Multiple sequence alignment - TraesCS1A01G065200

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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 TraesCS1A01G065200 chr1A 100.000 2538 0 0 1 2538 47379105 47376568 0.000000e+00 4687
1 TraesCS1A01G065200 chr1A 91.624 1576 114 12 373 1939 17306508 17304942 0.000000e+00 2163
2 TraesCS1A01G065200 chr7A 97.279 2168 33 5 373 2538 415463728 415461585 0.000000e+00 3653
3 TraesCS1A01G065200 chr7A 98.057 1132 20 1 373 1502 415923126 415921995 0.000000e+00 1967
4 TraesCS1A01G065200 chr7A 98.082 365 6 1 2146 2510 415922003 415921640 3.560000e-178 634
5 TraesCS1A01G065200 chr7A 94.865 370 19 0 3 372 582097133 582096764 1.690000e-161 579
6 TraesCS1A01G065200 chr6A 98.346 1814 28 2 725 2538 589252444 589250633 0.000000e+00 3182
7 TraesCS1A01G065200 chr3A 92.609 2192 120 19 373 2538 723838464 723840639 0.000000e+00 3112
8 TraesCS1A01G065200 chr3A 94.865 370 19 0 3 372 328821852 328821483 1.690000e-161 579
9 TraesCS1A01G065200 chr3A 83.092 621 73 20 373 971 746942392 746943002 1.030000e-148 536
10 TraesCS1A01G065200 chr4D 95.393 369 16 1 4 372 321842162 321841795 1.010000e-163 586
11 TraesCS1A01G065200 chr4D 94.823 367 19 0 3 369 40947020 40947386 7.880000e-160 573
12 TraesCS1A01G065200 chr5D 95.135 370 18 0 3 372 107612212 107612581 3.640000e-163 584
13 TraesCS1A01G065200 chr5D 94.595 370 20 0 3 372 120234233 120233864 7.880000e-160 573
14 TraesCS1A01G065200 chr5D 94.595 370 20 0 3 372 221321985 221321616 7.880000e-160 573
15 TraesCS1A01G065200 chr3D 95.330 364 17 0 3 366 22616848 22617211 1.690000e-161 579
16 TraesCS1A01G065200 chr5A 94.624 372 20 0 1 372 310101478 310101107 6.090000e-161 577
17 TraesCS1A01G065200 chr4B 86.460 517 59 8 368 875 41007211 41007725 7.930000e-155 556
18 TraesCS1A01G065200 chr6B 83.601 561 66 13 1547 2088 643521460 643520907 1.050000e-138 503
19 TraesCS1A01G065200 chr3B 85.023 434 47 8 1714 2133 703832095 703831666 2.330000e-115 425
20 TraesCS1A01G065200 chr3B 84.793 434 48 8 1714 2133 73184005 73183576 1.090000e-113 420
21 TraesCS1A01G065200 chr2A 86.453 406 33 10 1714 2101 541819051 541818650 2.330000e-115 425
22 TraesCS1A01G065200 chr2A 82.759 290 40 6 1239 1525 541819817 541819535 1.510000e-62 250
23 TraesCS1A01G065200 chr2A 83.333 132 21 1 372 502 269086077 269085946 1.230000e-23 121


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 TraesCS1A01G065200 chr1A 47376568 47379105 2537 True 4687.0 4687 100.0000 1 2538 1 chr1A.!!$R2 2537
