Multiple sequence alignment - TraesCS3A01G475400

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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 TraesCS3A01G475400 chr3A 100.000 2959 0 0 1 2959 706922129 706925087 0.000000e+00 5465.0
1 TraesCS3A01G475400 chr3A 87.920 1101 123 4 728 1828 706851422 706852512 0.000000e+00 1288.0
2 TraesCS3A01G475400 chr3D 93.400 2394 129 14 572 2950 572046195 572043816 0.000000e+00 3518.0
3 TraesCS3A01G475400 chr3D 88.638 1109 119 2 706 1814 572085520 572084419 0.000000e+00 1343.0
4 TraesCS3A01G475400 chr3D 88.095 1092 123 2 728 1819 572101787 572100703 0.000000e+00 1290.0
5 TraesCS3A01G475400 chr3D 87.843 255 22 5 14 267 300710588 300710834 1.040000e-74 291.0
6 TraesCS3A01G475400 chr3D 92.718 206 6 3 262 467 572047619 572047423 3.730000e-74 289.0
7 TraesCS3A01G475400 chr3B 92.248 2335 151 15 637 2959 761936827 761939143 0.000000e+00 3282.0
8 TraesCS3A01G475400 chr3B 87.648 1101 126 3 728 1828 761902263 761903353 0.000000e+00 1271.0
9 TraesCS3A01G475400 chr3B 90.514 253 15 2 14 265 462864909 462865153 2.840000e-85 326.0
10 TraesCS3A01G475400 chr3B 88.038 209 12 5 262 469 761934879 761935075 4.930000e-58 235.0
11 TraesCS3A01G475400 chr2B 85.781 1069 144 3 755 1820 390925520 390926583 0.000000e+00 1125.0
12 TraesCS3A01G475400 chr2D 85.460 1066 147 6 758 1820 323076870 323077930 0.000000e+00 1103.0
13 TraesCS3A01G475400 chr2D 88.583 254 19 3 14 265 628560051 628560296 1.720000e-77 300.0
14 TraesCS3A01G475400 chr2D 88.189 254 19 4 14 265 628689420 628689176 2.880000e-75 292.0
15 TraesCS3A01G475400 chr2D 78.512 121 17 8 2517 2633 636609198 636609083 1.470000e-08 71.3
16 TraesCS3A01G475400 chr2A 84.991 1066 152 6 758 1820 407740545 407739485 0.000000e+00 1075.0
17 TraesCS3A01G475400 chr2A 76.580 269 44 16 2557 2816 564615763 564615505 2.390000e-26 130.0
18 TraesCS3A01G475400 chr2A 83.333 102 10 4 164 265 19695611 19695517 1.460000e-13 87.9
19 TraesCS3A01G475400 chr2A 82.524 103 9 7 163 265 689767037 689766944 6.800000e-12 82.4
20 TraesCS3A01G475400 chr2A 97.727 44 1 0 222 265 740011777 740011734 3.160000e-10 76.8
21 TraesCS3A01G475400 chr2A 91.667 48 4 0 218 265 57972093 57972046 1.900000e-07 67.6
22 TraesCS3A01G475400 chr6A 88.672 256 17 3 14 268 526018789 526018545 4.790000e-78 302.0
23 TraesCS3A01G475400 chr6D 88.889 243 18 6 14 255 121065887 121066121 1.040000e-74 291.0
24 TraesCS3A01G475400 chr6D 86.029 136 14 4 2602 2734 30131232 30131099 1.110000e-29 141.0
25 TraesCS3A01G475400 chr5D 88.000 250 19 4 14 262 541625642 541625881 4.830000e-73 285.0
26 TraesCS3A01G475400 chr5D 83.516 91 8 3 1966 2055 168496532 168496448 8.790000e-11 78.7
27 TraesCS3A01G475400 chr6B 85.385 260 27 8 10 265 708040427 708040679 2.930000e-65 259.0
28 TraesCS3A01G475400 chr7D 84.942 259 27 5 10 265 540241479 540241728 4.900000e-63 252.0
29 TraesCS3A01G475400 chr7D 84.397 141 20 2 2603 2742 197675602 197675463 1.430000e-28 137.0
30 TraesCS3A01G475400 chr7D 82.051 156 21 6 2561 2712 530843453 530843301 3.100000e-25 126.0
31 TraesCS3A01G475400 chr7B 76.038 313 59 14 2439 2745 123654422 123654724 6.610000e-32 148.0
32 TraesCS3A01G475400 chr7B 76.981 265 42 16 2520 2772 727871889 727872146 1.850000e-27 134.0
33 TraesCS3A01G475400 chr7B 90.909 55 5 0 2783 2837 47980150 47980204 1.140000e-09 75.0
34 TraesCS3A01G475400 chr1D 76.052 309 56 14 2523 2828 20065304 20065011 8.550000e-31 145.0
35 TraesCS3A01G475400 chr1A 74.455 321 56 15 2524 2838 133157306 133157006 6.700000e-22 115.0
36 TraesCS3A01G475400 chr7A 74.894 235 47 9 2520 2750 508651622 508651848 2.430000e-16 97.1
37 TraesCS3A01G475400 chr5B 84.746 59 8 1 1998 2055 84935022 84935080 1.150000e-04 58.4


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 TraesCS3A01G475400 chr3A 706922129 706925087 2958 False 5465.0 5465 100.000 1 2959 1 chr3A.!!$F2 2958
1 TraesCS3A01G475400 chr3A 706851422 706852512 1090 False 1288.0 1288 87.920 728 1828 1 chr3A.!!$F1 1100
2 TraesCS3A01G475400 chr3D 572043816 572047619 3803 True 1903.5 3518 93.059 262 2950 2 chr3D.!!$R3 2688
3 TraesCS3A01G475400 chr3D 572084419 572085520 1101 True 1343.0 1343 88.638 706 1814 1 chr3D.!!$R1 1108
4 TraesCS3A01G475400 chr3D 572100703 572101787 1084 True 1290.0 1290 88.095 728 1819 1 chr3D.!!$R2 1091
5 TraesCS3A01G475400 chr3B 761934879 761939143 4264 False 1758.5 3282 90.143 262 2959 2 chr3B.!!$F3 2697
6 TraesCS3A01G475400 chr3B 761902263 761903353 1090 False 1271.0 1271 87.648 728 1828 1 chr3B.!!$F2 1100
7 TraesCS3A01G475400 chr2B 390925520 390926583 1063 False 1125.0 1125 85.781 755 1820 1 chr2B.!!$F1 1065
8 TraesCS3A01G475400 chr2D 323076870 323077930 1060 False 1103.0 1103 85.460 758 1820 1 chr2D.!!$F1 1062
9 TraesCS3A01G475400 chr2A 407739485 407740545 1060 True 1075.0 1075 84.991 758 1820 1 chr2A.!!$R3 1062

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
77 78 0.034756 TGTCGGGTCTGTGGATGTTG 59.965 55.0 0.0 0.0 0.0 3.33 F
79 80 0.034756 TCGGGTCTGTGGATGTTGTG 59.965 55.0 0.0 0.0 0.0 3.33 F
127 128 0.183014 TGCGGTTGTGGGGTTTCTTA 59.817 50.0 0.0 0.0 0.0 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 3457 0.179029 CCAGTGTCCCTTCCAAACGT 60.179 55.000 0.00 0.0 0.00 3.99 R
1773 3461 1.142870 CAGAACCAGTGTCCCTTCCAA 59.857 52.381 0.00 0.0 0.00 3.53 R
