Multiple sequence alignment - TraesCS3D01G149400

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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 TraesCS3D01G149400 chr3D 100.000 2421 0 0 1 2421 114235511 114233091 0.000000e+00 4471.0
1 TraesCS3D01G149400 chr3D 95.357 280 10 3 1810 2087 598164032 598164310 2.210000e-120 442.0
2 TraesCS3D01G149400 chr3A 87.998 1708 142 43 142 1808 110152763 110151078 0.000000e+00 1960.0
3 TraesCS3D01G149400 chr3A 80.921 152 27 2 111 261 587391993 587392143 4.230000e-23 119.0
4 TraesCS3D01G149400 chr3B 86.782 749 37 26 1003 1733 166555501 166556205 0.000000e+00 778.0
5 TraesCS3D01G149400 chr3B 90.504 516 37 4 598 1112 166555052 166555556 0.000000e+00 671.0
6 TraesCS3D01G149400 chr3B 82.432 444 54 18 156 595 166532455 166532878 1.370000e-97 366.0
7 TraesCS3D01G149400 chr3B 86.869 198 15 6 1615 1810 166556165 166556353 6.780000e-51 211.0
8 TraesCS3D01G149400 chr6D 94.805 308 8 1 2122 2421 82223579 82223272 7.830000e-130 473.0
9 TraesCS3D01G149400 chr6D 94.156 308 10 1 2122 2421 78503467 78503774 1.700000e-126 462.0
10 TraesCS3D01G149400 chr6D 93.831 308 11 1 2122 2421 68636839 68637146 7.890000e-125 457.0
11 TraesCS3D01G149400 chr6D 97.015 268 7 1 1820 2087 82223934 82223668 1.320000e-122 449.0
12 TraesCS3D01G149400 chr6D 93.182 308 13 1 2122 2421 7235752 7236059 1.710000e-121 446.0
13 TraesCS3D01G149400 chr6D 93.182 308 13 1 2122 2421 37105966 37106273 1.710000e-121 446.0
14 TraesCS3D01G149400 chr6D 94.700 283 12 2 1807 2087 240910468 240910749 1.030000e-118 436.0
15 TraesCS3D01G149400 chr6D 91.883 308 17 1 2122 2421 34185317 34185010 8.000000e-115 424.0
16 TraesCS3D01G149400 chr2D 94.481 308 9 1 2122 2421 21631088 21630781 3.640000e-128 468.0
17 TraesCS3D01G149400 chr2D 95.357 280 11 2 1810 2087 34543647 34543926 6.140000e-121 444.0
18 TraesCS3D01G149400 chr2D 92.642 299 18 4 1791 2087 66825674 66825970 6.190000e-116 427.0
19 TraesCS3D01G149400 chr1D 94.481 308 9 1 2122 2421 383728884 383729191 3.640000e-128 468.0
20 TraesCS3D01G149400 chr1D 94.156 308 10 1 2122 2421 301738877 301739184 1.700000e-126 462.0
21 TraesCS3D01G149400 chr7D 94.156 308 10 1 2122 2421 9364576 9364883 1.700000e-126 462.0
22 TraesCS3D01G149400 chr7D 95.324 278 12 1 1810 2087 9364211 9364487 7.950000e-120 440.0
23 TraesCS3D01G149400 chr7D 95.324 278 11 2 1811 2087 113131253 113130977 7.950000e-120 440.0
24 TraesCS3D01G149400 chr7D 94.118 289 15 2 1800 2087 192661681 192661968 2.860000e-119 438.0
25 TraesCS3D01G149400 chr5D 94.156 308 10 1 2122 2421 555899603 555899910 1.700000e-126 462.0
26 TraesCS3D01G149400 chr5D 95.000 280 13 1 1809 2087 301614961 301615240 2.860000e-119 438.0
27 TraesCS3D01G149400 chr5D 91.883 308 17 1 2122 2421 62533752 62533445 8.000000e-115 424.0
28 TraesCS3D01G149400 chr5D 82.418 182 31 1 179 359 42044401 42044220 8.960000e-35 158.0
29 TraesCS3D01G149400 chr4D 94.156 308 10 1 2122 2421 309538741 309539048 1.700000e-126 462.0
30 TraesCS3D01G149400 chr4D 93.831 308 11 1 2122 2421 402968016 402967709 7.890000e-125 457.0
31 TraesCS3D01G149400 chr4D 95.699 279 10 2 1810 2087 402968382 402968105 4.750000e-122 448.0
32 TraesCS3D01G149400 chrUn 92.857 308 14 1 2122 2421 95570977 95571284 7.950000e-120 440.0
33 TraesCS3D01G149400 chrUn 92.857 308 14 5 2122 2421 126746583 126746276 7.950000e-120 440.0
34 TraesCS3D01G149400 chrUn 91.593 226 11 1 2122 2339 393079032 393078807 3.020000e-79 305.0
35 TraesCS3D01G149400 chr5A 75.920 299 63 6 63 356 552061432 552061726 6.980000e-31 145.0
36 TraesCS3D01G149400 chr2A 78.667 150 27 4 109 255 637233419 637233272 7.130000e-16 95.3


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 TraesCS3D01G149400 chr3D 114233091 114235511 2420 True 4471.000000 4471 100.000000 1 2421 1 chr3D.!!$R1 2420
1 TraesCS3D01G149400 chr3A 110151078 110152763 1685 True 1960.000000 1960 87.998000 142 1808 1 chr3A.!!$R1 1666
2 TraesCS3D01G149400 chr3B 166555052 166556353 1301 False 553.333333 778 88.051667 598 1810 3 chr3B.!!$F2 1212
3 TraesCS3D01G149400 chr6D 82223272 82223934 662 True 461.000000 473 95.910000 1820 2421 2 chr6D.!!$R2 601
4 TraesCS3D01G149400 chr7D 9364211 9364883 672 False 451.000000 462 94.740000 1810 2421 2 chr7D.!!$F2 611
5 TraesCS3D01G149400 chr4D 402967709 402968382 673 True 452.500000 457 94.765000 1810 2421 2 chr4D.!!$R1 611

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
222 223 0.167689 GACGACGGTAGACACTCCAC 59.832 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1719 0.026803 GTAGCCAGACGTACGTACCG 59.973 60.0 22.87 16.17 0.0 4.02 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
21 22 4.431661 AGTTGGCTACTAACACGTAGAC 57.568 45.455 0.00 0.00 44.18 2.59
22 23 3.192212 AGTTGGCTACTAACACGTAGACC 59.808 47.826 0.00 3.77 43.45 3.85
