Multiple sequence alignment - TraesCS6D01G186300

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 TraesCS6D01G186300 chr6D 100.000 4475 0 0 1 4475 244541201 244545675 0.000000e+00 8264
1 TraesCS6D01G186300 chr6D 97.260 73 0 1 4352 4424 244545482 244545552 6.080000e-24 122
2 TraesCS6D01G186300 chr6D 97.260 73 0 1 4282 4352 244545552 244545624 6.080000e-24 122
3 TraesCS6D01G186300 chr6A 97.055 3531 66 6 854 4352 334511145 334514669 0.000000e+00 5910
4 TraesCS6D01G186300 chr6A 81.965 743 95 21 138 852 1834225 1834956 1.070000e-165 593
5 TraesCS6D01G186300 chr6A 95.745 94 2 1 4352 4445 334514599 334514690 2.790000e-32 150
6 TraesCS6D01G186300 chr6B 98.030 3045 56 3 936 3977 334839297 334842340 0.000000e+00 5288
7 TraesCS6D01G186300 chr2B 90.682 719 61 5 138 852 647094082 647094798 0.000000e+00 952
8 TraesCS6D01G186300 chr5A 88.999 709 72 5 146 852 367594087 367594791 0.000000e+00 872
9 TraesCS6D01G186300 chr5B 86.011 722 92 7 136 855 292489745 292490459 0.000000e+00 765
10 TraesCS6D01G186300 chr1B 85.417 720 92 9 139 852 527289171 527289883 0.000000e+00 736
11 TraesCS6D01G186300 chr1A 84.882 721 99 7 138 855 393998003 393997290 0.000000e+00 719
12 TraesCS6D01G186300 chr7A 87.879 594 56 11 273 856 126085729 126086316 0.000000e+00 684
13 TraesCS6D01G186300 chr7A 82.256 727 83 26 140 856 98101339 98100649 1.790000e-163 586
14 TraesCS6D01G186300 chr7D 84.000 725 100 12 136 854 496775913 496776627 0.000000e+00 682
15 TraesCS6D01G186300 chr7D 85.816 141 19 1 134 274 48543769 48543908 1.000000e-31 148
16 TraesCS6D01G186300 chr7B 84.854 581 76 7 266 844 671279025 671278455 3.880000e-160 575
17 TraesCS6D01G186300 chr7B 86.765 136 18 0 138 273 748957173 748957038 7.750000e-33 152


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 TraesCS6D01G186300 chr6D 244541201 244545675 4474 False 2836 8264 98.173333 1 4475 3 chr6D.!!$F1 4474
1 TraesCS6D01G186300 chr6A 334511145 334514690 3545 False 3030 5910 96.400000 854 4445 2 chr6A.!!$F2 3591
2 TraesCS6D01G186300 chr6A 1834225 1834956 731 False 593 593 81.965000 138 852 1 chr6A.!!$F1 714
3 TraesCS6D01G186300 chr6B 334839297 334842340 3043 False 5288 5288 98.030000 936 3977 1 chr6B.!!$F1 3041
4 TraesCS6D01G186300 chr2B 647094082 647094798 716 False 952 952 90.682000 138 852 1 chr2B.!!$F1 714
5 TraesCS6D01G186300 chr5A 367594087 367594791 704 False 872 872 88.999000 146 852 1 chr5A.!!$F1 706
6 TraesCS6D01G186300 chr5B 292489745 292490459 714 False 765 765 86.011000 136 855 1 chr5B.!!$F1 719
7 TraesCS6D01G186300 chr1B 527289171 527289883 712 False 736 736 85.417000 139 852 1 chr1B.!!$F1 713
8 TraesCS6D01G186300 chr1A 393997290 393998003 713 True 719 719 84.882000 138 855 1 chr1A.!!$R1 717
9 TraesCS6D01G186300 chr7A 126085729 126086316 587 False 684 684 87.879000 273 856 1 chr7A.!!$F1 583
10 TraesCS6D01G186300 chr7A 98100649 98101339 690 True 586 586 82.256000 140 856 1 chr7A.!!$R1 716
11 TraesCS6D01G186300 chr7D 496775913 496776627 714 False 682 682 84.000000 136 854 1 chr7D.!!$F2 718
12 TraesCS6D01G186300 chr7B 671278455 671279025 570 True 575 575 84.854000 266 844 1 chr7B.!!$R1 578

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
64 65 0.110373 CCGCGTTGAAGTTGGCTTAC 60.110 55.000 4.92 0.0 34.61 2.34 F
323 328 0.673437 TTAGCACTGCAAACAAGCCC 59.327 50.000 3.30 0.0 0.00 5.19 F
867 934 0.679960 GCCTAAACCGCACTGGGAAT 60.680 55.000 0.00 0.0 44.64 3.01 F
1659 1728 1.749334 GCGAGACGGGGAGGATTGAT 61.749 60.000 0.00 0.0 0.00 2.57 F
2542 2635 1.878088 AGAGTGTTAAGCTCACGACGA 59.122 47.619 0.00 0.0 40.28 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1121 1188 1.229209 AGGGACGGAGCAAGGAGAA 60.229 57.895 0.00 0.00 0.00 2.87 R
1215 1282 1.280457 GGAGGGAAAGGCTGAGAAGA 58.720 55.000 0.00 0.00 0.00 2.87 R
2775 2868 0.381801 GTCCAATACTTGCATGCCCG 59.618 55.000 16.68 8.56 0.00 6.13 R
3291 3384 5.916661 TGTAGTCTTCCCATCTACAGTTC 57.083 43.478 0.00 0.00 38.98 3.01 R
4427 4529 0.438830 GGTTAACGCGCAGTCTGAAG 59.561 55.000 5.73 0.00 0.00 3.02 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
18 19 4.243008 TGGCCTCGCGGACACAAA 62.243 61.111 6.13 0.00 45.79 2.83
19 20 2.746277 GGCCTCGCGGACACAAAT 60.746 61.111 6.13 0.00 38.64 2.32
20 21 2.480555 GCCTCGCGGACACAAATG 59.519 61.111 6.13 0.00 0.00 2.32
21 22 3.039202 GCCTCGCGGACACAAATGG 62.039 63.158 6.13 0.00 0.00 3.16
22 23 1.375396 CCTCGCGGACACAAATGGA 60.375 57.895 6.13 0.00 0.00 3.41
23 24 1.635663 CCTCGCGGACACAAATGGAC 61.636 60.000 6.13 0.00 0.00 4.02