1986 3675 1.376683 GGCACTGGCACGTGGATTA 60.377 57.895 18.88 0.0 43.71 1.75 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
22 23 5.574891 AATCTGCTTTGTGTTGTGTACAA 57.425 34.783 0.00 0.00 38.80 2.41
23 24 4.614555 TCTGCTTTGTGTTGTGTACAAG 57.385 40.909 0.00 0.00 39.03 3.16
24 25 4.006989 TCTGCTTTGTGTTGTGTACAAGT 58.993 39.130 0.00 0.00 39.03 3.16
25 26 4.090138 TGCTTTGTGTTGTGTACAAGTG 57.910 40.909 0.00 0.00 39.03 3.16
26 27 3.504134 TGCTTTGTGTTGTGTACAAGTGT 59.496 39.130 0.00 0.00 39.03 3.55
27 28 4.022762 TGCTTTGTGTTGTGTACAAGTGTT 60.023 37.500 0.00 0.00 39.03 3.32
28 29 4.557301 GCTTTGTGTTGTGTACAAGTGTTC 59.443 41.667 0.00 0.00 39.03 3.18
29 30 5.619086 GCTTTGTGTTGTGTACAAGTGTTCT 60.619 40.000 0.00 0.00 39.03 3.01
30 31 5.950758 TTGTGTTGTGTACAAGTGTTCTT 57.049 34.783 0.00 0.00 38.80 2.52
38 39 2.307363 CAAGTGTTCTTGTCGGCGT 58.693 52.632 6.85 0.00 44.09 5.68
39 40 0.655733 CAAGTGTTCTTGTCGGCGTT 59.344 50.000 6.85 0.00 44.09 4.84
40 41 0.935196 AAGTGTTCTTGTCGGCGTTC 59.065 50.000 6.85 2.07 32.09 3.95
41 42 0.104304 AGTGTTCTTGTCGGCGTTCT 59.896 50.000 6.85 0.00 0.00 3.01
42 43 0.935196 GTGTTCTTGTCGGCGTTCTT 59.065 50.000 6.85 0.00 0.00 2.52
43 44 1.329599 GTGTTCTTGTCGGCGTTCTTT 59.670 47.619 6.85 0.00 0.00 2.52
44 45 2.011222 TGTTCTTGTCGGCGTTCTTTT 58.989 42.857 6.85 0.00 0.00 2.27
45 46 2.223157 TGTTCTTGTCGGCGTTCTTTTG 60.223 45.455 6.85 0.00 0.00 2.44
46 47 0.941542 TCTTGTCGGCGTTCTTTTGG 59.058 50.000 6.85 0.00 0.00 3.28
47 48 0.661020 CTTGTCGGCGTTCTTTTGGT 59.339 50.000 6.85 0.00 0.00 3.67
48 49 0.378962 TTGTCGGCGTTCTTTTGGTG 59.621 50.000 6.85 0.00 0.00 4.17
49 50 0.745128 TGTCGGCGTTCTTTTGGTGT 60.745 50.000 6.85 0.00 0.00 4.16
50 51 1.219646 GTCGGCGTTCTTTTGGTGTA 58.780 50.000 6.85 0.00 0.00 2.90
51 52 1.193874 GTCGGCGTTCTTTTGGTGTAG 59.806 52.381 6.85 0.00 0.00 2.74
52 53 1.202557 TCGGCGTTCTTTTGGTGTAGT 60.203 47.619 6.85 0.00 0.00 2.73
53 54 2.035704 TCGGCGTTCTTTTGGTGTAGTA 59.964 45.455 6.85 0.00 0.00 1.82
54 55 2.410730 CGGCGTTCTTTTGGTGTAGTAG 59.589 50.000 0.00 0.00 0.00 2.57
55 56 2.159037 GGCGTTCTTTTGGTGTAGTAGC 59.841 50.000 0.00 0.00 0.00 3.58
56 57 2.803956 GCGTTCTTTTGGTGTAGTAGCA 59.196 45.455 0.00 0.00 34.39 3.49
57 58 3.249080 GCGTTCTTTTGGTGTAGTAGCAA 59.751 43.478 0.00 0.00 44.45 3.91
58 59 4.083484 GCGTTCTTTTGGTGTAGTAGCAAT 60.083 41.667 0.00 0.00 45.35 3.56
59 60 5.382303 CGTTCTTTTGGTGTAGTAGCAATG 58.618 41.667 0.00 0.00 45.35 2.82
60 61 5.049680 CGTTCTTTTGGTGTAGTAGCAATGT 60.050 40.000 0.00 0.00 45.35 2.71
61 62 6.371389 GTTCTTTTGGTGTAGTAGCAATGTC 58.629 40.000 0.00 0.00 45.35 3.06
62 63 4.688879 TCTTTTGGTGTAGTAGCAATGTCG 59.311 41.667 0.00 0.00 45.35 4.35
63 64 2.665649 TGGTGTAGTAGCAATGTCGG 57.334 50.000 0.00 0.00 33.01 4.79
64 65 1.206132 TGGTGTAGTAGCAATGTCGGG 59.794 52.381 0.00 0.00 33.01 5.14
65 66 1.206371 GGTGTAGTAGCAATGTCGGGT 59.794 52.381 0.00 0.00 0.00 5.28
66 67 2.537401 GTGTAGTAGCAATGTCGGGTC 58.463 52.381 0.00 0.00 0.00 4.46
67 68 2.165845 GTGTAGTAGCAATGTCGGGTCT 59.834 50.000 0.00 0.00 0.00 3.85
68 69 2.165641 TGTAGTAGCAATGTCGGGTCTG 59.834 50.000 0.00 0.00 0.00 3.51
69 70 1.267121 AGTAGCAATGTCGGGTCTGT 58.733 50.000 0.00 0.00 0.00 3.41
70 71 1.066858 AGTAGCAATGTCGGGTCTGTG 60.067 52.381 0.00 0.00 0.00 3.66
71 72 0.249120 TAGCAATGTCGGGTCTGTGG 59.751 55.000 0.00 0.00 0.00 4.17
72 73 1.003839 GCAATGTCGGGTCTGTGGA 60.004 57.895 0.00 0.00 0.00 4.02
73 74 0.392998 GCAATGTCGGGTCTGTGGAT 60.393 55.000 0.00 0.00 0.00 3.41
74 75 1.372582 CAATGTCGGGTCTGTGGATG 58.627 55.000 0.00 0.00 0.00 3.51
75 76 0.984230 AATGTCGGGTCTGTGGATGT 59.016 50.000 0.00 0.00 0.00 3.06
76 77 0.984230 ATGTCGGGTCTGTGGATGTT 59.016 50.000 0.00 0.00 0.00 2.71
77 78 0.034756 TGTCGGGTCTGTGGATGTTG 59.965 55.000 0.00 0.00 0.00 3.33
78 79 0.034896 GTCGGGTCTGTGGATGTTGT 59.965 55.000 0.00 0.00 0.00 3.32
79 80 0.034756 TCGGGTCTGTGGATGTTGTG 59.965 55.000 0.00 0.00 0.00 3.33
80 81 0.250295 CGGGTCTGTGGATGTTGTGT 60.250 55.000 0.00 0.00 0.00 3.72
81 82 1.001520 CGGGTCTGTGGATGTTGTGTA 59.998 52.381 0.00 0.00 0.00 2.90
82 83 2.354704 CGGGTCTGTGGATGTTGTGTAT 60.355 50.000 0.00 0.00 0.00 2.29
83 84 3.686016 GGGTCTGTGGATGTTGTGTATT 58.314 45.455 0.00 0.00 0.00 1.89
84 85 3.689649 GGGTCTGTGGATGTTGTGTATTC 59.310 47.826 0.00 0.00 0.00 1.75
85 86 3.370978 GGTCTGTGGATGTTGTGTATTCG 59.629 47.826 0.00 0.00 0.00 3.34
86 87 4.242475 GTCTGTGGATGTTGTGTATTCGA 58.758 43.478 0.00 0.00 0.00 3.71
87 88 4.688879 GTCTGTGGATGTTGTGTATTCGAA 59.311 41.667 0.00 0.00 0.00 3.71
88 89 4.929211 TCTGTGGATGTTGTGTATTCGAAG 59.071 41.667 3.35 0.00 0.00 3.79
89 90 4.888917 TGTGGATGTTGTGTATTCGAAGA 58.111 39.130 3.35 0.00 0.00 2.87
90 91 4.929211 TGTGGATGTTGTGTATTCGAAGAG 59.071 41.667 3.35 0.00 38.43 2.85
91 92 5.168569 GTGGATGTTGTGTATTCGAAGAGA 58.831 41.667 3.35 0.00 38.43 3.10
92 93 5.062308 GTGGATGTTGTGTATTCGAAGAGAC 59.938 44.000 12.70 12.70 38.43 3.36
93 94 5.047306 TGGATGTTGTGTATTCGAAGAGACT 60.047 40.000 19.15 0.84 38.43 3.24
94 95 5.289675 GGATGTTGTGTATTCGAAGAGACTG 59.710 44.000 19.15 0.00 38.43 3.51
95 96 4.556233 TGTTGTGTATTCGAAGAGACTGG 58.444 43.478 19.15 0.00 38.43 4.00
96 97 3.232213 TGTGTATTCGAAGAGACTGGC 57.768 47.619 19.15 6.21 38.43 4.85
97 98 2.186076 GTGTATTCGAAGAGACTGGCG 58.814 52.381 12.36 0.00 38.43 5.69