23 24 2.794103 TGGCTACTAACACGTAGACCA 58.206 47.619 1.72 5.91 43.45 4.02
24 25 3.359033 TGGCTACTAACACGTAGACCAT 58.641 45.455 1.72 0.00 43.45 3.55
25 26 4.525996 TGGCTACTAACACGTAGACCATA 58.474 43.478 1.72 0.00 43.45 2.74
26 27 4.336433 TGGCTACTAACACGTAGACCATAC 59.664 45.833 1.72 0.00 43.45 2.39
27 28 4.578105 GGCTACTAACACGTAGACCATACT 59.422 45.833 2.40 0.00 39.18 2.12
28 29 5.067023 GGCTACTAACACGTAGACCATACTT 59.933 44.000 2.40 0.00 39.18 2.24
29 30 6.405176 GGCTACTAACACGTAGACCATACTTT 60.405 42.308 2.40 0.00 39.18 2.66
30 31 6.471519 GCTACTAACACGTAGACCATACTTTG 59.528 42.308 2.40 0.00 39.33 2.77
31 32 5.166398 ACTAACACGTAGACCATACTTTGC 58.834 41.667 0.00 0.00 33.61 3.68
32 33 3.671008 ACACGTAGACCATACTTTGCA 57.329 42.857 0.00 0.00 0.00 4.08
33 34 3.997762 ACACGTAGACCATACTTTGCAA 58.002 40.909 0.00 0.00 0.00 4.08
34 35 4.382291 ACACGTAGACCATACTTTGCAAA 58.618 39.130 12.14 12.14 0.00 3.68
35 36 4.817464 ACACGTAGACCATACTTTGCAAAA 59.183 37.500 13.84 0.00 0.00 2.44
36 37 5.049680 ACACGTAGACCATACTTTGCAAAAG 60.050 40.000 13.84 9.83 0.00 2.27
37 38 5.178623 CACGTAGACCATACTTTGCAAAAGA 59.821 40.000 13.84 4.22 0.00 2.52
38 39 5.408604 ACGTAGACCATACTTTGCAAAAGAG 59.591 40.000 13.84 4.09 0.00 2.85
39 40 5.408604 CGTAGACCATACTTTGCAAAAGAGT 59.591 40.000 13.84 10.29 0.00 3.24
40 41 6.073222 CGTAGACCATACTTTGCAAAAGAGTT 60.073 38.462 13.84 0.00 0.00 3.01
41 42 6.715347 AGACCATACTTTGCAAAAGAGTTT 57.285 33.333 13.84 0.14 0.00 2.66
42 43 6.739112 AGACCATACTTTGCAAAAGAGTTTC 58.261 36.000 13.84 6.37 0.00 2.78
43 44 6.547510 AGACCATACTTTGCAAAAGAGTTTCT 59.452 34.615 13.84 8.45 0.00 2.52
44 45 7.068716 AGACCATACTTTGCAAAAGAGTTTCTT 59.931 33.333 13.84 0.00 38.59 2.52
45 46 8.232913 ACCATACTTTGCAAAAGAGTTTCTTA 57.767 30.769 13.84 0.00 35.27 2.10
46 47 8.691797 ACCATACTTTGCAAAAGAGTTTCTTAA 58.308 29.630 13.84 0.00 35.27 1.85
47 48 9.528018 CCATACTTTGCAAAAGAGTTTCTTAAA 57.472 29.630 13.84 0.00 35.27 1.52
50 51 8.825667 ACTTTGCAAAAGAGTTTCTTAAAACA 57.174 26.923 13.84 0.00 45.94 2.83
51 52 9.435688 ACTTTGCAAAAGAGTTTCTTAAAACAT 57.564 25.926 13.84 0.00 45.94 2.71
52 53 9.693157 CTTTGCAAAAGAGTTTCTTAAAACATG 57.307 29.630 13.84 0.00 45.94 3.21
53 54 7.232945 TGCAAAAGAGTTTCTTAAAACATGC 57.767 32.000 0.00 6.40 45.94 4.06
54 55 6.257630 TGCAAAAGAGTTTCTTAAAACATGCC 59.742 34.615 0.00 0.00 45.94 4.40
55 56 6.479990 GCAAAAGAGTTTCTTAAAACATGCCT 59.520 34.615 0.00 0.00 45.94 4.75
56 57 7.306807 GCAAAAGAGTTTCTTAAAACATGCCTC 60.307 37.037 0.00 0.00 45.94 4.70
57 58 7.588497 AAAGAGTTTCTTAAAACATGCCTCT 57.412 32.000 0.00 0.00 45.94 3.69
58 59 8.691661 AAAGAGTTTCTTAAAACATGCCTCTA 57.308 30.769 0.00 0.00 45.94 2.43
59 60 8.691661 AAGAGTTTCTTAAAACATGCCTCTAA 57.308 30.769 0.00 0.00 45.94 2.10
60 61 8.100508 AGAGTTTCTTAAAACATGCCTCTAAC 57.899 34.615 0.00 0.00 45.94 2.34
61 62 7.719633 AGAGTTTCTTAAAACATGCCTCTAACA 59.280 33.333 0.00 0.00 45.94 2.41
62 63 8.232913 AGTTTCTTAAAACATGCCTCTAACAA 57.767 30.769 0.00 0.00 45.94 2.83
63 64 8.691797 AGTTTCTTAAAACATGCCTCTAACAAA 58.308 29.630 0.00 0.00 45.94 2.83
64 65 8.968242 GTTTCTTAAAACATGCCTCTAACAAAG 58.032 33.333 0.00 0.00 43.52 2.77
65 66 8.458573 TTCTTAAAACATGCCTCTAACAAAGA 57.541 30.769 0.00 0.00 0.00 2.52
78 79 6.080648 TCTAACAAAGAGAAGCGTAGTTCA 57.919 37.500 0.00 0.00 0.00 3.18
79 80 6.509656 TCTAACAAAGAGAAGCGTAGTTCAA 58.490 36.000 0.00 0.00 0.00 2.69
80 81 6.982141 TCTAACAAAGAGAAGCGTAGTTCAAA 59.018 34.615 0.00 0.00 0.00 2.69
81 82 6.431198 AACAAAGAGAAGCGTAGTTCAAAA 57.569 33.333 0.00 0.00 0.00 2.44
82 83 6.049263 ACAAAGAGAAGCGTAGTTCAAAAG 57.951 37.500 0.00 0.00 0.00 2.27
83 84 5.815740 ACAAAGAGAAGCGTAGTTCAAAAGA 59.184 36.000 0.00 0.00 0.00 2.52
84 85 6.315393 ACAAAGAGAAGCGTAGTTCAAAAGAA 59.685 34.615 0.00 0.00 0.00 2.52
85 86 7.012421 ACAAAGAGAAGCGTAGTTCAAAAGAAT 59.988 33.333 0.00 0.00 0.00 2.40
86 87 7.497925 AAGAGAAGCGTAGTTCAAAAGAATT 57.502 32.000 0.00 0.00 0.00 2.17
87 88 7.123160 AGAGAAGCGTAGTTCAAAAGAATTC 57.877 36.000 0.00 0.00 0.00 2.17
88 89 6.706270 AGAGAAGCGTAGTTCAAAAGAATTCA 59.294 34.615 8.44 0.00 0.00 2.57
89 90 7.226720 AGAGAAGCGTAGTTCAAAAGAATTCAA 59.773 33.333 8.44 0.00 0.00 2.69
90 91 7.703328 AGAAGCGTAGTTCAAAAGAATTCAAA 58.297 30.769 8.44 0.00 0.00 2.69
91 92 8.352942 AGAAGCGTAGTTCAAAAGAATTCAAAT 58.647 29.630 8.44 0.00 0.00 2.32
92 93 7.858052 AGCGTAGTTCAAAAGAATTCAAATG 57.142 32.000 8.44 3.31 0.00 2.32
93 94 7.648142 AGCGTAGTTCAAAAGAATTCAAATGA 58.352 30.769 8.44 5.67 0.00 2.57
94 95 8.134895 AGCGTAGTTCAAAAGAATTCAAATGAA 58.865 29.630 8.44 11.19 38.56 2.57
95 96 8.420189 GCGTAGTTCAAAAGAATTCAAATGAAG 58.580 33.333 15.69 8.69 37.48 3.02
96 97 9.663904 CGTAGTTCAAAAGAATTCAAATGAAGA 57.336 29.630 15.69 8.03 37.48 2.87
101 102 8.301730 TCAAAAGAATTCAAATGAAGACATGC 57.698 30.769 8.44 0.00 37.48 4.06
