Multiple sequence alignment - TraesCS1A01G113700

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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 TraesCS1A01G113700 chr1A 100.000 5998 0 0 1 5998 117199223 117193226 0.000000e+00 11077.0
1 TraesCS1A01G113700 chr1A 91.071 112 9 1 78 189 117199042 117198932 3.740000e-32 150.0
2 TraesCS1A01G113700 chr1A 91.071 112 9 1 182 292 117199146 117199035 3.740000e-32 150.0
3 TraesCS1A01G113700 chr1B 95.101 3082 108 20 1902 4948 169664961 169661888 0.000000e+00 4815.0
4 TraesCS1A01G113700 chr1B 91.171 1008 46 16 968 1962 169665939 169664962 0.000000e+00 1328.0
5 TraesCS1A01G113700 chr1B 89.556 1082 42 20 4944 5998 169644268 169643231 0.000000e+00 1306.0
6 TraesCS1A01G113700 chr1B 88.080 797 61 19 182 973 169666735 169665968 0.000000e+00 915.0
7 TraesCS1A01G113700 chr1B 87.975 316 35 2 5651 5966 2557232 2556920 2.640000e-98 370.0
8 TraesCS1A01G113700 chr1B 87.975 316 35 2 5651 5966 2613967 2613655 2.640000e-98 370.0
9 TraesCS1A01G113700 chr1D 92.068 2723 100 43 571 3256 111039374 111036731 0.000000e+00 3725.0
10 TraesCS1A01G113700 chr1D 93.839 1753 69 10 3356 5070 111036735 111034984 0.000000e+00 2603.0
11 TraesCS1A01G113700 chr1D 90.305 918 32 18 5099 5998 111016208 111015330 0.000000e+00 1149.0
12 TraesCS1A01G113700 chr1D 84.655 391 44 10 182 570 111040267 111039891 5.680000e-100 375.0
13 TraesCS1A01G113700 chr2A 83.678 435 40 11 5293 5720 596358568 596358158 1.220000e-101 381.0
14 TraesCS1A01G113700 chrUn 87.975 316 35 2 5651 5966 297916728 297916416 2.640000e-98 370.0
15 TraesCS1A01G113700 chr7B 89.437 284 30 0 2483 2766 394213336 394213619 5.720000e-95 359.0
16 TraesCS1A01G113700 chr7A 86.164 318 41 1 5649 5966 134016521 134016207 2.070000e-89 340.0
17 TraesCS1A01G113700 chr7A 85.971 278 31 7 2486 2758 563154284 563154558 2.110000e-74 291.0
18 TraesCS1A01G113700 chr2D 83.529 340 46 3 5387 5720 22816100 22815765 5.840000e-80 309.0
19 TraesCS1A01G113700 chr2D 88.646 229 22 1 5757 5985 22815765 22815541 5.920000e-70 276.0
20 TraesCS1A01G113700 chr2D 85.606 264 24 6 5462 5715 453570405 453570146 1.280000e-66 265.0
21 TraesCS1A01G113700 chr2D 91.667 168 14 0 5757 5924 453570141 453569974 3.610000e-57 233.0
22 TraesCS1A01G113700 chr2D 88.800 125 8 5 5293 5417 453570521 453570403 1.350000e-31 148.0
23 TraesCS1A01G113700 chr4B 87.938 257 29 2 2502 2756 188515105 188515361 9.770000e-78 302.0
24 TraesCS1A01G113700 chr2B 86.842 266 31 4 2494 2756 790086982 790087246 1.630000e-75 294.0
25 TraesCS1A01G113700 chr7D 87.027 185 19 2 5801 5985 561875545 561875366 2.830000e-48 204.0
26 TraesCS1A01G113700 chr4A 86.395 147 17 3 2623 2766 464804050 464803904 2.240000e-34 158.0
27 TraesCS1A01G113700 chr4D 100.000 28 0 0 2190 2217 136627842 136627869 1.100000e-02 52.8


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 TraesCS1A01G113700 chr1A 117193226 117199223 5997 True 3792.333333 11077 94.047333 1 5998 3 chr1A.!!$R1 5997
1 TraesCS1A01G113700 chr1B 169661888 169666735 4847 True 2352.666667 4815 91.450667 182 4948 3 chr1B.!!$R4 4766
2 TraesCS1A01G113700 chr1B 169643231 169644268 1037 True 1306.000000 1306 89.556000 4944 5998 1 chr1B.!!$R3 1054
3 TraesCS1A01G113700 chr1D 111034984 111040267 5283 True 2234.333333 3725 90.187333 182 5070 3 chr1D.!!$R2 4888
4 TraesCS1A01G113700 chr1D 111015330 111016208 878 True 1149.000000 1149 90.305000 5099 5998 1 chr1D.!!$R1 899
5 TraesCS1A01G113700 chr2D 22815541 22816100 559 True 292.500000 309 86.087500 5387 5985 2 chr2D.!!$R1 598
6 TraesCS1A01G113700 chr2D 453569974 453570521 547 True 215.333333 265 88.691000 5293 5924 3 chr2D.!!$R2 631

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
40 41 0.038166 AATTCCTTCGAGCCTGCCAA 59.962 50.000 0.00 0.0 0.00 4.52 F
73 74 0.038310 GACTTGGTTGAAGGAGGGGG 59.962 60.000 0.00 0.0 35.78 5.40 F
896 1427 0.177373 GGAACTACGGCCCACCTTAG 59.823 60.000 0.00 0.0 42.26 2.18 F
1769 2364 0.460459 GGTCGGCTGCTTACTCCTTC 60.460 60.000 0.00 0.0 0.00 3.46 F
1772 2367 0.532573 CGGCTGCTTACTCCTTCTCA 59.467 55.000 0.00 0.0 0.00 3.27 F
2689 3355 0.827925 TGAGGACTCTGTTGGCGAGT 60.828 55.000 0.56 0.0 43.97 4.18 F
3272 3954 1.219664 CAAGGGCACAATGGCATGG 59.780 57.895 0.00 0.0 45.76 3.66 F
4557 5249 0.253610 ACGTGGTGGACAAGGTTTCA 59.746 50.000 0.00 0.0 32.45 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1999 0.250513 GACTGAAGGTGGCCAGGTAG 59.749 60.000 5.11 3.02 34.85 3.18 R
1512 2086 1.022451 GGGCGCAACGGAATTCTACA 61.022 55.000 10.83 0.00 0.00 2.74 R
2715 3381 0.109597 GTTTTCCATCAGTGCTGCCG 60.110 55.000 0.00 0.00 0.00 5.69 R
3322 4004 1.134580 AGACATGAAGCGCACTAGCAT 60.135 47.619 11.47 2.19 42.27 3.79 R
3679 4365 2.295349 CAGCACTGGCATTTTCTGACTT 59.705 45.455 0.00 0.00 44.61 3.01 R
4076 4762 0.111639 GGGGTTAACACTTCCAGGCA 59.888 55.000 7.98 0.00 0.00 4.75 R
4805 5516 1.136336 CGGTAGCAGCAAACGAGAAAC 60.136 52.381 0.00 0.00 0.00 2.78 R
5624 6392 1.299850 GAACCAAAACCGGCAGTGC 60.300 57.895 6.55 6.55 0.00 4.40 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
26 27 9.922305 CTTTCTTCAGTCGTTGAATATAATTCC 57.078 33.333 5.77 0.00 44.48 3.01
27 28 9.667107 TTTCTTCAGTCGTTGAATATAATTCCT 57.333 29.630 5.77 0.00 44.48 3.36
28 29 9.667107 TTCTTCAGTCGTTGAATATAATTCCTT 57.333 29.630 5.77 0.00 44.48 3.36