98 99 1.134367 TGTATTCGAAGAGACTGGCGG 59.866 52.381 3.35 0.00 38.43 6.13
99 100 0.744874 TATTCGAAGAGACTGGCGGG 59.255 55.000 3.35 0.00 38.43 6.13
100 101 1.961180 ATTCGAAGAGACTGGCGGGG 61.961 60.000 3.35 0.00 38.43 5.73
101 102 3.382832 CGAAGAGACTGGCGGGGT 61.383 66.667 0.00 0.00 0.00 4.95
102 103 2.579738 GAAGAGACTGGCGGGGTC 59.420 66.667 0.00 0.00 0.00 4.46
103 104 2.203788 AAGAGACTGGCGGGGTCA 60.204 61.111 0.00 0.00 36.29 4.02
104 105 2.508586 GAAGAGACTGGCGGGGTCAC 62.509 65.000 0.00 0.00 36.29 3.67
105 106 4.083862 GAGACTGGCGGGGTCACC 62.084 72.222 0.00 0.00 36.29 4.02
106 107 4.640690 AGACTGGCGGGGTCACCT 62.641 66.667 0.00 0.00 36.29 4.00
107 108 4.394712 GACTGGCGGGGTCACCTG 62.395 72.222 0.00 0.00 46.56 4.00
109 110 4.704833 CTGGCGGGGTCACCTGTG 62.705 72.222 0.00 0.00 45.50 3.66
114 115 4.265056 GGGGTCACCTGTGCGGTT 62.265 66.667 0.00 0.00 46.37 4.44
115 116 2.978010 GGGTCACCTGTGCGGTTG 60.978 66.667 0.00 0.00 46.37 3.77
116 117 2.203153 GGTCACCTGTGCGGTTGT 60.203 61.111 0.00 0.00 46.37 3.32
117 118 2.542907 GGTCACCTGTGCGGTTGTG 61.543 63.158 0.00 0.00 46.37 3.33
118 119 2.203139 TCACCTGTGCGGTTGTGG 60.203 61.111 0.00 0.00 46.37 4.17
119 120 3.286751 CACCTGTGCGGTTGTGGG 61.287 66.667 0.00 0.00 46.37 4.61
120 121 4.579384 ACCTGTGCGGTTGTGGGG 62.579 66.667 0.00 0.00 46.37 4.96
121 122 4.579384 CCTGTGCGGTTGTGGGGT 62.579 66.667 0.00 0.00 0.00 4.95
122 123 2.518349 CTGTGCGGTTGTGGGGTT 60.518 61.111 0.00 0.00 0.00 4.11
123 124 2.043852 TGTGCGGTTGTGGGGTTT 60.044 55.556 0.00 0.00 0.00 3.27
124 125 2.070654 CTGTGCGGTTGTGGGGTTTC 62.071 60.000 0.00 0.00 0.00 2.78
125 126 1.826487 GTGCGGTTGTGGGGTTTCT 60.826 57.895 0.00 0.00 0.00 2.52
126 127 1.076632 TGCGGTTGTGGGGTTTCTT 60.077 52.632 0.00 0.00 0.00 2.52
127 128 0.183014 TGCGGTTGTGGGGTTTCTTA 59.817 50.000 0.00 0.00 0.00 2.10
128 129 0.594602 GCGGTTGTGGGGTTTCTTAC 59.405 55.000 0.00 0.00 0.00 2.34
129 130 1.816572 GCGGTTGTGGGGTTTCTTACT 60.817 52.381 0.00 0.00 0.00 2.24
130 131 1.877443 CGGTTGTGGGGTTTCTTACTG 59.123 52.381 0.00 0.00 0.00 2.74
131 132 2.747135 CGGTTGTGGGGTTTCTTACTGT 60.747 50.000 0.00 0.00 0.00 3.55
132 133 2.621526 GGTTGTGGGGTTTCTTACTGTG 59.378 50.000 0.00 0.00 0.00 3.66
133 134 3.284617 GTTGTGGGGTTTCTTACTGTGT 58.715 45.455 0.00 0.00 0.00 3.72
134 135 2.925724 TGTGGGGTTTCTTACTGTGTG 58.074 47.619 0.00 0.00 0.00 3.82
135 136 2.506231 TGTGGGGTTTCTTACTGTGTGA 59.494 45.455 0.00 0.00 0.00 3.58
136 137 3.139077 GTGGGGTTTCTTACTGTGTGAG 58.861 50.000 0.00 0.00 0.00 3.51
137 138 2.775384 TGGGGTTTCTTACTGTGTGAGT 59.225 45.455 0.00 0.00 38.88 3.41
138 139 3.968649 TGGGGTTTCTTACTGTGTGAGTA 59.031 43.478 0.00 0.00 35.96 2.59
139 140 4.039973 TGGGGTTTCTTACTGTGTGAGTAG 59.960 45.833 0.00 0.00 38.45 2.57
140 141 4.040095 GGGGTTTCTTACTGTGTGAGTAGT 59.960 45.833 0.00 0.00 38.45 2.73
141 142 5.454329 GGGGTTTCTTACTGTGTGAGTAGTT 60.454 44.000 0.00 0.00 38.45 2.24
142 143 6.239402 GGGGTTTCTTACTGTGTGAGTAGTTA 60.239 42.308 0.00 0.00 38.45 2.24
143 144 6.867293 GGGTTTCTTACTGTGTGAGTAGTTAG 59.133 42.308 0.00 0.00 38.45 2.34
144 145 7.432059 GGTTTCTTACTGTGTGAGTAGTTAGT 58.568 38.462 0.00 0.00 38.45 2.24
145 146 8.571336 GGTTTCTTACTGTGTGAGTAGTTAGTA 58.429 37.037 0.00 0.00 38.45 1.82
148 149 8.859236 TCTTACTGTGTGAGTAGTTAGTATGT 57.141 34.615 0.00 0.00 38.45 2.29
149 150 8.727910 TCTTACTGTGTGAGTAGTTAGTATGTG 58.272 37.037 0.00 0.00 38.45 3.21
150 151 5.710984 ACTGTGTGAGTAGTTAGTATGTGC 58.289 41.667 0.00 0.00 30.86 4.57
151 152 5.477291 ACTGTGTGAGTAGTTAGTATGTGCT 59.523 40.000 0.00 0.00 30.86 4.40
152 153 6.015350 ACTGTGTGAGTAGTTAGTATGTGCTT 60.015 38.462 0.00 0.00 30.86 3.91
153 154 6.387465 TGTGTGAGTAGTTAGTATGTGCTTC 58.613 40.000 0.00 0.00 0.00 3.86
154 155 6.015772 TGTGTGAGTAGTTAGTATGTGCTTCA 60.016 38.462 0.00 0.00 0.00 3.02
155 156 7.036220 GTGTGAGTAGTTAGTATGTGCTTCAT 58.964 38.462 0.00 0.00 40.25 2.57
156 157 7.545965 GTGTGAGTAGTTAGTATGTGCTTCATT 59.454 37.037 0.89 0.00 37.91 2.57
157 158 8.094548 TGTGAGTAGTTAGTATGTGCTTCATTT 58.905 33.333 0.89 0.00 37.91 2.32
158 159 8.383619 GTGAGTAGTTAGTATGTGCTTCATTTG 58.616 37.037 0.89 0.00 37.91 2.32
159 160 8.094548 TGAGTAGTTAGTATGTGCTTCATTTGT 58.905 33.333 0.89 0.00 37.91 2.83
160 161 9.582431 GAGTAGTTAGTATGTGCTTCATTTGTA 57.418 33.333 0.89 0.00 37.91 2.41
164 165 8.677300 AGTTAGTATGTGCTTCATTTGTATTGG 58.323 33.333 0.89 0.00 37.91 3.16
165 166 8.458843 GTTAGTATGTGCTTCATTTGTATTGGT 58.541 33.333 0.89 0.00 37.91 3.67
166 167 7.466746 AGTATGTGCTTCATTTGTATTGGTT 57.533 32.000 0.89 0.00 37.91 3.67
167 168 7.895759 AGTATGTGCTTCATTTGTATTGGTTT 58.104 30.769 0.89 0.00 37.91 3.27
168 169 8.367156 AGTATGTGCTTCATTTGTATTGGTTTT 58.633 29.630 0.89 0.00 37.91 2.43
169 170 7.656707 ATGTGCTTCATTTGTATTGGTTTTC 57.343 32.000 0.00 0.00 32.08 2.29
170 171 6.577103 TGTGCTTCATTTGTATTGGTTTTCA 58.423 32.000 0.00 0.00 0.00 2.69
171 172 6.478344 TGTGCTTCATTTGTATTGGTTTTCAC 59.522 34.615 0.00 0.00 0.00 3.18
172 173 5.988561 TGCTTCATTTGTATTGGTTTTCACC 59.011 36.000 0.00 0.00 44.56 4.02
173 174 5.408299 GCTTCATTTGTATTGGTTTTCACCC 59.592 40.000 0.00 0.00 43.49 4.61
174 175 5.127693 TCATTTGTATTGGTTTTCACCCG 57.872 39.130 0.00 0.00 43.49 5.28
175 176 4.021894 TCATTTGTATTGGTTTTCACCCGG 60.022 41.667 0.00 0.00 43.49 5.73
176 177 2.660670 TGTATTGGTTTTCACCCGGT 57.339 45.000 0.00 0.00 43.49 5.28
