Multiple sequence alignment - TraesCS5D01G304100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G304100 chr5D 100.000 6158 0 0 1 6158 399285116 399291273 0.000000e+00 11372.0
1 TraesCS5D01G304100 chr5D 96.344 2270 50 19 325 2578 399299496 399297244 0.000000e+00 3701.0
2 TraesCS5D01G304100 chr5D 91.503 1424 80 15 74 1485 399249530 399250924 0.000000e+00 1921.0
3 TraesCS5D01G304100 chr5D 86.230 443 27 12 73 502 399248325 399248746 3.390000e-122 449.0
4 TraesCS5D01G304100 chr5D 98.551 69 1 0 1 69 399258016 399258084 8.380000e-24 122.0
5 TraesCS5D01G304100 chr5B 93.650 4646 188 48 74 4669 479638952 479643540 0.000000e+00 6846.0
6 TraesCS5D01G304100 chr5B 91.231 707 30 10 4669 5353 479643578 479644274 0.000000e+00 933.0
7 TraesCS5D01G304100 chr5B 95.238 42 1 1 4666 4706 27817262 27817221 1.430000e-06 65.8
8 TraesCS5D01G304100 chr5A 94.366 3674 136 40 73 3712 504875184 504878820 0.000000e+00 5572.0
9 TraesCS5D01G304100 chr5A 93.498 1615 61 22 3690 5271 504879877 504881480 0.000000e+00 2361.0
10 TraesCS5D01G304100 chr5A 94.214 674 21 2 5411 6067 435709795 435710467 0.000000e+00 1013.0
11 TraesCS5D01G304100 chr5A 89.504 686 43 16 73 743 504883039 504882368 0.000000e+00 841.0
12 TraesCS5D01G304100 chr5A 92.208 77 6 0 1 77 294899350 294899426 6.530000e-20 110.0
13 TraesCS5D01G304100 chr2B 94.659 674 18 2 5411 6067 168631863 168632535 0.000000e+00 1029.0
14 TraesCS5D01G304100 chr1A 94.510 674 18 3 5411 6067 13006490 13007161 0.000000e+00 1022.0
15 TraesCS5D01G304100 chr6B 94.362 674 20 2 5411 6067 687137854 687137182 0.000000e+00 1018.0
16 TraesCS5D01G304100 chr6B 94.214 674 21 4 5411 6067 194690 194018 0.000000e+00 1013.0
17 TraesCS5D01G304100 chr2A 94.362 674 20 2 5411 6067 607490901 607490229 0.000000e+00 1018.0
18 TraesCS5D01G304100 chr2A 88.608 79 7 2 6070 6146 671709963 671709885 1.830000e-15 95.3
19 TraesCS5D01G304100 chr4B 94.214 674 21 2 5411 6067 672925160 672925832 0.000000e+00 1013.0
20 TraesCS5D01G304100 chr3A 94.214 674 21 2 5411 6067 121401821 121402493 0.000000e+00 1013.0
21 TraesCS5D01G304100 chr3A 95.122 41 1 1 4666 4705 543729655 543729615 5.150000e-06 63.9
22 TraesCS5D01G304100 chr7A 94.065 674 22 2 5411 6067 38120214 38120886 0.000000e+00 1007.0
23 TraesCS5D01G304100 chr7A 93.789 644 22 2 5441 6067 662092953 662093595 0.000000e+00 952.0
24 TraesCS5D01G304100 chr7A 97.101 69 1 1 429 496 725645352 725645420 1.400000e-21 115.0
25 TraesCS5D01G304100 chr3B 94.065 674 22 2 5411 6067 805267804 805267132 0.000000e+00 1007.0
26 TraesCS5D01G304100 chr3B 86.667 60 3 4 4658 4714 758394797 758394854 1.850000e-05 62.1
27 TraesCS5D01G304100 chr1B 94.065 674 22 2 5411 6067 66136315 66135643 0.000000e+00 1007.0
28 TraesCS5D01G304100 chr1B 94.065 674 22 2 5411 6067 676771106 676770434 0.000000e+00 1007.0
29 TraesCS5D01G304100 chr7B 93.917 674 23 2 5411 6067 706279327 706279999 0.000000e+00 1002.0
30 TraesCS5D01G304100 chr3D 93.926 675 18 5 5411 6067 33194256 33193587 0.000000e+00 998.0
31 TraesCS5D01G304100 chr3D 94.521 73 4 0 1 73 183665 183737 5.040000e-21 113.0
32 TraesCS5D01G304100 chr3D 90.385 52 2 3 4666 4716 457058513 457058464 1.430000e-06 65.8
33 TraesCS5D01G304100 chrUn 96.653 478 15 1 5411 5888 432143101 432143577 0.000000e+00 793.0
34 TraesCS5D01G304100 chrUn 94.595 74 4 0 1 74 81128789 81128862 1.400000e-21 115.0
35 TraesCS5D01G304100 chrUn 91.139 79 5 1 6070 6146 19232316 19232238 8.440000e-19 106.0
36 TraesCS5D01G304100 chr4D 95.714 70 3 0 1 70 354099080 354099011 5.040000e-21 113.0
37 TraesCS5D01G304100 chr4D 86.250 80 6 3 6070 6146 43147638 43147715 1.420000e-11 82.4
38 TraesCS5D01G304100 chr2D 94.521 73 4 0 1 73 50654793 50654865 5.040000e-21 113.0
39 TraesCS5D01G304100 chr2D 90.000 50 2 2 4666 4714 118378493 118378446 1.850000e-05 62.1
40 TraesCS5D01G304100 chr2D 90.000 50 2 2 4666 4714 575265294 575265247 1.850000e-05 62.1
41 TraesCS5D01G304100 chr1D 94.521 73 4 0 1 73 383763245 383763173 5.040000e-21 113.0
42 TraesCS5D01G304100 chr6D 92.405 79 4 2 1 77 372406523 372406601 1.810000e-20 111.0
43 TraesCS5D01G304100 chr6D 93.333 75 4 1 1 75 245255919 245255992 6.530000e-20 110.0
44 TraesCS5D01G304100 chr6A 86.667 60 2 5 4658 4714 393802318 393802374 1.850000e-05 62.1


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 TraesCS5D01G304100 chr5D 399285116 399291273 6157 False 11372.0 11372 100.0000 1 6158 1 chr5D.!!$F2 6157
1 TraesCS5D01G304100 chr5D 399297244 399299496 2252 True 3701.0 3701 96.3440 325 2578 1 chr5D.!!$R1 2253
2 TraesCS5D01G304100 chr5D 399248325 399250924 2599 False 1185.0 1921 88.8665 73 1485 2 chr5D.!!$F3 1412