1 TraesCS1A01G065200 chr1A 17304942 17306508 1566 True 2163.0 2163 91.6240 373 1939 1 chr1A.!!$R1 1566
2 TraesCS1A01G065200 chr7A 415461585 415463728 2143 True 3653.0 3653 97.2790 373 2538 1 chr7A.!!$R1 2165
3 TraesCS1A01G065200 chr7A 415921640 415923126 1486 True 1300.5 1967 98.0695 373 2510 2 chr7A.!!$R3 2137
4 TraesCS1A01G065200 chr6A 589250633 589252444 1811 True 3182.0 3182 98.3460 725 2538 1 chr6A.!!$R1 1813
5 TraesCS1A01G065200 chr3A 723838464 723840639 2175 False 3112.0 3112 92.6090 373 2538 1 chr3A.!!$F1 2165
6 TraesCS1A01G065200 chr3A 746942392 746943002 610 False 536.0 536 83.0920 373 971 1 chr3A.!!$F2 598
7 TraesCS1A01G065200 chr4B 41007211 41007725 514 False 556.0 556 86.4600 368 875 1 chr4B.!!$F1 507
8 TraesCS1A01G065200 chr6B 643520907 643521460 553 True 503.0 503 83.6010 1547 2088 1 chr6B.!!$R1 541
9 TraesCS1A01G065200 chr2A 541818650 541819817 1167 True 337.5 425 84.6060 1239 2101 2 chr2A.!!$R2 862

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
303 304 0.036577 CTCCCAGCTGAGTCAAGTGG 60.037 60.0 17.39 11.92 0.0 4.00 F
305 306 0.109342 CCCAGCTGAGTCAAGTGGTT 59.891 55.0 17.39 0.00 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1326 2.818432 CCTCTGAGCAGCTGACAAATTT 59.182 45.455 20.43 0.0 0.0 1.82 R
1708 1840 8.717821 TCCTCTCAAATAAATCACTTGTTAACG 58.282 33.333 0.26 0.0 0.0 3.18 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
24 25 1.814793 GTCCAGACTTGGGCTTCTTC 58.185 55.000 0.00 0.00 45.96 2.87
25 26 1.072331 GTCCAGACTTGGGCTTCTTCA 59.928 52.381 0.00 0.00 45.96 3.02
26 27 1.072331 TCCAGACTTGGGCTTCTTCAC 59.928 52.381 0.00 0.00 45.10 3.18
27 28 1.072965 CCAGACTTGGGCTTCTTCACT 59.927 52.381 0.00 0.00 41.05 3.41
28 29 2.487986 CCAGACTTGGGCTTCTTCACTT 60.488 50.000 0.00 0.00 41.05 3.16
29 30 2.551459 CAGACTTGGGCTTCTTCACTTG 59.449 50.000 0.00 0.00 0.00 3.16
30 31 2.439507 AGACTTGGGCTTCTTCACTTGA 59.560 45.455 0.00 0.00 0.00 3.02
31 32 2.810852 GACTTGGGCTTCTTCACTTGAG 59.189 50.000 0.00 0.00 0.00 3.02
32 33 1.538950 CTTGGGCTTCTTCACTTGAGC 59.461 52.381 0.00 0.00 0.00 4.26
33 34 0.473755 TGGGCTTCTTCACTTGAGCA 59.526 50.000 0.00 0.00 0.00 4.26
34 35 1.163554 GGGCTTCTTCACTTGAGCAG 58.836 55.000 0.00 0.00 0.00 4.24
35 36 0.520847 GGCTTCTTCACTTGAGCAGC 59.479 55.000 0.00 0.00 0.00 5.25
36 37 1.233019 GCTTCTTCACTTGAGCAGCA 58.767 50.000 0.00 0.00 0.00 4.41
37 38 1.605710 GCTTCTTCACTTGAGCAGCAA 59.394 47.619 0.00 0.00 34.73 3.91
38 39 2.228343 GCTTCTTCACTTGAGCAGCAAT 59.772 45.455 0.00 0.00 35.59 3.56
39 40 3.305199 GCTTCTTCACTTGAGCAGCAATT 60.305 43.478 0.00 0.00 35.59 2.32