24 25 1.635663 CTCGCGGACACAAATGGACC 61.636 60.000 6.13 0.00 0.00 4.46
25 26 1.963855 CGCGGACACAAATGGACCA 60.964 57.895 0.00 0.00 0.00 4.02
26 27 1.511318 CGCGGACACAAATGGACCAA 61.511 55.000 0.00 0.00 0.00 3.67
27 28 0.671251 GCGGACACAAATGGACCAAA 59.329 50.000 0.00 0.00 0.00 3.28
28 29 1.067821 GCGGACACAAATGGACCAAAA 59.932 47.619 0.00 0.00 0.00 2.44
29 30 2.738135 CGGACACAAATGGACCAAAAC 58.262 47.619 0.00 0.00 0.00 2.43
30 31 2.099921 CGGACACAAATGGACCAAAACA 59.900 45.455 0.00 0.00 0.00 2.83
31 32 3.429547 CGGACACAAATGGACCAAAACAA 60.430 43.478 0.00 0.00 0.00 2.83
32 33 4.508662 GGACACAAATGGACCAAAACAAA 58.491 39.130 0.00 0.00 0.00 2.83
33 34 4.331443 GGACACAAATGGACCAAAACAAAC 59.669 41.667 0.00 0.00 0.00 2.93
34 35 3.929610 ACACAAATGGACCAAAACAAACG 59.070 39.130 0.00 0.00 0.00 3.60
35 36 4.177026 CACAAATGGACCAAAACAAACGA 58.823 39.130 0.00 0.00 0.00 3.85
36 37 4.627467 CACAAATGGACCAAAACAAACGAA 59.373 37.500 0.00 0.00 0.00 3.85
37 38 5.120830 CACAAATGGACCAAAACAAACGAAA 59.879 36.000 0.00 0.00 0.00 3.46
38 39 5.877564 ACAAATGGACCAAAACAAACGAAAT 59.122 32.000 0.00 0.00 0.00 2.17
39 40 5.982465 AATGGACCAAAACAAACGAAATG 57.018 34.783 0.00 0.00 0.00 2.32
40 41 3.786635 TGGACCAAAACAAACGAAATGG 58.213 40.909 0.00 0.00 0.00 3.16
41 42 3.127589 GGACCAAAACAAACGAAATGGG 58.872 45.455 0.00 0.00 32.21 4.00
42 43 3.431068 GGACCAAAACAAACGAAATGGGT 60.431 43.478 0.00 0.00 32.21 4.51
43 44 3.787785 ACCAAAACAAACGAAATGGGTC 58.212 40.909 0.00 0.00 32.21 4.46
44 45 3.195825 ACCAAAACAAACGAAATGGGTCA 59.804 39.130 0.00 0.00 32.21 4.02
45 46 3.553917 CCAAAACAAACGAAATGGGTCAC 59.446 43.478 0.00 0.00 0.00 3.67
46 47 3.446310 AAACAAACGAAATGGGTCACC 57.554 42.857 0.00 0.00 37.24 4.02
47 48 0.948678 ACAAACGAAATGGGTCACCG 59.051 50.000 0.00 0.00 40.75 4.94
48 49 0.386731 CAAACGAAATGGGTCACCGC 60.387 55.000 0.00 0.00 40.75 5.68
49 50 1.847890 AAACGAAATGGGTCACCGCG 61.848 55.000 0.00 0.00 40.75 6.46
50 51 2.740826 CGAAATGGGTCACCGCGT 60.741 61.111 4.92 0.00 40.75 6.01
51 52 2.322081 CGAAATGGGTCACCGCGTT 61.322 57.895 4.92 0.00 40.75 4.84
52 53 1.209127 GAAATGGGTCACCGCGTTG 59.791 57.895 4.92 0.00 40.75 4.10
53 54 1.228003 AAATGGGTCACCGCGTTGA 60.228 52.632 0.74 0.74 40.75 3.18
54 55 0.820074 AAATGGGTCACCGCGTTGAA 60.820 50.000 8.29 0.00 40.75 2.69
55 56 1.234615 AATGGGTCACCGCGTTGAAG 61.235 55.000 8.29 0.00 40.75 3.02
56 57 2.280592 GGGTCACCGCGTTGAAGT 60.281 61.111 8.29 0.00 0.00 3.01
57 58 1.890510 GGGTCACCGCGTTGAAGTT 60.891 57.895 8.29 0.00 0.00 2.66
58 59 1.278637 GGTCACCGCGTTGAAGTTG 59.721 57.895 8.29 0.00 0.00 3.16
59 60 1.278637 GTCACCGCGTTGAAGTTGG 59.721 57.895 8.29 0.00 0.00 3.77
60 61 2.051345 CACCGCGTTGAAGTTGGC 60.051 61.111 4.92 0.00 0.00 4.52
61 62 2.203153 ACCGCGTTGAAGTTGGCT 60.203 55.556 4.92 0.00 0.00 4.75
62 63 1.822186 ACCGCGTTGAAGTTGGCTT 60.822 52.632 4.92 0.00 37.71 4.35
63 64 0.533308 ACCGCGTTGAAGTTGGCTTA 60.533 50.000 4.92 0.00 34.61 3.09
64 65 0.110373 CCGCGTTGAAGTTGGCTTAC 60.110 55.000 4.92 0.00 34.61 2.34
65 66 0.110373 CGCGTTGAAGTTGGCTTACC 60.110 55.000 0.00 0.00 34.61 2.85
66 67 1.235724 GCGTTGAAGTTGGCTTACCT 58.764 50.000 0.00 0.00 34.61 3.08
67 68 1.607148 GCGTTGAAGTTGGCTTACCTT 59.393 47.619 0.00 0.00 34.61 3.50
68 69 2.034179 GCGTTGAAGTTGGCTTACCTTT 59.966 45.455 0.00 0.00 34.61 3.11
69 70 3.490249 GCGTTGAAGTTGGCTTACCTTTT 60.490 43.478 0.00 0.00 34.61 2.27
70 71 4.287720 CGTTGAAGTTGGCTTACCTTTTC 58.712 43.478 0.00 0.00 34.61 2.29
71 72 4.036380 CGTTGAAGTTGGCTTACCTTTTCT 59.964 41.667 0.00 0.00 34.61 2.52
72 73 5.520632 GTTGAAGTTGGCTTACCTTTTCTC 58.479 41.667 0.00 0.00 34.61 2.87
73 74 4.787551 TGAAGTTGGCTTACCTTTTCTCA 58.212 39.130 0.00 0.00 34.61 3.27
74 75 4.821805 TGAAGTTGGCTTACCTTTTCTCAG 59.178 41.667 0.00 0.00 34.61 3.35
75 76 3.149981 AGTTGGCTTACCTTTTCTCAGC 58.850 45.455 0.00 0.00 36.63 4.26
76 77 2.884639 GTTGGCTTACCTTTTCTCAGCA 59.115 45.455 0.00 0.00 36.63 4.41
77 78 3.222173 TGGCTTACCTTTTCTCAGCAA 57.778 42.857 0.00 0.00 36.63 3.91
78 79 3.149196 TGGCTTACCTTTTCTCAGCAAG 58.851 45.455 0.00 0.00 36.63 4.01
79 80 2.489722 GGCTTACCTTTTCTCAGCAAGG 59.510 50.000 1.65 1.65 44.68 3.61
80 81 3.412386 GCTTACCTTTTCTCAGCAAGGA 58.588 45.455 9.04 0.00 42.11 3.36
81 82 3.821033 GCTTACCTTTTCTCAGCAAGGAA 59.179 43.478 9.04 0.00 42.11 3.36
82 83 4.278419 GCTTACCTTTTCTCAGCAAGGAAA 59.722 41.667 9.04 0.00 42.11 3.13
83 84 5.763088 CTTACCTTTTCTCAGCAAGGAAAC 58.237 41.667 9.04 0.00 42.11 2.78
84 85 3.631250 ACCTTTTCTCAGCAAGGAAACA 58.369 40.909 9.04 0.00 42.11 2.83