29 30 9.314321 TCTTCAGTCGTTGAATATAATTCCTTC 57.686 33.333 5.77 0.00 44.48 3.46
30 31 7.694388 TCAGTCGTTGAATATAATTCCTTCG 57.306 36.000 0.00 1.16 31.34 3.79
31 32 7.485810 TCAGTCGTTGAATATAATTCCTTCGA 58.514 34.615 0.00 3.12 31.34 3.71
32 33 7.648112 TCAGTCGTTGAATATAATTCCTTCGAG 59.352 37.037 9.42 0.00 31.34 4.04
33 34 6.421202 AGTCGTTGAATATAATTCCTTCGAGC 59.579 38.462 9.42 0.00 0.00 5.03
34 35 5.694910 TCGTTGAATATAATTCCTTCGAGCC 59.305 40.000 0.00 0.00 0.00 4.70
35 36 5.696724 CGTTGAATATAATTCCTTCGAGCCT 59.303 40.000 0.00 0.00 0.00 4.58
36 37 6.346919 CGTTGAATATAATTCCTTCGAGCCTG 60.347 42.308 0.00 0.00 0.00 4.85
37 38 4.997395 TGAATATAATTCCTTCGAGCCTGC 59.003 41.667 0.00 0.00 0.00 4.85
38 39 2.262423 ATAATTCCTTCGAGCCTGCC 57.738 50.000 0.00 0.00 0.00 4.85
39 40 0.908910 TAATTCCTTCGAGCCTGCCA 59.091 50.000 0.00 0.00 0.00 4.92
40 41 0.038166 AATTCCTTCGAGCCTGCCAA 59.962 50.000 0.00 0.00 0.00 4.52
41 42 0.038166 ATTCCTTCGAGCCTGCCAAA 59.962 50.000 0.00 0.00 0.00 3.28
42 43 0.889186 TTCCTTCGAGCCTGCCAAAC 60.889 55.000 0.00 0.00 0.00 2.93
43 44 1.302832 CCTTCGAGCCTGCCAAACT 60.303 57.895 0.00 0.00 0.00 2.66
44 45 1.580845 CCTTCGAGCCTGCCAAACTG 61.581 60.000 0.00 0.00 0.00 3.16
45 46 2.192608 CTTCGAGCCTGCCAAACTGC 62.193 60.000 0.00 0.00 0.00 4.40
46 47 2.670934 CGAGCCTGCCAAACTGCT 60.671 61.111 0.00 0.00 36.62 4.24
47 48 2.684843 CGAGCCTGCCAAACTGCTC 61.685 63.158 0.00 0.00 45.19 4.26
48 49 1.303155 GAGCCTGCCAAACTGCTCT 60.303 57.895 0.00 0.00 45.21 4.09
49 50 1.303155 AGCCTGCCAAACTGCTCTC 60.303 57.895 0.00 0.00 0.00 3.20
50 51 2.684843 GCCTGCCAAACTGCTCTCG 61.685 63.158 0.00 0.00 0.00 4.04
51 52 1.302033 CCTGCCAAACTGCTCTCGT 60.302 57.895 0.00 0.00 0.00 4.18
52 53 0.886490 CCTGCCAAACTGCTCTCGTT 60.886 55.000 0.00 0.00 0.00 3.85
53 54 0.947244 CTGCCAAACTGCTCTCGTTT 59.053 50.000 0.00 0.00 35.12 3.60
54 55 0.662619 TGCCAAACTGCTCTCGTTTG 59.337 50.000 8.28 8.28 46.57 2.93
59 60 3.951979 AAACTGCTCTCGTTTGACTTG 57.048 42.857 0.00 0.00 33.64 3.16
60 61 1.871080 ACTGCTCTCGTTTGACTTGG 58.129 50.000 0.00 0.00 0.00 3.61
61 62 1.139058 ACTGCTCTCGTTTGACTTGGT 59.861 47.619 0.00 0.00 0.00 3.67
62 63 2.213499 CTGCTCTCGTTTGACTTGGTT 58.787 47.619 0.00 0.00 0.00 3.67
63 64 1.939934 TGCTCTCGTTTGACTTGGTTG 59.060 47.619 0.00 0.00 0.00 3.77
64 65 2.210116 GCTCTCGTTTGACTTGGTTGA 58.790 47.619 0.00 0.00 0.00 3.18
65 66 2.612212 GCTCTCGTTTGACTTGGTTGAA 59.388 45.455 0.00 0.00 0.00 2.69
66 67 3.303395 GCTCTCGTTTGACTTGGTTGAAG 60.303 47.826 0.00 0.00 37.73 3.02
67 68 3.202906 TCTCGTTTGACTTGGTTGAAGG 58.797 45.455 0.00 0.00 35.78 3.46
68 69 3.118555 TCTCGTTTGACTTGGTTGAAGGA 60.119 43.478 0.00 0.00 35.78 3.36
69 70 3.202906 TCGTTTGACTTGGTTGAAGGAG 58.797 45.455 0.00 0.00 35.78 3.69
70 71 2.290641 CGTTTGACTTGGTTGAAGGAGG 59.709 50.000 0.00 0.00 35.78 4.30
71 72 2.623416 GTTTGACTTGGTTGAAGGAGGG 59.377 50.000 0.00 0.00 35.78 4.30
72 73 0.771127 TGACTTGGTTGAAGGAGGGG 59.229 55.000 0.00 0.00 35.78 4.79
73 74 0.038310 GACTTGGTTGAAGGAGGGGG 59.962 60.000 0.00 0.00 35.78 5.40
74 75 0.402861 ACTTGGTTGAAGGAGGGGGA 60.403 55.000 0.00 0.00 35.78 4.81
75 76 0.777446 CTTGGTTGAAGGAGGGGGAA 59.223 55.000 0.00 0.00 0.00 3.97
76 77 1.146982 CTTGGTTGAAGGAGGGGGAAA 59.853 52.381 0.00 0.00 0.00 3.13
77 78 0.777446 TGGTTGAAGGAGGGGGAAAG 59.223 55.000 0.00 0.00 0.00 2.62
78 79 1.073098 GGTTGAAGGAGGGGGAAAGA 58.927 55.000 0.00 0.00 0.00 2.52
79 80 1.427753 GGTTGAAGGAGGGGGAAAGAA 59.572 52.381 0.00 0.00 0.00 2.52
80 81 2.158370 GGTTGAAGGAGGGGGAAAGAAA 60.158 50.000 0.00 0.00 0.00 2.52
81 82 2.891580 GTTGAAGGAGGGGGAAAGAAAC 59.108 50.000 0.00 0.00 0.00 2.78
82 83 2.140224 TGAAGGAGGGGGAAAGAAACA 58.860 47.619 0.00 0.00 0.00 2.83
83 84 2.721906 TGAAGGAGGGGGAAAGAAACAT 59.278 45.455 0.00 0.00 0.00 2.71
84 85 3.920197 TGAAGGAGGGGGAAAGAAACATA 59.080 43.478 0.00 0.00 0.00 2.29
85 86 4.544152 TGAAGGAGGGGGAAAGAAACATAT 59.456 41.667 0.00 0.00 0.00 1.78
86 87 4.526438 AGGAGGGGGAAAGAAACATATG 57.474 45.455 0.00 0.00 0.00 1.78
87 88 2.959030 GGAGGGGGAAAGAAACATATGC 59.041 50.000 1.58 0.00 0.00 3.14
88 89 2.959030 GAGGGGGAAAGAAACATATGCC 59.041 50.000 1.58 0.00 0.00 4.40
89 90 2.587307 AGGGGGAAAGAAACATATGCCT 59.413 45.455 1.58 0.00 0.00 4.75
90 91 3.012844 AGGGGGAAAGAAACATATGCCTT 59.987 43.478 1.58 1.35 0.00 4.35
91 92 3.132824 GGGGGAAAGAAACATATGCCTTG 59.867 47.826 1.58 0.00 0.00 3.61
92 93 3.769300 GGGGAAAGAAACATATGCCTTGT 59.231 43.478 1.58 0.00 0.00 3.16
93 94 4.222810 GGGGAAAGAAACATATGCCTTGTT 59.777 41.667 1.58 0.00 38.91 2.83
94 95 5.420739 GGGGAAAGAAACATATGCCTTGTTA 59.579 40.000 1.58 0.00 36.32 2.41
95 96 6.330278 GGGAAAGAAACATATGCCTTGTTAC 58.670 40.000 1.58 0.00 36.32 2.50
96 97 6.152831 GGGAAAGAAACATATGCCTTGTTACT 59.847 38.462 1.58 0.00 36.32 2.24
97 98 7.338449 GGGAAAGAAACATATGCCTTGTTACTA 59.662 37.037 1.58 0.00 36.32 1.82
98 99 8.398665 GGAAAGAAACATATGCCTTGTTACTAG 58.601 37.037 1.58 0.00 36.32 2.57
99 100 6.927294 AGAAACATATGCCTTGTTACTAGC 57.073 37.500 1.58 0.00 36.32 3.42
100 101 5.823045 AGAAACATATGCCTTGTTACTAGCC 59.177 40.000 1.58 0.00 36.32 3.93
101 102 4.771114 ACATATGCCTTGTTACTAGCCA 57.229 40.909 1.58 0.00 0.00 4.75
102 103 5.310409 ACATATGCCTTGTTACTAGCCAT 57.690 39.130 1.58 0.00 0.00 4.40
103 104 5.308825 ACATATGCCTTGTTACTAGCCATC 58.691 41.667 1.58 0.00 0.00 3.51