3 TraesCS5D01G304100 chr5B 479638952 479644274 5322 False 3889.5 6846 92.4405 74 5353 2 chr5B.!!$F1 5279
4 TraesCS5D01G304100 chr5A 504875184 504881480 6296 False 3966.5 5572 93.9320 73 5271 2 chr5A.!!$F3 5198
5 TraesCS5D01G304100 chr5A 435709795 435710467 672 False 1013.0 1013 94.2140 5411 6067 1 chr5A.!!$F2 656
6 TraesCS5D01G304100 chr5A 504882368 504883039 671 True 841.0 841 89.5040 73 743 1 chr5A.!!$R1 670
7 TraesCS5D01G304100 chr2B 168631863 168632535 672 False 1029.0 1029 94.6590 5411 6067 1 chr2B.!!$F1 656
8 TraesCS5D01G304100 chr1A 13006490 13007161 671 False 1022.0 1022 94.5100 5411 6067 1 chr1A.!!$F1 656
9 TraesCS5D01G304100 chr6B 687137182 687137854 672 True 1018.0 1018 94.3620 5411 6067 1 chr6B.!!$R2 656
10 TraesCS5D01G304100 chr6B 194018 194690 672 True 1013.0 1013 94.2140 5411 6067 1 chr6B.!!$R1 656
11 TraesCS5D01G304100 chr2A 607490229 607490901 672 True 1018.0 1018 94.3620 5411 6067 1 chr2A.!!$R1 656
12 TraesCS5D01G304100 chr4B 672925160 672925832 672 False 1013.0 1013 94.2140 5411 6067 1 chr4B.!!$F1 656
13 TraesCS5D01G304100 chr3A 121401821 121402493 672 False 1013.0 1013 94.2140 5411 6067 1 chr3A.!!$F1 656
14 TraesCS5D01G304100 chr7A 38120214 38120886 672 False 1007.0 1007 94.0650 5411 6067 1 chr7A.!!$F1 656
15 TraesCS5D01G304100 chr7A 662092953 662093595 642 False 952.0 952 93.7890 5441 6067 1 chr7A.!!$F2 626
16 TraesCS5D01G304100 chr3B 805267132 805267804 672 True 1007.0 1007 94.0650 5411 6067 1 chr3B.!!$R1 656
17 TraesCS5D01G304100 chr1B 66135643 66136315 672 True 1007.0 1007 94.0650 5411 6067 1 chr1B.!!$R1 656
18 TraesCS5D01G304100 chr1B 676770434 676771106 672 True 1007.0 1007 94.0650 5411 6067 1 chr1B.!!$R2 656
19 TraesCS5D01G304100 chr7B 706279327 706279999 672 False 1002.0 1002 93.9170 5411 6067 1 chr7B.!!$F1 656
20 TraesCS5D01G304100 chr3D 33193587 33194256 669 True 998.0 998 93.9260 5411 6067 1 chr3D.!!$R1 656

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
561 1798 0.470456 TCCTCCGGCGGTATGGTATT 60.470 55.000 27.32 0.0 0.00 1.89 F
1419 2688 0.458543 CGATGAACTGTACGCTGGCT 60.459 55.000 0.00 0.0 0.00 4.75 F
1891 3164 0.394192 TATGAGGAATCGCAGGGCTG 59.606 55.000 0.00 0.0 0.00 4.85 F
2067 3340 6.627395 ACATTTTGACGTTGATTTCAGGTA 57.373 33.333 0.00 0.0 0.00 3.08 F
3435 4710 5.626578 GCCATTTTTGTTGTATACTGGCCAT 60.627 40.000 5.51 0.0 41.57 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 3156 1.078143 CTACCAGTTCCAGCCCTGC 60.078 63.158 0.0 0.0 0.00 4.85 R
3306 4580 6.486657 TCAGTTGCTTCATACAAAACTAGCTT 59.513 34.615 0.0 0.0 30.20 3.74 R
3435 4710 5.405935 TGTCTCTAGTAAATGAGCTTGCA 57.594 39.130 0.0 0.0 0.00 4.08 R
3948 6309 3.510388 TCTGGTAGTTCAGCATTCTCG 57.490 47.619 0.0 0.0 34.91 4.04 R
5375 7819 0.036010 AGAGCCCAACGTCCAATCAG 60.036 55.000 0.0 0.0 0.00 2.90 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
19 20 1.186200 TGAGTCCCTGATCTTGGTCG 58.814 55.000 0.00 0.00 0.00 4.79
20 21 1.187087 GAGTCCCTGATCTTGGTCGT 58.813 55.000 0.00 0.00 0.00 4.34
21 22 2.291346 TGAGTCCCTGATCTTGGTCGTA 60.291 50.000 0.00 0.00 0.00 3.43
22 23 2.099427 GAGTCCCTGATCTTGGTCGTAC 59.901 54.545 0.00 0.00 0.00 3.67
23 24 1.822990 GTCCCTGATCTTGGTCGTACA 59.177 52.381 0.00 0.00 0.00 2.90
24 25 1.822990 TCCCTGATCTTGGTCGTACAC 59.177 52.381 0.00 0.00 0.00 2.90
25 26 1.548719 CCCTGATCTTGGTCGTACACA 59.451 52.381 0.00 0.00 0.00 3.72
26 27 2.168521 CCCTGATCTTGGTCGTACACAT 59.831 50.000 0.00 0.00 0.00 3.21
27 28 3.369471 CCCTGATCTTGGTCGTACACATT 60.369 47.826 0.00 0.00 0.00 2.71
28 29 4.253685 CCTGATCTTGGTCGTACACATTT 58.746 43.478 0.00 0.00 0.00 2.32
29 30 4.695455 CCTGATCTTGGTCGTACACATTTT 59.305 41.667 0.00 0.00 0.00 1.82
30 31 5.163854 CCTGATCTTGGTCGTACACATTTTC 60.164 44.000 0.00 0.00 0.00 2.29
31 32 4.387559 TGATCTTGGTCGTACACATTTTCG 59.612 41.667 0.00 0.00 0.00 3.46
32 33 3.719924 TCTTGGTCGTACACATTTTCGT 58.280 40.909 0.00 0.00 0.00 3.85
33 34 3.491639 TCTTGGTCGTACACATTTTCGTG 59.508 43.478 0.00 0.00 42.81 4.35
34 35 1.527736 TGGTCGTACACATTTTCGTGC 59.472 47.619 0.00 0.00 40.73 5.34
35 36 1.527736 GGTCGTACACATTTTCGTGCA 59.472 47.619 0.00 0.00 40.73 4.57
36 37 2.158841 GGTCGTACACATTTTCGTGCAT 59.841 45.455 0.00 0.00 40.73 3.96
37 38 3.152983 GTCGTACACATTTTCGTGCATG 58.847 45.455 0.00 0.00 40.73 4.06
38 39 3.060602 TCGTACACATTTTCGTGCATGA 58.939 40.909 3.97 3.97 40.73 3.07
39 40 3.682377 TCGTACACATTTTCGTGCATGAT 59.318 39.130 9.96 0.00 40.73 2.45
40 41 4.153296 TCGTACACATTTTCGTGCATGATT 59.847 37.500 9.96 0.00 40.73 2.57
41 42 5.348997 TCGTACACATTTTCGTGCATGATTA 59.651 36.000 9.96 1.02 40.73 1.75
42 43 5.672426 CGTACACATTTTCGTGCATGATTAG 59.328 40.000 9.96 3.25 40.73 1.73
43 44 5.627499 ACACATTTTCGTGCATGATTAGT 57.373 34.783 9.96 3.88 40.73 2.24