85 86 4.023291 ACCTTTTCTCAGCAAGGAAACAA 58.977 39.130 9.04 0.00 42.11 2.83
86 87 4.466015 ACCTTTTCTCAGCAAGGAAACAAA 59.534 37.500 9.04 0.00 42.11 2.83
87 88 4.805719 CCTTTTCTCAGCAAGGAAACAAAC 59.194 41.667 0.00 0.00 42.11 2.93
88 89 5.394553 CCTTTTCTCAGCAAGGAAACAAACT 60.395 40.000 0.00 0.00 42.11 2.66
89 90 4.900635 TTCTCAGCAAGGAAACAAACTC 57.099 40.909 0.00 0.00 0.00 3.01
90 91 3.214328 TCTCAGCAAGGAAACAAACTCC 58.786 45.455 0.00 0.00 0.00 3.85
91 92 3.117888 TCTCAGCAAGGAAACAAACTCCT 60.118 43.478 0.00 0.00 45.66 3.69
92 93 4.102524 TCTCAGCAAGGAAACAAACTCCTA 59.897 41.667 0.00 0.00 42.77 2.94
93 94 4.985538 TCAGCAAGGAAACAAACTCCTAT 58.014 39.130 0.00 0.00 42.77 2.57
94 95 5.385198 TCAGCAAGGAAACAAACTCCTATT 58.615 37.500 0.00 0.00 42.77 1.73
95 96 5.473504 TCAGCAAGGAAACAAACTCCTATTC 59.526 40.000 0.00 0.00 42.77 1.75
96 97 4.455877 AGCAAGGAAACAAACTCCTATTCG 59.544 41.667 0.00 0.00 42.77 3.34
97 98 4.723248 CAAGGAAACAAACTCCTATTCGC 58.277 43.478 0.00 0.00 42.77 4.70
98 99 3.000727 AGGAAACAAACTCCTATTCGCG 58.999 45.455 0.00 0.00 41.73 5.87
99 100 2.740447 GGAAACAAACTCCTATTCGCGT 59.260 45.455 5.77 0.00 0.00 6.01
100 101 3.424433 GGAAACAAACTCCTATTCGCGTG 60.424 47.826 5.77 0.00 0.00 5.34
101 102 1.722011 ACAAACTCCTATTCGCGTGG 58.278 50.000 5.77 4.91 0.00 4.94
102 103 1.274167 ACAAACTCCTATTCGCGTGGA 59.726 47.619 5.77 9.21 0.00 4.02
103 104 1.659098 CAAACTCCTATTCGCGTGGAC 59.341 52.381 5.77 0.00 0.00 4.02
104 105 0.892755 AACTCCTATTCGCGTGGACA 59.107 50.000 5.77 0.00 0.00 4.02
105 106 0.892755 ACTCCTATTCGCGTGGACAA 59.107 50.000 5.77 0.00 0.00 3.18
106 107 1.274167 ACTCCTATTCGCGTGGACAAA 59.726 47.619 5.77 0.00 0.00 2.83
107 108 2.093658 ACTCCTATTCGCGTGGACAAAT 60.094 45.455 5.77 0.00 0.00 2.32
108 109 2.936498 CTCCTATTCGCGTGGACAAATT 59.064 45.455 5.77 0.00 0.00 1.82
109 110 3.340034 TCCTATTCGCGTGGACAAATTT 58.660 40.909 5.77 0.00 0.00 1.82
110 111 3.372822 TCCTATTCGCGTGGACAAATTTC 59.627 43.478 5.77 0.00 0.00 2.17
111 112 3.126171 CCTATTCGCGTGGACAAATTTCA 59.874 43.478 5.77 0.00 0.00 2.69
112 113 3.848272 ATTCGCGTGGACAAATTTCAT 57.152 38.095 5.77 0.00 0.00 2.57
113 114 2.610219 TCGCGTGGACAAATTTCATG 57.390 45.000 5.77 0.00 0.00 3.07
114 115 1.876799 TCGCGTGGACAAATTTCATGT 59.123 42.857 5.77 0.00 0.00 3.21
115 116 1.978097 CGCGTGGACAAATTTCATGTG 59.022 47.619 0.00 0.00 0.00 3.21
116 117 2.350293 CGCGTGGACAAATTTCATGTGA 60.350 45.455 0.00 0.00 31.71 3.58
117 118 2.979813 GCGTGGACAAATTTCATGTGAC 59.020 45.455 0.00 0.00 0.00 3.67
118 119 3.564511 CGTGGACAAATTTCATGTGACC 58.435 45.455 0.00 0.00 0.00 4.02
119 120 3.004210 CGTGGACAAATTTCATGTGACCA 59.996 43.478 1.34 1.34 35.25 4.02
120 121 4.321156 CGTGGACAAATTTCATGTGACCAT 60.321 41.667 7.50 0.00 38.88 3.55
121 122 5.540911 GTGGACAAATTTCATGTGACCATT 58.459 37.500 7.50 0.00 38.88 3.16
122 123 5.634859 GTGGACAAATTTCATGTGACCATTC 59.365 40.000 7.50 0.00 38.88 2.67
123 124 4.858692 GGACAAATTTCATGTGACCATTCG 59.141 41.667 0.00 0.00 0.00 3.34
124 125 4.808558 ACAAATTTCATGTGACCATTCGG 58.191 39.130 0.00 0.00 38.77 4.30
125 126 4.175516 CAAATTTCATGTGACCATTCGGG 58.824 43.478 0.00 0.00 44.81 5.14
238 239 5.885912 ACCACAGTTTTGACATAACAGAGTT 59.114 36.000 10.77 0.00 0.00 3.01
323 328 0.673437 TTAGCACTGCAAACAAGCCC 59.327 50.000 3.30 0.00 0.00 5.19
329 334 1.066502 ACTGCAAACAAGCCCGTTTTT 60.067 42.857 0.00 0.00 36.98 1.94
357 368 2.121645 GCTGGCTAGCCATTGCATT 58.878 52.632 35.93 0.00 46.15 3.56
374 392 2.410322 ATTCAGCAACAGACCGGCCA 62.410 55.000 0.00 0.00 0.00 5.36
393 428 2.744202 CCAAAGAACAACGCTGCTCTAT 59.256 45.455 0.00 0.00 27.67 1.98
411 452 3.641436 TCTATGTGGCTGGTCGTATCATT 59.359 43.478 0.00 0.00 0.00 2.57
745 811 7.608308 AAATACCGCGGTATTAAAACTACAA 57.392 32.000 46.37 24.38 46.76 2.41
748 814 8.885494 ATACCGCGGTATTAAAACTACAATTA 57.115 30.769 38.70 15.91 38.02 1.40
751 817 8.676401 ACCGCGGTATTAAAACTACAATTATTT 58.324 29.630 33.34 0.00 0.00 1.40
767 833 6.427547 ACAATTATTTGTGGCAATCAAACAGG 59.572 34.615 5.52 0.00 44.36 4.00
769 835 2.886862 TTGTGGCAATCAAACAGGTG 57.113 45.000 0.00 0.00 0.00 4.00
772 838 1.000274 GTGGCAATCAAACAGGTGGTC 60.000 52.381 0.00 0.00 0.00 4.02
783 849 7.330900 TCAAACAGGTGGTCGTAAATAAAAA 57.669 32.000 0.00 0.00 0.00 1.94
867 934 0.679960 GCCTAAACCGCACTGGGAAT 60.680 55.000 0.00 0.00 44.64 3.01
1121 1188 3.790437 CCTGCCGCATCTCCCTGT 61.790 66.667 0.00 0.00 0.00 4.00
1267 1334 3.273654 TCCACTCCCTCTCCCCGT 61.274 66.667 0.00 0.00 0.00 5.28
1659 1728 1.749334 GCGAGACGGGGAGGATTGAT 61.749 60.000 0.00 0.00 0.00 2.57
1785 1854 2.398252 TGCTGCAGAGGATGAAGAAG 57.602 50.000 20.43 0.00 36.54 2.85