177 178 2.946785 TGTATTGGTTTTCACCCGGTT 58.053 42.857 0.00 0.00 43.49 4.44
178 179 3.297736 TGTATTGGTTTTCACCCGGTTT 58.702 40.909 0.00 0.00 43.49 3.27
179 180 3.705072 TGTATTGGTTTTCACCCGGTTTT 59.295 39.130 0.00 0.00 43.49 2.43
180 181 2.963548 TTGGTTTTCACCCGGTTTTC 57.036 45.000 0.00 0.00 43.49 2.29
181 182 1.112950 TGGTTTTCACCCGGTTTTCC 58.887 50.000 0.00 0.00 43.49 3.13
197 198 6.806388 GGTTTTCCGTAAATTAACTGGAGA 57.194 37.500 0.00 0.00 0.00 3.71
198 199 7.205737 GGTTTTCCGTAAATTAACTGGAGAA 57.794 36.000 0.00 0.00 0.00 2.87
199 200 7.823665 GGTTTTCCGTAAATTAACTGGAGAAT 58.176 34.615 0.00 0.00 0.00 2.40
200 201 8.301720 GGTTTTCCGTAAATTAACTGGAGAATT 58.698 33.333 0.00 0.00 0.00 2.17
201 202 9.338291 GTTTTCCGTAAATTAACTGGAGAATTC 57.662 33.333 0.00 0.00 0.00 2.17
202 203 8.857694 TTTCCGTAAATTAACTGGAGAATTCT 57.142 30.769 7.95 7.95 0.00 2.40
203 204 8.488651 TTCCGTAAATTAACTGGAGAATTCTC 57.511 34.615 24.68 24.68 42.14 2.87
204 205 7.848128 TCCGTAAATTAACTGGAGAATTCTCT 58.152 34.615 29.64 15.83 42.48 3.10
205 206 8.319146 TCCGTAAATTAACTGGAGAATTCTCTT 58.681 33.333 29.64 20.31 42.48 2.85
206 207 8.604890 CCGTAAATTAACTGGAGAATTCTCTTC 58.395 37.037 29.64 17.47 42.48 2.87
207 208 9.372369 CGTAAATTAACTGGAGAATTCTCTTCT 57.628 33.333 29.64 16.64 42.48 2.85
240 241 7.992180 AATTCATTAATCGATGAGGCAAAAC 57.008 32.000 0.00 0.00 37.35 2.43
241 242 6.757897 TTCATTAATCGATGAGGCAAAACT 57.242 33.333 0.00 0.00 37.35 2.66
242 243 6.757897 TCATTAATCGATGAGGCAAAACTT 57.242 33.333 0.00 0.00 32.50 2.66
243 244 7.156876 TCATTAATCGATGAGGCAAAACTTT 57.843 32.000 0.00 0.00 32.50 2.66
244 245 7.601856 TCATTAATCGATGAGGCAAAACTTTT 58.398 30.769 0.00 0.00 32.50 2.27
245 246 7.541783 TCATTAATCGATGAGGCAAAACTTTTG 59.458 33.333 9.54 9.54 32.50 2.44
246 247 3.011949 TCGATGAGGCAAAACTTTTGC 57.988 42.857 25.11 25.11 44.22 3.68
252 253 3.659850 GCAAAACTTTTGCCTCCGT 57.340 47.368 23.40 0.00 39.38 4.69
253 254 1.934589 GCAAAACTTTTGCCTCCGTT 58.065 45.000 23.40 0.00 39.38 4.44
254 255 2.276201 GCAAAACTTTTGCCTCCGTTT 58.724 42.857 23.40 0.00 39.38 3.60
255 256 2.284150 GCAAAACTTTTGCCTCCGTTTC 59.716 45.455 23.40 0.00 39.38 2.78
256 257 3.516615 CAAAACTTTTGCCTCCGTTTCA 58.483 40.909 1.30 0.00 0.00 2.69
257 258 3.878160 AAACTTTTGCCTCCGTTTCAA 57.122 38.095 0.00 0.00 0.00 2.69
258 259 3.436700 AACTTTTGCCTCCGTTTCAAG 57.563 42.857 0.00 0.00 0.00 3.02
259 260 2.650322 ACTTTTGCCTCCGTTTCAAGA 58.350 42.857 0.00 0.00 0.00 3.02
260 261 3.020984 ACTTTTGCCTCCGTTTCAAGAA 58.979 40.909 0.00 0.00 0.00 2.52
306 307 5.933463 TGGGCACAATTCATTTCTTCATTTC 59.067 36.000 0.00 0.00 0.00 2.17
332 333 0.615850 TTCGGGTCATGCATGTACCA 59.384 50.000 31.59 19.38 32.90 3.25
407 410 5.184096 TGAAAAAGTACAAAACTGCCACTCA 59.816 36.000 0.00 0.00 38.88 3.41
408 411 4.632538 AAAGTACAAAACTGCCACTCAC 57.367 40.909 0.00 0.00 38.88 3.51
489 664 2.080693 AGTGTTGTTGCGTGTTCTTGA 58.919 42.857 0.00 0.00 0.00 3.02
500 675 3.425625 GCGTGTTCTTGATTTTCGGCATA 60.426 43.478 0.00 0.00 0.00 3.14
546 737 9.825109 TTTTTCCCTTTTCCTAATTTAACTGTG 57.175 29.630 0.00 0.00 0.00 3.66
547 738 8.541899 TTTCCCTTTTCCTAATTTAACTGTGT 57.458 30.769 0.00 0.00 0.00 3.72
548 739 9.643735 TTTCCCTTTTCCTAATTTAACTGTGTA 57.356 29.630 0.00 0.00 0.00 2.90
552 743 9.462606 CCTTTTCCTAATTTAACTGTGTATCCT 57.537 33.333 0.00 0.00 0.00 3.24
567 758 9.823647 ACTGTGTATCCTTATTAATGTCTTGAG 57.176 33.333 0.00 0.00 0.00 3.02
568 759 9.823647 CTGTGTATCCTTATTAATGTCTTGAGT 57.176 33.333 0.00 0.00 0.00 3.41
593 1763 7.630242 AACTGTAGATCATGTTATTGGGTTG 57.370 36.000 0.00 0.00 0.00 3.77
594 1764 6.721318 ACTGTAGATCATGTTATTGGGTTGT 58.279 36.000 0.00 0.00 0.00 3.32
635 1805 9.878667 TGTCGGTCTATTGAAAATTATAGTCAA 57.121 29.630 0.00 0.00 35.83 3.18
691 2368 9.419297 GGTACGCATTAAAGAACATATATCTCA 57.581 33.333 0.00 0.00 0.00 3.27
756 2441 9.891828 TTGAATGATTATTTTGGTATACGCATC 57.108 29.630 0.00 0.00 0.00 3.91
981 2666 4.821589 GGCGCACTCTTCCTCCCG 62.822 72.222 10.83 0.00 0.00 5.14
1124 2812 7.201767 GGAAATATCAAAGCAAGTACAGCATCT 60.202 37.037 12.08 0.00 0.00 2.90
1318 3006 4.710167 TCCTCGTGCTCGGGTCGA 62.710 66.667 7.35 4.86 35.53 4.20
1506 3194 1.736282 CATCTGCGTGTACGTGGCA 60.736 57.895 0.00 1.51 42.22 4.92
1660 3348 1.748122 CTCACCATGCTCTGCCACC 60.748 63.158 0.00 0.00 0.00 4.61
1769 3457 1.638679 CCCATGGAGGAGATGGTGCA 61.639 60.000 15.22 0.00 39.08 4.57
1773 3461 1.296715 GGAGGAGATGGTGCACGTT 59.703 57.895 11.45 0.00 0.00 3.99
1850 3538 2.487762 CCGGTGTCAATGTGTTAGCATT 59.512 45.455 0.00 0.00 39.42 3.56
1964 3653 7.558161 CATCACTGCAGGAAAATAGTTATGA 57.442 36.000 19.93 8.16 30.27 2.15
1968 3657 7.446931 TCACTGCAGGAAAATAGTTATGAACAA 59.553 33.333 19.93 0.00 0.00 2.83
1986 3675 2.218603 CAAGGGTGCGTGAAAGTTAGT 58.781 47.619 0.00 0.00 0.00 2.24
1987 3676 3.181463 ACAAGGGTGCGTGAAAGTTAGTA 60.181 43.478 0.00 0.00 0.00 1.82
2024 3713 7.119699 CAGTGCCAGAACTATGAGTTGATTTTA 59.880 37.037 0.00 0.00 38.80 1.52
2053 3742 6.321690 TCTTATGGGTTTCAGCTCTAGTCTAC 59.678 42.308 0.00 0.00 0.00 2.59
2062 3751 9.089601 GTTTCAGCTCTAGTCTACCTTATTTTC 57.910 37.037 0.00 0.00 0.00 2.29
2130 3819 4.018960 AGGTGGACAATGCTTCATAAGTCT 60.019 41.667 10.18 0.00 32.97 3.24
2241 3930 6.070938 TCAGATCAATCGAATCCATATGCTCT 60.071 38.462 0.00 0.00 0.00 4.09
2248 3937 3.990469 CGAATCCATATGCTCTAGCGTTT 59.010 43.478 1.35 0.00 45.83 3.60