44 45 5.393124 ACACATTTTCGTGCATGATTAGTG 58.607 37.500 20.44 20.44 40.73 2.74
45 46 5.048782 ACACATTTTCGTGCATGATTAGTGT 60.049 36.000 21.33 21.33 40.73 3.55
46 47 6.148645 ACACATTTTCGTGCATGATTAGTGTA 59.851 34.615 23.68 3.37 40.73 2.90
47 48 6.465781 CACATTTTCGTGCATGATTAGTGTAC 59.534 38.462 9.96 0.00 0.00 2.90
50 51 2.536365 CGTGCATGATTAGTGTACGGT 58.464 47.619 0.00 0.00 46.91 4.83
51 52 2.534349 CGTGCATGATTAGTGTACGGTC 59.466 50.000 0.00 0.00 46.91 4.79
52 53 2.534349 GTGCATGATTAGTGTACGGTCG 59.466 50.000 0.00 0.00 0.00 4.79
53 54 2.424246 TGCATGATTAGTGTACGGTCGA 59.576 45.455 0.00 0.00 0.00 4.20
54 55 3.043586 GCATGATTAGTGTACGGTCGAG 58.956 50.000 0.00 0.00 0.00 4.04
55 56 3.242969 GCATGATTAGTGTACGGTCGAGA 60.243 47.826 0.00 0.00 0.00 4.04
56 57 4.280461 CATGATTAGTGTACGGTCGAGAC 58.720 47.826 0.00 0.00 0.00 3.36
57 58 2.349580 TGATTAGTGTACGGTCGAGACG 59.650 50.000 7.80 7.80 37.36 4.18
58 59 1.078709 TTAGTGTACGGTCGAGACGG 58.921 55.000 13.20 8.89 37.61 4.79
59 60 0.740868 TAGTGTACGGTCGAGACGGG 60.741 60.000 13.20 4.08 36.16 5.28
60 61 2.747460 TGTACGGTCGAGACGGGG 60.747 66.667 13.20 1.90 36.16 5.73
61 62 3.512516 GTACGGTCGAGACGGGGG 61.513 72.222 13.20 0.00 36.16 5.40
69 70 3.771160 GAGACGGGGGCGTCACAT 61.771 66.667 0.00 0.00 40.96 3.21
70 71 2.363276 AGACGGGGGCGTCACATA 60.363 61.111 0.00 0.00 40.96 2.29
71 72 2.202837 GACGGGGGCGTCACATAC 60.203 66.667 0.00 0.00 38.62 2.39
83 84 3.611530 GCGTCACATACAAAAGGCATGTT 60.612 43.478 0.00 0.00 30.89 2.71
87 88 6.158598 GTCACATACAAAAGGCATGTTTGAT 58.841 36.000 12.69 2.07 38.05 2.57
89 90 6.645827 TCACATACAAAAGGCATGTTTGATTG 59.354 34.615 12.69 11.13 38.05 2.67
93 94 5.184711 ACAAAAGGCATGTTTGATTGTGTT 58.815 33.333 12.69 0.00 38.05 3.32
95 96 6.820656 ACAAAAGGCATGTTTGATTGTGTTTA 59.179 30.769 12.69 0.00 38.05 2.01
99 100 9.723601 AAAGGCATGTTTGATTGTGTTTATATT 57.276 25.926 0.00 0.00 0.00 1.28
180 1393 5.642165 TGTGTCCTAAAGAGTAGAACCTCT 58.358 41.667 0.00 0.00 43.65 3.69
206 1419 4.461198 ACCTACACCAAGAAAAAGAGTGG 58.539 43.478 0.00 0.00 37.17 4.00
207 1420 4.079958 ACCTACACCAAGAAAAAGAGTGGT 60.080 41.667 0.00 0.00 45.32 4.16
258 1473 3.542712 AAACAAGAGCGCAATGTGTAG 57.457 42.857 11.47 0.00 0.00 2.74
294 1510 5.845065 AGTTTCTGGGAGGTACTAAAAGAGT 59.155 40.000 0.00 0.00 41.55 3.24
560 1797 0.898789 CTCCTCCGGCGGTATGGTAT 60.899 60.000 27.32 0.00 0.00 2.73
561 1798 0.470456 TCCTCCGGCGGTATGGTATT 60.470 55.000 27.32 0.00 0.00 1.89
562 1799 1.203038 TCCTCCGGCGGTATGGTATTA 60.203 52.381 27.32 7.95 0.00 0.98
643 1891 2.278206 CGTCGTGGATCCTCGCTG 60.278 66.667 27.29 18.76 33.63 5.18
1150 2399 2.133641 GGGTTGTGGCTTGGCTTGT 61.134 57.895 0.00 0.00 0.00 3.16
1413 2682 2.024875 CGTTCGTTCGATGAACTGTACG 59.975 50.000 21.54 11.31 40.90 3.67
1419 2688 0.458543 CGATGAACTGTACGCTGGCT 60.459 55.000 0.00 0.00 0.00 4.75
1459 2730 0.680618 CCTTTTTGTGAGCATGGCCA 59.319 50.000 8.56 8.56 0.00 5.36
1629 2900 6.037726 GTCCTTTTAGCTTACTAGTGCTCTC 58.962 44.000 10.75 0.00 40.35 3.20
1656 2927 5.911178 AGAATGGATAACAGGATAGGGACAA 59.089 40.000 0.00 0.00 0.00 3.18
1698 2969 8.243426 GGACTGTAAATTGCATTTAGATTGTGA 58.757 33.333 0.00 0.00 35.56 3.58
1716 2987 5.160607 TGTGAACCGACTAGGATGAAAAT 57.839 39.130 0.00 0.00 45.00 1.82
1717 2988 5.175859 TGTGAACCGACTAGGATGAAAATC 58.824 41.667 0.00 0.00 45.00 2.17
1735 3007 6.152661 TGAAAATCTGGATTTATGTGGACCAC 59.847 38.462 18.28 18.28 39.88 4.16
1737 3009 2.835156 TCTGGATTTATGTGGACCACGA 59.165 45.455 19.67 7.53 37.14 4.35
1761 3034 5.957842 TGCTTACCACAGGACAAAAATAG 57.042 39.130 0.00 0.00 0.00 1.73
1883 3156 7.710896 TGATCTATGCAGTATATGAGGAATCG 58.289 38.462 0.00 0.00 0.00 3.34
1891 3164 0.394192 TATGAGGAATCGCAGGGCTG 59.606 55.000 0.00 0.00 0.00 4.85
2067 3340 6.627395 ACATTTTGACGTTGATTTCAGGTA 57.373 33.333 0.00 0.00 0.00 3.08
2093 3366 7.390718 AGAATTAATTCCGTAACTGCTGAGTTT 59.609 33.333 21.86 0.00 39.14 2.66
3401 4675 9.554395 TTCATACTCACTTCTACATGTTTTTGA 57.446 29.630 2.30 0.00 0.00 2.69
3402 4676 9.725019 TCATACTCACTTCTACATGTTTTTGAT 57.275 29.630 2.30 0.00 0.00 2.57
3435 4710 5.626578 GCCATTTTTGTTGTATACTGGCCAT 60.627 40.000 5.51 0.00 41.57 4.40
3844 6205 8.244802 TCTTAGTCAGCTACTTGTTTGATACTC 58.755 37.037 0.00 0.00 39.80 2.59
3948 6309 1.671845 ACTGAGACTCGCCGTATTCTC 59.328 52.381 0.00 5.73 35.93 2.87
4258 6619 3.990092 TGATGTTCGCTTCACAGTAGTT 58.010 40.909 0.00 0.00 0.00 2.24
4508 6870 3.973657 TCCGTTACTTGAAGTCTGACAC 58.026 45.455 10.88 4.46 0.00 3.67
4585 6947 7.454694 TCCTATTGTCAGCCTACATACACATAT 59.545 37.037 0.00 0.00 0.00 1.78
4603 6965 2.062971 ATGTGGATGGAGATTGCACC 57.937 50.000 0.00 0.00 34.85 5.01
4696 7096 7.627513 GCAAAAACATCTTATATTGTGGGACGA 60.628 37.037 0.00 0.00 0.00 4.20