2354 2447 7.337480 TGGTGACATTCAATTCATTGATAGG 57.663 36.000 3.06 0.00 40.22 2.57
2542 2635 1.878088 AGAGTGTTAAGCTCACGACGA 59.122 47.619 0.00 0.00 40.28 4.20
2704 2797 3.072915 TGAAGGAAGACTCATTGAAGCCA 59.927 43.478 0.00 0.00 0.00 4.75
3132 3225 3.435275 TGAGGACATCTACACTGCTCTT 58.565 45.455 0.00 0.00 0.00 2.85
3199 3292 3.159213 TGCTTCACTCCATGATTGGTT 57.841 42.857 0.00 0.00 44.06 3.67
3291 3384 6.642430 TCATATGGCTGAAGAAATTTTTGGG 58.358 36.000 2.13 0.00 0.00 4.12
3495 3589 7.766278 GGATAATATACTGCTACATTCACCAGG 59.234 40.741 0.00 0.00 0.00 4.45
3653 3747 6.615088 TCATGTTTTATTGCTCTCTCAAAGC 58.385 36.000 0.00 0.00 40.26 3.51
3790 3884 7.069569 CACCTAAAGATAACAAGTCAACAACG 58.930 38.462 0.00 0.00 0.00 4.10
4040 4134 2.961741 TGGGCTTGTTGTGCTCATTTTA 59.038 40.909 0.00 0.00 35.80 1.52
4068 4162 1.134340 TCAACACAAGTAACCTGCCGT 60.134 47.619 0.00 0.00 0.00 5.68
4122 4216 8.319146 CAAGGTTGGAAATAGACTAGGAACTAA 58.681 37.037 0.00 0.00 42.17 2.24
4182 4276 2.557924 TGCTTAGCACATGTTCCTTTGG 59.442 45.455 1.39 0.00 31.71 3.28
4255 4357 6.668323 AGAAACATCCGTTTTGATAACACAG 58.332 36.000 0.00 0.00 45.40 3.66
4328 4430 6.477053 TTGACATCCTGTCCAATTTTTCAA 57.523 33.333 4.91 0.00 46.40 2.69
4336 4438 5.336150 TGTCCAATTTTTCAAAGCAGTGA 57.664 34.783 0.00 0.00 0.00 3.41
4337 4439 5.728471 TGTCCAATTTTTCAAAGCAGTGAA 58.272 33.333 0.00 0.00 35.72 3.18
4338 4440 5.811613 TGTCCAATTTTTCAAAGCAGTGAAG 59.188 36.000 0.00 0.00 38.69 3.02
4339 4441 5.812127 GTCCAATTTTTCAAAGCAGTGAAGT 59.188 36.000 0.00 0.00 38.69 3.01
4340 4442 6.978080 GTCCAATTTTTCAAAGCAGTGAAGTA 59.022 34.615 0.00 0.00 38.69 2.24
4341 4443 7.653311 GTCCAATTTTTCAAAGCAGTGAAGTAT 59.347 33.333 0.00 0.00 38.69 2.12
4342 4444 8.203485 TCCAATTTTTCAAAGCAGTGAAGTATT 58.797 29.630 0.00 4.55 38.69 1.89
4343 4445 8.829612 CCAATTTTTCAAAGCAGTGAAGTATTT 58.170 29.630 0.00 0.00 38.69 1.40
4344 4446 9.853921 CAATTTTTCAAAGCAGTGAAGTATTTC 57.146 29.630 0.00 0.00 38.69 2.17
4345 4447 7.678194 TTTTTCAAAGCAGTGAAGTATTTCG 57.322 32.000 0.00 0.00 38.69 3.46
4346 4448 6.612247 TTTCAAAGCAGTGAAGTATTTCGA 57.388 33.333 0.00 0.00 38.69 3.71
4347 4449 6.612247 TTCAAAGCAGTGAAGTATTTCGAA 57.388 33.333 0.00 0.00 36.04 3.71
4348 4450 6.228273 TCAAAGCAGTGAAGTATTTCGAAG 57.772 37.500 0.00 0.00 36.04 3.79
4349 4451 5.758296 TCAAAGCAGTGAAGTATTTCGAAGT 59.242 36.000 0.00 0.00 36.04 3.01
4350 4452 6.260050 TCAAAGCAGTGAAGTATTTCGAAGTT 59.740 34.615 0.00 0.00 36.04 2.66
4351 4453 7.439955 TCAAAGCAGTGAAGTATTTCGAAGTTA 59.560 33.333 0.00 0.00 36.04 2.24
4352 4454 6.707599 AGCAGTGAAGTATTTCGAAGTTAC 57.292 37.500 0.00 5.45 36.04 2.50
4353 4455 6.220930 AGCAGTGAAGTATTTCGAAGTTACA 58.779 36.000 17.47 5.75 36.04 2.41
4354 4456 6.145696 AGCAGTGAAGTATTTCGAAGTTACAC 59.854 38.462 17.47 14.37 36.04 2.90
4355 4457 6.145696 GCAGTGAAGTATTTCGAAGTTACACT 59.854 38.462 17.47 15.80 36.04 3.55
4356 4458 7.307219 GCAGTGAAGTATTTCGAAGTTACACTT 60.307 37.037 17.47 12.71 41.95 3.16
4357 4459 8.004344 CAGTGAAGTATTTCGAAGTTACACTTG 58.996 37.037 17.47 11.52 38.80 3.16
4358 4460 7.709613 AGTGAAGTATTTCGAAGTTACACTTGT 59.290 33.333 17.47 0.00 38.80 3.16
4359 4461 8.971321 GTGAAGTATTTCGAAGTTACACTTGTA 58.029 33.333 17.47 4.64 38.80 2.41
4360 4462 9.701098 TGAAGTATTTCGAAGTTACACTTGTAT 57.299 29.630 17.47 0.89 38.80 2.29
4362 4464 8.699283 AGTATTTCGAAGTTACACTTGTATCC 57.301 34.615 17.47 0.00 38.80 2.59
4363 4465 6.980051 ATTTCGAAGTTACACTTGTATCCC 57.020 37.500 0.00 0.00 38.80 3.85
4364 4466 5.471556 TTCGAAGTTACACTTGTATCCCA 57.528 39.130 0.00 0.00 38.80 4.37
4365 4467 5.471556 TCGAAGTTACACTTGTATCCCAA 57.528 39.130 0.00 0.00 38.80 4.12
4366 4468 5.856156 TCGAAGTTACACTTGTATCCCAAA 58.144 37.500 0.00 0.00 38.80 3.28
4367 4469 6.289834 TCGAAGTTACACTTGTATCCCAAAA 58.710 36.000 0.00 0.00 38.80 2.44
4368 4470 6.938030 TCGAAGTTACACTTGTATCCCAAAAT 59.062 34.615 0.00 0.00 38.80 1.82
4369 4471 7.118680 TCGAAGTTACACTTGTATCCCAAAATC 59.881 37.037 0.00 0.00 38.80 2.17
4370 4472 7.094975 CGAAGTTACACTTGTATCCCAAAATCA 60.095 37.037 0.00 0.00 38.80 2.57
4371 4473 8.650143 AAGTTACACTTGTATCCCAAAATCAT 57.350 30.769 0.00 0.00 37.00 2.45
4372 4474 9.747898 AAGTTACACTTGTATCCCAAAATCATA 57.252 29.630 0.00 0.00 37.00 2.15
4373 4475 9.747898 AGTTACACTTGTATCCCAAAATCATAA 57.252 29.630 0.00 0.00 31.20 1.90
4377 4479 9.874205 ACACTTGTATCCCAAAATCATAATTTG 57.126 29.630 0.00 0.00 35.27 2.32
4383 4485 9.696917 GTATCCCAAAATCATAATTTGACATCC 57.303 33.333 0.83 0.00 39.56 3.51
4384 4486 7.976414 TCCCAAAATCATAATTTGACATCCT 57.024 32.000 0.83 0.00 39.56 3.24