104 105 2.710096 TGCCTTGTTACTAGCCATCC 57.290 50.000 0.00 0.00 0.00 3.51
105 106 2.196595 TGCCTTGTTACTAGCCATCCT 58.803 47.619 0.00 0.00 0.00 3.24
106 107 2.576191 TGCCTTGTTACTAGCCATCCTT 59.424 45.455 0.00 0.00 0.00 3.36
107 108 3.778075 TGCCTTGTTACTAGCCATCCTTA 59.222 43.478 0.00 0.00 0.00 2.69
108 109 4.127907 GCCTTGTTACTAGCCATCCTTAC 58.872 47.826 0.00 0.00 0.00 2.34
109 110 4.383770 GCCTTGTTACTAGCCATCCTTACA 60.384 45.833 0.00 0.00 0.00 2.41
110 111 5.687706 GCCTTGTTACTAGCCATCCTTACAT 60.688 44.000 0.00 0.00 0.00 2.29
111 112 6.463897 GCCTTGTTACTAGCCATCCTTACATA 60.464 42.308 0.00 0.00 0.00 2.29
112 113 7.680730 CCTTGTTACTAGCCATCCTTACATAT 58.319 38.462 0.00 0.00 0.00 1.78
113 114 7.819900 CCTTGTTACTAGCCATCCTTACATATC 59.180 40.741 0.00 0.00 0.00 1.63
114 115 7.849322 TGTTACTAGCCATCCTTACATATCA 57.151 36.000 0.00 0.00 0.00 2.15
115 116 8.257602 TGTTACTAGCCATCCTTACATATCAA 57.742 34.615 0.00 0.00 0.00 2.57
116 117 8.880244 TGTTACTAGCCATCCTTACATATCAAT 58.120 33.333 0.00 0.00 0.00 2.57
117 118 9.372369 GTTACTAGCCATCCTTACATATCAATC 57.628 37.037 0.00 0.00 0.00 2.67
118 119 7.805083 ACTAGCCATCCTTACATATCAATCT 57.195 36.000 0.00 0.00 0.00 2.40
119 120 7.619050 ACTAGCCATCCTTACATATCAATCTG 58.381 38.462 0.00 0.00 0.00 2.90
120 121 5.813383 AGCCATCCTTACATATCAATCTGG 58.187 41.667 0.00 0.00 0.00 3.86
121 122 5.311649 AGCCATCCTTACATATCAATCTGGT 59.688 40.000 0.00 0.00 0.00 4.00
122 123 6.501805 AGCCATCCTTACATATCAATCTGGTA 59.498 38.462 0.00 0.00 0.00 3.25
123 124 6.595716 GCCATCCTTACATATCAATCTGGTAC 59.404 42.308 0.00 0.00 0.00 3.34
124 125 7.106239 CCATCCTTACATATCAATCTGGTACC 58.894 42.308 4.43 4.43 0.00 3.34
125 126 7.256655 CCATCCTTACATATCAATCTGGTACCA 60.257 40.741 15.39 15.39 0.00 3.25
126 127 7.872061 TCCTTACATATCAATCTGGTACCAT 57.128 36.000 16.75 1.23 0.00 3.55
127 128 7.907389 TCCTTACATATCAATCTGGTACCATC 58.093 38.462 16.75 0.00 0.00 3.51
128 129 7.038302 TCCTTACATATCAATCTGGTACCATCC 60.038 40.741 16.75 0.00 0.00 3.51
129 130 5.152623 ACATATCAATCTGGTACCATCCG 57.847 43.478 16.75 3.90 0.00 4.18
130 131 4.020218 ACATATCAATCTGGTACCATCCGG 60.020 45.833 16.75 3.48 38.77 5.14
139 140 4.480480 ACCATCCGGTGACAGGAT 57.520 55.556 11.59 11.59 46.79 3.24
140 141 2.212327 ACCATCCGGTGACAGGATC 58.788 57.895 14.43 0.00 46.79 3.36
141 142 0.617535 ACCATCCGGTGACAGGATCA 60.618 55.000 14.43 0.00 46.79 2.92
142 143 0.761187 CCATCCGGTGACAGGATCAT 59.239 55.000 14.43 0.00 46.04 2.45
143 144 1.541889 CCATCCGGTGACAGGATCATG 60.542 57.143 14.43 5.68 46.04 3.07
144 145 0.761187 ATCCGGTGACAGGATCATGG 59.239 55.000 11.59 0.00 44.68 3.66
145 146 0.617535 TCCGGTGACAGGATCATGGT 60.618 55.000 12.66 0.00 40.28 3.55
146 147 1.119684 CCGGTGACAGGATCATGGTA 58.880 55.000 12.66 0.00 40.28 3.25
147 148 1.484653 CCGGTGACAGGATCATGGTAA 59.515 52.381 12.66 0.00 40.28 2.85
148 149 2.550978 CGGTGACAGGATCATGGTAAC 58.449 52.381 12.66 6.56 40.28 2.50
149 150 2.741878 CGGTGACAGGATCATGGTAACC 60.742 54.545 12.66 13.91 40.28 2.85
150 151 2.550978 GTGACAGGATCATGGTAACCG 58.449 52.381 12.66 0.00 40.28 4.44
151 152 2.093658 GTGACAGGATCATGGTAACCGT 60.094 50.000 12.66 0.00 40.28 4.83
152 153 2.569853 TGACAGGATCATGGTAACCGTT 59.430 45.455 12.66 0.00 29.99 4.44
153 154 3.770388 TGACAGGATCATGGTAACCGTTA 59.230 43.478 12.66 0.00 29.99 3.18
154 155 4.223255 TGACAGGATCATGGTAACCGTTAA 59.777 41.667 12.66 0.00 29.99 2.01
155 156 5.168647 ACAGGATCATGGTAACCGTTAAA 57.831 39.130 12.66 0.00 0.00 1.52
156 157 5.562635 ACAGGATCATGGTAACCGTTAAAA 58.437 37.500 12.66 0.00 0.00 1.52
157 158 6.005198 ACAGGATCATGGTAACCGTTAAAAA 58.995 36.000 12.66 0.00 0.00 1.94
202 203 5.353394 TGAAACATAGGCCTTGGTACTAG 57.647 43.478 12.58 0.00 0.00 2.57
209 210 1.132500 GCCTTGGTACTAGCCATCCT 58.868 55.000 0.00 0.00 38.48 3.24
211 212 2.704065 GCCTTGGTACTAGCCATCCTTA 59.296 50.000 0.00 0.00 38.48 2.69
213 214 3.709653 CCTTGGTACTAGCCATCCTTACA 59.290 47.826 0.00 0.00 38.48 2.41
230 231 7.062749 TCCTTACATATCAATCTGGTACCAC 57.937 40.000 11.60 0.00 0.00 4.16
253 254 7.038017 CCACCAGGTGATAGGATTATGATAACT 60.038 40.741 22.37 0.00 35.23 2.24
291 292 9.513906 TCAATGAGAAGTGGTACAATGAAAATA 57.486 29.630 0.00 0.00 44.16 1.40
330 331 9.707957 TTATTTATAAGTTGTCCCATGTTGGAT 57.292 29.630 0.00 0.00 40.96 3.41
342 343 0.687920 TGTTGGATGGTTAGACGGCA 59.312 50.000 0.00 0.00 0.00 5.69
421 424 2.159226 GCATAGAGTGGTTAGTGCTCGT 60.159 50.000 0.00 0.00 34.69 4.18
455 458 6.613233 CCTTACCACGTTATAAACAATGCAA 58.387 36.000 0.00 0.00 0.00 4.08
603 1122 0.818296 AGAATTACGAGTCCGCTGCT 59.182 50.000 0.00 0.00 39.95 4.24
604 1123 0.924090 GAATTACGAGTCCGCTGCTG 59.076 55.000 0.00 0.00 39.95 4.41
605 1124 1.084370 AATTACGAGTCCGCTGCTGC 61.084 55.000 5.34 5.34 39.95 5.25
720 1241 2.652496 GACGCAGCTCCGACGATC 60.652 66.667 2.80 0.00 0.00 3.69
850 1381 3.557595 CACACTTATGCCGATTCCTTCTC 59.442 47.826 0.00 0.00 0.00 2.87
863 1394 1.134220 TCCTTCTCGCCCGCAATTAAT 60.134 47.619 0.00 0.00 0.00 1.40
888 1419 1.515736 CGAGAACGGAACTACGGCC 60.516 63.158 0.00 0.00 38.39 6.13
896 1427 0.177373 GGAACTACGGCCCACCTTAG 59.823 60.000 0.00 0.00 42.26 2.18
897 1428 4.881224 ACTACGGCCCACCTTAGT 57.119 55.556 0.00 0.00 44.12 2.24
899 1430 2.236489 ACTACGGCCCACCTTAGTAA 57.764 50.000 0.00 0.00 46.33 2.24
900 1431 2.755686 ACTACGGCCCACCTTAGTAAT 58.244 47.619 0.00 0.00 46.33 1.89