4767 7177 7.102847 ACTTTAGCTGATACTCCTCTAACAC 57.897 40.000 0.00 0.00 0.00 3.32
4840 7256 4.044336 TGCAATGTGTTTCTGTTCCTTG 57.956 40.909 0.00 0.00 0.00 3.61
4851 7267 2.821378 TCTGTTCCTTGTCGGACGATAA 59.179 45.455 3.34 0.29 42.97 1.75
4868 7284 9.622004 CGGACGATAACATATCTATTTACAACT 57.378 33.333 0.00 0.00 0.00 3.16
4923 7339 5.999205 AACCTTGCCATTCACAATATTGA 57.001 34.783 22.16 0.00 0.00 2.57
4945 7362 0.251165 TTACAAGCTTCCCCTGCACC 60.251 55.000 0.00 0.00 0.00 5.01
5083 7500 1.403972 GCTCGGCGTAAGTGAGAACG 61.404 60.000 6.85 0.00 42.21 3.95
5161 7578 3.117360 TGATCAGGCCAGTCTCTGATAGA 60.117 47.826 5.01 0.00 46.89 1.98
5251 7691 7.413219 CGATGTACCGGTAATTGTGTACAAAAT 60.413 37.037 17.78 5.37 44.58 1.82
5297 7737 8.076910 TGTGAAAAACTTCATGGGCATATATT 57.923 30.769 0.00 0.00 33.02 1.28
5300 7740 8.349245 TGAAAAACTTCATGGGCATATATTACG 58.651 33.333 0.00 0.00 0.00 3.18
5301 7741 7.817418 AAAACTTCATGGGCATATATTACGT 57.183 32.000 0.00 0.00 0.00 3.57
5342 7786 1.251251 ATGTGCCTGGAAACTTCTGC 58.749 50.000 0.00 0.00 0.00 4.26
5343 7787 0.106769 TGTGCCTGGAAACTTCTGCA 60.107 50.000 0.00 0.00 0.00 4.41
5349 7793 4.022068 TGCCTGGAAACTTCTGCAAAATAG 60.022 41.667 0.00 0.00 0.00 1.73
5353 7797 6.461509 CCTGGAAACTTCTGCAAAATAGTGTT 60.462 38.462 0.00 0.00 0.00 3.32
5354 7798 6.272318 TGGAAACTTCTGCAAAATAGTGTTG 58.728 36.000 0.00 0.00 0.00 3.33
5359 7803 2.736890 GCAAAATAGTGTTGCCCGC 58.263 52.632 0.00 0.00 44.53 6.13
5360 7804 0.735978 GCAAAATAGTGTTGCCCGCC 60.736 55.000 0.00 0.00 44.53 6.13
5361 7805 0.887933 CAAAATAGTGTTGCCCGCCT 59.112 50.000 0.00 0.00 0.00 5.52
5362 7806 1.135402 CAAAATAGTGTTGCCCGCCTC 60.135 52.381 0.00 0.00 0.00 4.70
5363 7807 0.679960 AAATAGTGTTGCCCGCCTCC 60.680 55.000 0.00 0.00 0.00 4.30
5364 7808 1.562672 AATAGTGTTGCCCGCCTCCT 61.563 55.000 0.00 0.00 0.00 3.69
5365 7809 1.562672 ATAGTGTTGCCCGCCTCCTT 61.563 55.000 0.00 0.00 0.00 3.36
5366 7810 2.463589 TAGTGTTGCCCGCCTCCTTG 62.464 60.000 0.00 0.00 0.00 3.61
5367 7811 4.659172 TGTTGCCCGCCTCCTTGG 62.659 66.667 0.00 0.00 39.35 3.61
5368 7812 4.344865 GTTGCCCGCCTCCTTGGA 62.345 66.667 0.00 0.00 38.35 3.53
5369 7813 3.338250 TTGCCCGCCTCCTTGGAT 61.338 61.111 0.00 0.00 38.35 3.41
5370 7814 3.643595 TTGCCCGCCTCCTTGGATG 62.644 63.158 0.00 0.00 38.35 3.51
5371 7815 4.115199 GCCCGCCTCCTTGGATGT 62.115 66.667 0.00 0.00 38.35 3.06
5372 7816 2.190578 CCCGCCTCCTTGGATGTC 59.809 66.667 0.00 0.00 38.35 3.06
5373 7817 2.190578 CCGCCTCCTTGGATGTCC 59.809 66.667 0.00 0.00 38.35 4.02
5374 7818 2.669133 CCGCCTCCTTGGATGTCCA 61.669 63.158 0.00 0.00 45.94 4.02
5391 7835 1.875963 CACTGATTGGACGTTGGGC 59.124 57.895 0.00 0.00 0.00 5.36
5392 7836 0.606401 CACTGATTGGACGTTGGGCT 60.606 55.000 0.00 0.00 0.00 5.19
5393 7837 0.321653 ACTGATTGGACGTTGGGCTC 60.322 55.000 0.00 0.00 0.00 4.70
5394 7838 0.036010 CTGATTGGACGTTGGGCTCT 60.036 55.000 0.00 0.00 0.00 4.09
5395 7839 0.400213 TGATTGGACGTTGGGCTCTT 59.600 50.000 0.00 0.00 0.00 2.85
5396 7840 0.804989 GATTGGACGTTGGGCTCTTG 59.195 55.000 0.00 0.00 0.00 3.02
5397 7841 0.110486 ATTGGACGTTGGGCTCTTGT 59.890 50.000 0.00 0.00 0.00 3.16
5398 7842 0.759959 TTGGACGTTGGGCTCTTGTA 59.240 50.000 0.00 0.00 0.00 2.41
5399 7843 0.759959 TGGACGTTGGGCTCTTGTAA 59.240 50.000 0.00 0.00 0.00 2.41
5400 7844 1.154197 GGACGTTGGGCTCTTGTAAC 58.846 55.000 0.00 0.00 0.00 2.50
5401 7845 1.270678 GGACGTTGGGCTCTTGTAACT 60.271 52.381 0.00 0.00 0.00 2.24
5402 7846 2.028748 GGACGTTGGGCTCTTGTAACTA 60.029 50.000 0.00 0.00 0.00 2.24
5403 7847 3.369157 GGACGTTGGGCTCTTGTAACTAT 60.369 47.826 0.00 0.00 0.00 2.12
5404 7848 4.142093 GGACGTTGGGCTCTTGTAACTATA 60.142 45.833 0.00 0.00 0.00 1.31
5405 7849 5.410355 ACGTTGGGCTCTTGTAACTATAA 57.590 39.130 0.00 0.00 0.00 0.98
5406 7850 5.173664 ACGTTGGGCTCTTGTAACTATAAC 58.826 41.667 0.00 0.00 0.00 1.89
5407 7851 4.569564 CGTTGGGCTCTTGTAACTATAACC 59.430 45.833 0.00 0.00 0.00 2.85
5408 7852 5.626116 CGTTGGGCTCTTGTAACTATAACCT 60.626 44.000 0.00 0.00 0.00 3.50
5409 7853 5.609533 TGGGCTCTTGTAACTATAACCTC 57.390 43.478 0.00 0.00 0.00 3.85
5583 8027 0.627469 ATTGGTGTCCCCCTATGGCT 60.627 55.000 0.00 0.00 0.00 4.75
5586 8030 3.096495 TGTCCCCCTATGGCTGGC 61.096 66.667 0.00 0.00 0.00 4.85
5611 8055 3.378427 GGTGAAACTGAATACTGATGGGC 59.622 47.826 0.00 0.00 36.74 5.36
5688 8132 5.423610 AGGTAATGTCATCTACTCAGCTTGT 59.576 40.000 0.00 0.00 0.00 3.16
5977 8438 0.603065 GAACAATGACCTGGGTTGGC 59.397 55.000 0.00 0.00 0.00 4.52
6083 8544 4.404185 AAAAACCCCTCATAGAAGGCTT 57.596 40.909 0.00 0.00 34.88 4.35
6084 8545 3.372440 AAACCCCTCATAGAAGGCTTG 57.628 47.619 3.46 0.00 34.88 4.01
6085 8546 1.972588 ACCCCTCATAGAAGGCTTGT 58.027 50.000 3.46 2.30 34.88 3.16