40 41 4.795308 GCTTCTTCACTTGAGCAGCAATTT 60.795 41.667 0.00 0.00 35.59 1.82
41 42 4.233123 TCTTCACTTGAGCAGCAATTTG 57.767 40.909 0.00 0.00 35.59 2.32
42 43 3.633525 TCTTCACTTGAGCAGCAATTTGT 59.366 39.130 0.00 0.00 35.59 2.83
43 44 4.098349 TCTTCACTTGAGCAGCAATTTGTT 59.902 37.500 0.00 0.00 35.59 2.83
44 45 4.389890 TCACTTGAGCAGCAATTTGTTT 57.610 36.364 0.00 0.00 35.59 2.83
45 46 4.114073 TCACTTGAGCAGCAATTTGTTTG 58.886 39.130 0.00 0.00 35.59 2.93
57 58 5.069485 CAATTTGTTTGCCGTTCTTCTTG 57.931 39.130 0.00 0.00 0.00 3.02
58 59 4.647424 ATTTGTTTGCCGTTCTTCTTGA 57.353 36.364 0.00 0.00 0.00 3.02
59 60 4.442375 TTTGTTTGCCGTTCTTCTTGAA 57.558 36.364 0.00 0.00 0.00 2.69
60 61 3.691049 TGTTTGCCGTTCTTCTTGAAG 57.309 42.857 4.13 4.13 35.01 3.02
61 62 3.013921 TGTTTGCCGTTCTTCTTGAAGT 58.986 40.909 9.80 0.00 35.01 3.01
62 63 3.442273 TGTTTGCCGTTCTTCTTGAAGTT 59.558 39.130 9.80 0.00 35.01 2.66
63 64 3.963383 TTGCCGTTCTTCTTGAAGTTC 57.037 42.857 9.80 0.00 35.01 3.01
64 65 2.218603 TGCCGTTCTTCTTGAAGTTCC 58.781 47.619 9.80 0.23 35.01 3.62
65 66 2.158813 TGCCGTTCTTCTTGAAGTTCCT 60.159 45.455 9.80 0.00 35.01 3.36
66 67 2.480802 GCCGTTCTTCTTGAAGTTCCTC 59.519 50.000 9.80 0.00 35.01 3.71
67 68 3.804063 GCCGTTCTTCTTGAAGTTCCTCT 60.804 47.826 9.80 0.00 35.01 3.69
68 69 4.381411 CCGTTCTTCTTGAAGTTCCTCTT 58.619 43.478 9.80 0.00 39.32 2.85
80 81 4.912317 AGTTCCTCTTCTTCCCTTTACC 57.088 45.455 0.00 0.00 0.00 2.85
81 82 3.587951 AGTTCCTCTTCTTCCCTTTACCC 59.412 47.826 0.00 0.00 0.00 3.69
82 83 3.579742 TCCTCTTCTTCCCTTTACCCT 57.420 47.619 0.00 0.00 0.00 4.34
83 84 3.883135 TCCTCTTCTTCCCTTTACCCTT 58.117 45.455 0.00 0.00 0.00 3.95
84 85 4.248652 TCCTCTTCTTCCCTTTACCCTTT 58.751 43.478 0.00 0.00 0.00 3.11
85 86 4.668335 TCCTCTTCTTCCCTTTACCCTTTT 59.332 41.667 0.00 0.00 0.00 2.27
86 87 5.135533 TCCTCTTCTTCCCTTTACCCTTTTT 59.864 40.000 0.00 0.00 0.00 1.94
87 88 5.477291 CCTCTTCTTCCCTTTACCCTTTTTC 59.523 44.000 0.00 0.00 0.00 2.29
88 89 6.275692 TCTTCTTCCCTTTACCCTTTTTCT 57.724 37.500 0.00 0.00 0.00 2.52
89 90 6.679542 TCTTCTTCCCTTTACCCTTTTTCTT 58.320 36.000 0.00 0.00 0.00 2.52
90 91 6.549736 TCTTCTTCCCTTTACCCTTTTTCTTG 59.450 38.462 0.00 0.00 0.00 3.02
91 92 6.020881 TCTTCCCTTTACCCTTTTTCTTGA 57.979 37.500 0.00 0.00 0.00 3.02
92 93 6.436890 TCTTCCCTTTACCCTTTTTCTTGAA 58.563 36.000 0.00 0.00 0.00 2.69
93 94 6.898521 TCTTCCCTTTACCCTTTTTCTTGAAA 59.101 34.615 0.00 0.00 0.00 2.69
94 95 6.474140 TCCCTTTACCCTTTTTCTTGAAAC 57.526 37.500 0.00 0.00 0.00 2.78