4385 4487 7.784037 TCCCAAAATCATAATTTGACATCCTG 58.216 34.615 0.83 0.00 39.56 3.86
4386 4488 7.399765 TCCCAAAATCATAATTTGACATCCTGT 59.600 33.333 0.83 0.00 39.56 4.00
4388 4490 7.707893 CCAAAATCATAATTTGACATCCTGTCC 59.292 37.037 4.91 0.00 46.40 4.02
4389 4491 7.959658 AAATCATAATTTGACATCCTGTCCA 57.040 32.000 4.91 0.00 46.40 4.02
4390 4492 7.959658 AATCATAATTTGACATCCTGTCCAA 57.040 32.000 4.91 1.03 46.40 3.53
4391 4493 8.543293 AATCATAATTTGACATCCTGTCCAAT 57.457 30.769 4.91 3.27 46.40 3.16
4393 4495 8.365060 TCATAATTTGACATCCTGTCCAATTT 57.635 30.769 18.56 11.41 44.93 1.82
4394 4496 8.814931 TCATAATTTGACATCCTGTCCAATTTT 58.185 29.630 18.56 11.66 44.93 1.82
4395 4497 9.439500 CATAATTTGACATCCTGTCCAATTTTT 57.561 29.630 18.56 8.99 44.93 1.94
4396 4498 7.967890 AATTTGACATCCTGTCCAATTTTTC 57.032 32.000 11.44 0.00 44.93 2.29
4397 4499 6.729690 TTTGACATCCTGTCCAATTTTTCT 57.270 33.333 4.91 0.00 46.40 2.52
4398 4500 5.964958 TGACATCCTGTCCAATTTTTCTC 57.035 39.130 4.91 0.00 46.40 2.87
4399 4501 5.384336 TGACATCCTGTCCAATTTTTCTCA 58.616 37.500 4.91 0.00 46.40 3.27
4400 4502 5.832595 TGACATCCTGTCCAATTTTTCTCAA 59.167 36.000 4.91 0.00 46.40 3.02
4401 4503 6.323482 TGACATCCTGTCCAATTTTTCTCAAA 59.677 34.615 4.91 0.00 46.40 2.69
4402 4504 6.752168 ACATCCTGTCCAATTTTTCTCAAAG 58.248 36.000 0.00 0.00 0.00 2.77
4403 4505 5.200368 TCCTGTCCAATTTTTCTCAAAGC 57.800 39.130 0.00 0.00 0.00 3.51
4404 4506 4.648762 TCCTGTCCAATTTTTCTCAAAGCA 59.351 37.500 0.00 0.00 0.00 3.91
4405 4507 4.986659 CCTGTCCAATTTTTCTCAAAGCAG 59.013 41.667 0.00 0.00 0.00 4.24
4406 4508 5.452356 CCTGTCCAATTTTTCTCAAAGCAGT 60.452 40.000 0.00 0.00 0.00 4.40
4407 4509 5.350633 TGTCCAATTTTTCTCAAAGCAGTG 58.649 37.500 0.00 0.00 0.00 3.66
4427 4529 6.183360 GCAGTGAAGTATTTCGAAGTTAGGAC 60.183 42.308 0.00 0.00 36.04 3.85
4445 4547 1.124477 GACTTCAGACTGCGCGTTAAC 59.876 52.381 8.43 0.00 0.00 2.01
4446 4548 0.438830 CTTCAGACTGCGCGTTAACC 59.561 55.000 8.43 0.00 0.00 2.85
4447 4549 0.032952 TTCAGACTGCGCGTTAACCT 59.967 50.000 8.43 0.00 0.00 3.50
4448 4550 0.666274 TCAGACTGCGCGTTAACCTG 60.666 55.000 8.43 9.44 0.00 4.00
4449 4551 2.027625 AGACTGCGCGTTAACCTGC 61.028 57.895 8.43 9.22 0.00 4.85
4450 4552 2.027625 GACTGCGCGTTAACCTGCT 61.028 57.895 8.43 0.00 0.00 4.24
4451 4553 2.227968 GACTGCGCGTTAACCTGCTG 62.228 60.000 8.43 16.82 0.00 4.41
4452 4554 2.280524 TGCGCGTTAACCTGCTGT 60.281 55.556 8.43 0.00 0.00 4.40
4453 4555 1.841663 CTGCGCGTTAACCTGCTGTT 61.842 55.000 8.43 0.00 41.11 3.16
4454 4556 0.600518 TGCGCGTTAACCTGCTGTTA 60.601 50.000 8.43 0.00 38.42 2.41
4455 4557 0.513820 GCGCGTTAACCTGCTGTTAA 59.486 50.000 8.43 7.71 45.01 2.01
4464 4566 6.588719 TTAACCTGCTGTTAATTTGAGCAT 57.411 33.333 7.71 0.00 42.94 3.79
4465 4567 5.473066 AACCTGCTGTTAATTTGAGCATT 57.527 34.783 0.00 0.00 41.74 3.56
4466 4568 5.473066 ACCTGCTGTTAATTTGAGCATTT 57.527 34.783 0.00 0.00 41.74 2.32
4467 4569 5.473039 ACCTGCTGTTAATTTGAGCATTTC 58.527 37.500 0.00 0.00 41.74 2.17
4468 4570 5.244626 ACCTGCTGTTAATTTGAGCATTTCT 59.755 36.000 0.00 0.00 41.74 2.52
4469 4571 6.161381 CCTGCTGTTAATTTGAGCATTTCTT 58.839 36.000 0.00 0.00 41.74 2.52
4470 4572 6.647895 CCTGCTGTTAATTTGAGCATTTCTTT 59.352 34.615 0.00 0.00 41.74 2.52
4471 4573 7.172019 CCTGCTGTTAATTTGAGCATTTCTTTT 59.828 33.333 0.00 0.00 41.74 2.27
4472 4574 7.853524 TGCTGTTAATTTGAGCATTTCTTTTG 58.146 30.769 0.00 0.00 37.81 2.44
4473 4575 7.495279 TGCTGTTAATTTGAGCATTTCTTTTGT 59.505 29.630 0.00 0.00 37.81 2.83
4474 4576 7.795272 GCTGTTAATTTGAGCATTTCTTTTGTG 59.205 33.333 0.00 0.00 32.70 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.635663 GGTCCATTTGTGTCCGCGAG 61.636 60.000 8.23 0.00 0.00 5.03
6 7 1.669760 GGTCCATTTGTGTCCGCGA 60.670 57.895 8.23 0.00 0.00 5.87
8 9 0.671251 TTTGGTCCATTTGTGTCCGC 59.329 50.000 0.00 0.00 0.00 5.54
10 11 3.810310 TGTTTTGGTCCATTTGTGTCC 57.190 42.857 0.00 0.00 0.00 4.02
12 13 3.929610 CGTTTGTTTTGGTCCATTTGTGT 59.070 39.130 0.00 0.00 0.00 3.72
14 15 4.457834 TCGTTTGTTTTGGTCCATTTGT 57.542 36.364 0.00 0.00 0.00 2.83
15 16 5.786401 TTTCGTTTGTTTTGGTCCATTTG 57.214 34.783 0.00 0.00 0.00 2.32
16 17 5.295540 CCATTTCGTTTGTTTTGGTCCATTT 59.704 36.000 0.00 0.00 0.00 2.32
17 18 4.813697 CCATTTCGTTTGTTTTGGTCCATT 59.186 37.500 0.00 0.00 0.00 3.16
18 19 4.376146 CCATTTCGTTTGTTTTGGTCCAT 58.624 39.130 0.00 0.00 0.00 3.41
19 20 3.430929 CCCATTTCGTTTGTTTTGGTCCA 60.431 43.478 0.00 0.00 0.00 4.02
20 21 3.127589 CCCATTTCGTTTGTTTTGGTCC 58.872 45.455 0.00 0.00 0.00 4.46