6086 8547 3.130734 ACCCCTCATAGAAGGCTTGTA 57.869 47.619 3.46 5.27 34.88 2.41
6087 8548 2.772515 ACCCCTCATAGAAGGCTTGTAC 59.227 50.000 3.46 0.00 34.88 2.90
6088 8549 3.041946 CCCCTCATAGAAGGCTTGTACT 58.958 50.000 3.46 0.00 34.88 2.73
6089 8550 3.070302 CCCCTCATAGAAGGCTTGTACTC 59.930 52.174 3.46 0.00 34.88 2.59
6090 8551 3.964031 CCCTCATAGAAGGCTTGTACTCT 59.036 47.826 3.46 0.00 34.88 3.24
6091 8552 4.038642 CCCTCATAGAAGGCTTGTACTCTC 59.961 50.000 3.46 0.00 34.88 3.20
6092 8553 4.892934 CCTCATAGAAGGCTTGTACTCTCT 59.107 45.833 3.46 0.00 0.00 3.10
6093 8554 5.009610 CCTCATAGAAGGCTTGTACTCTCTC 59.990 48.000 3.46 0.00 0.00 3.20
6094 8555 5.510430 TCATAGAAGGCTTGTACTCTCTCA 58.490 41.667 3.46 0.00 0.00 3.27
6095 8556 6.132658 TCATAGAAGGCTTGTACTCTCTCAT 58.867 40.000 3.46 0.00 0.00 2.90
6096 8557 6.264292 TCATAGAAGGCTTGTACTCTCTCATC 59.736 42.308 3.46 0.00 0.00 2.92
6097 8558 4.609301 AGAAGGCTTGTACTCTCTCATCT 58.391 43.478 3.46 0.00 0.00 2.90
6098 8559 5.022787 AGAAGGCTTGTACTCTCTCATCTT 58.977 41.667 3.46 0.00 0.00 2.40
6099 8560 5.483583 AGAAGGCTTGTACTCTCTCATCTTT 59.516 40.000 3.46 0.00 0.00 2.52
6100 8561 5.753721 AGGCTTGTACTCTCTCATCTTTT 57.246 39.130 0.00 0.00 0.00 2.27
6101 8562 5.729510 AGGCTTGTACTCTCTCATCTTTTC 58.270 41.667 0.00 0.00 0.00 2.29
6102 8563 5.247110 AGGCTTGTACTCTCTCATCTTTTCA 59.753 40.000 0.00 0.00 0.00 2.69
6103 8564 5.934625 GGCTTGTACTCTCTCATCTTTTCAA 59.065 40.000 0.00 0.00 0.00 2.69
6104 8565 6.597280 GGCTTGTACTCTCTCATCTTTTCAAT 59.403 38.462 0.00 0.00 0.00 2.57
6105 8566 7.413877 GGCTTGTACTCTCTCATCTTTTCAATG 60.414 40.741 0.00 0.00 0.00 2.82
6106 8567 6.974932 TGTACTCTCTCATCTTTTCAATGC 57.025 37.500 0.00 0.00 0.00 3.56
6107 8568 6.466812 TGTACTCTCTCATCTTTTCAATGCA 58.533 36.000 0.00 0.00 0.00 3.96
6108 8569 6.936335 TGTACTCTCTCATCTTTTCAATGCAA 59.064 34.615 0.00 0.00 0.00 4.08
6109 8570 7.609146 TGTACTCTCTCATCTTTTCAATGCAAT 59.391 33.333 0.00 0.00 0.00 3.56
6110 8571 6.853720 ACTCTCTCATCTTTTCAATGCAATG 58.146 36.000 0.00 0.00 0.00 2.82
6111 8572 6.127703 ACTCTCTCATCTTTTCAATGCAATGG 60.128 38.462 1.05 0.00 0.00 3.16
6112 8573 5.947566 TCTCTCATCTTTTCAATGCAATGGA 59.052 36.000 1.05 0.00 0.00 3.41
6113 8574 6.434965 TCTCTCATCTTTTCAATGCAATGGAA 59.565 34.615 1.05 0.00 33.50 3.53
6114 8575 6.392354 TCTCATCTTTTCAATGCAATGGAAC 58.608 36.000 1.05 0.00 35.58 3.62
6115 8576 5.162794 TCATCTTTTCAATGCAATGGAACG 58.837 37.500 1.05 0.00 35.58 3.95
6116 8577 3.316283 TCTTTTCAATGCAATGGAACGC 58.684 40.909 1.05 0.00 35.58 4.84
6117 8578 2.808523 TTTCAATGCAATGGAACGCA 57.191 40.000 1.05 0.00 35.58 5.24
6118 8579 2.808523 TTCAATGCAATGGAACGCAA 57.191 40.000 1.05 0.00 42.37 4.85
6119 8580 2.808523 TCAATGCAATGGAACGCAAA 57.191 40.000 1.05 0.00 42.37 3.68
6120 8581 2.674954 TCAATGCAATGGAACGCAAAG 58.325 42.857 1.05 0.00 42.37 2.77
6121 8582 2.295629 TCAATGCAATGGAACGCAAAGA 59.704 40.909 1.05 0.00 42.37 2.52
6122 8583 3.056678 TCAATGCAATGGAACGCAAAGAT 60.057 39.130 1.05 0.00 42.37 2.40
6123 8584 2.634982 TGCAATGGAACGCAAAGATC 57.365 45.000 0.00 0.00 34.59 2.75
6124 8585 1.202114 TGCAATGGAACGCAAAGATCC 59.798 47.619 0.00 0.00 41.70 3.36
6125 8586 1.474077 GCAATGGAACGCAAAGATCCT 59.526 47.619 0.00 0.00 41.85 3.24
6126 8587 2.094545 GCAATGGAACGCAAAGATCCTT 60.095 45.455 0.00 0.00 41.85 3.36
6127 8588 3.614870 GCAATGGAACGCAAAGATCCTTT 60.615 43.478 0.00 0.00 41.85 3.11
6128 8589 4.559153 CAATGGAACGCAAAGATCCTTTT 58.441 39.130 0.00 0.00 41.85 2.27
6129 8590 3.641437 TGGAACGCAAAGATCCTTTTG 57.359 42.857 3.64 3.64 41.85 2.44
6137 8598 3.905784 CAAAGATCCTTTTGCGCTTTCT 58.094 40.909 9.73 0.00 31.96 2.52
6138 8599 5.046910 CAAAGATCCTTTTGCGCTTTCTA 57.953 39.130 9.73 0.00 31.96 2.10
6139 8600 5.460646 CAAAGATCCTTTTGCGCTTTCTAA 58.539 37.500 9.73 0.00 31.96 2.10
6140 8601 5.705609 AAGATCCTTTTGCGCTTTCTAAA 57.294 34.783 9.73 0.00 0.00 1.85
6141 8602 5.705609 AGATCCTTTTGCGCTTTCTAAAA 57.294 34.783 9.73 5.65 0.00 1.52
6142 8603 6.084326 AGATCCTTTTGCGCTTTCTAAAAA 57.916 33.333 9.73 4.87 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.186200 CGACCAAGATCAGGGACTCA 58.814 55.000 9.43 0.00 34.60 3.41
1 2 1.187087 ACGACCAAGATCAGGGACTC 58.813 55.000 9.43 0.00 34.60 3.36
5 6 1.548719 TGTGTACGACCAAGATCAGGG 59.451 52.381 8.82 5.29 0.00 4.45
6 7 3.526931 ATGTGTACGACCAAGATCAGG 57.473 47.619 0.00 0.00 0.00 3.86
7 8 5.444613 CGAAAATGTGTACGACCAAGATCAG 60.445 44.000 0.00 0.00 0.00 2.90
8 9 4.387559 CGAAAATGTGTACGACCAAGATCA 59.612 41.667 0.00 0.00 0.00 2.92
9 10 4.387862 ACGAAAATGTGTACGACCAAGATC 59.612 41.667 0.00 0.00 0.00 2.75
10 11 4.151689 CACGAAAATGTGTACGACCAAGAT 59.848 41.667 0.00 0.00 35.12 2.40