901 1432 3.914771 ACTACGGCCCACCTTAGTAATA 58.085 45.455 0.00 0.00 46.33 0.98
918 1449 2.008242 ATACTGCAGCCCACCAAAAA 57.992 45.000 15.27 0.00 0.00 1.94
1018 1583 1.810755 GAAACAAATCCCACCGACCTC 59.189 52.381 0.00 0.00 0.00 3.85
1048 1613 2.039724 CCTACCCCTCCCCTTCCC 60.040 72.222 0.00 0.00 0.00 3.97
1049 1614 2.039724 CTACCCCTCCCCTTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
1050 1615 2.882676 TACCCCTCCCCTTCCCCA 60.883 66.667 0.00 0.00 0.00 4.96
1051 1616 3.277514 TACCCCTCCCCTTCCCCAC 62.278 68.421 0.00 0.00 0.00 4.61
1053 1618 4.371231 CCCTCCCCTTCCCCACCT 62.371 72.222 0.00 0.00 0.00 4.00
1054 1619 2.204306 CCTCCCCTTCCCCACCTT 60.204 66.667 0.00 0.00 0.00 3.50
1055 1620 2.309504 CCTCCCCTTCCCCACCTTC 61.310 68.421 0.00 0.00 0.00 3.46
1056 1621 2.204244 TCCCCTTCCCCACCTTCC 60.204 66.667 0.00 0.00 0.00 3.46
1057 1622 3.728373 CCCCTTCCCCACCTTCCG 61.728 72.222 0.00 0.00 0.00 4.30
1058 1623 4.426313 CCCTTCCCCACCTTCCGC 62.426 72.222 0.00 0.00 0.00 5.54
1326 1897 3.577334 TTCCAACCCATCCGCACCC 62.577 63.158 0.00 0.00 0.00 4.61
1425 1999 4.877823 CGTCCCCCAAACTTAAGGTAATAC 59.122 45.833 7.53 0.00 0.00 1.89
1447 2021 3.612247 CTGGCCACCTTCAGTCCGG 62.612 68.421 0.00 0.00 0.00 5.14
1512 2086 1.185618 TAGTGCTGGTCTGCTCGGTT 61.186 55.000 1.84 0.00 0.00 4.44
1526 2100 2.093783 GCTCGGTTGTAGAATTCCGTTG 59.906 50.000 0.65 0.00 42.95 4.10
1529 2103 1.465187 GGTTGTAGAATTCCGTTGCGC 60.465 52.381 0.00 0.00 0.00 6.09
1545 2119 1.144969 GCGCCCATAAATCGAATCGA 58.855 50.000 8.12 8.12 41.13 3.59
1550 2124 3.120199 GCCCATAAATCGAATCGATGTGG 60.120 47.826 25.11 25.11 46.30 4.17
1599 2173 7.923414 TTCAGATAGAAAAGGGAAAAGTAGC 57.077 36.000 0.00 0.00 32.05 3.58
1628 2204 2.203280 TGGTTCCGGTGCTTGTGG 60.203 61.111 0.00 0.00 0.00 4.17
1686 2281 7.933033 AGGTTTTTGTACGTACTTTTAGGATGA 59.067 33.333 25.12 0.00 0.00 2.92
1768 2363 1.192146 TGGTCGGCTGCTTACTCCTT 61.192 55.000 0.00 0.00 0.00 3.36
1769 2364 0.460459 GGTCGGCTGCTTACTCCTTC 60.460 60.000 0.00 0.00 0.00 3.46
1770 2365 0.533032 GTCGGCTGCTTACTCCTTCT 59.467 55.000 0.00 0.00 0.00 2.85
1771 2366 0.818296 TCGGCTGCTTACTCCTTCTC 59.182 55.000 0.00 0.00 0.00 2.87
1772 2367 0.532573 CGGCTGCTTACTCCTTCTCA 59.467 55.000 0.00 0.00 0.00 3.27
1773 2368 1.137872 CGGCTGCTTACTCCTTCTCAT 59.862 52.381 0.00 0.00 0.00 2.90
1774 2369 2.362397 CGGCTGCTTACTCCTTCTCATA 59.638 50.000 0.00 0.00 0.00 2.15
1775 2370 3.551863 CGGCTGCTTACTCCTTCTCATAG 60.552 52.174 0.00 0.00 0.00 2.23
1776 2371 3.386402 GGCTGCTTACTCCTTCTCATAGT 59.614 47.826 0.00 0.00 0.00 2.12
1777 2372 4.500716 GGCTGCTTACTCCTTCTCATAGTC 60.501 50.000 0.00 0.00 0.00 2.59
1778 2373 4.340950 GCTGCTTACTCCTTCTCATAGTCT 59.659 45.833 0.00 0.00 0.00 3.24
1779 2374 5.163457 GCTGCTTACTCCTTCTCATAGTCTT 60.163 44.000 0.00 0.00 0.00 3.01
1780 2375 6.039941 GCTGCTTACTCCTTCTCATAGTCTTA 59.960 42.308 0.00 0.00 0.00 2.10
1809 2404 6.874134 GCCTCATATTGATGTACCTAAATCGT 59.126 38.462 0.00 0.00 34.41 3.73
1810 2405 7.063544 GCCTCATATTGATGTACCTAAATCGTC 59.936 40.741 0.00 0.00 34.41 4.20
1828 2423 3.849708 TCGTCTGATGTTCAACGAATACG 59.150 43.478 10.34 0.00 45.75 3.06
1829 2424 3.001070 CGTCTGATGTTCAACGAATACGG 60.001 47.826 0.00 0.00 44.46 4.02
1857 2454 5.307196 CACTTTAGTGGGGGTGTATATAGCT 59.693 44.000 1.88 0.00 42.10 3.32
2019 2683 6.484643 AGCTGCATTTATGGTAACTATGACAG 59.515 38.462 1.02 0.00 37.61 3.51
2057 2721 9.173021 TGTGTGATAGTTTTAATCATGGGTTAG 57.827 33.333 0.00 0.00 35.87 2.34
2084 2748 0.954452 GTTAGGCAGCAGCAAACAGT 59.046 50.000 2.65 0.00 44.61 3.55
2244 2908 2.742372 GCGCACAGTGGTAGGGTG 60.742 66.667 0.30 0.00 35.68 4.61
2252 2916 2.576191 ACAGTGGTAGGGTGTGCAATAT 59.424 45.455 0.00 0.00 0.00 1.28
2339 3003 5.826737 ACCGTATACTTCTGTAGCTGTATGT 59.173 40.000 0.00 0.00 31.51 2.29
2364 3028 9.574516 GTGATATTAATAACCAATCCAAGAGGT 57.425 33.333 0.00 0.00 37.20 3.85
2689 3355 0.827925 TGAGGACTCTGTTGGCGAGT 60.828 55.000 0.56 0.00 43.97 4.18
2893 3559 5.059404 CAATAACTTGCTTACTGGTTGGG 57.941 43.478 0.00 0.00 0.00 4.12
2906 3572 4.796606 ACTGGTTGGGATAATCAAGATGG 58.203 43.478 0.00 0.00 0.00 3.51
2907 3573 4.478317 ACTGGTTGGGATAATCAAGATGGA 59.522 41.667 0.00 0.00 0.00 3.41
2915 3581 7.413446 TGGGATAATCAAGATGGAAAAGAACT 58.587 34.615 0.00 0.00 0.00 3.01
3135 3801 2.012673 CTGGTCATTTGTCCAGCTAGC 58.987 52.381 6.62 6.62 42.57 3.42
3253 3935 3.795688 TGAGTTTCCTTCAGCTCCATT 57.204 42.857 0.00 0.00 0.00 3.16
3272 3954 1.219664 CAAGGGCACAATGGCATGG 59.780 57.895 0.00 0.00 45.76 3.66
3315 3997 1.470996 TTTGTGGCCCCTGTTGCATC 61.471 55.000 0.00 0.00 0.00 3.91
3367 4049 4.774726 TCTTCTGCCTTCTTCATCTAGTGT 59.225 41.667 0.00 0.00 0.00 3.55
3392 4074 1.699634 ACATGCCTTCACCTAGTGTGT 59.300 47.619 10.08 0.00 45.61 3.72
3481 4166 7.163001 AGGAAGATTTCTTTTGGTGCTTATC 57.837 36.000 0.00 0.00 36.11 1.75
3495 4181 6.575267 TGGTGCTTATCGTACTAATTTGCTA 58.425 36.000 0.00 0.00 0.00 3.49
3507 4193 4.943705 ACTAATTTGCTACCTGGACACATG 59.056 41.667 0.00 0.00 0.00 3.21
3549 4235 3.589988 ACTATCGCCAGTGTTTCTTCAG 58.410 45.455 0.00 0.00 0.00 3.02
3558 4244 4.252073 CAGTGTTTCTTCAGCAGCTAGAT 58.748 43.478 0.00 0.00 0.00 1.98
3679 4365 6.014584 TCAAGTGTCTAAAGCAGAGGATGTTA 60.015 38.462 0.00 0.00 32.51 2.41
3788 4474 1.454539 CTCCTTCCCAACCAACGGT 59.545 57.895 0.00 0.00 37.65 4.83
