTCC 58.369 40.000 0.00 0.00 0.00 3.85
5718 10168 9.239002 GTATCACAACATAGTTCTGACATACTC 57.761 37.037 0.00 0.00 0.00 2.59
5719 10169 8.749354 TGTATCACAACATAGTTCTGACATACT 58.251 33.333 0.00 0.00 0.00 2.12
5720 10170 8.926715 TGTATCACAACATAGTTCTGACATAC 57.073 34.615 0.00 0.00 0.00 2.39
5721 10171 9.936759 TTTGTATCACAACATAGTTCTGACATA 57.063 29.630 0.00 0.00 37.90 2.29
5722 10172 8.846943 TTTGTATCACAACATAGTTCTGACAT 57.153 30.769 0.00 0.00 37.90 3.06
5723 10173 8.846943 ATTTGTATCACAACATAGTTCTGACA 57.153 30.769 0.00 0.00 37.90 3.58
5793 10297 2.957402 AGTCTTGCCCTTGACAATGA 57.043 45.000 0.00 0.00 35.81 2.57
5805 10309 6.401153 CGTTTGTAGGATTCTTGTAGTCTTGC 60.401 42.308 0.00 0.00 0.00 4.01
6205 10841 0.683179 ATGATCGGGTCAGTCCACGA 60.683 55.000 0.00 0.00 40.92 4.35
6380 11037 3.181484 CGTTCCGGTGATACTTGATGGTA 60.181 47.826 0.00 0.00 0.00 3.25
6382 11039 2.201732 CGTTCCGGTGATACTTGATGG 58.798 52.381 0.00 0.00 0.00 3.51
6641 11900 2.974489 GAAGGAGACGACGGCGACA 61.974 63.158 22.49 0.00 41.64 4.35
6670 11946 6.704493 ACTGTTAGCGAGTGAAATAAACAGAA 59.296 34.615 16.62 0.00 43.01 3.02
6704 11980 2.427506 ACCCGTGAGAGAAAATGAAGC 58.572 47.619 0.00 0.00 0.00 3.86
6705 11981 4.787598 CAAACCCGTGAGAGAAAATGAAG 58.212 43.478 0.00 0.00 0.00 3.02
6706 11982 3.004315 GCAAACCCGTGAGAGAAAATGAA 59.996 43.478 0.00 0.00 0.00 2.57
6708 11984 2.293122 TGCAAACCCGTGAGAGAAAATG 59.707 45.455 0.00 0.00 0.00 2.32
6709 11985 2.554032 CTGCAAACCCGTGAGAGAAAAT 59.446 45.455 0.00 0.00 0.00 1.82
6712 11990 0.756294 TCTGCAAACCCGTGAGAGAA 59.244 50.000 0.00 0.00 0.00 2.87
6716 11994 1.197721 GTGAATCTGCAAACCCGTGAG 59.802 52.381 0.00 0.00 0.00 3.51
6986 12305 5.705441 CACAAGGTTCTACATGTACATGGTT 59.295 40.000 33.32 19.54 42.91 3.67
7023 12342 3.979948 TGGATGTGCATGTTTGTTCAAG 58.020 40.909 0.00 0.00 0.00 3.02
7058 12377 5.914635 CGCAAAGTCACAAACTCACATATTT 59.085 36.000 0.00 0.00 37.17 1.40
7061 12380 3.874543 ACGCAAAGTCACAAACTCACATA 59.125 39.130 0.00 0.00 37.17 2.29
7239 12562 8.087982 TCAGAATGATTTGTAGAAGACAACAC 57.912 34.615 0.00 0.00 44.26 3.32
7300 12623 2.747177 ACACCGATCCAAGGTCTATCA 58.253 47.619 0.00 0.00 40.59 2.15
7301 12624 3.256136 CCTACACCGATCCAAGGTCTATC 59.744 52.174 0.00 0.00 40.59 2.08
7302 12625 3.231818 CCTACACCGATCCAAGGTCTAT 58.768 50.000 0.00 0.00 40.59 1.98
7303 12626 2.662866 CCTACACCGATCCAAGGTCTA 58.337 52.381 0.00 0.00 40.59 2.59
7304 12627 1.486211 CCTACACCGATCCAAGGTCT 58.514 55.000 0.00 0.00 40.59 3.85
7305 12628 0.179081 GCCTACACCGATCCAAGGTC 60.179 60.000 0.00 0.00 40.59 3.85
7308 12631 2.032620 ACTAGCCTACACCGATCCAAG 58.967 52.381 0.00 0.00 0.00 3.61
7318 12641 2.440627 TCACCGGATCTACTAGCCTACA 59.559 50.000 9.46 0.00 0.00 2.74
7354 12678 1.591863 GACCGAGCTTATCCGCACC 60.592 63.158 0.00 0.00 0.00 5.01
7532 12859 4.674623 CGCGCTATATAAACAGAGGTAGGG 60.675 50.000 5.56 0.00 0.00 3.53
7535 12862 3.192001 CCCGCGCTATATAAACAGAGGTA 59.808 47.826 5.56 0.00 0.00 3.08
7628 12955 3.060615 CTCTCCCGTTCGACCCGT 61.061 66.667 3.33 0.00 0.00 5.28
7630 12957 0.752376 ATCTCTCTCCCGTTCGACCC 60.752 60.000 0.00 0.00 0.00 4.46
7632 12959 1.380524 TGATCTCTCTCCCGTTCGAC 58.619 55.000 0.00 0.00 0.00 4.20
7813 13145 2.314549 TGGATAGGCCCAAAAGGAACAT 59.685 45.455 0.00 0.00 38.24 2.71


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

AutoCloner maintained by Alex Coulton.