95 96 6.199376 TCCCTTTACCCTTTTTCTTGAAACT 58.801 36.000 0.00 0.00 0.00 2.66
96 97 6.097696 TCCCTTTACCCTTTTTCTTGAAACTG 59.902 38.462 0.00 0.00 0.00 3.16
97 98 6.280643 CCTTTACCCTTTTTCTTGAAACTGG 58.719 40.000 0.00 1.90 0.00 4.00
98 99 6.127168 CCTTTACCCTTTTTCTTGAAACTGGT 60.127 38.462 12.10 12.10 36.14 4.00
99 100 4.736126 ACCCTTTTTCTTGAAACTGGTG 57.264 40.909 8.59 5.66 32.76 4.17
100 101 4.349365 ACCCTTTTTCTTGAAACTGGTGA 58.651 39.130 8.59 0.00 32.76 4.02
101 102 4.962362 ACCCTTTTTCTTGAAACTGGTGAT 59.038 37.500 8.59 0.00 32.76 3.06
102 103 5.069119 ACCCTTTTTCTTGAAACTGGTGATC 59.931 40.000 8.59 0.00 32.76 2.92
103 104 5.302823 CCCTTTTTCTTGAAACTGGTGATCT 59.697 40.000 0.00 0.00 0.00 2.75
104 105 6.183360 CCCTTTTTCTTGAAACTGGTGATCTT 60.183 38.462 0.00 0.00 0.00 2.40
105 106 6.698766 CCTTTTTCTTGAAACTGGTGATCTTG 59.301 38.462 0.00 0.00 0.00 3.02
106 107 6.773976 TTTTCTTGAAACTGGTGATCTTGT 57.226 33.333 0.00 0.00 0.00 3.16
107 108 6.773976 TTTCTTGAAACTGGTGATCTTGTT 57.226 33.333 0.00 0.00 0.00 2.83
108 109 5.756195 TCTTGAAACTGGTGATCTTGTTG 57.244 39.130 0.00 0.00 0.00 3.33
109 110 5.436175 TCTTGAAACTGGTGATCTTGTTGA 58.564 37.500 0.00 0.00 0.00 3.18
110 111 5.296780 TCTTGAAACTGGTGATCTTGTTGAC 59.703 40.000 0.00 0.00 0.00 3.18
111 112 3.882888 TGAAACTGGTGATCTTGTTGACC 59.117 43.478 0.00 0.00 0.00 4.02
112 113 3.576078 AACTGGTGATCTTGTTGACCA 57.424 42.857 0.87 0.87 36.98 4.02
113 114 3.795688 ACTGGTGATCTTGTTGACCAT 57.204 42.857 1.16 0.00 37.83 3.55
114 115 3.679389 ACTGGTGATCTTGTTGACCATC 58.321 45.455 1.16 0.00 37.83 3.51
115 116 3.072915 ACTGGTGATCTTGTTGACCATCA 59.927 43.478 1.16 0.00 37.83 3.07
116 117 4.074259 CTGGTGATCTTGTTGACCATCAA 58.926 43.478 1.16 0.00 37.83 2.57
147 148 9.838339 TGATATTCTTTCTTGATTTCTACCTCC 57.162 33.333 0.00 0.00 0.00 4.30
148 149 8.894768 ATATTCTTTCTTGATTTCTACCTCCG 57.105 34.615 0.00 0.00 0.00 4.63
149 150 4.504858 TCTTTCTTGATTTCTACCTCCGC 58.495 43.478 0.00 0.00 0.00 5.54
150 151 3.973206 TTCTTGATTTCTACCTCCGCA 57.027 42.857 0.00 0.00 0.00 5.69
151 152 3.526931 TCTTGATTTCTACCTCCGCAG 57.473 47.619 0.00 0.00 0.00 5.18
152 153 2.832129 TCTTGATTTCTACCTCCGCAGT 59.168 45.455 0.00 0.00 0.00 4.40
153 154 2.961526 TGATTTCTACCTCCGCAGTC 57.038 50.000 0.00 0.00 0.00 3.51
154 155 2.457598 TGATTTCTACCTCCGCAGTCT 58.542 47.619 0.00 0.00 0.00 3.24
155 156 2.832129 TGATTTCTACCTCCGCAGTCTT 59.168 45.455 0.00 0.00 0.00 3.01
156 157 3.260884 TGATTTCTACCTCCGCAGTCTTT 59.739 43.478 0.00 0.00 0.00 2.52
157 158 4.464951 TGATTTCTACCTCCGCAGTCTTTA 59.535 41.667 0.00 0.00 0.00 1.85