2264 3953 2.673368 GCGTTTGGTCTGTCCTCTAATG 59.327 50.000 0.00 0.00 37.07 1.90
2278 3967 4.078571 TCCTCTAATGGAGCTCCCTTCTTA 60.079 45.833 29.95 18.84 40.57 2.10
2305 3994 2.755103 GGATCCGTGAATCCAAAGCTTT 59.245 45.455 5.69 5.69 44.04 3.51
2333 4022 5.063060 AGCAGATAAACACGGTCGTATTTTC 59.937 40.000 5.11 3.99 0.00 2.29
2365 4054 1.469917 CGCATGCTCGGCTTAAAATG 58.530 50.000 17.13 0.00 0.00 2.32
2390 4079 3.067040 GGCCCTTACGAGTTCAACAAAAA 59.933 43.478 0.00 0.00 0.00 1.94
2420 4109 7.843490 TCCAGAGAAATGAAAATAAGTACGG 57.157 36.000 0.00 0.00 0.00 4.02
2448 4137 2.085320 AGTACGCGTCTGTTCTGATCT 58.915 47.619 18.63 0.00 0.00 2.75
2475 4164 5.934625 AGTTCATGTGAGTTCAGGTGAATAC 59.065 40.000 10.46 0.00 34.84 1.89
2483 4172 8.154203 TGTGAGTTCAGGTGAATACTAAAATCA 58.846 33.333 0.00 0.00 36.33 2.57
2629 4318 5.616488 ACAAAATTGATGCTCCAAAATGC 57.384 34.783 0.00 0.00 0.00 3.56
2635 4324 7.548196 AATTGATGCTCCAAAATGCTATTTG 57.452 32.000 7.54 7.54 39.47 2.32
2637 4326 2.878580 TGCTCCAAAATGCTATTTGCG 58.121 42.857 8.67 4.52 46.63 4.85
2816 4507 1.821136 ACACGATCTCATGTGAGCTCA 59.179 47.619 13.74 13.74 41.80 4.26
2818 4509 2.098770 CACGATCTCATGTGAGCTCAGA 59.901 50.000 18.89 17.80 41.80 3.27
2871 4562 0.035534 ACAATGCCACCATAGCGACA 60.036 50.000 0.00 0.00 0.00 4.35
2874 4565 0.035534 ATGCCACCATAGCGACACAA 60.036 50.000 0.00 0.00 0.00 3.33
2885 4576 2.310233 CGACACAACGCCTGACAGG 61.310 63.158 17.83 17.83 38.80 4.00
2897 4588 1.610522 CCTGACAGGACAAAGCAAAGG 59.389 52.381 17.22 0.00 37.67 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.125417 ACTTGTACACAACACAAAGCAGATT 59.875 36.000 0.00 0.00 38.00 2.40
1 2 4.640201 ACTTGTACACAACACAAAGCAGAT 59.360 37.500 0.00 0.00 38.00 2.90
2 3 4.006989 ACTTGTACACAACACAAAGCAGA 58.993 39.130 0.00 0.00 38.00 4.26
3 4 4.097714 CACTTGTACACAACACAAAGCAG 58.902 43.478 0.00 0.00 38.00 4.24
4 5 3.504134 ACACTTGTACACAACACAAAGCA 59.496 39.130 0.00 0.00 38.00 3.91
5 6 4.091453 ACACTTGTACACAACACAAAGC 57.909 40.909 0.00 0.00 38.00 3.51
6 7 5.938322 AGAACACTTGTACACAACACAAAG 58.062 37.500 0.00 0.00 38.00 2.77
7 8 5.950758 AGAACACTTGTACACAACACAAA 57.049 34.783 0.00 0.00 38.00 2.83
8 9 5.694816 CAAGAACACTTGTACACAACACAA 58.305 37.500 0.00 0.00 38.00 3.33
9 10 5.289917 CAAGAACACTTGTACACAACACA 57.710 39.130 0.00 0.00 38.00 3.72
20 21 0.655733 AACGCCGACAAGAACACTTG 59.344 50.000 8.18 8.18 44.35 3.16
21 22 0.935196 GAACGCCGACAAGAACACTT 59.065 50.000 0.00 0.00 0.00 3.16
22 23 0.104304 AGAACGCCGACAAGAACACT 59.896 50.000 0.00 0.00 0.00 3.55
23 24 0.935196 AAGAACGCCGACAAGAACAC 59.065 50.000 0.00 0.00 0.00 3.32
24 25 1.658994 AAAGAACGCCGACAAGAACA 58.341 45.000 0.00 0.00 0.00 3.18
25 26 2.372350 CAAAAGAACGCCGACAAGAAC 58.628 47.619 0.00 0.00 0.00 3.01
26 27 1.332375 CCAAAAGAACGCCGACAAGAA 59.668 47.619 0.00 0.00 0.00 2.52
27 28 0.941542 CCAAAAGAACGCCGACAAGA 59.058 50.000 0.00 0.00 0.00 3.02
28 29 0.661020 ACCAAAAGAACGCCGACAAG 59.339 50.000 0.00 0.00 0.00 3.16
29 30 0.378962 CACCAAAAGAACGCCGACAA 59.621 50.000 0.00 0.00 0.00 3.18
30 31 0.745128 ACACCAAAAGAACGCCGACA 60.745 50.000 0.00 0.00 0.00 4.35
31 32 1.193874 CTACACCAAAAGAACGCCGAC 59.806 52.381 0.00 0.00 0.00 4.79
32 33 1.202557 ACTACACCAAAAGAACGCCGA 60.203 47.619 0.00 0.00 0.00 5.54
33 34 1.223187 ACTACACCAAAAGAACGCCG 58.777 50.000 0.00 0.00 0.00 6.46
34 35 2.159037 GCTACTACACCAAAAGAACGCC 59.841 50.000 0.00 0.00 0.00 5.68
35 36 2.803956 TGCTACTACACCAAAAGAACGC 59.196 45.455 0.00 0.00 0.00 4.84
36 37 5.049680 ACATTGCTACTACACCAAAAGAACG 60.050 40.000 0.00 0.00 0.00 3.95
37 38 6.313744 ACATTGCTACTACACCAAAAGAAC 57.686 37.500 0.00 0.00 0.00 3.01
38 39 5.178623 CGACATTGCTACTACACCAAAAGAA 59.821 40.000 0.00 0.00 0.00 2.52
39 40 4.688879 CGACATTGCTACTACACCAAAAGA 59.311 41.667 0.00 0.00 0.00 2.52
40 41 4.142902 CCGACATTGCTACTACACCAAAAG 60.143 45.833 0.00 0.00 0.00 2.27
41 42 3.749088 CCGACATTGCTACTACACCAAAA 59.251 43.478 0.00 0.00 0.00 2.44
42 43 3.331150 CCGACATTGCTACTACACCAAA 58.669 45.455 0.00 0.00 0.00 3.28
43 44 2.354303 CCCGACATTGCTACTACACCAA 60.354 50.000 0.00 0.00 0.00 3.67
44 45 1.206132 CCCGACATTGCTACTACACCA 59.794 52.381 0.00 0.00 0.00 4.17
45 46 1.206371 ACCCGACATTGCTACTACACC 59.794 52.381 0.00 0.00 0.00 4.16
46 47 2.165845 AGACCCGACATTGCTACTACAC 59.834 50.000 0.00 0.00 0.00 2.90
47 48 2.165641 CAGACCCGACATTGCTACTACA 59.834 50.000 0.00 0.00 0.00 2.74
48 49 2.165845 ACAGACCCGACATTGCTACTAC 59.834 50.000 0.00 0.00 0.00 2.73
49 50 2.165641 CACAGACCCGACATTGCTACTA 59.834 50.000 0.00 0.00 0.00 1.82
50 51 1.066858 CACAGACCCGACATTGCTACT 60.067 52.381 0.00 0.00 0.00 2.57
51 52 1.359848 CACAGACCCGACATTGCTAC 58.640 55.000 0.00 0.00 0.00 3.58
52 53 0.249120 CCACAGACCCGACATTGCTA 59.751 55.000 0.00 0.00 0.00 3.49
53 54 1.003355 CCACAGACCCGACATTGCT 60.003 57.895 0.00 0.00 0.00 3.91
54 55 0.392998 ATCCACAGACCCGACATTGC 60.393 55.000 0.00 0.00 0.00 3.56
55 56 1.339055 ACATCCACAGACCCGACATTG 60.339 52.381 0.00 0.00 0.00 2.82
56 57 0.984230 ACATCCACAGACCCGACATT 59.016 50.000 0.00 0.00 0.00 2.71
57 58 0.984230 AACATCCACAGACCCGACAT 59.016 50.000 0.00 0.00 0.00 3.06
58 59 0.034756 CAACATCCACAGACCCGACA 59.965 55.000 0.00 0.00 0.00 4.35
59 60 0.034896 ACAACATCCACAGACCCGAC 59.965 55.000 0.00 0.00 0.00 4.79
60 61 0.034756 CACAACATCCACAGACCCGA 59.965 55.000 0.00 0.00 0.00 5.14