3819 4505 3.830192 CCTGCTCCAAATGCGCCC 61.830 66.667 4.18 0.00 0.00 6.13
4076 4762 2.366916 CTCCATATTCTCAACCTCCGCT 59.633 50.000 0.00 0.00 0.00 5.52
4172 4858 0.975040 CCTGCTCAGAGCTACCCACT 60.975 60.000 23.15 0.00 42.97 4.00
4301 4987 3.000819 TCCACCACCGCCCTACAG 61.001 66.667 0.00 0.00 0.00 2.74
4302 4988 4.778143 CCACCACCGCCCTACAGC 62.778 72.222 0.00 0.00 0.00 4.40
4497 5189 4.756458 GCAGCGCCAGTGAGCTCT 62.756 66.667 16.19 0.89 45.08 4.09
4498 5190 2.814341 CAGCGCCAGTGAGCTCTG 60.814 66.667 16.19 5.58 45.08 3.35
4500 5192 4.756458 GCGCCAGTGAGCTCTGCT 62.756 66.667 16.19 10.29 43.88 4.24
4557 5249 0.253610 ACGTGGTGGACAAGGTTTCA 59.746 50.000 0.00 0.00 32.45 2.69
4572 5264 2.500229 GTTTCAACGATGGGGTTCTCA 58.500 47.619 0.00 0.00 0.00 3.27
4664 5356 1.388093 CGACAAGCTGATGAACGACAG 59.612 52.381 0.00 0.00 37.22 3.51
4764 5475 2.209838 CGATGAGCGAACACCTATGT 57.790 50.000 0.00 0.00 44.57 2.29
4794 5505 2.359900 GTGCATTCACGAGGGATTTCT 58.640 47.619 0.00 0.00 32.98 2.52
4805 5516 5.065218 CACGAGGGATTTCTTATTTGTCAGG 59.935 44.000 0.00 0.00 0.00 3.86
4817 5528 3.414549 TTTGTCAGGTTTCTCGTTTGC 57.585 42.857 0.00 0.00 0.00 3.68
4818 5529 2.325583 TGTCAGGTTTCTCGTTTGCT 57.674 45.000 0.00 0.00 0.00 3.91
4819 5530 1.939934 TGTCAGGTTTCTCGTTTGCTG 59.060 47.619 0.00 0.00 0.00 4.41
4820 5531 0.944386 TCAGGTTTCTCGTTTGCTGC 59.056 50.000 0.00 0.00 0.00 5.25
4821 5532 0.947244 CAGGTTTCTCGTTTGCTGCT 59.053 50.000 0.00 0.00 0.00 4.24
4851 5567 9.252962 GTACAGTTAGTGTTAGCTCTTTTGTTA 57.747 33.333 0.00 0.00 40.94 2.41
4860 5583 6.204108 TGTTAGCTCTTTTGTTAACTAGTGCC 59.796 38.462 17.89 9.68 0.00 5.01
4879 5602 3.395607 TGCCCTAGTGATTGCTATCCATT 59.604 43.478 5.67 0.00 0.00 3.16
4886 5609 5.503927 AGTGATTGCTATCCATTGTCAGTT 58.496 37.500 5.67 0.00 0.00 3.16
5003 5733 1.744522 GACGGTGACCTCTCTAACCTC 59.255 57.143 0.00 0.00 0.00 3.85
5008 5738 3.083293 GTGACCTCTCTAACCTCTTCGT 58.917 50.000 0.00 0.00 0.00 3.85
5013 5743 1.544691 TCTCTAACCTCTTCGTGTGGC 59.455 52.381 0.00 0.00 32.83 5.01
5020 5750 3.414700 CTTCGTGTGGCTGGCGAC 61.415 66.667 0.88 0.88 34.21 5.19
5076 5806 4.205996 CAGAGACAAATCGTTAGATCGCTG 59.794 45.833 0.00 0.00 35.74 5.18
5284 6036 2.669133 CCCACCGAGGATCAGCCAA 61.669 63.158 0.00 0.00 41.22 4.52
5435 6190 2.124320 GCCCGCAGCCCAAGATAA 60.124 61.111 0.00 0.00 34.35 1.75
5564 6319 2.355837 TCGAGCTGTGCGTGTTCC 60.356 61.111 0.00 0.00 0.00 3.62
5568 6325 2.356553 GCTGTGCGTGTTCCCGTA 60.357 61.111 0.00 0.00 0.00 4.02
5569 6326 1.957186 GCTGTGCGTGTTCCCGTAA 60.957 57.895 0.00 0.00 0.00 3.18
5577 6334 2.222574 GCGTGTTCCCGTAACGTATTTC 60.223 50.000 0.00 0.00 41.30 2.17
5600 6364 0.725117 CGCGATTGGGTAAGGTGTTC 59.275 55.000 0.00 0.00 0.00 3.18
5603 6367 2.354805 GCGATTGGGTAAGGTGTTCTCT 60.355 50.000 0.00 0.00 0.00 3.10
5624 6392 3.281751 CTGACAACGTGCTTCGCCG 62.282 63.158 0.00 0.00 44.19 6.46
5965 6737 1.526917 GGCGCCCTACTACTCGGTA 60.527 63.158 18.11 0.00 0.00 4.02
5966 6738 0.892814 GGCGCCCTACTACTCGGTAT 60.893 60.000 18.11 0.00 0.00 2.73
5967 6739 0.957362 GCGCCCTACTACTCGGTATT 59.043 55.000 0.00 0.00 0.00 1.89
5968 6740 1.339291 GCGCCCTACTACTCGGTATTT 59.661 52.381 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.567771 GCTCGAAGGAATTATATTCAACGACTG 60.568 40.741 0.00 0.00 0.00 3.51
8 9 6.421202 GCTCGAAGGAATTATATTCAACGACT 59.579 38.462 0.00 0.00 0.00 4.18
9 10 6.346678 GGCTCGAAGGAATTATATTCAACGAC 60.347 42.308 0.00 0.00 0.00 4.34
10 11 5.694910 GGCTCGAAGGAATTATATTCAACGA 59.305 40.000 0.00 0.00 0.00 3.85
11 12 5.696724 AGGCTCGAAGGAATTATATTCAACG 59.303 40.000 2.24 0.00 0.00 4.10
12 13 6.566753 GCAGGCTCGAAGGAATTATATTCAAC 60.567 42.308 2.24 0.00 0.00 3.18
13 14 5.470098 GCAGGCTCGAAGGAATTATATTCAA 59.530 40.000 2.24 0.00 0.00 2.69
14 15 4.997395 GCAGGCTCGAAGGAATTATATTCA 59.003 41.667 2.24 0.00 0.00 2.57
15 16 4.393371 GGCAGGCTCGAAGGAATTATATTC 59.607 45.833 0.00 0.00 0.00 1.75
16 17 4.202461 TGGCAGGCTCGAAGGAATTATATT 60.202 41.667 0.00 0.00 0.00 1.28
17 18 3.327757 TGGCAGGCTCGAAGGAATTATAT 59.672 43.478 0.00 0.00 0.00 0.86
18 19 2.703536 TGGCAGGCTCGAAGGAATTATA 59.296 45.455 0.00 0.00 0.00 0.98
19 20 1.490490 TGGCAGGCTCGAAGGAATTAT 59.510 47.619 0.00 0.00 0.00 1.28
20 21 0.908910 TGGCAGGCTCGAAGGAATTA 59.091 50.000 0.00 0.00 0.00 1.40
21 22 0.038166 TTGGCAGGCTCGAAGGAATT 59.962 50.000 0.00 0.00 0.00 2.17
22 23 0.038166 TTTGGCAGGCTCGAAGGAAT 59.962 50.000 0.00 0.00 0.00 3.01
23 24 0.889186 GTTTGGCAGGCTCGAAGGAA 60.889 55.000 0.00 0.00 0.00 3.36
24 25 1.302511 GTTTGGCAGGCTCGAAGGA 60.303 57.895 0.00 0.00 0.00 3.36
25 26 1.302832 AGTTTGGCAGGCTCGAAGG 60.303 57.895 0.00 0.00 0.00 3.46
26 27 1.871772 CAGTTTGGCAGGCTCGAAG 59.128 57.895 0.00 0.00 0.00 3.79
27 28 2.260869 GCAGTTTGGCAGGCTCGAA 61.261 57.895 0.00 0.00 0.00 3.71
28 29 2.669569 GCAGTTTGGCAGGCTCGA 60.670 61.111 0.00 0.00 0.00 4.04
29 30 2.670934 AGCAGTTTGGCAGGCTCG 60.671 61.111 0.00 0.00 35.83 5.03
30 31 3.272031 GAGCAGTTTGGCAGGCTC 58.728 61.111 13.89 13.89 44.97 4.70
31 32 1.303155 GAGAGCAGTTTGGCAGGCT 60.303 57.895 5.00 5.00 39.75 4.58
32 33 2.684843 CGAGAGCAGTTTGGCAGGC 61.685 63.158 0.00 0.00 35.83 4.85
33 34 0.886490 AACGAGAGCAGTTTGGCAGG 60.886 55.000 0.00 0.00 35.83 4.85
34 35 0.947244 AAACGAGAGCAGTTTGGCAG 59.053 50.000 0.00 0.00 39.96 4.85