102 103 6.939551 AAAGAATTCAAATGAAGACATGCG 57.060 33.333 8.44 0.00 37.48 4.73
103 104 5.885230 AGAATTCAAATGAAGACATGCGA 57.115 34.783 8.44 0.00 37.48 5.10
104 105 6.258230 AGAATTCAAATGAAGACATGCGAA 57.742 33.333 8.44 0.00 37.48 4.70
105 106 6.088824 AGAATTCAAATGAAGACATGCGAAC 58.911 36.000 8.44 0.00 37.48 3.95
106 107 4.827304 TTCAAATGAAGACATGCGAACA 57.173 36.364 0.00 0.00 36.79 3.18
107 108 5.375417 TTCAAATGAAGACATGCGAACAT 57.625 34.783 0.00 0.00 36.79 2.71
108 109 6.493449 TTCAAATGAAGACATGCGAACATA 57.507 33.333 0.00 0.00 36.79 2.29
109 110 6.110543 TCAAATGAAGACATGCGAACATAG 57.889 37.500 0.00 0.00 36.79 2.23
110 111 5.874261 TCAAATGAAGACATGCGAACATAGA 59.126 36.000 0.00 0.00 36.79 1.98
111 112 5.725110 AATGAAGACATGCGAACATAGAC 57.275 39.130 0.00 0.00 36.79 2.59
112 113 4.186856 TGAAGACATGCGAACATAGACA 57.813 40.909 0.00 0.00 33.67 3.41
113 114 4.565022 TGAAGACATGCGAACATAGACAA 58.435 39.130 0.00 0.00 33.67 3.18
114 115 4.994217 TGAAGACATGCGAACATAGACAAA 59.006 37.500 0.00 0.00 33.67 2.83
115 116 4.928661 AGACATGCGAACATAGACAAAC 57.071 40.909 0.00 0.00 33.67 2.93
116 117 4.314961 AGACATGCGAACATAGACAAACA 58.685 39.130 0.00 0.00 33.67 2.83
117 118 4.754618 AGACATGCGAACATAGACAAACAA 59.245 37.500 0.00 0.00 33.67 2.83
118 119 5.238432 AGACATGCGAACATAGACAAACAAA 59.762 36.000 0.00 0.00 33.67 2.83
119 120 5.451908 ACATGCGAACATAGACAAACAAAG 58.548 37.500 0.00 0.00 33.67 2.77
120 121 5.238432 ACATGCGAACATAGACAAACAAAGA 59.762 36.000 0.00 0.00 33.67 2.52
121 122 5.090652 TGCGAACATAGACAAACAAAGAC 57.909 39.130 0.00 0.00 0.00 3.01
122 123 4.024387 TGCGAACATAGACAAACAAAGACC 60.024 41.667 0.00 0.00 0.00 3.85
123 124 4.698276 CGAACATAGACAAACAAAGACCG 58.302 43.478 0.00 0.00 0.00 4.79
124 125 4.446385 CGAACATAGACAAACAAAGACCGA 59.554 41.667 0.00 0.00 0.00 4.69
125 126 5.050634 CGAACATAGACAAACAAAGACCGAA 60.051 40.000 0.00 0.00 0.00 4.30
126 127 6.347402 CGAACATAGACAAACAAAGACCGAAT 60.347 38.462 0.00 0.00 0.00 3.34
127 128 6.481954 ACATAGACAAACAAAGACCGAATC 57.518 37.500 0.00 0.00 0.00 2.52
128 129 5.411669 ACATAGACAAACAAAGACCGAATCC 59.588 40.000 0.00 0.00 0.00 3.01
129 130 3.815809 AGACAAACAAAGACCGAATCCA 58.184 40.909 0.00 0.00 0.00 3.41
130 131 4.204012 AGACAAACAAAGACCGAATCCAA 58.796 39.130 0.00 0.00 0.00 3.53
131 132 4.275936 AGACAAACAAAGACCGAATCCAAG 59.724 41.667 0.00 0.00 0.00 3.61
132 133 3.243401 ACAAACAAAGACCGAATCCAAGC 60.243 43.478 0.00 0.00 0.00 4.01
133 134 2.270352 ACAAAGACCGAATCCAAGCA 57.730 45.000 0.00 0.00 0.00 3.91
134 135 2.154462 ACAAAGACCGAATCCAAGCAG 58.846 47.619 0.00 0.00 0.00 4.24
135 136 2.224523 ACAAAGACCGAATCCAAGCAGA 60.225 45.455 0.00 0.00 0.00 4.26
136 137 3.012518 CAAAGACCGAATCCAAGCAGAT 58.987 45.455 0.00 0.00 0.00 2.90
137 138 3.356529 AAGACCGAATCCAAGCAGATT 57.643 42.857 0.00 0.00 39.19 2.40
138 139 2.911484 AGACCGAATCCAAGCAGATTC 58.089 47.619 11.92 11.92 45.75 2.52
153 154 3.366374 GCAGATTCACTAAAGGCAACCAC 60.366 47.826 0.00 0.00 37.17 4.16
165 166 1.295423 CAACCACCGACCGAATCCT 59.705 57.895 0.00 0.00 0.00 3.24
166 167 1.019278 CAACCACCGACCGAATCCTG 61.019 60.000 0.00 0.00 0.00 3.86
167 168 1.477685 AACCACCGACCGAATCCTGT 61.478 55.000 0.00 0.00 0.00 4.00
168 169 1.447838 CCACCGACCGAATCCTGTG 60.448 63.158 0.00 0.00 0.00 3.66
171 172 0.611062 ACCGACCGAATCCTGTGAGA 60.611 55.000 0.00 0.00 0.00 3.27
175 176 2.035632 GACCGAATCCTGTGAGATCCT 58.964 52.381 0.00 0.00 0.00 3.24
179 180 2.544694 CGAATCCTGTGAGATCCTTCGG 60.545 54.545 0.00 0.00 0.00 4.30
182 183 0.749649 CCTGTGAGATCCTTCGGAGG 59.250 60.000 2.10 2.10 45.02 4.30
197 198 3.161450 AGGCACACCTCCACACGT 61.161 61.111 0.00 0.00 46.34 4.49
202 203 2.207924 ACACCTCCACACGTCCTCC 61.208 63.158 0.00 0.00 0.00 4.30
203 204 2.989824 ACCTCCACACGTCCTCCG 60.990 66.667 0.00 0.00 44.03 4.63
220 221 1.423056 CGACGACGGTAGACACTCC 59.577 63.158 0.00 0.00 35.72 3.85
222 223 0.167689 GACGACGGTAGACACTCCAC 59.832 60.000 0.00 0.00 0.00 4.02
230 231 0.178955 TAGACACTCCACCGGGACAA 60.179 55.000 6.32 0.00 38.64 3.18
231 232 1.004918 GACACTCCACCGGGACAAG 60.005 63.158 6.32 0.00 38.64 3.16
233 234 2.928396 ACTCCACCGGGACAAGGG 60.928 66.667 6.32 0.00 38.64 3.95
235 236 4.974438 TCCACCGGGACAAGGGCT 62.974 66.667 6.32 0.00 38.64 5.19
238 239 1.987855 CACCGGGACAAGGGCTAGA 60.988 63.158 6.32 0.00 0.00 2.43
239 240 1.988406 ACCGGGACAAGGGCTAGAC 60.988 63.158 6.32 0.00 0.00 2.59
241 242 2.901042 GGGACAAGGGCTAGACGG 59.099 66.667 0.00 0.00 0.00 4.79
244 245 1.677637 GGACAAGGGCTAGACGGGAG 61.678 65.000 0.00 0.00 0.00 4.30
248 249 0.976590 AAGGGCTAGACGGGAGAACC 60.977 60.000 0.00 0.00 0.00 3.62
255 256 3.243805 GCTAGACGGGAGAACCTTATTCC 60.244 52.174 0.00 0.00 36.97 3.01
261 262 4.227527 ACGGGAGAACCTTATTCCATCTTT 59.772 41.667 0.00 0.00 36.97 2.52