21 22 3.787785 ACCCATTTCGTTTGTTTTGGTC 58.212 40.909 0.00 0.00 0.00 4.02
22 23 3.195825 TGACCCATTTCGTTTGTTTTGGT 59.804 39.130 0.00 0.00 0.00 3.67
23 24 3.553917 GTGACCCATTTCGTTTGTTTTGG 59.446 43.478 0.00 0.00 0.00 3.28
24 25 3.553917 GGTGACCCATTTCGTTTGTTTTG 59.446 43.478 0.00 0.00 0.00 2.44
25 26 3.735514 CGGTGACCCATTTCGTTTGTTTT 60.736 43.478 0.00 0.00 0.00 2.43
26 27 2.223618 CGGTGACCCATTTCGTTTGTTT 60.224 45.455 0.00 0.00 0.00 2.83
27 28 1.335496 CGGTGACCCATTTCGTTTGTT 59.665 47.619 0.00 0.00 0.00 2.83
28 29 0.948678 CGGTGACCCATTTCGTTTGT 59.051 50.000 0.00 0.00 0.00 2.83
29 30 0.386731 GCGGTGACCCATTTCGTTTG 60.387 55.000 0.00 0.00 0.00 2.93
30 31 1.847890 CGCGGTGACCCATTTCGTTT 61.848 55.000 0.00 0.00 0.00 3.60
31 32 2.322081 CGCGGTGACCCATTTCGTT 61.322 57.895 0.00 0.00 0.00 3.85
32 33 2.740826 CGCGGTGACCCATTTCGT 60.741 61.111 0.00 0.00 0.00 3.85
33 34 2.322081 AACGCGGTGACCCATTTCG 61.322 57.895 12.47 0.00 0.00 3.46
34 35 1.209127 CAACGCGGTGACCCATTTC 59.791 57.895 22.23 0.00 0.00 2.17
35 36 0.820074 TTCAACGCGGTGACCCATTT 60.820 50.000 29.42 0.00 0.00 2.32
36 37 1.228003 TTCAACGCGGTGACCCATT 60.228 52.632 29.42 0.00 0.00 3.16
37 38 1.671054 CTTCAACGCGGTGACCCAT 60.671 57.895 29.42 0.00 0.00 4.00
38 39 2.280524 CTTCAACGCGGTGACCCA 60.281 61.111 29.42 12.15 0.00 4.51
39 40 1.890510 AACTTCAACGCGGTGACCC 60.891 57.895 29.42 0.00 0.00 4.46
40 41 1.278637 CAACTTCAACGCGGTGACC 59.721 57.895 29.42 0.00 0.00 4.02
41 42 1.278637 CCAACTTCAACGCGGTGAC 59.721 57.895 29.42 0.00 0.00 3.67
42 43 2.539338 GCCAACTTCAACGCGGTGA 61.539 57.895 25.58 25.58 0.00 4.02
43 44 2.051345 GCCAACTTCAACGCGGTG 60.051 61.111 20.47 20.47 0.00 4.94
44 45 0.533308 TAAGCCAACTTCAACGCGGT 60.533 50.000 12.47 0.00 37.33 5.68
45 46 0.110373 GTAAGCCAACTTCAACGCGG 60.110 55.000 12.47 0.00 37.33 6.46
46 47 0.110373 GGTAAGCCAACTTCAACGCG 60.110 55.000 3.53 3.53 37.33 6.01
47 48 1.235724 AGGTAAGCCAACTTCAACGC 58.764 50.000 0.00 0.00 37.33 4.84
48 49 3.982576 AAAGGTAAGCCAACTTCAACG 57.017 42.857 0.00 0.00 37.33 4.10
49 50 5.067283 TGAGAAAAGGTAAGCCAACTTCAAC 59.933 40.000 0.00 0.00 37.33 3.18
50 51 5.197451 TGAGAAAAGGTAAGCCAACTTCAA 58.803 37.500 0.00 0.00 37.33 2.69
51 52 4.787551 TGAGAAAAGGTAAGCCAACTTCA 58.212 39.130 0.00 0.00 37.33 3.02
52 53 4.320567 GCTGAGAAAAGGTAAGCCAACTTC 60.321 45.833 0.00 0.00 37.33 3.01
53 54 3.570125 GCTGAGAAAAGGTAAGCCAACTT 59.430 43.478 0.00 0.00 40.07 2.66
54 55 3.149981 GCTGAGAAAAGGTAAGCCAACT 58.850 45.455 0.00 0.00 37.19 3.16
55 56 2.884639 TGCTGAGAAAAGGTAAGCCAAC 59.115 45.455 0.00 0.00 37.19 3.77
56 57 3.222173 TGCTGAGAAAAGGTAAGCCAA 57.778 42.857 0.00 0.00 37.19 4.52
57 58 2.949177 TGCTGAGAAAAGGTAAGCCA 57.051 45.000 0.00 0.00 37.19 4.75
58 59 2.489722 CCTTGCTGAGAAAAGGTAAGCC 59.510 50.000 6.28 0.00 38.53 4.35
59 60 3.412386 TCCTTGCTGAGAAAAGGTAAGC 58.588 45.455 12.35 0.00 43.02 3.09
60 61 5.299279 TGTTTCCTTGCTGAGAAAAGGTAAG 59.701 40.000 12.35 0.00 43.02 2.34
61 62 5.197451 TGTTTCCTTGCTGAGAAAAGGTAA 58.803 37.500 12.35 7.86 43.02 2.85
62 63 4.787551 TGTTTCCTTGCTGAGAAAAGGTA 58.212 39.130 12.35 2.85 43.02 3.08
63 64 3.631250 TGTTTCCTTGCTGAGAAAAGGT 58.369 40.909 12.35 0.00 43.02 3.50
64 65 4.654091 TTGTTTCCTTGCTGAGAAAAGG 57.346 40.909 7.77 7.77 43.72 3.11
65 66 5.654497 AGTTTGTTTCCTTGCTGAGAAAAG 58.346 37.500 0.00 0.00 33.98 2.27
66 67 5.394115 GGAGTTTGTTTCCTTGCTGAGAAAA 60.394 40.000 0.00 0.00 33.98 2.29
67 68 4.097892 GGAGTTTGTTTCCTTGCTGAGAAA 59.902 41.667 0.00 0.00 0.00 2.52
68 69 3.632145 GGAGTTTGTTTCCTTGCTGAGAA 59.368 43.478 0.00 0.00 0.00 2.87
69 70 3.117888 AGGAGTTTGTTTCCTTGCTGAGA 60.118 43.478 0.00 0.00 42.40 3.27
70 71 3.217626 AGGAGTTTGTTTCCTTGCTGAG 58.782 45.455 0.00 0.00 42.40 3.35
71 72 3.297134 AGGAGTTTGTTTCCTTGCTGA 57.703 42.857 0.00 0.00 42.40 4.26
72 73 5.617751 CGAATAGGAGTTTGTTTCCTTGCTG 60.618 44.000 0.00 0.00 42.40 4.41
73 74 4.455877 CGAATAGGAGTTTGTTTCCTTGCT 59.544 41.667 0.00 0.00 42.40 3.91
74 75 4.723248 CGAATAGGAGTTTGTTTCCTTGC 58.277 43.478 0.00 0.00 42.40 4.01
75 76 4.669197 CGCGAATAGGAGTTTGTTTCCTTG 60.669 45.833 0.00 0.00 42.40 3.61
76 77 3.435671 CGCGAATAGGAGTTTGTTTCCTT 59.564 43.478 0.00 0.00 42.40 3.36
77 78 3.000727 CGCGAATAGGAGTTTGTTTCCT 58.999 45.455 0.00 0.00 46.58 3.36
78 79 2.740447 ACGCGAATAGGAGTTTGTTTCC 59.260 45.455 15.93 0.00 34.83 3.13
79 80 3.424433 CCACGCGAATAGGAGTTTGTTTC 60.424 47.826 15.93 0.00 0.00 2.78
80 81 2.482721 CCACGCGAATAGGAGTTTGTTT 59.517 45.455 15.93 0.00 0.00 2.83
81 82 2.073816 CCACGCGAATAGGAGTTTGTT 58.926 47.619 15.93 0.00 0.00 2.83