35 36 3.094386 AAACGAGAGCAGTTTGGCA 57.906 47.368 0.00 0.00 39.96 4.92
39 40 2.614057 CCAAGTCAAACGAGAGCAGTTT 59.386 45.455 0.00 0.00 41.90 2.66
40 41 2.213499 CCAAGTCAAACGAGAGCAGTT 58.787 47.619 0.00 0.00 0.00 3.16
41 42 1.139058 ACCAAGTCAAACGAGAGCAGT 59.861 47.619 0.00 0.00 0.00 4.40
42 43 1.871080 ACCAAGTCAAACGAGAGCAG 58.129 50.000 0.00 0.00 0.00 4.24
43 44 1.939934 CAACCAAGTCAAACGAGAGCA 59.060 47.619 0.00 0.00 0.00 4.26
44 45 2.210116 TCAACCAAGTCAAACGAGAGC 58.790 47.619 0.00 0.00 0.00 4.09
45 46 3.248602 CCTTCAACCAAGTCAAACGAGAG 59.751 47.826 0.00 0.00 0.00 3.20
46 47 3.118555 TCCTTCAACCAAGTCAAACGAGA 60.119 43.478 0.00 0.00 0.00 4.04
47 48 3.202906 TCCTTCAACCAAGTCAAACGAG 58.797 45.455 0.00 0.00 0.00 4.18
48 49 3.202906 CTCCTTCAACCAAGTCAAACGA 58.797 45.455 0.00 0.00 0.00 3.85
49 50 2.290641 CCTCCTTCAACCAAGTCAAACG 59.709 50.000 0.00 0.00 0.00 3.60
50 51 2.623416 CCCTCCTTCAACCAAGTCAAAC 59.377 50.000 0.00 0.00 0.00 2.93
51 52 2.424234 CCCCTCCTTCAACCAAGTCAAA 60.424 50.000 0.00 0.00 0.00 2.69
52 53 1.144913 CCCCTCCTTCAACCAAGTCAA 59.855 52.381 0.00 0.00 0.00 3.18
53 54 0.771127 CCCCTCCTTCAACCAAGTCA 59.229 55.000 0.00 0.00 0.00 3.41
54 55 0.038310 CCCCCTCCTTCAACCAAGTC 59.962 60.000 0.00 0.00 0.00 3.01
55 56 0.402861 TCCCCCTCCTTCAACCAAGT 60.403 55.000 0.00 0.00 0.00 3.16
56 57 0.777446 TTCCCCCTCCTTCAACCAAG 59.223 55.000 0.00 0.00 0.00 3.61
57 58 1.146982 CTTTCCCCCTCCTTCAACCAA 59.853 52.381 0.00 0.00 0.00 3.67
58 59 0.777446 CTTTCCCCCTCCTTCAACCA 59.223 55.000 0.00 0.00 0.00 3.67
59 60 1.073098 TCTTTCCCCCTCCTTCAACC 58.927 55.000 0.00 0.00 0.00 3.77
60 61 2.891580 GTTTCTTTCCCCCTCCTTCAAC 59.108 50.000 0.00 0.00 0.00 3.18
61 62 2.516277 TGTTTCTTTCCCCCTCCTTCAA 59.484 45.455 0.00 0.00 0.00 2.69
62 63 2.140224 TGTTTCTTTCCCCCTCCTTCA 58.860 47.619 0.00 0.00 0.00 3.02
63 64 2.971901 TGTTTCTTTCCCCCTCCTTC 57.028 50.000 0.00 0.00 0.00 3.46
64 65 4.871822 CATATGTTTCTTTCCCCCTCCTT 58.128 43.478 0.00 0.00 0.00 3.36
65 66 3.373110 GCATATGTTTCTTTCCCCCTCCT 60.373 47.826 4.29 0.00 0.00 3.69
66 67 2.959030 GCATATGTTTCTTTCCCCCTCC 59.041 50.000 4.29 0.00 0.00 4.30
67 68 2.959030 GGCATATGTTTCTTTCCCCCTC 59.041 50.000 4.29 0.00 0.00 4.30
68 69 2.587307 AGGCATATGTTTCTTTCCCCCT 59.413 45.455 4.29 0.00 0.00 4.79
69 70 3.032265 AGGCATATGTTTCTTTCCCCC 57.968 47.619 4.29 0.00 0.00 5.40
70 71 3.769300 ACAAGGCATATGTTTCTTTCCCC 59.231 43.478 4.29 0.00 0.00 4.81
71 72 5.405935 AACAAGGCATATGTTTCTTTCCC 57.594 39.130 4.29 0.00 37.74 3.97
72 73 7.158099 AGTAACAAGGCATATGTTTCTTTCC 57.842 36.000 4.29 0.00 41.11 3.13
73 74 7.910683 GCTAGTAACAAGGCATATGTTTCTTTC 59.089 37.037 4.29 5.04 41.11 2.62
74 75 7.148069 GGCTAGTAACAAGGCATATGTTTCTTT 60.148 37.037 4.29 0.00 41.11 2.52
75 76 6.318900 GGCTAGTAACAAGGCATATGTTTCTT 59.681 38.462 4.29 3.76 41.11 2.52
76 77 5.823045 GGCTAGTAACAAGGCATATGTTTCT 59.177 40.000 4.29 10.46 41.11 2.52
77 78 5.588648 TGGCTAGTAACAAGGCATATGTTTC 59.411 40.000 4.29 4.57 43.79 2.78
78 79 5.505780 TGGCTAGTAACAAGGCATATGTTT 58.494 37.500 4.29 0.00 43.79 2.83
79 80 5.110814 TGGCTAGTAACAAGGCATATGTT 57.889 39.130 4.29 8.13 43.79 2.71
80 81 4.771114 TGGCTAGTAACAAGGCATATGT 57.229 40.909 4.29 0.00 43.79 2.29
86 87 3.283259 AAGGATGGCTAGTAACAAGGC 57.717 47.619 0.00 0.00 39.83 4.35
87 88 5.353394 TGTAAGGATGGCTAGTAACAAGG 57.647 43.478 0.00 0.00 0.00 3.61
88 89 8.367911 TGATATGTAAGGATGGCTAGTAACAAG 58.632 37.037 0.00 0.00 0.00 3.16
89 90 8.257602 TGATATGTAAGGATGGCTAGTAACAA 57.742 34.615 0.00 0.00 0.00 2.83
90 91 7.849322 TGATATGTAAGGATGGCTAGTAACA 57.151 36.000 0.00 0.00 0.00 2.41
91 92 9.372369 GATTGATATGTAAGGATGGCTAGTAAC 57.628 37.037 0.00 0.00 0.00 2.50
92 93 9.326489 AGATTGATATGTAAGGATGGCTAGTAA 57.674 33.333 0.00 0.00 0.00 2.24
93 94 8.753133 CAGATTGATATGTAAGGATGGCTAGTA 58.247 37.037 0.00 0.00 0.00 1.82
94 95 7.310921 CCAGATTGATATGTAAGGATGGCTAGT 60.311 40.741 0.00 0.00 0.00 2.57
95 96 7.046652 CCAGATTGATATGTAAGGATGGCTAG 58.953 42.308 0.00 0.00 0.00 3.42
96 97 6.501805 ACCAGATTGATATGTAAGGATGGCTA 59.498 38.462 0.00 0.00 0.00 3.93
97 98 5.311649 ACCAGATTGATATGTAAGGATGGCT 59.688 40.000 0.00 0.00 0.00 4.75
98 99 5.564550 ACCAGATTGATATGTAAGGATGGC 58.435 41.667 0.00 0.00 0.00 4.40
99 100 7.106239 GGTACCAGATTGATATGTAAGGATGG 58.894 42.308 7.15 0.00 0.00 3.51
100 101 7.679783 TGGTACCAGATTGATATGTAAGGATG 58.320 38.462 11.60 0.00 0.00 3.51
101 102 7.872061 TGGTACCAGATTGATATGTAAGGAT 57.128 36.000 11.60 0.00 0.00 3.24
102 103 7.038302 GGATGGTACCAGATTGATATGTAAGGA 60.038 40.741 21.41 0.00 0.00 3.36
103 104 7.106239 GGATGGTACCAGATTGATATGTAAGG 58.894 42.308 21.41 0.00 0.00 2.69
104 105 6.813649 CGGATGGTACCAGATTGATATGTAAG 59.186 42.308 21.41 0.00 0.00 2.34
105 106 6.295632 CCGGATGGTACCAGATTGATATGTAA 60.296 42.308 21.41 0.00 0.00 2.41
106 107 5.186992 CCGGATGGTACCAGATTGATATGTA 59.813 44.000 21.41 0.00 0.00 2.29
107 108 4.020218 CCGGATGGTACCAGATTGATATGT 60.020 45.833 21.41 0.00 0.00 2.29
108 109 4.507710 CCGGATGGTACCAGATTGATATG 58.492 47.826 21.41 2.43 0.00 1.78
109 110 4.826274 CCGGATGGTACCAGATTGATAT 57.174 45.455 21.41 0.00 0.00 1.63
123 124 0.761187 ATGATCCTGTCACCGGATGG 59.239 55.000 9.46 2.26 41.24 3.51
124 125 1.541889 CCATGATCCTGTCACCGGATG 60.542 57.143 9.46 2.48 41.24 3.51
125 126 0.761187 CCATGATCCTGTCACCGGAT 59.239 55.000 9.46 0.00 43.77 4.18