158 159 4.451629 TTTCTACCTCCGCAGTCTTTAG 57.548 45.455 0.00 0.00 0.00 1.85
159 160 1.749634 TCTACCTCCGCAGTCTTTAGC 59.250 52.381 0.00 0.00 0.00 3.09
160 161 1.476891 CTACCTCCGCAGTCTTTAGCA 59.523 52.381 0.00 0.00 0.00 3.49
161 162 0.905357 ACCTCCGCAGTCTTTAGCAT 59.095 50.000 0.00 0.00 0.00 3.79
162 163 1.279271 ACCTCCGCAGTCTTTAGCATT 59.721 47.619 0.00 0.00 0.00 3.56
163 164 1.667724 CCTCCGCAGTCTTTAGCATTG 59.332 52.381 0.00 0.00 0.00 2.82
164 165 1.063174 CTCCGCAGTCTTTAGCATTGC 59.937 52.381 0.00 0.00 0.00 3.56
167 168 2.900122 GCAGTCTTTAGCATTGCGAA 57.100 45.000 2.38 0.93 0.00 4.70
168 169 2.778659 GCAGTCTTTAGCATTGCGAAG 58.221 47.619 16.74 16.74 0.00 3.79
169 170 2.416547 GCAGTCTTTAGCATTGCGAAGA 59.583 45.455 19.72 19.72 34.90 2.87
170 171 3.484886 GCAGTCTTTAGCATTGCGAAGAG 60.485 47.826 22.41 15.94 36.72 2.85
182 183 3.976339 CGAAGAGCTCGGGAATCAT 57.024 52.632 8.37 0.00 44.20 2.45
183 184 1.777101 CGAAGAGCTCGGGAATCATC 58.223 55.000 8.37 0.00 44.20 2.92
184 185 1.339610 CGAAGAGCTCGGGAATCATCT 59.660 52.381 8.37 0.00 44.20 2.90
185 186 2.223923 CGAAGAGCTCGGGAATCATCTT 60.224 50.000 8.37 0.00 44.20 2.40
186 187 3.004839 CGAAGAGCTCGGGAATCATCTTA 59.995 47.826 8.37 0.00 44.20 2.10
187 188 4.321601 CGAAGAGCTCGGGAATCATCTTAT 60.322 45.833 8.37 0.00 44.20 1.73
188 189 4.799564 AGAGCTCGGGAATCATCTTATC 57.200 45.455 8.37 0.00 0.00 1.75
189 190 3.513515 AGAGCTCGGGAATCATCTTATCC 59.486 47.826 8.37 0.00 0.00 2.59
190 191 3.242867 AGCTCGGGAATCATCTTATCCA 58.757 45.455 0.00 0.00 34.82 3.41
191 192 3.843027 AGCTCGGGAATCATCTTATCCAT 59.157 43.478 0.00 0.00 34.82 3.41
192 193 4.081198 AGCTCGGGAATCATCTTATCCATC 60.081 45.833 0.00 0.00 34.82 3.51
193 194 4.764172 CTCGGGAATCATCTTATCCATCC 58.236 47.826 0.00 0.00 34.82 3.51
194 195 3.519510 TCGGGAATCATCTTATCCATCCC 59.480 47.826 0.00 0.00 41.32 3.85
195 196 3.521126 CGGGAATCATCTTATCCATCCCT 59.479 47.826 6.40 0.00 42.33 4.20
196 197 4.018960 CGGGAATCATCTTATCCATCCCTT 60.019 45.833 6.40 0.00 42.33 3.95
197 198 5.259632 GGGAATCATCTTATCCATCCCTTG 58.740 45.833 0.00 0.00 41.48 3.61
198 199 4.704057 GGAATCATCTTATCCATCCCTTGC 59.296 45.833 0.00 0.00 33.30 4.01
199 200 5.319453 GAATCATCTTATCCATCCCTTGCA 58.681 41.667 0.00 0.00 0.00 4.08
200 201 5.531753 ATCATCTTATCCATCCCTTGCAT 57.468 39.130 0.00 0.00 0.00 3.96
201 202 6.647461 ATCATCTTATCCATCCCTTGCATA 57.353 37.500 0.00 0.00 0.00 3.14
202 203 6.647461 TCATCTTATCCATCCCTTGCATAT 57.353 37.500 0.00 0.00 0.00 1.78
203 204 7.036154 TCATCTTATCCATCCCTTGCATATT 57.964 36.000 0.00 0.00 0.00 1.28