82 83 1.274167 TCCACGCGAATAGGAGTTTGT 59.726 47.619 15.93 0.00 0.00 2.83
83 84 1.659098 GTCCACGCGAATAGGAGTTTG 59.341 52.381 15.93 0.00 30.78 2.93
84 85 1.274167 TGTCCACGCGAATAGGAGTTT 59.726 47.619 15.93 0.00 30.78 2.66
85 86 0.892755 TGTCCACGCGAATAGGAGTT 59.107 50.000 15.93 0.00 30.78 3.01
86 87 0.892755 TTGTCCACGCGAATAGGAGT 59.107 50.000 15.93 0.00 30.78 3.85
87 88 2.004583 TTTGTCCACGCGAATAGGAG 57.995 50.000 15.93 0.00 30.78 3.69
88 89 2.684001 ATTTGTCCACGCGAATAGGA 57.316 45.000 15.93 11.82 0.00 2.94
89 90 3.126171 TGAAATTTGTCCACGCGAATAGG 59.874 43.478 15.93 9.35 0.00 2.57
90 91 4.335082 TGAAATTTGTCCACGCGAATAG 57.665 40.909 15.93 0.00 0.00 1.73
91 92 4.155099 ACATGAAATTTGTCCACGCGAATA 59.845 37.500 15.93 0.00 0.00 1.75
92 93 3.057596 ACATGAAATTTGTCCACGCGAAT 60.058 39.130 15.93 0.00 0.00 3.34
93 94 2.292016 ACATGAAATTTGTCCACGCGAA 59.708 40.909 15.93 0.00 0.00 4.70
94 95 1.876799 ACATGAAATTTGTCCACGCGA 59.123 42.857 15.93 0.00 0.00 5.87
95 96 1.978097 CACATGAAATTTGTCCACGCG 59.022 47.619 3.53 3.53 0.00 6.01
96 97 2.979813 GTCACATGAAATTTGTCCACGC 59.020 45.455 0.00 0.00 0.00 5.34
97 98 3.004210 TGGTCACATGAAATTTGTCCACG 59.996 43.478 0.00 0.00 37.31 4.94
98 99 4.582701 TGGTCACATGAAATTTGTCCAC 57.417 40.909 0.00 0.00 37.31 4.02
99 100 5.564455 CGAATGGTCACATGAAATTTGTCCA 60.564 40.000 0.00 0.29 44.10 4.02
100 101 4.858692 CGAATGGTCACATGAAATTTGTCC 59.141 41.667 0.00 0.00 37.40 4.02
101 102 4.858692 CCGAATGGTCACATGAAATTTGTC 59.141 41.667 0.00 0.00 37.40 3.18
102 103 4.321899 CCCGAATGGTCACATGAAATTTGT 60.322 41.667 0.00 0.00 37.40 2.83
103 104 4.175516 CCCGAATGGTCACATGAAATTTG 58.824 43.478 0.00 0.00 37.40 2.32
104 105 4.454728 CCCGAATGGTCACATGAAATTT 57.545 40.909 0.00 0.00 37.40 1.82
117 118 4.440112 GCCTTAATCTTTTCACCCGAATGG 60.440 45.833 0.00 0.00 41.37 3.16
118 119 4.440112 GGCCTTAATCTTTTCACCCGAATG 60.440 45.833 0.00 0.00 0.00 2.67
119 120 3.699538 GGCCTTAATCTTTTCACCCGAAT 59.300 43.478 0.00 0.00 0.00 3.34
120 121 3.086282 GGCCTTAATCTTTTCACCCGAA 58.914 45.455 0.00 0.00 0.00 4.30
121 122 2.619590 GGGCCTTAATCTTTTCACCCGA 60.620 50.000 0.84 0.00 0.00 5.14
122 123 1.749063 GGGCCTTAATCTTTTCACCCG 59.251 52.381 0.84 0.00 0.00 5.28
123 124 2.760650 CAGGGCCTTAATCTTTTCACCC 59.239 50.000 1.32 0.00 36.29 4.61
124 125 3.431415 ACAGGGCCTTAATCTTTTCACC 58.569 45.455 1.32 0.00 0.00 4.02
125 126 5.010617 TCAAACAGGGCCTTAATCTTTTCAC 59.989 40.000 1.32 0.00 0.00 3.18
126 127 5.144100 TCAAACAGGGCCTTAATCTTTTCA 58.856 37.500 1.32 0.00 0.00 2.69
127 128 5.722021 TCAAACAGGGCCTTAATCTTTTC 57.278 39.130 1.32 0.00 0.00 2.29
128 129 6.127338 GCTATCAAACAGGGCCTTAATCTTTT 60.127 38.462 1.32 0.00 0.00 2.27
129 130 5.360999 GCTATCAAACAGGGCCTTAATCTTT 59.639 40.000 1.32 0.00 0.00 2.52
130 131 4.889995 GCTATCAAACAGGGCCTTAATCTT 59.110 41.667 1.32 0.00 0.00 2.40
131 132 4.079787 TGCTATCAAACAGGGCCTTAATCT 60.080 41.667 1.32 0.00 0.00 2.40
132 133 4.207165 TGCTATCAAACAGGGCCTTAATC 58.793 43.478 1.32 0.00 0.00 1.75
133 134 4.249638 TGCTATCAAACAGGGCCTTAAT 57.750 40.909 1.32 0.00 0.00 1.40
134 135 3.730215 TGCTATCAAACAGGGCCTTAA 57.270 42.857 1.32 0.00 0.00 1.85
238 239 5.000591 TCTGCATCACGAATACTCCAAAAA 58.999 37.500 0.00 0.00 0.00 1.94
357 368 2.616797 TTTGGCCGGTCTGTTGCTGA 62.617 55.000 7.97 0.00 0.00 4.26
374 392 3.187227 CACATAGAGCAGCGTTGTTCTTT 59.813 43.478 22.39 12.89 41.46 2.52
393 428 1.552792 TGAATGATACGACCAGCCACA 59.447 47.619 0.00 0.00 0.00 4.17
411 452 3.489229 CGTGGATCTCTGCGTTCTTATGA 60.489 47.826 0.00 0.00 0.00 2.15
488 535 1.216444 CGCTGCTGCTACCAAGAGA 59.784 57.895 14.03 0.00 36.97 3.10
493 540 1.607801 ATGACTCGCTGCTGCTACCA 61.608 55.000 14.03 6.64 36.97 3.25
529 577 4.082523 TCTCCCTCGGCGGCAAAG 62.083 66.667 10.53 5.52 0.00 2.77
561 609 4.999939 CCGTTGCCACCGCTTTGC 63.000 66.667 0.00 0.00 35.36 3.68
708 764 3.813166 CGCGGTATTTAGGAAACCATGAT 59.187 43.478 0.00 0.00 32.55 2.45
709 765 3.199677 CGCGGTATTTAGGAAACCATGA 58.800 45.455 0.00 0.00 32.55 3.07
745 811 5.933463 CACCTGTTTGATTGCCACAAATAAT 59.067 36.000 0.00 0.00 39.01 1.28
748 814 3.494749 CCACCTGTTTGATTGCCACAAAT 60.495 43.478 0.00 0.00 39.01 2.32
751 817 1.039068 CCACCTGTTTGATTGCCACA 58.961 50.000 0.00 0.00 0.00 4.17
832 899 1.589414 AGGCCCTGTTTGATAGCTCT 58.411 50.000 0.00 0.00 0.00 4.09
833 900 3.560636 TTAGGCCCTGTTTGATAGCTC 57.439 47.619 0.00 0.00 0.00 4.09
834 901 3.621558 GTTTAGGCCCTGTTTGATAGCT 58.378 45.455 0.00 0.00 0.00 3.32
867 934 3.686405 GCCATTGTTGGGATCTCATCTCA 60.686 47.826 0.00 0.00 43.84 3.27