264 265 6.299922 GGGAGAACCTTATTCCATCTTTAGG 58.700 44.000 0.00 0.00 35.85 2.69
276 277 2.125832 TTTAGGAAGCCGTCGCCG 60.126 61.111 0.00 0.00 34.57 6.46
289 290 0.306840 GTCGCCGTCTCGTCATCATA 59.693 55.000 0.00 0.00 0.00 2.15
291 292 1.002792 TCGCCGTCTCGTCATCATAAG 60.003 52.381 0.00 0.00 0.00 1.73
294 295 2.864097 GCCGTCTCGTCATCATAAGCAT 60.864 50.000 0.00 0.00 0.00 3.79
316 317 4.469657 TGACACAAACCCTAGCAAATCTT 58.530 39.130 0.00 0.00 0.00 2.40
320 321 6.981722 ACACAAACCCTAGCAAATCTTAAAG 58.018 36.000 0.00 0.00 0.00 1.85
324 325 8.141909 ACAAACCCTAGCAAATCTTAAAGAAAC 58.858 33.333 0.00 0.00 0.00 2.78
327 328 8.422577 ACCCTAGCAAATCTTAAAGAAACATT 57.577 30.769 0.00 0.00 0.00 2.71
329 330 9.143631 CCCTAGCAAATCTTAAAGAAACATTTG 57.856 33.333 0.00 0.00 37.46 2.32
344 345 4.830826 ACATTTGAAAACGAAGTCCTCC 57.169 40.909 0.00 0.00 45.00 4.30
345 346 3.568430 ACATTTGAAAACGAAGTCCTCCC 59.432 43.478 0.00 0.00 45.00 4.30
346 347 3.284793 TTTGAAAACGAAGTCCTCCCA 57.715 42.857 0.00 0.00 45.00 4.37
348 349 3.053831 TGAAAACGAAGTCCTCCCATC 57.946 47.619 0.00 0.00 45.00 3.51
350 351 0.249398 AAACGAAGTCCTCCCATCGG 59.751 55.000 0.00 0.00 45.00 4.18
351 352 2.107141 CGAAGTCCTCCCATCGGC 59.893 66.667 0.00 0.00 0.00 5.54
371 372 2.609350 CAAGGGCCAAAATTCATCACG 58.391 47.619 6.18 0.00 0.00 4.35
372 373 0.532115 AGGGCCAAAATTCATCACGC 59.468 50.000 6.18 0.00 0.00 5.34
377 378 2.159198 GCCAAAATTCATCACGCCTCAT 60.159 45.455 0.00 0.00 0.00 2.90
378 379 3.441163 CCAAAATTCATCACGCCTCATG 58.559 45.455 0.00 0.00 0.00 3.07
397 403 1.439644 GCTCTAAGGCCAGACGAGG 59.560 63.158 5.01 0.00 0.00 4.63
405 411 4.910956 CCAGACGAGGCAAATCGA 57.089 55.556 11.51 0.00 45.56 3.59
413 419 3.602103 GGCAAATCGATGGCACCA 58.398 55.556 20.03 0.00 44.66 4.17
414 420 1.139520 GGCAAATCGATGGCACCAC 59.860 57.895 20.03 3.46 44.66 4.16
415 421 1.139520 GCAAATCGATGGCACCACC 59.860 57.895 15.27 0.00 39.84 4.61
416 422 1.429021 CAAATCGATGGCACCACCG 59.571 57.895 0.00 0.00 43.94 4.94
417 423 1.748879 AAATCGATGGCACCACCGG 60.749 57.895 3.05 0.00 43.94 5.28
418 424 2.478335 AAATCGATGGCACCACCGGT 62.478 55.000 0.00 0.00 43.94 5.28
434 440 1.602771 GGTGGTAGGAGGCAGGAAC 59.397 63.158 0.00 0.00 0.00 3.62
455 461 3.070446 ACCCTAATCGTGTGTTCACTTGA 59.930 43.478 4.59 3.00 41.89 3.02
478 485 2.579860 AGGAGAGACGAAGGGGTAAGTA 59.420 50.000 0.00 0.00 0.00 2.24
504 511 0.824109 TTCCCTGCGTCACCTCTATG 59.176 55.000 0.00 0.00 0.00 2.23
508 515 0.174389 CTGCGTCACCTCTATGCAGT 59.826 55.000 8.73 0.00 46.97 4.40
680 693 2.689785 GCGTGCAATGTGCTGGCTA 61.690 57.895 1.43 0.00 45.31 3.93
804 821 4.132441 CGCGCCCCATGCATGTTT 62.132 61.111 24.58 0.00 41.33 2.83
914 933 2.555325 TCACGACCTATATAAGTGGCCG 59.445 50.000 0.00 0.00 33.98 6.13
915 934 1.891150 ACGACCTATATAAGTGGCCGG 59.109 52.381 0.00 0.00 0.00 6.13
916 935 2.165167 CGACCTATATAAGTGGCCGGA 58.835 52.381 5.05 0.00 0.00 5.14
917 936 2.559668 CGACCTATATAAGTGGCCGGAA 59.440 50.000 5.05 0.00 0.00 4.30
918 937 3.613432 CGACCTATATAAGTGGCCGGAAC 60.613 52.174 5.05 1.67 0.00 3.62
945 964 0.461548 TCCGGTGAAGCAGAGCATAG 59.538 55.000 0.00 0.00 0.00 2.23
962 981 4.906792 GCAGCAGGCTAGCGGAGG 62.907 72.222 9.00 0.00 40.25 4.30
1052 1116 1.000993 AGGTGCAGGACTCGGAGAT 59.999 57.895 12.86 0.00 33.89 2.75
1055 1119 1.000359 TGCAGGACTCGGAGATCCA 60.000 57.895 21.00 6.85 36.91 3.41
1232 1296 0.315059 CGTTCATGCGTTGGCGTATC 60.315 55.000 0.00 0.00 41.30 2.24
1490 1603 3.121559 TCGTACGTGTGTATGTACTGC 57.878 47.619 16.05 0.00 43.83 4.40
1492 1605 2.591148 CGTACGTGTGTATGTACTGCAC 59.409 50.000 7.22 1.48 43.83 4.57
1493 1606 3.668757 CGTACGTGTGTATGTACTGCACT 60.669 47.826 7.22 0.00 43.83 4.40
1494 1607 2.672714 ACGTGTGTATGTACTGCACTG 58.327 47.619 13.23 9.60 40.74 3.66
1495 1608 2.035449 ACGTGTGTATGTACTGCACTGT 59.965 45.455 13.23 10.03 40.74 3.55
1552 1665 3.995636 AGGCTAGGTTGAAGGATGTAGA 58.004 45.455 0.00 0.00 0.00 2.59
1578 1695 1.656652 AGTAGCGTTGATGCATGTCC 58.343 50.000 2.46 0.00 37.31 4.02
1636 1753 2.635427 TGGCTACAAAATTTTGGTCCCC 59.365 45.455 29.37 22.84 42.34 4.81
1666 1842 0.456221 CGCCGTAGCCCCTCTATATG 59.544 60.000 0.00 0.00 34.57 1.78
1715 1892 1.200484 GGCTGCAAAATTTTGGCATGG 59.800 47.619 27.60 16.73 38.57 3.66
1750 1927 2.505819 AGCCAATGATCCCCGGATATAC 59.494 50.000 0.73 0.00 34.60 1.47
1751 1928 2.505819 GCCAATGATCCCCGGATATACT 59.494 50.000 0.73 0.00 34.60 2.12
1752 1929 3.054361 GCCAATGATCCCCGGATATACTT 60.054 47.826 0.73 0.00 34.60 2.24
1753 1930 4.163458 GCCAATGATCCCCGGATATACTTA 59.837 45.833 0.73 0.00 34.60 2.24
1755 1932 6.042781 GCCAATGATCCCCGGATATACTTATA 59.957 42.308 0.73 0.00 34.60 0.98
1756 1933 7.256691 GCCAATGATCCCCGGATATACTTATAT 60.257 40.741 0.73 0.00 34.60 0.86
1761 1938 9.947189 TGATCCCCGGATATACTTATATAAGTT 57.053 33.333 28.42 19.15 39.82 2.66