126 127 0.617535 ACCATGATCCTGTCACCGGA 60.618 55.000 9.46 0.00 40.28 5.14
127 128 1.119684 TACCATGATCCTGTCACCGG 58.880 55.000 0.00 0.00 40.28 5.28
128 129 2.550978 GTTACCATGATCCTGTCACCG 58.449 52.381 0.00 0.00 40.28 4.94
129 130 2.741878 CGGTTACCATGATCCTGTCACC 60.742 54.545 1.13 0.00 40.28 4.02
130 131 2.093658 ACGGTTACCATGATCCTGTCAC 60.094 50.000 1.13 0.00 40.28 3.67
131 132 2.184533 ACGGTTACCATGATCCTGTCA 58.815 47.619 1.13 0.00 42.06 3.58
132 133 2.981859 ACGGTTACCATGATCCTGTC 57.018 50.000 1.13 0.00 0.00 3.51
133 134 4.829872 TTAACGGTTACCATGATCCTGT 57.170 40.909 1.13 0.00 0.00 4.00
134 135 6.503589 TTTTTAACGGTTACCATGATCCTG 57.496 37.500 1.13 0.00 0.00 3.86
156 157 8.859090 TCATTGTACCACTTCTCATTGATTTTT 58.141 29.630 0.00 0.00 0.00 1.94
157 158 8.408043 TCATTGTACCACTTCTCATTGATTTT 57.592 30.769 0.00 0.00 0.00 1.82
158 159 8.408043 TTCATTGTACCACTTCTCATTGATTT 57.592 30.769 0.00 0.00 0.00 2.17
159 160 8.299570 GTTTCATTGTACCACTTCTCATTGATT 58.700 33.333 0.00 0.00 0.00 2.57
160 161 7.448161 TGTTTCATTGTACCACTTCTCATTGAT 59.552 33.333 0.00 0.00 0.00 2.57
161 162 6.770303 TGTTTCATTGTACCACTTCTCATTGA 59.230 34.615 0.00 0.00 0.00 2.57
162 163 6.969366 TGTTTCATTGTACCACTTCTCATTG 58.031 36.000 0.00 0.00 0.00 2.82
163 164 7.765695 ATGTTTCATTGTACCACTTCTCATT 57.234 32.000 0.00 0.00 0.00 2.57
164 165 7.554118 CCTATGTTTCATTGTACCACTTCTCAT 59.446 37.037 0.00 0.00 0.00 2.90
165 166 6.878923 CCTATGTTTCATTGTACCACTTCTCA 59.121 38.462 0.00 0.00 0.00 3.27
166 167 6.183360 GCCTATGTTTCATTGTACCACTTCTC 60.183 42.308 0.00 0.00 0.00 2.87
167 168 5.648092 GCCTATGTTTCATTGTACCACTTCT 59.352 40.000 0.00 0.00 0.00 2.85
168 169 5.163652 GGCCTATGTTTCATTGTACCACTTC 60.164 44.000 0.00 0.00 0.00 3.01
169 170 4.705023 GGCCTATGTTTCATTGTACCACTT 59.295 41.667 0.00 0.00 0.00 3.16
170 171 4.018415 AGGCCTATGTTTCATTGTACCACT 60.018 41.667 1.29 0.00 0.00 4.00
171 172 4.270008 AGGCCTATGTTTCATTGTACCAC 58.730 43.478 1.29 0.00 0.00 4.16
172 173 4.584638 AGGCCTATGTTTCATTGTACCA 57.415 40.909 1.29 0.00 0.00 3.25
173 174 4.097892 CCAAGGCCTATGTTTCATTGTACC 59.902 45.833 5.16 0.00 0.00 3.34
174 175 4.705023 ACCAAGGCCTATGTTTCATTGTAC 59.295 41.667 5.16 0.00 0.00 2.90
175 176 4.929479 ACCAAGGCCTATGTTTCATTGTA 58.071 39.130 5.16 0.00 0.00 2.41
176 177 3.778265 ACCAAGGCCTATGTTTCATTGT 58.222 40.909 5.16 0.00 0.00 2.71
177 178 4.949856 AGTACCAAGGCCTATGTTTCATTG 59.050 41.667 5.16 0.00 0.00 2.82
178 179 5.193099 AGTACCAAGGCCTATGTTTCATT 57.807 39.130 5.16 0.00 0.00 2.57
179 180 4.862641 AGTACCAAGGCCTATGTTTCAT 57.137 40.909 5.16 0.00 0.00 2.57
180 181 4.383770 GCTAGTACCAAGGCCTATGTTTCA 60.384 45.833 5.16 0.00 0.00 2.69
202 203 5.564550 ACCAGATTGATATGTAAGGATGGC 58.435 41.667 0.00 0.00 0.00 4.40
209 210 6.816616 TGGTGGTACCAGATTGATATGTAA 57.183 37.500 16.93 0.00 44.79 2.41
230 231 7.911651 ACAGTTATCATAATCCTATCACCTGG 58.088 38.462 0.00 0.00 0.00 4.45
260 261 8.859090 TCATTGTACCACTTCTCATTGATTTTT 58.141 29.630 0.00 0.00 0.00 1.94
262 263 8.408043 TTCATTGTACCACTTCTCATTGATTT 57.592 30.769 0.00 0.00 0.00 2.17
263 264 8.408043 TTTCATTGTACCACTTCTCATTGATT 57.592 30.769 0.00 0.00 0.00 2.57
322 323 1.280710 TGCCGTCTAACCATCCAACAT 59.719 47.619 0.00 0.00 0.00 2.71
326 327 0.251916 CCTTGCCGTCTAACCATCCA 59.748 55.000 0.00 0.00 0.00 3.41
330 331 2.047655 CGCCTTGCCGTCTAACCA 60.048 61.111 0.00 0.00 0.00 3.67
384 386 0.177141 ATGCCTAAGCGACGCCTAAA 59.823 50.000 17.79 0.00 44.31 1.85
421 424 2.372264 ACGTGGTAAGGCGATCTAAGA 58.628 47.619 0.00 0.00 0.00 2.10
475 478 9.897744 CATATTTTCCTCCGTATTACGTTACTA 57.102 33.333 14.62 0.00 40.58 1.82
482 485 9.978044 AGTACTTCATATTTTCCTCCGTATTAC 57.022 33.333 0.00 0.00 0.00 1.89
563 566 6.961360 TCTCACGAGTAGTATCATTTCCAT 57.039 37.500 0.00 0.00 0.00 3.41
566 569 8.893884 CGTAATTCTCACGAGTAGTATCATTTC 58.106 37.037 0.00 0.00 41.91 2.17
623 1142 0.736053 GCTACCTGTCGTCTCCTGAG 59.264 60.000 0.00 0.00 0.00 3.35
817 1347 0.907704 ATAAGTGTGTGGAGGCCCGA 60.908 55.000 0.00 0.00 34.29 5.14
850 1381 1.654220 CCCAGATTAATTGCGGGCG 59.346 57.895 5.19 0.00 0.00 6.13
888 1419 3.467803 GGCTGCAGTATTACTAAGGTGG 58.532 50.000 16.64 0.00 0.00 4.61
896 1427 2.122783 TTGGTGGGCTGCAGTATTAC 57.877 50.000 16.64 9.48 0.00 1.89
897 1428 2.889170 TTTGGTGGGCTGCAGTATTA 57.111 45.000 16.64 0.00 0.00 0.98
899 1430 1.895131 CTTTTTGGTGGGCTGCAGTAT 59.105 47.619 16.64 0.00 0.00 2.12
900 1431 1.133637 TCTTTTTGGTGGGCTGCAGTA 60.134 47.619 16.64 0.00 0.00 2.74
901 1432 0.396974 TCTTTTTGGTGGGCTGCAGT 60.397 50.000 16.64 0.00 0.00 4.40
1018 1583 1.550976 GGGGTAGGAGGCAATCTATCG 59.449 57.143 0.00 0.00 0.00 2.92
1425 1999 0.250513 GACTGAAGGTGGCCAGGTAG 59.749 60.000 5.11 3.02 34.85 3.18
1429 2003 2.046892 CGGACTGAAGGTGGCCAG 60.047 66.667 5.11 0.00 36.53 4.85
1447 2021 3.529533 ACAGATCTATGAACAGCAGTGC 58.470 45.455 7.13 7.13 0.00 4.40
1512 2086 1.022451 GGGCGCAACGGAATTCTACA 61.022 55.000 10.83 0.00 0.00 2.74
1526 2100 1.144969 TCGATTCGATTTATGGGCGC 58.855 50.000 4.29 0.00 0.00 6.53
1529 2103 4.065088 ACCACATCGATTCGATTTATGGG 58.935 43.478 29.38 22.42 44.59 4.00
1599 2173 1.206371 CCGGAACCACAACTACTAGGG 59.794 57.143 0.00 0.00 0.00 3.53
1628 2204 2.478134 GTCATGGATATGCGTCAGCTTC 59.522 50.000 0.00 0.00 45.42 3.86
1671 2247 6.653183 CATCTGCAATCATCCTAAAAGTACG 58.347 40.000 0.00 0.00 0.00 3.67