204 205 8.161640 TCATCTTATCCATCCCTTGCATATTA 57.838 34.615 0.00 0.00 0.00 0.98
205 206 8.784880 TCATCTTATCCATCCCTTGCATATTAT 58.215 33.333 0.00 0.00 0.00 1.28
208 209 9.284131 TCTTATCCATCCCTTGCATATTATAGT 57.716 33.333 0.00 0.00 0.00 2.12
209 210 9.911788 CTTATCCATCCCTTGCATATTATAGTT 57.088 33.333 0.00 0.00 0.00 2.24
210 211 9.905713 TTATCCATCCCTTGCATATTATAGTTC 57.094 33.333 0.00 0.00 0.00 3.01
211 212 7.328404 TCCATCCCTTGCATATTATAGTTCA 57.672 36.000 0.00 0.00 0.00 3.18
212 213 7.932134 TCCATCCCTTGCATATTATAGTTCAT 58.068 34.615 0.00 0.00 0.00 2.57
213 214 8.049117 TCCATCCCTTGCATATTATAGTTCATC 58.951 37.037 0.00 0.00 0.00 2.92
214 215 7.830697 CCATCCCTTGCATATTATAGTTCATCA 59.169 37.037 0.00 0.00 0.00 3.07
215 216 9.404848 CATCCCTTGCATATTATAGTTCATCAT 57.595 33.333 0.00 0.00 0.00 2.45
216 217 8.797350 TCCCTTGCATATTATAGTTCATCATG 57.203 34.615 0.00 0.00 0.00 3.07
217 218 8.605065 TCCCTTGCATATTATAGTTCATCATGA 58.395 33.333 0.00 0.00 0.00 3.07
218 219 9.234827 CCCTTGCATATTATAGTTCATCATGAA 57.765 33.333 0.00 0.00 33.32 2.57
220 221 9.770503 CTTGCATATTATAGTTCATCATGAAGC 57.229 33.333 0.00 0.00 37.00 3.86
221 222 9.511272 TTGCATATTATAGTTCATCATGAAGCT 57.489 29.630 0.00 4.22 37.00 3.74
222 223 9.159364 TGCATATTATAGTTCATCATGAAGCTC 57.841 33.333 0.00 0.00 37.00 4.09
223 224 9.381033 GCATATTATAGTTCATCATGAAGCTCT 57.619 33.333 0.00 0.00 37.00 4.09
228 229 9.755804 TTATAGTTCATCATGAAGCTCTTGTAG 57.244 33.333 0.00 0.00 37.00 2.74
238 239 3.631453 CTCTTGTAGCTTGGTGGCA 57.369 52.632 0.00 0.00 34.17 4.92
239 240 1.446907 CTCTTGTAGCTTGGTGGCAG 58.553 55.000 0.00 0.00 34.17 4.85
240 241 0.764890 TCTTGTAGCTTGGTGGCAGT 59.235 50.000 0.00 0.00 34.17 4.40
241 242 0.877071 CTTGTAGCTTGGTGGCAGTG 59.123 55.000 0.00 0.00 34.17 3.66
242 243 0.472044 TTGTAGCTTGGTGGCAGTGA 59.528 50.000 0.00 0.00 34.17 3.41
243 244 0.692476 TGTAGCTTGGTGGCAGTGAT 59.308 50.000 0.00 0.00 34.17 3.06
244 245 1.073763 TGTAGCTTGGTGGCAGTGATT 59.926 47.619 0.00 0.00 34.17 2.57
245 246 1.470098 GTAGCTTGGTGGCAGTGATTG 59.530 52.381 0.00 0.00 34.17 2.67
246 247 0.111061 AGCTTGGTGGCAGTGATTGA 59.889 50.000 0.00 0.00 34.17 2.57
247 248 0.961019 GCTTGGTGGCAGTGATTGAA 59.039 50.000 0.00 0.00 0.00 2.69
248 249 1.068055 GCTTGGTGGCAGTGATTGAAG 60.068 52.381 0.00 0.00 0.00 3.02
249 250 2.507484 CTTGGTGGCAGTGATTGAAGA 58.493 47.619 0.00 0.00 0.00 2.87
250 251 2.655090 TGGTGGCAGTGATTGAAGAA 57.345 45.000 0.00 0.00 0.00 2.52
251 252 2.229792 TGGTGGCAGTGATTGAAGAAC 58.770 47.619 0.00 0.00 0.00 3.01