1791 1968 1.067364 TGGTCGTGTCTGCGAAAACTA 59.933 47.619 0.00 0.00 42.82 2.24
1793 1970 1.121967 GTCGTGTCTGCGAAAACTACG 59.878 52.381 0.00 0.00 42.82 3.51
1874 2052 7.180408 AGTGATGTATACGGCCCTCTTATTAAT 59.820 37.037 0.00 0.00 0.00 1.40
1879 2057 8.212312 TGTATACGGCCCTCTTATTAATGAAAA 58.788 33.333 0.00 0.00 0.00 2.29
1902 2080 4.736126 AAAGGTTCCAACAAGGTTTCAG 57.264 40.909 0.00 0.00 39.02 3.02
2087 2265 0.833834 CCCGAGCTACCATCTCCCAT 60.834 60.000 0.00 0.00 0.00 4.00
2088 2266 1.051812 CCGAGCTACCATCTCCCATT 58.948 55.000 0.00 0.00 0.00 3.16
2089 2267 1.001406 CCGAGCTACCATCTCCCATTC 59.999 57.143 0.00 0.00 0.00 2.67
2090 2268 1.001406 CGAGCTACCATCTCCCATTCC 59.999 57.143 0.00 0.00 0.00 3.01
2091 2269 1.349357 GAGCTACCATCTCCCATTCCC 59.651 57.143 0.00 0.00 0.00 3.97
2093 2271 1.072965 GCTACCATCTCCCATTCCCTG 59.927 57.143 0.00 0.00 0.00 4.45
2094 2272 2.694397 CTACCATCTCCCATTCCCTGA 58.306 52.381 0.00 0.00 0.00 3.86
2095 2273 1.216990 ACCATCTCCCATTCCCTGAC 58.783 55.000 0.00 0.00 0.00 3.51
2100 2278 1.010046 TCTCCCATTCCCTGACTCCAT 59.990 52.381 0.00 0.00 0.00 3.41
2101 2279 1.419387 CTCCCATTCCCTGACTCCATC 59.581 57.143 0.00 0.00 0.00 3.51
2102 2280 0.107456 CCCATTCCCTGACTCCATCG 59.893 60.000 0.00 0.00 0.00 3.84
2117 2324 0.385751 CATCGGAGTAGCGACCATGT 59.614 55.000 0.00 0.00 0.00 3.21
2153 2385 6.861065 AAGTGAATACGTGATGTTCTGTTT 57.139 33.333 0.00 0.00 30.03 2.83
2169 2409 7.715657 TGTTCTGTTTATCATTTCTGCAAGTT 58.284 30.769 0.00 0.00 33.76 2.66
2180 2420 3.895232 TCTGCAAGTTCAGATAGTCCC 57.105 47.619 0.00 0.00 38.11 4.46
2257 2497 5.132502 CAGTGAGCCATATCCCAAATAACA 58.867 41.667 0.00 0.00 0.00 2.41
2303 2543 6.885735 AATATTAAAAGCAATGTGAACCGC 57.114 33.333 0.00 0.00 0.00 5.68
2307 2547 0.827507 AAGCAATGTGAACCGCCCTT 60.828 50.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.192212 GGTCTACGTGTTAGTAGCCAACT 59.808 47.826 0.00 0.00 42.73 3.16
1 2 3.057315 TGGTCTACGTGTTAGTAGCCAAC 60.057 47.826 0.00 3.30 42.32 3.77
2 3 3.156293 TGGTCTACGTGTTAGTAGCCAA 58.844 45.455 0.00 0.00 42.32 4.52
3 4 2.794103 TGGTCTACGTGTTAGTAGCCA 58.206 47.619 0.00 12.67 42.66 4.75
4 5 4.578105 AGTATGGTCTACGTGTTAGTAGCC 59.422 45.833 0.00 5.36 42.73 3.93
5 6 5.747951 AGTATGGTCTACGTGTTAGTAGC 57.252 43.478 0.00 0.00 42.73 3.58
6 7 6.471519 GCAAAGTATGGTCTACGTGTTAGTAG 59.528 42.308 0.00 0.00 43.97 2.57
7 8 6.072008 TGCAAAGTATGGTCTACGTGTTAGTA 60.072 38.462 0.00 0.00 0.00 1.82
8 9 5.166398 GCAAAGTATGGTCTACGTGTTAGT 58.834 41.667 0.00 0.00 0.00 2.24
9 10 5.165676 TGCAAAGTATGGTCTACGTGTTAG 58.834 41.667 0.00 0.00 0.00 2.34
10 11 5.136816 TGCAAAGTATGGTCTACGTGTTA 57.863 39.130 0.00 0.00 0.00 2.41
11 12 3.997762 TGCAAAGTATGGTCTACGTGTT 58.002 40.909 0.00 0.00 0.00 3.32
12 13 3.671008 TGCAAAGTATGGTCTACGTGT 57.329 42.857 0.00 0.00 0.00 4.49
13 14 5.178623 TCTTTTGCAAAGTATGGTCTACGTG 59.821 40.000 12.41 0.00 0.00 4.49
14 15 5.302360 TCTTTTGCAAAGTATGGTCTACGT 58.698 37.500 12.41 0.00 0.00 3.57
15 16 5.408604 ACTCTTTTGCAAAGTATGGTCTACG 59.591 40.000 12.41 0.00 0.00 3.51
16 17 6.803154 ACTCTTTTGCAAAGTATGGTCTAC 57.197 37.500 12.41 0.00 0.00 2.59
17 18 7.719633 AGAAACTCTTTTGCAAAGTATGGTCTA 59.280 33.333 12.41 0.00 0.00 2.59
18 19 6.547510 AGAAACTCTTTTGCAAAGTATGGTCT 59.452 34.615 12.41 9.73 0.00 3.85
19 20 6.739112 AGAAACTCTTTTGCAAAGTATGGTC 58.261 36.000 12.41 7.72 0.00 4.02
20 21 6.715347 AGAAACTCTTTTGCAAAGTATGGT 57.285 33.333 12.41 5.87 0.00 3.55
21 22 9.528018 TTTAAGAAACTCTTTTGCAAAGTATGG 57.472 29.630 12.41 5.28 37.89 2.74
24 25 9.915629 TGTTTTAAGAAACTCTTTTGCAAAGTA 57.084 25.926 12.41 3.78 44.33 2.24
25 26 8.825667 TGTTTTAAGAAACTCTTTTGCAAAGT 57.174 26.923 12.41 4.08 44.33 2.66
26 27 9.693157 CATGTTTTAAGAAACTCTTTTGCAAAG 57.307 29.630 12.41 3.37 44.33 2.77
27 28 8.174422 GCATGTTTTAAGAAACTCTTTTGCAAA 58.826 29.630 8.05 8.05 44.33 3.68
28 29 7.201600 GGCATGTTTTAAGAAACTCTTTTGCAA 60.202 33.333 0.00 0.00 44.33 4.08
29 30 6.257630 GGCATGTTTTAAGAAACTCTTTTGCA 59.742 34.615 0.00 0.00 44.33 4.08
30 31 6.479990 AGGCATGTTTTAAGAAACTCTTTTGC 59.520 34.615 0.00 0.00 44.33 3.68
31 32 7.922811 AGAGGCATGTTTTAAGAAACTCTTTTG 59.077 33.333 0.00 0.00 44.33 2.44
32 33 8.011844 AGAGGCATGTTTTAAGAAACTCTTTT 57.988 30.769 0.00 0.00 44.33 2.27
33 34 7.588497 AGAGGCATGTTTTAAGAAACTCTTT 57.412 32.000 0.00 0.00 44.33 2.52
34 35 8.568794 GTTAGAGGCATGTTTTAAGAAACTCTT 58.431 33.333 0.00 0.00 44.33 2.85
35 36 7.719633 TGTTAGAGGCATGTTTTAAGAAACTCT 59.280 33.333 0.00 0.00 44.33 3.24
36 37 7.871853 TGTTAGAGGCATGTTTTAAGAAACTC 58.128 34.615 0.00 0.00 44.33 3.01
37 38 7.817418 TGTTAGAGGCATGTTTTAAGAAACT 57.183 32.000 0.00 0.00 44.33 2.66
38 39 8.865590 TTTGTTAGAGGCATGTTTTAAGAAAC 57.134 30.769 0.00 0.00 44.29 2.78
39 40 8.908903 TCTTTGTTAGAGGCATGTTTTAAGAAA 58.091 29.630 0.00 0.81 0.00 2.52
40 41 8.458573 TCTTTGTTAGAGGCATGTTTTAAGAA 57.541 30.769 0.00 0.00 0.00 2.52