1672 2248 6.261826 AGCATCTGCAATCATCCTAAAAGTAC 59.738 38.462 4.79 0.00 45.16 2.73
1738 2333 1.869767 CAGCCGACCATAAAGAGCATC 59.130 52.381 0.00 0.00 0.00 3.91
1775 2370 9.319143 GGTACATCAATATGAGGCATATAAGAC 57.681 37.037 0.00 0.00 36.20 3.01
1776 2371 9.271921 AGGTACATCAATATGAGGCATATAAGA 57.728 33.333 0.00 0.00 36.20 2.10
1809 2404 2.927477 GCCGTATTCGTTGAACATCAGA 59.073 45.455 0.00 0.00 35.01 3.27
1810 2405 2.670905 TGCCGTATTCGTTGAACATCAG 59.329 45.455 0.00 0.00 35.01 2.90
2019 2683 3.748048 ACTATCACACACATGCACACTTC 59.252 43.478 0.00 0.00 0.00 3.01
2057 2721 2.363680 TGCTGCTGCCTAACTATCTCTC 59.636 50.000 13.47 0.00 38.71 3.20
2084 2748 2.832838 TCCCTGCAGTTCTGGAGATAA 58.167 47.619 19.94 4.98 35.98 1.75
2101 2765 0.398948 ATGGCCAAATGGTCCATCCC 60.399 55.000 10.96 4.54 43.66 3.85
2244 2908 6.979817 TCAATCAGTTGCCAATTATATTGCAC 59.020 34.615 0.00 0.00 35.26 4.57
2252 2916 9.679661 TTCTTATACTCAATCAGTTGCCAATTA 57.320 29.630 0.00 0.00 36.43 1.40
2689 3355 8.667463 GTTGTAGTTACCAACTGTTAACTTCAA 58.333 33.333 16.19 16.19 42.84 2.69
2715 3381 0.109597 GTTTTCCATCAGTGCTGCCG 60.110 55.000 0.00 0.00 0.00 5.69
2884 3550 4.478317 TCCATCTTGATTATCCCAACCAGT 59.522 41.667 0.00 0.00 0.00 4.00
2893 3559 8.743714 ACCAAGTTCTTTTCCATCTTGATTATC 58.256 33.333 0.00 0.00 38.06 1.75
3007 3673 1.597742 TCAGCCAACAAGCTTCAGTC 58.402 50.000 0.00 0.00 42.61 3.51
3135 3801 6.072838 ACTGCAAACTATCAACAAGATGTGAG 60.073 38.462 0.00 0.00 37.57 3.51
3253 3935 1.259142 CCATGCCATTGTGCCCTTGA 61.259 55.000 0.00 0.00 0.00 3.02
3286 3968 5.772004 ACAGGGGCCACAAACATATTAATA 58.228 37.500 8.31 0.00 0.00 0.98
3294 3976 2.430610 GCAACAGGGGCCACAAACA 61.431 57.895 8.31 0.00 0.00 2.83
3295 3977 1.757423 ATGCAACAGGGGCCACAAAC 61.757 55.000 8.31 0.00 0.00 2.93
3301 3983 1.607467 ACAAGATGCAACAGGGGCC 60.607 57.895 0.00 0.00 0.00 5.80
3315 3997 1.226211 GCGCACTAGCATGCACAAG 60.226 57.895 21.98 16.01 46.47 3.16
3322 4004 1.134580 AGACATGAAGCGCACTAGCAT 60.135 47.619 11.47 2.19 42.27 3.79
3367 4049 5.381757 ACACTAGGTGAAGGCATGTAAAAA 58.618 37.500 4.62 0.00 36.96 1.94
3481 4166 4.565564 GTGTCCAGGTAGCAAATTAGTACG 59.434 45.833 0.00 0.00 0.00 3.67
3495 4181 7.775053 AATTAATACAAACATGTGTCCAGGT 57.225 32.000 0.00 0.00 37.14 4.00
3549 4235 8.261492 AGTGCATACATAATTAATCTAGCTGC 57.739 34.615 0.00 0.00 0.00 5.25
3558 4244 6.645003 CCTGCGAGTAGTGCATACATAATTAA 59.355 38.462 0.00 0.00 42.32 1.40
3679 4365 2.295349 CAGCACTGGCATTTTCTGACTT 59.705 45.455 0.00 0.00 44.61 3.01
3788 4474 2.971598 GCAGGAAGGGCAGGCAGTA 61.972 63.158 0.00 0.00 0.00 2.74
3835 4521 2.593436 CGGCGGAGGTTGGTTGTT 60.593 61.111 0.00 0.00 0.00 2.83
4004 4690 2.623915 GCTGCTGGAGGTGCTTGTG 61.624 63.158 0.00 0.00 0.00 3.33
4076 4762 0.111639 GGGGTTAACACTTCCAGGCA 59.888 55.000 7.98 0.00 0.00 4.75
4301 4987 2.711924 GCTGCTTGTATCCAGCGC 59.288 61.111 0.00 0.00 44.12 5.92
4428 5120 1.298859 CGTAGTTGCCACTTCCAGCC 61.299 60.000 0.00 0.00 34.06 4.85
4533 5225 2.014554 CTTGTCCACCACGTCGTCG 61.015 63.158 0.00 0.00 43.34 5.12
4557 5249 1.702957 TCCTTTGAGAACCCCATCGTT 59.297 47.619 0.00 0.00 0.00 3.85
4572 5264 1.302832 CGCCCTCACTTGCTCCTTT 60.303 57.895 0.00 0.00 0.00 3.11
4758 5469 5.065859 TGAATGCACGAATTGGTTACATAGG 59.934 40.000 6.37 0.00 0.00 2.57
4794 5505 5.298276 AGCAAACGAGAAACCTGACAAATAA 59.702 36.000 0.00 0.00 0.00 1.40
4805 5516 1.136336 CGGTAGCAGCAAACGAGAAAC 60.136 52.381 0.00 0.00 0.00 2.78
4817 5528 3.844577 ACACTAACTGTACGGTAGCAG 57.155 47.619 8.00 8.42 38.58 4.24
4818 5529 4.379813 GCTAACACTAACTGTACGGTAGCA 60.380 45.833 8.00 0.00 30.51 3.49
4819 5530 4.101235 GCTAACACTAACTGTACGGTAGC 58.899 47.826 8.00 7.73 30.51 3.58
4820 5531 5.353678 AGAGCTAACACTAACTGTACGGTAG 59.646 44.000 8.00 7.90 30.51 3.18
4821 5532 5.248640 AGAGCTAACACTAACTGTACGGTA 58.751 41.667 8.00 0.00 30.51 4.02
4855 5578 2.370189 GGATAGCAATCACTAGGGCACT 59.630 50.000 0.00 0.00 33.41 4.40
4860 5583 5.614308 TGACAATGGATAGCAATCACTAGG 58.386 41.667 0.00 0.00 33.41 3.02
4886 5609 3.118775 ACACTTGCAGACACACTAGTCAA 60.119 43.478 0.00 0.00 40.98 3.18
4892 5615 4.199310 ACAATAACACTTGCAGACACACT 58.801 39.130 0.00 0.00 0.00 3.55
5003 5733 3.414700 GTCGCCAGCCACACGAAG 61.415 66.667 0.00 0.00 37.60 3.79
5013 5743 3.463505 GTGATCACACGTCGCCAG 58.536 61.111 21.07 0.00 37.28 4.85
5218 5961 2.378858 GCAGCTCACGCAGACAGAC 61.379 63.158 0.00 0.00 39.10 3.51
5219 5962 2.048784 GCAGCTCACGCAGACAGA 60.049 61.111 0.00 0.00 39.10 3.41
5220 5963 2.048409 AGCAGCTCACGCAGACAG 60.048 61.111 0.00 0.00 39.10 3.51
5221 5964 2.356673 CAGCAGCTCACGCAGACA 60.357 61.111 0.00 0.00 39.10 3.41
5284 6036 4.505742 GGGATGAGAAGAGGTGTTTTCTGT 60.506 45.833 0.00 0.00 33.97 3.41
5418 6173 2.124320 TTATCTTGGGCTGCGGGC 60.124 61.111 11.40 11.40 40.90 6.13
5421 6176 4.147701 CCCTTATCTTGGGCTGCG 57.852 61.111 0.00 0.00 37.99 5.18
5577 6334 2.701006 CTTACCCAATCGCGCACG 59.299 61.111 8.75 0.00 42.01 5.34
5588 6351 4.710375 TGTCAGATAGAGAACACCTTACCC 59.290 45.833 0.00 0.00 0.00 3.69
5589 6352 5.916661 TGTCAGATAGAGAACACCTTACC 57.083 43.478 0.00 0.00 0.00 2.85
5600 6364 2.848887 CGAAGCACGTTGTCAGATAGAG 59.151 50.000 0.00 0.00 37.22 2.43
5624 6392 1.299850 GAACCAAAACCGGCAGTGC 60.300 57.895 6.55 6.55 0.00 4.40


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

AutoCloner maintained by Alex Coulton.