11 12 3.491639 CACGAAAATGTGTACGACCAAGA 59.508 43.478 0.00 0.00 35.12 3.02
12 13 3.794536 CACGAAAATGTGTACGACCAAG 58.205 45.455 0.00 0.00 35.12 3.61
13 14 2.032722 GCACGAAAATGTGTACGACCAA 60.033 45.455 0.00 0.00 41.94 3.67
14 15 1.527736 GCACGAAAATGTGTACGACCA 59.472 47.619 0.00 0.00 41.94 4.02
15 16 1.527736 TGCACGAAAATGTGTACGACC 59.472 47.619 0.00 0.00 41.94 4.79
16 17 2.934107 TGCACGAAAATGTGTACGAC 57.066 45.000 0.00 0.00 41.94 4.34
17 18 3.060602 TCATGCACGAAAATGTGTACGA 58.939 40.909 0.00 0.00 41.94 3.43
18 19 3.447752 TCATGCACGAAAATGTGTACG 57.552 42.857 0.00 0.00 41.94 3.67
19 20 6.465781 CACTAATCATGCACGAAAATGTGTAC 59.534 38.462 0.00 0.00 41.94 2.90
20 21 6.148645 ACACTAATCATGCACGAAAATGTGTA 59.851 34.615 10.73 0.00 41.94 2.90
21 22 5.048782 ACACTAATCATGCACGAAAATGTGT 60.049 36.000 7.88 7.88 41.94 3.72
22 23 5.393124 ACACTAATCATGCACGAAAATGTG 58.607 37.500 0.00 0.00 42.81 3.21
23 24 5.627499 ACACTAATCATGCACGAAAATGT 57.373 34.783 0.00 0.00 0.00 2.71
24 25 5.672426 CGTACACTAATCATGCACGAAAATG 59.328 40.000 0.00 0.00 38.80 2.32
25 26 5.220586 CCGTACACTAATCATGCACGAAAAT 60.221 40.000 0.00 0.00 38.80 1.82
26 27 4.092237 CCGTACACTAATCATGCACGAAAA 59.908 41.667 0.00 0.00 38.80 2.29
27 28 3.615056 CCGTACACTAATCATGCACGAAA 59.385 43.478 0.00 0.00 38.80 3.46
28 29 3.183754 CCGTACACTAATCATGCACGAA 58.816 45.455 0.00 0.00 38.80 3.85
29 30 2.164827 ACCGTACACTAATCATGCACGA 59.835 45.455 0.00 0.00 38.80 4.35
30 31 2.534349 GACCGTACACTAATCATGCACG 59.466 50.000 0.00 0.00 36.74 5.34
31 32 2.534349 CGACCGTACACTAATCATGCAC 59.466 50.000 0.00 0.00 0.00 4.57
32 33 2.424246 TCGACCGTACACTAATCATGCA 59.576 45.455 0.00 0.00 0.00 3.96
33 34 3.043586 CTCGACCGTACACTAATCATGC 58.956 50.000 0.00 0.00 0.00 4.06
34 35 4.280461 GTCTCGACCGTACACTAATCATG 58.720 47.826 0.00 0.00 0.00 3.07
35 36 3.002042 CGTCTCGACCGTACACTAATCAT 59.998 47.826 0.00 0.00 0.00 2.45
36 37 2.349580 CGTCTCGACCGTACACTAATCA 59.650 50.000 0.00 0.00 0.00 2.57
37 38 2.286067 CCGTCTCGACCGTACACTAATC 60.286 54.545 0.00 0.00 0.00 1.75
38 39 1.667724 CCGTCTCGACCGTACACTAAT 59.332 52.381 0.00 0.00 0.00 1.73
39 40 1.078709 CCGTCTCGACCGTACACTAA 58.921 55.000 0.00 0.00 0.00 2.24
40 41 0.740868 CCCGTCTCGACCGTACACTA 60.741 60.000 0.00 0.00 0.00 2.74
41 42 2.037136 CCCGTCTCGACCGTACACT 61.037 63.158 0.00 0.00 0.00 3.55
42 43 2.482374 CCCGTCTCGACCGTACAC 59.518 66.667 0.00 0.00 0.00 2.90
43 44 2.747460 CCCCGTCTCGACCGTACA 60.747 66.667 0.00 0.00 0.00 2.90
44 45 3.512516 CCCCCGTCTCGACCGTAC 61.513 72.222 0.00 0.00 0.00 3.67
56 57 0.956410 TTTTGTATGTGACGCCCCCG 60.956 55.000 0.00 0.00 41.14 5.73
57 58 0.808755 CTTTTGTATGTGACGCCCCC 59.191 55.000 0.00 0.00 0.00 5.40
58 59 0.808755 CCTTTTGTATGTGACGCCCC 59.191 55.000 0.00 0.00 0.00 5.80
59 60 0.170339 GCCTTTTGTATGTGACGCCC 59.830 55.000 0.00 0.00 0.00 6.13
60 61 0.878416 TGCCTTTTGTATGTGACGCC 59.122 50.000 0.00 0.00 0.00 5.68
61 62 2.095263 ACATGCCTTTTGTATGTGACGC 60.095 45.455 0.00 0.00 46.84 5.19
62 63 3.829886 ACATGCCTTTTGTATGTGACG 57.170 42.857 0.00 0.00 46.84 4.35
67 68 6.424509 ACACAATCAAACATGCCTTTTGTATG 59.575 34.615 7.04 9.05 42.23 2.39
68 69 6.523840 ACACAATCAAACATGCCTTTTGTAT 58.476 32.000 7.04 0.00 35.75 2.29
69 70 5.911752 ACACAATCAAACATGCCTTTTGTA 58.088 33.333 7.04 0.00 35.75 2.41
70 71 4.768583 ACACAATCAAACATGCCTTTTGT 58.231 34.783 7.04 2.58 35.75 2.83
71 72 5.738118 AACACAATCAAACATGCCTTTTG 57.262 34.783 0.00 0.00 35.61 2.44
180 1393 7.067737 CCACTCTTTTTCTTGGTGTAGGTTAAA 59.932 37.037 0.00 0.00 0.00 1.52
206 1419 4.154613 CGACCTCGTCAGCTTCAC 57.845 61.111 0.00 0.00 32.09 3.18
258 1473 2.618709 CCCAGAAACTGAGTTTGTGACC 59.381 50.000 29.65 10.51 45.53 4.02
1150 2399 0.108585 GAACAGCTGGGGAACACAGA 59.891 55.000 19.93 0.00 38.20 3.41
1629 2900 4.081420 CCCTATCCTGTTATCCATTCTCCG 60.081 50.000 0.00 0.00 0.00 4.63
1656 2927 5.116084 ACAGTCCATATGTACCAAATGCT 57.884 39.130 1.24 0.00 0.00 3.79
1698 2969 4.469945 TCCAGATTTTCATCCTAGTCGGTT 59.530 41.667 0.00 0.00 0.00 4.44
1716 2987 2.835156 TCGTGGTCCACATAAATCCAGA 59.165 45.455 21.91 4.71 33.40 3.86
1717 2988 3.260475 TCGTGGTCCACATAAATCCAG 57.740 47.619 21.91 2.31 33.40 3.86
1735 3007 2.093306 TGTCCTGTGGTAAGCAATCG 57.907 50.000 0.00 0.00 0.00 3.34
1737 3009 5.806654 ATTTTTGTCCTGTGGTAAGCAAT 57.193 34.783 0.00 0.00 0.00 3.56
1883 3156 1.078143 CTACCAGTTCCAGCCCTGC 60.078 63.158 0.00 0.00 0.00 4.85
1891 3164 3.686016 TCCATTTTCAGCTACCAGTTCC 58.314 45.455 0.00 0.00 0.00 3.62
2067 3340 6.407202 ACTCAGCAGTTACGGAATTAATTCT 58.593 36.000 23.85 10.79 37.00 2.40
2849 4123 9.754382 ATGCAAATCCATTTATTGACATACTTC 57.246 29.630 0.00 0.00 0.00 3.01
2956 4230 8.099537 ACCTGCCAAGATATGAGAACTAATATG 58.900 37.037 0.00 0.00 0.00 1.78