41 42 8.099364 CTCTTTGTTAGAGGCATGTTTTAAGA 57.901 34.615 0.00 0.00 45.61 2.10
55 56 6.080648 TGAACTACGCTTCTCTTTGTTAGA 57.919 37.500 0.00 0.00 0.00 2.10
56 57 6.764877 TTGAACTACGCTTCTCTTTGTTAG 57.235 37.500 0.00 0.00 0.00 2.34
57 58 7.493320 TCTTTTGAACTACGCTTCTCTTTGTTA 59.507 33.333 0.00 0.00 0.00 2.41
58 59 6.315393 TCTTTTGAACTACGCTTCTCTTTGTT 59.685 34.615 0.00 0.00 0.00 2.83
59 60 5.815740 TCTTTTGAACTACGCTTCTCTTTGT 59.184 36.000 0.00 0.00 0.00 2.83
60 61 6.287107 TCTTTTGAACTACGCTTCTCTTTG 57.713 37.500 0.00 0.00 0.00 2.77
61 62 6.920569 TTCTTTTGAACTACGCTTCTCTTT 57.079 33.333 0.00 0.00 32.77 2.52
62 63 7.226720 TGAATTCTTTTGAACTACGCTTCTCTT 59.773 33.333 7.05 0.00 41.77 2.85
63 64 6.706270 TGAATTCTTTTGAACTACGCTTCTCT 59.294 34.615 7.05 0.00 41.77 3.10
64 65 6.888430 TGAATTCTTTTGAACTACGCTTCTC 58.112 36.000 7.05 0.00 41.77 2.87
65 66 6.861065 TGAATTCTTTTGAACTACGCTTCT 57.139 33.333 7.05 0.00 41.77 2.85
66 67 7.908193 TTTGAATTCTTTTGAACTACGCTTC 57.092 32.000 7.05 0.00 41.77 3.86
67 68 8.134895 TCATTTGAATTCTTTTGAACTACGCTT 58.865 29.630 7.05 0.00 41.77 4.68
68 69 7.648142 TCATTTGAATTCTTTTGAACTACGCT 58.352 30.769 7.05 0.00 41.77 5.07
69 70 7.851822 TCATTTGAATTCTTTTGAACTACGC 57.148 32.000 7.05 0.00 41.77 4.42
70 71 9.663904 TCTTCATTTGAATTCTTTTGAACTACG 57.336 29.630 7.05 2.46 41.77 3.51
75 76 8.767085 GCATGTCTTCATTTGAATTCTTTTGAA 58.233 29.630 7.05 11.04 36.07 2.69
76 77 7.115236 CGCATGTCTTCATTTGAATTCTTTTGA 59.885 33.333 7.05 4.11 33.01 2.69
77 78 7.115236 TCGCATGTCTTCATTTGAATTCTTTTG 59.885 33.333 7.05 1.78 33.01 2.44
78 79 7.147312 TCGCATGTCTTCATTTGAATTCTTTT 58.853 30.769 7.05 0.00 33.01 2.27
79 80 6.680810 TCGCATGTCTTCATTTGAATTCTTT 58.319 32.000 7.05 0.00 33.01 2.52
80 81 6.258230 TCGCATGTCTTCATTTGAATTCTT 57.742 33.333 7.05 0.00 33.01 2.52
81 82 5.885230 TCGCATGTCTTCATTTGAATTCT 57.115 34.783 7.05 0.00 33.01 2.40
82 83 5.858049 TGTTCGCATGTCTTCATTTGAATTC 59.142 36.000 0.00 0.00 31.71 2.17
83 84 5.771469 TGTTCGCATGTCTTCATTTGAATT 58.229 33.333 0.00 0.00 31.71 2.17
84 85 5.375417 TGTTCGCATGTCTTCATTTGAAT 57.625 34.783 0.00 0.00 31.71 2.57
85 86 4.827304 TGTTCGCATGTCTTCATTTGAA 57.173 36.364 0.00 0.00 31.15 2.69
86 87 5.874261 TCTATGTTCGCATGTCTTCATTTGA 59.126 36.000 0.00 0.00 38.47 2.69
87 88 5.961843 GTCTATGTTCGCATGTCTTCATTTG 59.038 40.000 0.00 0.00 38.47 2.32
88 89 5.643348 TGTCTATGTTCGCATGTCTTCATTT 59.357 36.000 0.00 0.00 38.47 2.32
89 90 5.178061 TGTCTATGTTCGCATGTCTTCATT 58.822 37.500 0.00 0.00 38.47 2.57
90 91 4.758688 TGTCTATGTTCGCATGTCTTCAT 58.241 39.130 0.00 0.00 38.47 2.57
91 92 4.186856 TGTCTATGTTCGCATGTCTTCA 57.813 40.909 0.00 0.00 38.47 3.02
92 93 5.107104 TGTTTGTCTATGTTCGCATGTCTTC 60.107 40.000 0.00 0.00 38.47 2.87
93 94 4.754618 TGTTTGTCTATGTTCGCATGTCTT 59.245 37.500 0.00 0.00 38.47 3.01
94 95 4.314961 TGTTTGTCTATGTTCGCATGTCT 58.685 39.130 0.00 0.00 38.47 3.41
95 96 4.661993 TGTTTGTCTATGTTCGCATGTC 57.338 40.909 0.00 0.00 38.47 3.06
96 97 5.238432 TCTTTGTTTGTCTATGTTCGCATGT 59.762 36.000 0.00 0.00 38.47 3.21
97 98 5.565259 GTCTTTGTTTGTCTATGTTCGCATG 59.435 40.000 0.00 0.00 38.47 4.06
98 99 5.334879 GGTCTTTGTTTGTCTATGTTCGCAT 60.335 40.000 0.00 0.00 41.41 4.73
99 100 4.024387 GGTCTTTGTTTGTCTATGTTCGCA 60.024 41.667 0.00 0.00 0.00 5.10
100 101 4.464112 GGTCTTTGTTTGTCTATGTTCGC 58.536 43.478 0.00 0.00 0.00 4.70
101 102 4.446385 TCGGTCTTTGTTTGTCTATGTTCG 59.554 41.667 0.00 0.00 0.00 3.95
102 103 5.917541 TCGGTCTTTGTTTGTCTATGTTC 57.082 39.130 0.00 0.00 0.00 3.18
103 104 6.072673 GGATTCGGTCTTTGTTTGTCTATGTT 60.073 38.462 0.00 0.00 0.00 2.71
104 105 5.411669 GGATTCGGTCTTTGTTTGTCTATGT 59.588 40.000 0.00 0.00 0.00 2.29
105 106 5.411361 TGGATTCGGTCTTTGTTTGTCTATG 59.589 40.000 0.00 0.00 0.00 2.23
106 107 5.556915 TGGATTCGGTCTTTGTTTGTCTAT 58.443 37.500 0.00 0.00 0.00 1.98
107 108 4.963373 TGGATTCGGTCTTTGTTTGTCTA 58.037 39.130 0.00 0.00 0.00 2.59
108 109 3.815809 TGGATTCGGTCTTTGTTTGTCT 58.184 40.909 0.00 0.00 0.00 3.41
109 110 4.537015 CTTGGATTCGGTCTTTGTTTGTC 58.463 43.478 0.00 0.00 0.00 3.18
110 111 3.243401 GCTTGGATTCGGTCTTTGTTTGT 60.243 43.478 0.00 0.00 0.00 2.83
111 112 3.243367 TGCTTGGATTCGGTCTTTGTTTG 60.243 43.478 0.00 0.00 0.00 2.93
112 113 2.955660 TGCTTGGATTCGGTCTTTGTTT 59.044 40.909 0.00 0.00 0.00 2.83
113 114 2.554032 CTGCTTGGATTCGGTCTTTGTT 59.446 45.455 0.00 0.00 0.00 2.83
114 115 2.154462 CTGCTTGGATTCGGTCTTTGT 58.846 47.619 0.00 0.00 0.00 2.83
115 116 2.426522 TCTGCTTGGATTCGGTCTTTG 58.573 47.619 0.00 0.00 0.00 2.77
116 117 2.859165 TCTGCTTGGATTCGGTCTTT 57.141 45.000 0.00 0.00 0.00 2.52
117 118 3.274288 GAATCTGCTTGGATTCGGTCTT 58.726 45.455 10.21 0.00 41.07 3.01
118 119 2.911484 GAATCTGCTTGGATTCGGTCT 58.089 47.619 10.21 0.00 41.07 3.85