61 62 0.250295 ACACAACATCCACAGACCCG 60.250 55.000 0.00 0.00 0.00 5.28
62 63 2.851263 TACACAACATCCACAGACCC 57.149 50.000 0.00 0.00 0.00 4.46
63 64 3.370978 CGAATACACAACATCCACAGACC 59.629 47.826 0.00 0.00 0.00 3.85
64 65 4.242475 TCGAATACACAACATCCACAGAC 58.758 43.478 0.00 0.00 0.00 3.51
65 66 4.529109 TCGAATACACAACATCCACAGA 57.471 40.909 0.00 0.00 0.00 3.41
66 67 4.929211 TCTTCGAATACACAACATCCACAG 59.071 41.667 0.00 0.00 0.00 3.66
67 68 4.888917 TCTTCGAATACACAACATCCACA 58.111 39.130 0.00 0.00 0.00 4.17
68 69 5.062308 GTCTCTTCGAATACACAACATCCAC 59.938 44.000 0.00 0.00 0.00 4.02
69 70 5.047306 AGTCTCTTCGAATACACAACATCCA 60.047 40.000 0.00 0.00 0.00 3.41
70 71 5.289675 CAGTCTCTTCGAATACACAACATCC 59.710 44.000 0.00 0.00 0.00 3.51
71 72 5.289675 CCAGTCTCTTCGAATACACAACATC 59.710 44.000 0.00 0.00 0.00 3.06
72 73 5.171476 CCAGTCTCTTCGAATACACAACAT 58.829 41.667 0.00 0.00 0.00 2.71
73 74 4.556233 CCAGTCTCTTCGAATACACAACA 58.444 43.478 0.00 0.00 0.00 3.33
74 75 3.368236 GCCAGTCTCTTCGAATACACAAC 59.632 47.826 0.00 0.00 0.00 3.32
75 76 3.585862 GCCAGTCTCTTCGAATACACAA 58.414 45.455 0.00 0.00 0.00 3.33
76 77 2.415491 CGCCAGTCTCTTCGAATACACA 60.415 50.000 0.00 0.00 0.00 3.72
77 78 2.186076 CGCCAGTCTCTTCGAATACAC 58.814 52.381 0.00 0.00 0.00 2.90
78 79 1.134367 CCGCCAGTCTCTTCGAATACA 59.866 52.381 0.00 0.00 0.00 2.29
79 80 1.536284 CCCGCCAGTCTCTTCGAATAC 60.536 57.143 0.00 0.00 0.00 1.89
80 81 0.744874 CCCGCCAGTCTCTTCGAATA 59.255 55.000 0.00 0.00 0.00 1.75
81 82 1.517832 CCCGCCAGTCTCTTCGAAT 59.482 57.895 0.00 0.00 0.00 3.34
82 83 2.646175 CCCCGCCAGTCTCTTCGAA 61.646 63.158 0.00 0.00 0.00 3.71
83 84 3.068691 CCCCGCCAGTCTCTTCGA 61.069 66.667 0.00 0.00 0.00 3.71
84 85 3.358076 GACCCCGCCAGTCTCTTCG 62.358 68.421 0.00 0.00 0.00 3.79
85 86 2.283529 TGACCCCGCCAGTCTCTTC 61.284 63.158 0.00 0.00 35.21 2.87
86 87 2.203788 TGACCCCGCCAGTCTCTT 60.204 61.111 0.00 0.00 35.21 2.85
87 88 2.997897 GTGACCCCGCCAGTCTCT 60.998 66.667 0.00 0.00 35.21 3.10
88 89 4.083862 GGTGACCCCGCCAGTCTC 62.084 72.222 0.00 0.00 42.48 3.36
89 90 4.640690 AGGTGACCCCGCCAGTCT 62.641 66.667 0.00 0.00 45.32 3.24
90 91 4.394712 CAGGTGACCCCGCCAGTC 62.395 72.222 0.00 0.00 45.32 3.51
92 93 4.704833 CACAGGTGACCCCGCCAG 62.705 72.222 0.00 0.00 45.32 4.85
105 106 2.070654 GAAACCCCACAACCGCACAG 62.071 60.000 0.00 0.00 0.00 3.66
106 107 2.043852 AAACCCCACAACCGCACA 60.044 55.556 0.00 0.00 0.00 4.57
107 108 1.388837 AAGAAACCCCACAACCGCAC 61.389 55.000 0.00 0.00 0.00 5.34
108 109 0.183014 TAAGAAACCCCACAACCGCA 59.817 50.000 0.00 0.00 0.00 5.69
109 110 0.594602 GTAAGAAACCCCACAACCGC 59.405 55.000 0.00 0.00 0.00 5.68
110 111 1.877443 CAGTAAGAAACCCCACAACCG 59.123 52.381 0.00 0.00 0.00 4.44
111 112 2.621526 CACAGTAAGAAACCCCACAACC 59.378 50.000 0.00 0.00 0.00 3.77
112 113 3.066203 CACACAGTAAGAAACCCCACAAC 59.934 47.826 0.00 0.00 0.00 3.32
113 114 3.054287 TCACACAGTAAGAAACCCCACAA 60.054 43.478 0.00 0.00 0.00 3.33
114 115 2.506231 TCACACAGTAAGAAACCCCACA 59.494 45.455 0.00 0.00 0.00 4.17
115 116 3.139077 CTCACACAGTAAGAAACCCCAC 58.861 50.000 0.00 0.00 0.00 4.61
116 117 2.775384 ACTCACACAGTAAGAAACCCCA 59.225 45.455 0.00 0.00 31.37 4.96
117 118 3.487120 ACTCACACAGTAAGAAACCCC 57.513 47.619 0.00 0.00 31.37 4.95
118 119 5.211174 ACTACTCACACAGTAAGAAACCC 57.789 43.478 0.00 0.00 37.13 4.11
119 120 7.432059 ACTAACTACTCACACAGTAAGAAACC 58.568 38.462 0.00 0.00 37.13 3.27
122 123 9.293404 ACATACTAACTACTCACACAGTAAGAA 57.707 33.333 0.00 0.00 37.13 2.52
123 124 8.727910 CACATACTAACTACTCACACAGTAAGA 58.272 37.037 0.00 0.00 37.13 2.10
124 125 7.485277 GCACATACTAACTACTCACACAGTAAG 59.515 40.741 0.00 0.00 37.13 2.34
125 126 7.176165 AGCACATACTAACTACTCACACAGTAA 59.824 37.037 0.00 0.00 37.13 2.24
126 127 6.657966 AGCACATACTAACTACTCACACAGTA 59.342 38.462 0.00 0.00 36.43 2.74
127 128 5.477291 AGCACATACTAACTACTCACACAGT 59.523 40.000 0.00 0.00 39.41 3.55
128 129 5.955488 AGCACATACTAACTACTCACACAG 58.045 41.667 0.00 0.00 0.00 3.66
129 130 5.977489 AGCACATACTAACTACTCACACA 57.023 39.130 0.00 0.00 0.00 3.72
130 131 6.387465 TGAAGCACATACTAACTACTCACAC 58.613 40.000 0.00 0.00 0.00 3.82
131 132 6.584185 TGAAGCACATACTAACTACTCACA 57.416 37.500 0.00 0.00 0.00 3.58
132 133 8.383619 CAAATGAAGCACATACTAACTACTCAC 58.616 37.037 0.00 0.00 38.38 3.51
133 134 8.094548 ACAAATGAAGCACATACTAACTACTCA 58.905 33.333 0.00 0.00 38.38 3.41
134 135 8.480643 ACAAATGAAGCACATACTAACTACTC 57.519 34.615 0.00 0.00 38.38 2.59
138 139 8.677300 CCAATACAAATGAAGCACATACTAACT 58.323 33.333 0.00 0.00 38.38 2.24
139 140 8.458843 ACCAATACAAATGAAGCACATACTAAC 58.541 33.333 0.00 0.00 38.38 2.34
140 141 8.574251 ACCAATACAAATGAAGCACATACTAA 57.426 30.769 0.00 0.00 38.38 2.24
141 142 8.574251 AACCAATACAAATGAAGCACATACTA 57.426 30.769 0.00 0.00 38.38 1.82
142 143 7.466746 AACCAATACAAATGAAGCACATACT 57.533 32.000 0.00 0.00 38.38 2.12
143 144 8.532977 AAAACCAATACAAATGAAGCACATAC 57.467 30.769 0.00 0.00 38.38 2.39
144 145 8.363390 TGAAAACCAATACAAATGAAGCACATA 58.637 29.630 0.00 0.00 38.38 2.29
145 146 7.171337 GTGAAAACCAATACAAATGAAGCACAT 59.829 33.333 0.00 0.00 41.45 3.21
146 147 6.478344 GTGAAAACCAATACAAATGAAGCACA 59.522 34.615 0.00 0.00 0.00 4.57
147 148 6.073819 GGTGAAAACCAATACAAATGAAGCAC 60.074 38.462 0.00 0.00 0.00 4.40
148 149 5.988561 GGTGAAAACCAATACAAATGAAGCA 59.011 36.000 0.00 0.00 0.00 3.91