252 253 2.158623 TGGTGGCAGTGATTGAAGAACT 60.159 45.455 0.00 0.00 0.00 3.01
253 254 2.485814 GGTGGCAGTGATTGAAGAACTC 59.514 50.000 0.00 0.00 0.00 3.01
254 255 3.406764 GTGGCAGTGATTGAAGAACTCT 58.593 45.455 0.00 0.00 0.00 3.24
255 256 3.188048 GTGGCAGTGATTGAAGAACTCTG 59.812 47.826 0.00 0.00 0.00 3.35
256 257 3.181451 TGGCAGTGATTGAAGAACTCTGT 60.181 43.478 0.00 0.00 0.00 3.41
257 258 3.434984 GGCAGTGATTGAAGAACTCTGTC 59.565 47.826 0.00 0.00 0.00 3.51
258 259 4.060900 GCAGTGATTGAAGAACTCTGTCA 58.939 43.478 0.00 0.00 0.00 3.58
259 260 4.512944 GCAGTGATTGAAGAACTCTGTCAA 59.487 41.667 0.00 6.73 35.83 3.18
260 261 5.180868 GCAGTGATTGAAGAACTCTGTCAAT 59.819 40.000 12.76 12.76 43.06 2.57
261 262 6.600350 CAGTGATTGAAGAACTCTGTCAATG 58.400 40.000 15.62 8.58 41.03 2.82
262 263 6.426025 CAGTGATTGAAGAACTCTGTCAATGA 59.574 38.462 15.62 9.14 41.03 2.57
263 264 6.426328 AGTGATTGAAGAACTCTGTCAATGAC 59.574 38.462 6.41 6.41 42.57 3.06
264 265 6.203530 GTGATTGAAGAACTCTGTCAATGACA 59.796 38.462 15.88 15.88 42.13 3.58
265 266 5.991328 TTGAAGAACTCTGTCAATGACAC 57.009 39.130 12.63 2.33 37.67 3.67
266 267 5.282055 TGAAGAACTCTGTCAATGACACT 57.718 39.130 12.63 4.81 37.67 3.55
267 268 6.405278 TGAAGAACTCTGTCAATGACACTA 57.595 37.500 12.63 2.84 37.67 2.74
268 269 6.997655 TGAAGAACTCTGTCAATGACACTAT 58.002 36.000 12.63 0.00 37.67 2.12
269 270 7.093354 TGAAGAACTCTGTCAATGACACTATC 58.907 38.462 12.63 8.48 37.67 2.08
270 271 6.596309 AGAACTCTGTCAATGACACTATCA 57.404 37.500 12.63 0.00 43.13 2.15
285 286 8.311395 TGACACTATCATCAGGAAGATTAACT 57.689 34.615 0.00 0.00 33.72 2.24
286 287 8.417106 TGACACTATCATCAGGAAGATTAACTC 58.583 37.037 0.00 0.00 33.72 3.01
287 288 7.731054 ACACTATCATCAGGAAGATTAACTCC 58.269 38.462 0.00 0.00 33.72 3.85
288 289 7.158021 CACTATCATCAGGAAGATTAACTCCC 58.842 42.308 0.00 0.00 33.72 4.30
289 290 6.846505 ACTATCATCAGGAAGATTAACTCCCA 59.153 38.462 0.00 0.00 33.72 4.37
290 291 5.620738 TCATCAGGAAGATTAACTCCCAG 57.379 43.478 0.00 0.00 33.72 4.45
291 292 3.914426 TCAGGAAGATTAACTCCCAGC 57.086 47.619 0.00 0.00 0.00 4.85
292 293 3.454858 TCAGGAAGATTAACTCCCAGCT 58.545 45.455 0.00 0.00 0.00 4.24
293 294 3.198635 TCAGGAAGATTAACTCCCAGCTG 59.801 47.826 6.78 6.78 0.00 4.24
294 295 3.198635 CAGGAAGATTAACTCCCAGCTGA 59.801 47.826 17.39 0.00 0.00 4.26
295 296 3.454082 AGGAAGATTAACTCCCAGCTGAG 59.546 47.826 17.39 8.22 38.37 3.35
297 298 4.438148 GAAGATTAACTCCCAGCTGAGTC 58.562 47.826 17.39 0.00 44.68 3.36
298 299 3.445008 AGATTAACTCCCAGCTGAGTCA 58.555 45.455 17.39 2.68 44.68 3.41