3306 4580 6.486657 TCAGTTGCTTCATACAAAACTAGCTT 59.513 34.615 0.00 0.00 30.20 3.74
3435 4710 5.405935 TGTCTCTAGTAAATGAGCTTGCA 57.594 39.130 0.00 0.00 0.00 4.08
3761 6120 7.730364 AGTTACATCAACTTCCACTTGTTAG 57.270 36.000 0.00 0.00 45.54 2.34
3948 6309 3.510388 TCTGGTAGTTCAGCATTCTCG 57.490 47.619 0.00 0.00 34.91 4.04
4218 6579 6.161381 ACATCAACAGGAAATTGCTTCATTC 58.839 36.000 0.00 0.00 35.55 2.67
4258 6619 5.804979 GCACTTGTTTTGAAGCTTAAAGTCA 59.195 36.000 0.00 0.00 0.00 3.41
4508 6870 3.624326 TGCAAGATTCCAACAAGAACG 57.376 42.857 0.00 0.00 0.00 3.95
4585 6947 0.392863 CGGTGCAATCTCCATCCACA 60.393 55.000 0.00 0.00 0.00 4.17
4603 6965 0.389817 TGGCTGATTCGACAGGAACG 60.390 55.000 5.31 0.00 37.50 3.95
4696 7096 7.231467 TCTGCTTTTAAAACAGATACTCCCTT 58.769 34.615 20.07 0.00 35.58 3.95
4840 7256 9.616634 TTGTAAATAGATATGTTATCGTCCGAC 57.383 33.333 0.00 0.00 0.00 4.79
4868 7284 4.960938 AGCCACGCTATCTGATAAAATCA 58.039 39.130 0.00 0.00 36.99 2.57
4923 7339 2.562738 GTGCAGGGGAAGCTTGTAAATT 59.437 45.455 2.10 0.00 0.00 1.82
4945 7362 6.183360 GCCTGTCAGCAAATATAGATGCATAG 60.183 42.308 0.00 6.76 44.95 2.23
5083 7500 4.446413 CGACACCCTACCCCGTGC 62.446 72.222 0.00 0.00 33.09 5.34
5251 7691 7.171653 TCACAATGTTCCACATGGTAGATAAA 58.828 34.615 0.00 0.00 40.64 1.40
5261 7701 6.638610 TGAAGTTTTTCACAATGTTCCACAT 58.361 32.000 0.00 0.00 38.20 3.21
5279 7719 6.770785 ACAACGTAATATATGCCCATGAAGTT 59.229 34.615 0.00 0.00 0.00 2.66
5326 7770 1.774110 TTTGCAGAAGTTTCCAGGCA 58.226 45.000 0.00 0.00 0.00 4.75
5342 7786 0.887933 AGGCGGGCAACACTATTTTG 59.112 50.000 3.78 0.00 39.74 2.44
5343 7787 1.173913 GAGGCGGGCAACACTATTTT 58.826 50.000 3.78 0.00 39.74 1.82
5349 7793 3.365265 CAAGGAGGCGGGCAACAC 61.365 66.667 3.78 0.00 39.74 3.32
5353 7797 4.113815 CATCCAAGGAGGCGGGCA 62.114 66.667 3.78 0.00 37.29 5.36
5354 7798 4.115199 ACATCCAAGGAGGCGGGC 62.115 66.667 0.00 0.00 37.29 6.13
5355 7799 2.190578 GACATCCAAGGAGGCGGG 59.809 66.667 0.00 0.00 37.29 6.13
5356 7800 2.190578 GGACATCCAAGGAGGCGG 59.809 66.667 0.00 0.00 37.29 6.13
5357 7801 2.989639 TGGACATCCAAGGAGGCG 59.010 61.111 0.00 0.00 44.35 5.52
5373 7817 0.606401 AGCCCAACGTCCAATCAGTG 60.606 55.000 0.00 0.00 0.00 3.66
5374 7818 0.321653 GAGCCCAACGTCCAATCAGT 60.322 55.000 0.00 0.00 0.00 3.41
5375 7819 0.036010 AGAGCCCAACGTCCAATCAG 60.036 55.000 0.00 0.00 0.00 2.90
5376 7820 0.400213 AAGAGCCCAACGTCCAATCA 59.600 50.000 0.00 0.00 0.00 2.57
5377 7821 0.804989 CAAGAGCCCAACGTCCAATC 59.195 55.000 0.00 0.00 0.00 2.67
5378 7822 0.110486 ACAAGAGCCCAACGTCCAAT 59.890 50.000 0.00 0.00 0.00 3.16
5379 7823 0.759959 TACAAGAGCCCAACGTCCAA 59.240 50.000 0.00 0.00 0.00 3.53
5380 7824 0.759959 TTACAAGAGCCCAACGTCCA 59.240 50.000 0.00 0.00 0.00 4.02
5381 7825 1.154197 GTTACAAGAGCCCAACGTCC 58.846 55.000 0.00 0.00 0.00 4.79
5382 7826 2.165319 AGTTACAAGAGCCCAACGTC 57.835 50.000 0.00 0.00 0.00 4.34
5383 7827 3.975168 ATAGTTACAAGAGCCCAACGT 57.025 42.857 0.00 0.00 0.00 3.99
5384 7828 4.569564 GGTTATAGTTACAAGAGCCCAACG 59.430 45.833 0.00 0.00 0.00 4.10
5385 7829 5.742063 AGGTTATAGTTACAAGAGCCCAAC 58.258 41.667 0.00 0.00 0.00 3.77
5386 7830 5.486063 TGAGGTTATAGTTACAAGAGCCCAA 59.514 40.000 0.00 0.00 0.00 4.12
5387 7831 5.027460 TGAGGTTATAGTTACAAGAGCCCA 58.973 41.667 0.00 0.00 0.00 5.36
5388 7832 5.609533 TGAGGTTATAGTTACAAGAGCCC 57.390 43.478 0.00 0.00 0.00 5.19
5389 7833 5.524281 GCTTGAGGTTATAGTTACAAGAGCC 59.476 44.000 0.00 0.00 37.49 4.70
5390 7834 5.232414 CGCTTGAGGTTATAGTTACAAGAGC 59.768 44.000 0.00 0.00 37.49 4.09
5391 7835 6.331061 ACGCTTGAGGTTATAGTTACAAGAG 58.669 40.000 0.00 0.00 39.58 2.85
5392 7836 6.276832 ACGCTTGAGGTTATAGTTACAAGA 57.723 37.500 0.00 0.00 37.49 3.02
5393 7837 5.519206 GGACGCTTGAGGTTATAGTTACAAG 59.481 44.000 0.00 0.00 38.07 3.16
5394 7838 5.047164 TGGACGCTTGAGGTTATAGTTACAA 60.047 40.000 0.00 0.00 0.00 2.41
5395 7839 4.463539 TGGACGCTTGAGGTTATAGTTACA 59.536 41.667 0.00 0.00 0.00 2.41
5396 7840 5.002464 TGGACGCTTGAGGTTATAGTTAC 57.998 43.478 0.00 0.00 0.00 2.50
5397 7841 4.098960 CCTGGACGCTTGAGGTTATAGTTA 59.901 45.833 0.00 0.00 0.00 2.24
5398 7842 3.118738 CCTGGACGCTTGAGGTTATAGTT 60.119 47.826 0.00 0.00 0.00 2.24
5399 7843 2.431057 CCTGGACGCTTGAGGTTATAGT 59.569 50.000 0.00 0.00 0.00 2.12
5400 7844 2.693591 TCCTGGACGCTTGAGGTTATAG 59.306 50.000 0.00 0.00 0.00 1.31
5401 7845 2.693591 CTCCTGGACGCTTGAGGTTATA 59.306 50.000 0.00 0.00 0.00 0.98
5402 7846 1.482593 CTCCTGGACGCTTGAGGTTAT 59.517 52.381 0.00 0.00 0.00 1.89
5403 7847 0.895530 CTCCTGGACGCTTGAGGTTA 59.104 55.000 0.00 0.00 0.00 2.85
5404 7848 1.674057 CTCCTGGACGCTTGAGGTT 59.326 57.895 0.00 0.00 0.00 3.50
5405 7849 2.286523 CCTCCTGGACGCTTGAGGT 61.287 63.158 0.00 0.00 39.64 3.85