149 150 5.408299 GGGTGAAAACCAATACAAATGAAGC 59.592 40.000 0.00 0.00 0.00 3.86
150 151 5.633182 CGGGTGAAAACCAATACAAATGAAG 59.367 40.000 0.00 0.00 0.00 3.02
151 152 5.509840 CCGGGTGAAAACCAATACAAATGAA 60.510 40.000 0.00 0.00 0.00 2.57
152 153 4.021894 CCGGGTGAAAACCAATACAAATGA 60.022 41.667 0.00 0.00 0.00 2.57
153 154 4.241681 CCGGGTGAAAACCAATACAAATG 58.758 43.478 0.00 0.00 0.00 2.32
154 155 3.898741 ACCGGGTGAAAACCAATACAAAT 59.101 39.130 6.32 0.00 0.00 2.32
155 156 3.297736 ACCGGGTGAAAACCAATACAAA 58.702 40.909 6.32 0.00 0.00 2.83
156 157 2.946785 ACCGGGTGAAAACCAATACAA 58.053 42.857 6.32 0.00 0.00 2.41
157 158 2.660670 ACCGGGTGAAAACCAATACA 57.339 45.000 6.32 0.00 0.00 2.29
158 159 4.300803 GAAAACCGGGTGAAAACCAATAC 58.699 43.478 6.32 0.00 0.00 1.89
159 160 3.321396 GGAAAACCGGGTGAAAACCAATA 59.679 43.478 6.32 0.00 0.00 1.90
160 161 2.103432 GGAAAACCGGGTGAAAACCAAT 59.897 45.455 6.32 0.00 0.00 3.16
161 162 1.481363 GGAAAACCGGGTGAAAACCAA 59.519 47.619 6.32 0.00 0.00 3.67
162 163 1.112950 GGAAAACCGGGTGAAAACCA 58.887 50.000 6.32 0.00 0.00 3.67
163 164 0.031043 CGGAAAACCGGGTGAAAACC 59.969 55.000 6.32 0.00 0.00 3.27
164 165 0.740149 ACGGAAAACCGGGTGAAAAC 59.260 50.000 6.32 0.00 37.53 2.43
165 166 2.338577 TACGGAAAACCGGGTGAAAA 57.661 45.000 6.32 0.00 37.53 2.29
166 167 2.338577 TTACGGAAAACCGGGTGAAA 57.661 45.000 6.32 0.00 37.53 2.69
167 168 2.338577 TTTACGGAAAACCGGGTGAA 57.661 45.000 6.32 0.00 37.53 3.18
168 169 2.565046 ATTTACGGAAAACCGGGTGA 57.435 45.000 6.32 0.00 37.53 4.02
169 170 4.216042 AGTTAATTTACGGAAAACCGGGTG 59.784 41.667 6.32 0.00 37.53 4.61
170 171 4.216042 CAGTTAATTTACGGAAAACCGGGT 59.784 41.667 6.32 0.00 37.53 5.28
171 172 4.379708 CCAGTTAATTTACGGAAAACCGGG 60.380 45.833 6.32 0.00 37.53 5.73
172 173 4.455190 TCCAGTTAATTTACGGAAAACCGG 59.545 41.667 13.05 0.00 37.53 5.28
173 174 5.409214 TCTCCAGTTAATTTACGGAAAACCG 59.591 40.000 0.00 7.12 39.31 4.44
174 175 6.806388 TCTCCAGTTAATTTACGGAAAACC 57.194 37.500 0.00 0.00 0.00 3.27
175 176 9.338291 GAATTCTCCAGTTAATTTACGGAAAAC 57.662 33.333 0.00 0.00 0.00 2.43
176 177 9.292195 AGAATTCTCCAGTTAATTTACGGAAAA 57.708 29.630 0.88 0.00 0.00 2.29
177 178 8.857694 AGAATTCTCCAGTTAATTTACGGAAA 57.142 30.769 0.88 0.00 0.00 3.13
178 179 8.319146 AGAGAATTCTCCAGTTAATTTACGGAA 58.681 33.333 28.01 0.00 43.88 4.30
179 180 7.848128 AGAGAATTCTCCAGTTAATTTACGGA 58.152 34.615 28.01 7.57 43.88 4.69
180 181 8.494016 AAGAGAATTCTCCAGTTAATTTACGG 57.506 34.615 28.01 0.00 43.88 4.02
181 182 9.372369 AGAAGAGAATTCTCCAGTTAATTTACG 57.628 33.333 28.01 0.00 43.88 3.18
214 215 9.515020 GTTTTGCCTCATCGATTAATGAATTAA 57.485 29.630 0.00 0.00 35.32 1.40
215 216 8.902806 AGTTTTGCCTCATCGATTAATGAATTA 58.097 29.630 0.00 0.00 35.32 1.40
216 217 7.775120 AGTTTTGCCTCATCGATTAATGAATT 58.225 30.769 0.00 0.00 35.32 2.17
217 218 7.338800 AGTTTTGCCTCATCGATTAATGAAT 57.661 32.000 0.00 0.00 35.32 2.57
218 219 6.757897 AGTTTTGCCTCATCGATTAATGAA 57.242 33.333 0.00 0.00 35.32 2.57
219 220 6.757897 AAGTTTTGCCTCATCGATTAATGA 57.242 33.333 0.00 0.00 34.55 2.57
220 221 7.669098 CAAAAGTTTTGCCTCATCGATTAATG 58.331 34.615 15.06 0.00 0.00 1.90
221 222 6.311200 GCAAAAGTTTTGCCTCATCGATTAAT 59.689 34.615 33.57 0.00 39.38 1.40
222 223 5.633182 GCAAAAGTTTTGCCTCATCGATTAA 59.367 36.000 33.57 0.00 39.38 1.40
223 224 5.160641 GCAAAAGTTTTGCCTCATCGATTA 58.839 37.500 33.57 0.00 39.38 1.75
224 225 3.989817 GCAAAAGTTTTGCCTCATCGATT 59.010 39.130 33.57 0.00 39.38 3.34
225 226 3.578688 GCAAAAGTTTTGCCTCATCGAT 58.421 40.909 33.57 0.00 39.38 3.59
226 227 3.011949 GCAAAAGTTTTGCCTCATCGA 57.988 42.857 33.57 0.00 39.38 3.59
234 235 1.934589 AACGGAGGCAAAAGTTTTGC 58.065 45.000 34.99 34.99 44.22 3.68
235 236 3.516615 TGAAACGGAGGCAAAAGTTTTG 58.483 40.909 21.60 21.60 37.00 2.44
236 237 3.878160 TGAAACGGAGGCAAAAGTTTT 57.122 38.095 0.00 0.00 37.00 2.43
237 238 3.445805 TCTTGAAACGGAGGCAAAAGTTT 59.554 39.130 0.00 0.37 39.21 2.66
238 239 3.020984 TCTTGAAACGGAGGCAAAAGTT 58.979 40.909 0.00 0.00 0.00 2.66
239 240 2.650322 TCTTGAAACGGAGGCAAAAGT 58.350 42.857 0.00 0.00 0.00 2.66
240 241 3.708563 TTCTTGAAACGGAGGCAAAAG 57.291 42.857 0.00 0.00 0.00 2.27
241 242 4.457834 TTTTCTTGAAACGGAGGCAAAA 57.542 36.364 0.00 0.00 0.00 2.44
242 243 4.457834 TTTTTCTTGAAACGGAGGCAAA 57.542 36.364 0.00 0.00 0.00 3.68
260 261 7.503902 GCCCAATATATGTCTCCTTCTCTTTTT 59.496 37.037 0.00 0.00 0.00 1.94
306 307 3.378112 ACATGCATGACCCGAAGTAAATG 59.622 43.478 32.75 2.21 0.00 2.32
332 333 3.393426 TCAAGTATACTCCTCCCCGTT 57.607 47.619 5.70 0.00 0.00 4.44
376 378 9.040939 GGCAGTTTTGTACTTTTTCATTTGTAT 57.959 29.630 0.00 0.00 33.85 2.29
377 379 8.035394 TGGCAGTTTTGTACTTTTTCATTTGTA 58.965 29.630 0.00 0.00 33.85 2.41
378 380 6.876257 TGGCAGTTTTGTACTTTTTCATTTGT 59.124 30.769 0.00 0.00 33.85 2.83
379 381 7.064490 AGTGGCAGTTTTGTACTTTTTCATTTG 59.936 33.333 0.00 0.00 33.85 2.32
380 382 7.102993 AGTGGCAGTTTTGTACTTTTTCATTT 58.897 30.769 0.00 0.00 33.85 2.32
381 383 6.639563 AGTGGCAGTTTTGTACTTTTTCATT 58.360 32.000 0.00 0.00 33.85 2.57
382 384 6.127479 TGAGTGGCAGTTTTGTACTTTTTCAT 60.127 34.615 0.00 0.00 33.85 2.57
383 385 5.184096 TGAGTGGCAGTTTTGTACTTTTTCA 59.816 36.000 0.00 0.00 33.85 2.69
384 386 5.515270 GTGAGTGGCAGTTTTGTACTTTTTC 59.485 40.000 0.00 0.00 33.85 2.29