123 124 5.449725 GCCTTTAGTGAATCTGCTTGGATTC 60.450 44.000 15.51 15.51 46.82 2.52
124 125 4.400567 GCCTTTAGTGAATCTGCTTGGATT 59.599 41.667 0.00 0.00 38.47 3.01
125 126 3.950395 GCCTTTAGTGAATCTGCTTGGAT 59.050 43.478 0.00 0.00 0.00 3.41
126 127 3.244875 TGCCTTTAGTGAATCTGCTTGGA 60.245 43.478 0.00 0.00 0.00 3.53
127 128 3.084039 TGCCTTTAGTGAATCTGCTTGG 58.916 45.455 0.00 0.00 0.00 3.61
128 129 4.479619 GTTGCCTTTAGTGAATCTGCTTG 58.520 43.478 0.00 0.00 0.00 4.01
129 130 3.507622 GGTTGCCTTTAGTGAATCTGCTT 59.492 43.478 0.00 0.00 0.00 3.91
130 131 3.084786 GGTTGCCTTTAGTGAATCTGCT 58.915 45.455 0.00 0.00 0.00 4.24
131 132 2.819608 TGGTTGCCTTTAGTGAATCTGC 59.180 45.455 0.00 0.00 0.00 4.26
132 133 3.191371 GGTGGTTGCCTTTAGTGAATCTG 59.809 47.826 0.00 0.00 0.00 2.90
133 134 3.421844 GGTGGTTGCCTTTAGTGAATCT 58.578 45.455 0.00 0.00 0.00 2.40
134 135 2.161609 CGGTGGTTGCCTTTAGTGAATC 59.838 50.000 0.00 0.00 0.00 2.52
135 136 2.159382 CGGTGGTTGCCTTTAGTGAAT 58.841 47.619 0.00 0.00 0.00 2.57
136 137 1.141254 TCGGTGGTTGCCTTTAGTGAA 59.859 47.619 0.00 0.00 0.00 3.18
137 138 0.759959 TCGGTGGTTGCCTTTAGTGA 59.240 50.000 0.00 0.00 0.00 3.41
138 139 0.872388 GTCGGTGGTTGCCTTTAGTG 59.128 55.000 0.00 0.00 0.00 2.74
139 140 0.250597 GGTCGGTGGTTGCCTTTAGT 60.251 55.000 0.00 0.00 0.00 2.24
140 141 1.296056 CGGTCGGTGGTTGCCTTTAG 61.296 60.000 0.00 0.00 0.00 1.85
146 147 2.396157 GGATTCGGTCGGTGGTTGC 61.396 63.158 0.00 0.00 0.00 4.17
153 154 0.747255 ATCTCACAGGATTCGGTCGG 59.253 55.000 0.00 0.00 0.00 4.79
182 183 2.665185 GGACGTGTGGAGGTGTGC 60.665 66.667 0.00 0.00 0.00 4.57
202 203 1.293963 TGGAGTGTCTACCGTCGTCG 61.294 60.000 0.00 0.00 0.00 5.12
203 204 0.167689 GTGGAGTGTCTACCGTCGTC 59.832 60.000 0.00 0.00 0.00 4.20
210 211 0.896940 TGTCCCGGTGGAGTGTCTAC 60.897 60.000 0.00 0.00 42.85 2.59
218 219 3.549433 TAGCCCTTGTCCCGGTGGA 62.549 63.158 0.00 0.00 38.75 4.02
220 221 1.987855 TCTAGCCCTTGTCCCGGTG 60.988 63.158 0.00 0.00 0.00 4.94
222 223 2.901042 GTCTAGCCCTTGTCCCGG 59.099 66.667 0.00 0.00 0.00 5.73
225 226 1.677637 CTCCCGTCTAGCCCTTGTCC 61.678 65.000 0.00 0.00 0.00 4.02
230 231 1.381463 GGTTCTCCCGTCTAGCCCT 60.381 63.158 0.00 0.00 0.00 5.19
231 232 0.976590 AAGGTTCTCCCGTCTAGCCC 60.977 60.000 0.00 0.00 38.74 5.19
233 234 3.243805 GGAATAAGGTTCTCCCGTCTAGC 60.244 52.174 0.00 0.00 38.74 3.42
235 236 3.985127 TGGAATAAGGTTCTCCCGTCTA 58.015 45.455 0.00 0.00 38.74 2.59
238 239 3.385115 AGATGGAATAAGGTTCTCCCGT 58.615 45.455 0.00 0.00 38.74 5.28
239 240 4.423625 AAGATGGAATAAGGTTCTCCCG 57.576 45.455 0.00 0.00 38.74 5.14
241 242 7.138054 TCCTAAAGATGGAATAAGGTTCTCC 57.862 40.000 0.00 0.00 0.00 3.71
244 245 6.263392 GGCTTCCTAAAGATGGAATAAGGTTC 59.737 42.308 0.00 0.00 42.03 3.62
248 249 5.368989 ACGGCTTCCTAAAGATGGAATAAG 58.631 41.667 0.00 0.00 42.03 1.73
255 256 0.931005 GCGACGGCTTCCTAAAGATG 59.069 55.000 0.00 0.00 34.14 2.90
276 277 4.963237 GTCATGCTTATGATGACGAGAC 57.037 45.455 0.00 0.00 40.16 3.36
281 282 5.335127 GGTTTGTGTCATGCTTATGATGAC 58.665 41.667 7.07 7.07 46.72 3.06
284 285 4.603131 AGGGTTTGTGTCATGCTTATGAT 58.397 39.130 0.00 0.00 32.61 2.45
289 290 2.162681 GCTAGGGTTTGTGTCATGCTT 58.837 47.619 0.00 0.00 0.00 3.91
291 292 1.533625 TGCTAGGGTTTGTGTCATGC 58.466 50.000 0.00 0.00 0.00 4.06
294 295 4.098914 AGATTTGCTAGGGTTTGTGTCA 57.901 40.909 0.00 0.00 0.00 3.58
303 304 9.143631 CAAATGTTTCTTTAAGATTTGCTAGGG 57.856 33.333 6.02 0.00 45.02 3.53
316 317 8.463607 AGGACTTCGTTTTCAAATGTTTCTTTA 58.536 29.630 0.00 0.00 0.00 1.85
320 321 5.685954 GGAGGACTTCGTTTTCAAATGTTTC 59.314 40.000 0.00 0.00 0.00 2.78
324 325 3.568007 TGGGAGGACTTCGTTTTCAAATG 59.432 43.478 0.00 0.00 0.00 2.32
327 328 3.408634 GATGGGAGGACTTCGTTTTCAA 58.591 45.455 0.00 0.00 0.00 2.69
329 330 2.000447 CGATGGGAGGACTTCGTTTTC 59.000 52.381 0.00 0.00 34.51 2.29
336 337 1.604378 CTTGCCGATGGGAGGACTT 59.396 57.895 0.00 0.00 34.06 3.01
350 351 2.349590 GTGATGAATTTTGGCCCTTGC 58.650 47.619 0.00 0.00 0.00 4.01
351 352 2.609350 CGTGATGAATTTTGGCCCTTG 58.391 47.619 0.00 0.00 0.00 3.61
359 360 3.788333 CCATGAGGCGTGATGAATTTT 57.212 42.857 7.46 0.00 0.00 1.82
381 382 3.617368 GCCTCGTCTGGCCTTAGA 58.383 61.111 3.32 0.00 46.82 2.10
397 403 1.139520 GGTGGTGCCATCGATTTGC 59.860 57.895 9.26 9.26 37.17 3.68
412 418 3.000819 TGCCTCCTACCACCGGTG 61.001 66.667 28.26 28.26 36.19 4.94
413 419 2.683933 CTGCCTCCTACCACCGGT 60.684 66.667 0.00 0.00 40.16 5.28
414 420 3.470888 CCTGCCTCCTACCACCGG 61.471 72.222 0.00 0.00 0.00 5.28
415 421 1.987855 TTCCTGCCTCCTACCACCG 60.988 63.158 0.00 0.00 0.00 4.94
416 422 1.602771 GTTCCTGCCTCCTACCACC 59.397 63.158 0.00 0.00 0.00 4.61
417 423 1.602771 GGTTCCTGCCTCCTACCAC 59.397 63.158 0.00 0.00 0.00 4.16
418 424 1.615424 GGGTTCCTGCCTCCTACCA 60.615 63.158 0.00 0.00 0.00 3.25
419 425 0.031414 TAGGGTTCCTGCCTCCTACC 60.031 60.000 0.00 0.00 34.61 3.18