958 1025 0.603975 AAAGAGAAGGACGCTGTGGC 60.604 55.000 0.00 0.00 0.00 5.01
959 1026 1.270305 TGAAAGAGAAGGACGCTGTGG 60.270 52.381 0.00 0.00 0.00 4.17
1121 1188 1.229209 AGGGACGGAGCAAGGAGAA 60.229 57.895 0.00 0.00 0.00 2.87
1215 1282 1.280457 GGAGGGAAAGGCTGAGAAGA 58.720 55.000 0.00 0.00 0.00 2.87
1404 1473 3.260884 GGGAGCGGATGAGGATATTGTAA 59.739 47.826 0.00 0.00 0.00 2.41
1659 1728 2.229792 GTGAACAAGTCCAATGCCTCA 58.770 47.619 0.00 0.00 0.00 3.86
1936 2005 2.595380 TCCTCCCCTCCTTACAATACCT 59.405 50.000 0.00 0.00 0.00 3.08
2354 2447 2.098934 TGATCACATTTGCATAACCCGC 59.901 45.455 0.00 0.00 0.00 6.13
2704 2797 7.067372 TCTGTTCATCTCACTCACAACATTTTT 59.933 33.333 0.00 0.00 0.00 1.94
2775 2868 0.381801 GTCCAATACTTGCATGCCCG 59.618 55.000 16.68 8.56 0.00 6.13
3132 3225 8.355913 TGTCTTGATTTGCATAAACACATAACA 58.644 29.630 0.00 0.00 0.00 2.41
3291 3384 5.916661 TGTAGTCTTCCCATCTACAGTTC 57.083 43.478 0.00 0.00 38.98 3.01
3721 3815 3.810310 ATTTTGGTCAAACGCTTTCCA 57.190 38.095 0.00 0.00 0.00 3.53
3759 3853 5.805728 ACTTGTTATCTTTAGGTGGGACAG 58.194 41.667 0.00 0.00 41.80 3.51
4040 4134 7.200455 GCAGGTTACTTGTGTTGATTTAAAGT 58.800 34.615 0.00 0.00 35.39 2.66
4068 4162 4.216042 CAGTAGTGACATGTCAATTTGGCA 59.784 41.667 31.18 12.46 41.85 4.92
4182 4276 8.890718 ACTACAAAGACAAAAAGGAAGTCTAAC 58.109 33.333 0.00 0.00 41.45 2.34
4255 4357 4.494350 TTCTGCTCAATTCTTCAACTGC 57.506 40.909 0.00 0.00 0.00 4.40
4328 4430 6.704493 TGTAACTTCGAAATACTTCACTGCTT 59.296 34.615 17.02 0.00 0.00 3.91
4351 4453 9.874205 CAAATTATGATTTTGGGATACAAGTGT 57.126 29.630 0.00 0.00 40.82 3.55
4357 4459 9.696917 GGATGTCAAATTATGATTTTGGGATAC 57.303 33.333 0.00 0.00 40.97 2.24
4358 4460 9.659135 AGGATGTCAAATTATGATTTTGGGATA 57.341 29.630 0.00 0.00 40.97 2.59
4359 4461 8.426489 CAGGATGTCAAATTATGATTTTGGGAT 58.574 33.333 0.00 0.00 40.97 3.85
4360 4462 7.784037 CAGGATGTCAAATTATGATTTTGGGA 58.216 34.615 0.00 0.00 40.97 4.37
4379 4481 5.636543 GCTTTGAGAAAAATTGGACAGGATG 59.363 40.000 0.00 0.00 46.00 3.51
4380 4482 5.305128 TGCTTTGAGAAAAATTGGACAGGAT 59.695 36.000 0.00 0.00 0.00 3.24
4381 4483 4.648762 TGCTTTGAGAAAAATTGGACAGGA 59.351 37.500 0.00 0.00 0.00 3.86
4382 4484 4.947645 TGCTTTGAGAAAAATTGGACAGG 58.052 39.130 0.00 0.00 0.00 4.00
4383 4485 5.461078 CACTGCTTTGAGAAAAATTGGACAG 59.539 40.000 0.00 0.00 0.00 3.51
4384 4486 5.126869 TCACTGCTTTGAGAAAAATTGGACA 59.873 36.000 0.00 0.00 0.00 4.02
4385 4487 5.591099 TCACTGCTTTGAGAAAAATTGGAC 58.409 37.500 0.00 0.00 0.00 4.02
4386 4488 5.850557 TCACTGCTTTGAGAAAAATTGGA 57.149 34.783 0.00 0.00 0.00 3.53
4387 4489 6.044682 ACTTCACTGCTTTGAGAAAAATTGG 58.955 36.000 0.00 0.00 0.00 3.16
4388 4490 8.807667 ATACTTCACTGCTTTGAGAAAAATTG 57.192 30.769 0.00 0.00 0.00 2.32
4389 4491 9.822185 AAATACTTCACTGCTTTGAGAAAAATT 57.178 25.926 0.00 0.00 0.00 1.82
4390 4492 9.468532 GAAATACTTCACTGCTTTGAGAAAAAT 57.531 29.630 0.00 0.00 0.00 1.82
4391 4493 7.643764 CGAAATACTTCACTGCTTTGAGAAAAA 59.356 33.333 0.00 0.00 0.00 1.94
4392 4494 7.011950 TCGAAATACTTCACTGCTTTGAGAAAA 59.988 33.333 0.00 0.00 0.00 2.29
4393 4495 6.481976 TCGAAATACTTCACTGCTTTGAGAAA 59.518 34.615 0.00 0.00 0.00 2.52
4394 4496 5.989168 TCGAAATACTTCACTGCTTTGAGAA 59.011 36.000 0.00 0.00 0.00 2.87
4395 4497 5.538118 TCGAAATACTTCACTGCTTTGAGA 58.462 37.500 0.00 0.00 0.00 3.27
4396 4498 5.845985 TCGAAATACTTCACTGCTTTGAG 57.154 39.130 0.00 0.00 0.00 3.02
4397 4499 5.758296 ACTTCGAAATACTTCACTGCTTTGA 59.242 36.000 0.00 0.00 0.00 2.69
4398 4500 5.990408 ACTTCGAAATACTTCACTGCTTTG 58.010 37.500 0.00 0.00 0.00 2.77
4399 4501 6.619801 AACTTCGAAATACTTCACTGCTTT 57.380 33.333 0.00 0.00 0.00 3.51
4400 4502 6.369065 CCTAACTTCGAAATACTTCACTGCTT 59.631 38.462 0.00 0.00 0.00 3.91
4401 4503 5.869888 CCTAACTTCGAAATACTTCACTGCT 59.130 40.000 0.00 0.00 0.00 4.24
4402 4504 5.867716 TCCTAACTTCGAAATACTTCACTGC 59.132 40.000 0.00 0.00 0.00 4.40
4403 4505 7.091443 AGTCCTAACTTCGAAATACTTCACTG 58.909 38.462 0.00 0.00 28.74 3.66
4404 4506 7.229581 AGTCCTAACTTCGAAATACTTCACT 57.770 36.000 0.00 0.00 28.74 3.41
4405 4507 7.886405 AAGTCCTAACTTCGAAATACTTCAC 57.114 36.000 0.00 0.00 42.10 3.18
4427 4529 0.438830 GGTTAACGCGCAGTCTGAAG 59.561 55.000 5.73 0.00 0.00 3.02
4445 4547 5.717119 AGAAATGCTCAAATTAACAGCAGG 58.283 37.500 10.61 0.00 46.06 4.85
4446 4548 7.647907 AAAGAAATGCTCAAATTAACAGCAG 57.352 32.000 10.61 0.00 46.06 4.24
4447 4549 7.495279 ACAAAAGAAATGCTCAAATTAACAGCA 59.505 29.630 8.01 8.01 46.87 4.41
4448 4550 7.795272 CACAAAAGAAATGCTCAAATTAACAGC 59.205 33.333 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.