5406 7850 2.581354 CCTCCTGGACGCTTGAGG 59.419 66.667 0.00 0.00 38.56 3.86
5407 7851 1.115467 ATACCTCCTGGACGCTTGAG 58.885 55.000 0.00 0.00 37.04 3.02
5408 7852 1.568504 AATACCTCCTGGACGCTTGA 58.431 50.000 0.00 0.00 37.04 3.02
5409 7853 2.009774 CAAATACCTCCTGGACGCTTG 58.990 52.381 0.00 0.00 37.04 4.01
5528 7972 6.036517 GCTCTCAACTATTCGAACATGTGAAT 59.963 38.462 13.97 13.97 38.34 2.57
5565 8009 1.230149 AGCCATAGGGGGACACCAA 60.230 57.895 0.00 0.00 42.91 3.67
5583 8027 2.375174 AGTATTCAGTTTCACCCAGCCA 59.625 45.455 0.00 0.00 0.00 4.75
5586 8030 4.637534 CCATCAGTATTCAGTTTCACCCAG 59.362 45.833 0.00 0.00 0.00 4.45
5934 8395 4.202419 TGCCCTCTTGTCTAGCAAACTTTA 60.202 41.667 0.00 0.00 36.53 1.85
5977 8438 2.503895 AAGAAACTGATGGGCCTGAG 57.496 50.000 4.53 0.00 0.00 3.35
6067 8528 3.041946 AGTACAAGCCTTCTATGAGGGG 58.958 50.000 0.00 0.00 37.29 4.79
6068 8529 3.964031 AGAGTACAAGCCTTCTATGAGGG 59.036 47.826 0.00 0.00 37.29 4.30
6069 8530 4.892934 AGAGAGTACAAGCCTTCTATGAGG 59.107 45.833 0.00 0.00 39.93 3.86
6070 8531 5.592282 TGAGAGAGTACAAGCCTTCTATGAG 59.408 44.000 0.00 0.00 0.00 2.90
6071 8532 5.510430 TGAGAGAGTACAAGCCTTCTATGA 58.490 41.667 0.00 0.00 0.00 2.15
6072 8533 5.843673 TGAGAGAGTACAAGCCTTCTATG 57.156 43.478 0.00 0.00 0.00 2.23
6073 8534 6.372931 AGATGAGAGAGTACAAGCCTTCTAT 58.627 40.000 0.00 0.00 0.00 1.98
6074 8535 5.761205 AGATGAGAGAGTACAAGCCTTCTA 58.239 41.667 0.00 0.00 0.00 2.10
6075 8536 4.609301 AGATGAGAGAGTACAAGCCTTCT 58.391 43.478 0.00 0.00 0.00 2.85
6076 8537 5.337578 AAGATGAGAGAGTACAAGCCTTC 57.662 43.478 0.00 0.00 0.00 3.46
6077 8538 5.753721 AAAGATGAGAGAGTACAAGCCTT 57.246 39.130 0.00 0.00 0.00 4.35
6078 8539 5.247110 TGAAAAGATGAGAGAGTACAAGCCT 59.753 40.000 0.00 0.00 0.00 4.58
6079 8540 5.482908 TGAAAAGATGAGAGAGTACAAGCC 58.517 41.667 0.00 0.00 0.00 4.35
6080 8541 7.462731 CATTGAAAAGATGAGAGAGTACAAGC 58.537 38.462 0.00 0.00 0.00 4.01
6081 8542 7.118825 TGCATTGAAAAGATGAGAGAGTACAAG 59.881 37.037 0.00 0.00 0.00 3.16
6082 8543 6.936335 TGCATTGAAAAGATGAGAGAGTACAA 59.064 34.615 0.00 0.00 0.00 2.41
6083 8544 6.466812 TGCATTGAAAAGATGAGAGAGTACA 58.533 36.000 0.00 0.00 0.00 2.90
6084 8545 6.974932 TGCATTGAAAAGATGAGAGAGTAC 57.025 37.500 0.00 0.00 0.00 2.73
6085 8546 7.066645 CCATTGCATTGAAAAGATGAGAGAGTA 59.933 37.037 10.14 0.00 0.00 2.59
6086 8547 6.127703 CCATTGCATTGAAAAGATGAGAGAGT 60.128 38.462 10.14 0.00 0.00 3.24
6087 8548 6.095021 TCCATTGCATTGAAAAGATGAGAGAG 59.905 38.462 10.14 0.00 0.00 3.20
6088 8549 5.947566 TCCATTGCATTGAAAAGATGAGAGA 59.052 36.000 10.14 0.00 0.00 3.10
6089 8550 6.203808 TCCATTGCATTGAAAAGATGAGAG 57.796 37.500 10.14 0.00 0.00 3.20
6090 8551 6.392354 GTTCCATTGCATTGAAAAGATGAGA 58.608 36.000 10.14 0.00 0.00 3.27
6091 8552 5.287752 CGTTCCATTGCATTGAAAAGATGAG 59.712 40.000 10.14 0.00 0.00 2.90
6092 8553 5.162794 CGTTCCATTGCATTGAAAAGATGA 58.837 37.500 10.14 0.00 0.00 2.92
6093 8554 4.201647 GCGTTCCATTGCATTGAAAAGATG 60.202 41.667 10.14 0.00 0.00 2.90
6094 8555 3.928375 GCGTTCCATTGCATTGAAAAGAT 59.072 39.130 10.14 0.00 0.00 2.40
6095 8556 3.243670 TGCGTTCCATTGCATTGAAAAGA 60.244 39.130 10.14 0.00 35.90 2.52
6096 8557 3.058450 TGCGTTCCATTGCATTGAAAAG 58.942 40.909 10.14 0.00 35.90 2.27
6097 8558 3.103447 TGCGTTCCATTGCATTGAAAA 57.897 38.095 10.14 1.90 35.90 2.29
6098 8559 2.808523 TGCGTTCCATTGCATTGAAA 57.191 40.000 10.14 0.00 35.90 2.69
6099 8560 2.808523 TTGCGTTCCATTGCATTGAA 57.191 40.000 10.14 0.00 41.42 2.69
6100 8561 2.295629 TCTTTGCGTTCCATTGCATTGA 59.704 40.909 10.14 0.00 41.42 2.57
6101 8562 2.674954 TCTTTGCGTTCCATTGCATTG 58.325 42.857 1.49 1.49 41.42 2.82
6102 8563 3.514645 GATCTTTGCGTTCCATTGCATT 58.485 40.909 0.00 0.00 41.42 3.56
6103 8564 2.159198 GGATCTTTGCGTTCCATTGCAT 60.159 45.455 0.00 0.00 41.42 3.96
6104 8565 1.202114 GGATCTTTGCGTTCCATTGCA 59.798 47.619 0.00 0.00 39.81 4.08
6105 8566 1.474077 AGGATCTTTGCGTTCCATTGC 59.526 47.619 0.00 0.00 34.50 3.56
6106 8567 3.855689 AAGGATCTTTGCGTTCCATTG 57.144 42.857 0.00 0.00 34.50 2.82
6107 8568 4.559153 CAAAAGGATCTTTGCGTTCCATT 58.441 39.130 0.00 0.00 34.50 3.16
6108 8569 4.178545 CAAAAGGATCTTTGCGTTCCAT 57.821 40.909 0.00 0.00 34.50 3.41
6109 8570 3.641437 CAAAAGGATCTTTGCGTTCCA 57.359 42.857 0.00 0.00 34.50 3.53
6116 8577 3.905784 AGAAAGCGCAAAAGGATCTTTG 58.094 40.909 11.47 3.64 38.97 2.77
6117 8578 5.705609 TTAGAAAGCGCAAAAGGATCTTT 57.294 34.783 11.47 0.00 0.00 2.52
6118 8579 5.705609 TTTAGAAAGCGCAAAAGGATCTT 57.294 34.783 11.47 0.00 0.00 2.40
6119 8580 5.705609 TTTTAGAAAGCGCAAAAGGATCT 57.294 34.783 11.47 4.56 0.00 2.75


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

AutoCloner maintained by Alex Coulton.