420 426 1.875488 TTAGGGTTCCTGCCTCCTAC 58.125 55.000 0.00 0.00 34.61 3.18
421 427 2.690840 GATTAGGGTTCCTGCCTCCTA 58.309 52.381 0.00 0.00 34.61 2.94
422 428 1.512735 GATTAGGGTTCCTGCCTCCT 58.487 55.000 0.00 0.00 34.61 3.69
434 440 3.659786 TCAAGTGAACACACGATTAGGG 58.340 45.455 7.68 0.00 39.25 3.53
455 461 1.296984 TACCCCTTCGTCTCTCCTCT 58.703 55.000 0.00 0.00 0.00 3.69
486 493 1.676678 GCATAGAGGTGACGCAGGGA 61.677 60.000 0.00 0.00 0.00 4.20
498 505 5.008019 ACAAACTGTTCACAACTGCATAGAG 59.992 40.000 0.00 0.00 34.11 2.43
504 511 5.231991 CCATAAACAAACTGTTCACAACTGC 59.768 40.000 0.00 0.00 40.14 4.40
508 515 6.767524 ACTCCATAAACAAACTGTTCACAA 57.232 33.333 0.00 0.00 40.14 3.33
561 569 4.695993 TGAAGCATGACGGGCGCA 62.696 61.111 10.83 0.00 36.08 6.09
587 595 1.873698 TCAGCACGTTGGGTACTTTC 58.126 50.000 0.00 0.00 0.00 2.62
680 693 3.322466 CGTGGAGGCCCTTCTGGT 61.322 66.667 0.00 0.00 36.04 4.00
760 776 4.216257 CACGTTTGATGGGAAGTGATTTCT 59.784 41.667 0.00 0.00 36.03 2.52
819 836 1.302993 TTACCGCTGCCTTTCACCC 60.303 57.895 0.00 0.00 0.00 4.61
832 849 3.773630 CGTGGTGCGCTGTTACCG 61.774 66.667 9.73 0.00 39.87 4.02
914 933 3.069318 ACCGGAGAGCGGAGTTCC 61.069 66.667 9.46 0.00 39.04 3.62
915 934 1.874345 TTCACCGGAGAGCGGAGTTC 61.874 60.000 9.46 0.00 38.31 3.01
916 935 1.878656 CTTCACCGGAGAGCGGAGTT 61.879 60.000 9.46 0.00 0.00 3.01
917 936 2.282958 TTCACCGGAGAGCGGAGT 60.283 61.111 9.46 0.00 0.00 3.85
918 937 2.492090 CTTCACCGGAGAGCGGAG 59.508 66.667 9.46 0.00 0.00 4.63
928 947 0.460811 TGCTATGCTCTGCTTCACCG 60.461 55.000 0.00 0.00 0.00 4.94
945 964 4.906792 CCTCCGCTAGCCTGCTGC 62.907 72.222 9.66 2.97 41.71 5.25
962 981 3.119792 CGTAACAAGTCTTCGAAGTCTGC 59.880 47.826 22.66 12.83 0.00 4.26
1013 1035 4.760047 GCTCCGGCGCCTTCTTCA 62.760 66.667 26.68 0.00 0.00 3.02
1036 1100 1.323271 TGGATCTCCGAGTCCTGCAC 61.323 60.000 14.41 0.00 39.43 4.57
1052 1116 0.394192 CTTCACCTGCTGTGTCTGGA 59.606 55.000 6.80 0.00 45.61 3.86
1055 1119 1.071385 CCTTCTTCACCTGCTGTGTCT 59.929 52.381 6.80 0.00 45.61 3.41
1232 1296 3.627577 ACACAAAGTTAGAGCAACACCAG 59.372 43.478 0.00 0.00 39.81 4.00
1490 1603 5.542616 AGCACTACGTACTAACTACAGTG 57.457 43.478 5.22 5.22 0.00 3.66
1492 1605 6.481313 TCCATAGCACTACGTACTAACTACAG 59.519 42.308 0.00 0.00 0.00 2.74
1493 1606 6.348498 TCCATAGCACTACGTACTAACTACA 58.652 40.000 0.00 0.00 0.00 2.74
1494 1607 6.851222 TCCATAGCACTACGTACTAACTAC 57.149 41.667 0.00 0.00 0.00 2.73
1495 1608 6.994496 ACATCCATAGCACTACGTACTAACTA 59.006 38.462 0.00 0.00 0.00 2.24
1602 1719 0.026803 GTAGCCAGACGTACGTACCG 59.973 60.000 22.87 16.17 0.00 4.02
1603 1720 1.086696 TGTAGCCAGACGTACGTACC 58.913 55.000 22.87 10.14 0.00 3.34
1613 1730 3.576550 GGGACCAAAATTTTGTAGCCAGA 59.423 43.478 25.25 0.00 36.45 3.86
1685 1861 1.544724 TTTTGCAGCCAGGGTACATC 58.455 50.000 0.00 0.00 0.00 3.06
1715 1892 4.430007 TCATTGGCTACAGAACGTACATC 58.570 43.478 0.00 0.00 0.00 3.06
1755 1932 8.475639 AGACACGACCACTATTTATCAACTTAT 58.524 33.333 0.00 0.00 0.00 1.73
1756 1933 7.758076 CAGACACGACCACTATTTATCAACTTA 59.242 37.037 0.00 0.00 0.00 2.24
1758 1935 6.100004 CAGACACGACCACTATTTATCAACT 58.900 40.000 0.00 0.00 0.00 3.16
1759 1936 5.220416 GCAGACACGACCACTATTTATCAAC 60.220 44.000 0.00 0.00 0.00 3.18
1760 1937 4.868171 GCAGACACGACCACTATTTATCAA 59.132 41.667 0.00 0.00 0.00 2.57
1761 1938 4.430007 GCAGACACGACCACTATTTATCA 58.570 43.478 0.00 0.00 0.00 2.15
1762 1939 3.486108 CGCAGACACGACCACTATTTATC 59.514 47.826 0.00 0.00 34.06 1.75
1774 1951 1.401530 CGTAGTTTTCGCAGACACGA 58.598 50.000 0.00 0.00 41.04 4.35
1791 1968 5.830000 AAAAAGGAAAGAAGTTAGTGCGT 57.170 34.783 0.00 0.00 0.00 5.24
1879 2057 5.247337 TCTGAAACCTTGTTGGAACCTTTTT 59.753 36.000 0.00 0.00 39.71 1.94
1954 2132 1.257743 GGCTAGTCTGTGTGTCCAGA 58.742 55.000 0.00 0.00 39.11 3.86
2087 2265 2.901975 CTCCGATGGAGTCAGGGAA 58.098 57.895 4.65 0.00 44.25 3.97
2088 2266 4.686695 CTCCGATGGAGTCAGGGA 57.313 61.111 4.65 0.00 44.25 4.20
2100 2278 1.019673 GTACATGGTCGCTACTCCGA 58.980 55.000 0.00 0.00 34.40 4.55
2101 2279 0.316772 CGTACATGGTCGCTACTCCG 60.317 60.000 0.00 0.00 0.00 4.63
2102 2280 1.019673 TCGTACATGGTCGCTACTCC 58.980 55.000 0.00 0.00 0.00 3.85
2117 2324 4.150980 CGTATTCACTTTTTGCAGGTCGTA 59.849 41.667 0.00 0.00 0.00 3.43
2153 2385 7.712639 GGACTATCTGAACTTGCAGAAATGATA 59.287 37.037 0.00 0.00 46.94 2.15
2169 2409 2.354704 CGCTTTGTTGGGGACTATCTGA 60.355 50.000 0.00 0.00 0.00 3.27
2180 2420 0.102120 TGGAGTTTGCGCTTTGTTGG 59.898 50.000 9.73 0.00 0.00 3.77
2257 2497 3.769844 ACTCCACCGAATTCTGTCACTAT 59.230 43.478 3.52 0.00 0.00 2.12
2303 2543 4.389077 CGTTTGCTAGAGTACTTTGAAGGG 59.611 45.833 0.00 0.00 0.00 3.95
2307 2547 3.863400 GCCCGTTTGCTAGAGTACTTTGA 60.863 47.826 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.