385 387 5.407502 GTGAGTGGCAGTTTTGTACTTTTT 58.592 37.500 0.00 0.00 33.85 1.94
407 410 2.584608 GCTAGTGGTCCATGCCGT 59.415 61.111 0.00 0.00 0.00 5.68
408 411 2.586079 CGCTAGTGGTCCATGCCG 60.586 66.667 0.00 0.00 0.00 5.69
489 664 7.551585 TGACCACAAAATATTATGCCGAAAAT 58.448 30.769 0.00 0.00 0.00 1.82
525 716 8.683615 GGATACACAGTTAAATTAGGAAAAGGG 58.316 37.037 0.00 0.00 0.00 3.95
526 717 9.462606 AGGATACACAGTTAAATTAGGAAAAGG 57.537 33.333 0.00 0.00 41.41 3.11
542 733 9.823647 ACTCAAGACATTAATAAGGATACACAG 57.176 33.333 0.00 0.00 41.41 3.66
557 748 8.535335 ACATGATCTACAGTTACTCAAGACATT 58.465 33.333 0.00 0.00 0.00 2.71
559 750 7.468141 ACATGATCTACAGTTACTCAAGACA 57.532 36.000 0.00 0.00 0.00 3.41
563 754 9.599866 CCAATAACATGATCTACAGTTACTCAA 57.400 33.333 0.00 0.00 30.97 3.02
565 756 8.204836 ACCCAATAACATGATCTACAGTTACTC 58.795 37.037 0.00 0.00 30.97 2.59
567 758 8.612619 CAACCCAATAACATGATCTACAGTTAC 58.387 37.037 0.00 0.00 30.97 2.50
568 759 8.325787 ACAACCCAATAACATGATCTACAGTTA 58.674 33.333 0.00 0.00 31.90 2.24
570 761 6.721318 ACAACCCAATAACATGATCTACAGT 58.279 36.000 0.00 0.00 0.00 3.55
593 1763 2.989840 CCGACACATTCTCAAGAGTGAC 59.010 50.000 9.24 1.79 35.63 3.67
594 1764 2.628178 ACCGACACATTCTCAAGAGTGA 59.372 45.455 9.24 0.00 35.63 3.41
645 1815 6.529125 CGTACCGTAGTAATCACTCAAATGTT 59.471 38.462 0.00 0.00 36.14 2.71
646 1816 6.032094 CGTACCGTAGTAATCACTCAAATGT 58.968 40.000 0.00 0.00 36.14 2.71
647 1817 5.051907 GCGTACCGTAGTAATCACTCAAATG 60.052 44.000 0.00 0.00 36.14 2.32
648 1818 5.039333 GCGTACCGTAGTAATCACTCAAAT 58.961 41.667 0.00 0.00 36.14 2.32
663 2340 8.086522 AGATATATGTTCTTTAATGCGTACCGT 58.913 33.333 0.00 0.00 0.00 4.83
664 2341 8.462143 AGATATATGTTCTTTAATGCGTACCG 57.538 34.615 0.00 0.00 0.00 4.02
698 2375 8.039538 TCATGTGGCATGCTTGATTTAAAAATA 58.960 29.630 18.92 0.00 0.00 1.40
699 2376 6.879993 TCATGTGGCATGCTTGATTTAAAAAT 59.120 30.769 18.92 0.00 0.00 1.82
981 2666 1.073199 CAGTGAGTTGGGGGTGTCC 59.927 63.158 0.00 0.00 0.00 4.02
1124 2812 1.002257 ATCAGGATGTTGCGCCACA 60.002 52.632 17.36 17.36 37.40 4.17
1506 3194 2.029073 CACGACCACACGAAGCCT 59.971 61.111 0.00 0.00 37.03 4.58
1660 3348 2.494073 AGTAGAAGAGCCCGAACTTCAG 59.506 50.000 0.00 0.00 43.13 3.02
1769 3457 0.179029 CCAGTGTCCCTTCCAAACGT 60.179 55.000 0.00 0.00 0.00 3.99
1773 3461 1.142870 CAGAACCAGTGTCCCTTCCAA 59.857 52.381 0.00 0.00 0.00 3.53
1952 3640 5.475564 ACGCACCCTTGTTCATAACTATTTT 59.524 36.000 0.00 0.00 0.00 1.82
1964 3653 1.470051 AACTTTCACGCACCCTTGTT 58.530 45.000 0.00 0.00 0.00 2.83
1968 3657 3.756933 TTACTAACTTTCACGCACCCT 57.243 42.857 0.00 0.00 0.00 4.34
1986 3675 1.376683 GGCACTGGCACGTGGATTA 60.377 57.895 18.88 0.00 43.71 1.75
1987 3676 2.672996 GGCACTGGCACGTGGATT 60.673 61.111 18.88 0.00 43.71 3.01
2024 3713 5.643421 AGAGCTGAAACCCATAAGATCAT 57.357 39.130 0.00 0.00 0.00 2.45
2053 3742 9.533253 AACTGATTCAACAACAAGAAAATAAGG 57.467 29.630 0.00 0.00 0.00 2.69
2062 3751 3.044986 CGGCAACTGATTCAACAACAAG 58.955 45.455 0.00 0.00 0.00 3.16
2130 3819 1.604308 CCAGTGGCCATGAGCACAA 60.604 57.895 9.72 0.00 46.50 3.33
2241 3930 1.629043 AGAGGACAGACCAAACGCTA 58.371 50.000 0.00 0.00 42.04 4.26
2248 3937 2.111384 GCTCCATTAGAGGACAGACCA 58.889 52.381 0.00 0.00 43.46 4.02
2264 3953 3.456277 TCCAAAGATAAGAAGGGAGCTCC 59.544 47.826 25.59 25.59 0.00 4.70
2305 3994 0.037697 ACCGTGTTTATCTGCTCGCA 60.038 50.000 0.00 0.00 0.00 5.10
2360 4049 2.420058 CTCGTAAGGGCCTCCATTTT 57.580 50.000 6.46 0.00 38.47 1.82
2420 4109 2.645936 GACGCGTACTCGGCGTAC 60.646 66.667 13.97 7.16 44.36 3.67
2427 4116 2.096174 AGATCAGAACAGACGCGTACTC 59.904 50.000 13.97 6.48 0.00 2.59
2428 4117 2.085320 AGATCAGAACAGACGCGTACT 58.915 47.619 13.97 8.73 0.00 2.73
2430 4119 2.081462 TGAGATCAGAACAGACGCGTA 58.919 47.619 13.97 0.00 0.00 4.42
2436 4125 5.930569 CACATGAACTTGAGATCAGAACAGA 59.069 40.000 0.00 0.00 30.38 3.41
2448 4137 4.129380 CACCTGAACTCACATGAACTTGA 58.871 43.478 0.00 0.00 0.00 3.02
2555 4244 4.885413 TCTGGTGATGAAATTTTGCAAGG 58.115 39.130 0.00 0.00 0.00 3.61
2614 4303 4.435425 GCAAATAGCATTTTGGAGCATCA 58.565 39.130 11.79 0.00 44.79 3.07
2629 4318 3.497118 TCCAAAATGCGTTCGCAAATAG 58.503 40.909 22.83 13.28 44.70 1.73
2635 4324 0.456653 ATGCTCCAAAATGCGTTCGC 60.457 50.000 10.34 10.34 0.00 4.70
2637 4326 2.945278 TCAATGCTCCAAAATGCGTTC 58.055 42.857 0.00 0.00 36.42 3.95
2649 4338 6.347160 GGCAAAGAAAAACAAGATCAATGCTC 60.347 38.462 0.00 0.00 31.61 4.26
2802 4493 6.071165 TGTTCTAATTCTGAGCTCACATGAGA 60.071 38.462 13.74 12.59 44.74 3.27
2808 4499 5.698545 AGTGTTGTTCTAATTCTGAGCTCAC 59.301 40.000 13.74 0.00 0.00 3.51
2816 4507 7.876068 TGTATCCGAAAGTGTTGTTCTAATTCT 59.124 33.333 0.00 0.00 0.00 2.40
2818 4509 7.094933 GGTGTATCCGAAAGTGTTGTTCTAATT 60.095 37.037 0.00 0.00 0.00 1.40
2847 4538 1.806542 GCTATGGTGGCATTGTATCGG 59.193 52.381 0.00 0.00 0.00 4.18
2871 4562 0.107410 TTTGTCCTGTCAGGCGTTGT 60.107 50.000 14.64 0.00 34.61 3.32
2874 4565 1.598130 GCTTTGTCCTGTCAGGCGT 60.598 57.895 14.64 0.00 34.61 5.68
2879 4570 1.214175 TCCCTTTGCTTTGTCCTGTCA 59.786 47.619 0.00 0.00 0.00 3.58
2885 4576 2.818130 TTGCATCCCTTTGCTTTGTC 57.182 45.000 0.00 0.00 43.18 3.18
2897 4588 7.212274 AGTCCTGCATTTTTATATTTGCATCC 58.788 34.615 0.00 0.00 43.51 3.51


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

AutoCloner maintained by Alex Coulton.