299 300 3.840666 AGATTAACTCCCAGCTGAGTCAA 59.159 43.478 17.39 4.26 44.68 3.18
300 301 3.685139 TTAACTCCCAGCTGAGTCAAG 57.315 47.619 17.39 7.22 44.68 3.02
301 302 1.428869 AACTCCCAGCTGAGTCAAGT 58.571 50.000 17.39 7.87 44.68 3.16
302 303 0.683973 ACTCCCAGCTGAGTCAAGTG 59.316 55.000 17.39 0.00 41.75 3.16
303 304 0.036577 CTCCCAGCTGAGTCAAGTGG 60.037 60.000 17.39 11.92 0.00 4.00
304 305 0.764369 TCCCAGCTGAGTCAAGTGGT 60.764 55.000 17.39 0.00 0.00 4.16
305 306 0.109342 CCCAGCTGAGTCAAGTGGTT 59.891 55.000 17.39 0.00 0.00 3.67
306 307 1.233019 CCAGCTGAGTCAAGTGGTTG 58.767 55.000 17.39 0.75 34.67 3.77
307 308 1.475751 CCAGCTGAGTCAAGTGGTTGT 60.476 52.381 17.39 0.00 34.98 3.32
308 309 2.224281 CCAGCTGAGTCAAGTGGTTGTA 60.224 50.000 17.39 0.00 34.98 2.41
309 310 3.062763 CAGCTGAGTCAAGTGGTTGTAG 58.937 50.000 8.42 0.00 34.98 2.74
310 311 2.700897 AGCTGAGTCAAGTGGTTGTAGT 59.299 45.455 0.00 0.00 34.98 2.73
311 312 3.895656 AGCTGAGTCAAGTGGTTGTAGTA 59.104 43.478 0.00 0.00 34.98 1.82
312 313 3.988517 GCTGAGTCAAGTGGTTGTAGTAC 59.011 47.826 0.00 0.00 34.98 2.73
313 314 4.500887 GCTGAGTCAAGTGGTTGTAGTACA 60.501 45.833 0.00 0.00 34.98 2.90
314 315 4.940463 TGAGTCAAGTGGTTGTAGTACAC 58.060 43.478 1.43 0.00 34.98 2.90
315 316 4.403113 TGAGTCAAGTGGTTGTAGTACACA 59.597 41.667 1.43 0.00 37.58 3.72
316 317 4.945246 AGTCAAGTGGTTGTAGTACACAG 58.055 43.478 1.43 0.00 38.72 3.66
317 318 4.647853 AGTCAAGTGGTTGTAGTACACAGA 59.352 41.667 1.43 0.00 38.72 3.41
318 319 4.743644 GTCAAGTGGTTGTAGTACACAGAC 59.256 45.833 1.43 0.00 38.72 3.51
319 320 4.403113 TCAAGTGGTTGTAGTACACAGACA 59.597 41.667 1.43 0.00 38.72 3.41
320 321 5.069914 TCAAGTGGTTGTAGTACACAGACAT 59.930 40.000 1.43 0.00 38.72 3.06
321 322 5.546621 AGTGGTTGTAGTACACAGACATT 57.453 39.130 1.43 0.00 38.72 2.71
322 323 5.539048 AGTGGTTGTAGTACACAGACATTC 58.461 41.667 1.43 0.00 38.72 2.67
323 324 5.304614 AGTGGTTGTAGTACACAGACATTCT 59.695 40.000 1.43 0.00 38.72 2.40
329 330 7.939784 TGTAGTACACAGACATTCTGAGTAT 57.060 36.000 14.08 8.06 46.61 2.12
330 331 9.457436 TTGTAGTACACAGACATTCTGAGTATA 57.543 33.333 14.08 7.37 46.61 1.47
331 332 9.628500 TGTAGTACACAGACATTCTGAGTATAT 57.372 33.333 14.08 9.98 46.61 0.86
332 333 9.885934 GTAGTACACAGACATTCTGAGTATATG 57.114 37.037 14.08 3.19 46.61 1.78
333 334 8.526667 AGTACACAGACATTCTGAGTATATGT 57.473 34.615 14.08 7.94 46.61 2.29
334 335 8.972127 AGTACACAGACATTCTGAGTATATGTT 58.028 33.333 14.08 0.64 46.61 2.71
335 336 9.239002 GTACACAGACATTCTGAGTATATGTTC 57.761 37.037 14.08 1.73 46.61 3.18
341 342 9.539825 AGACATTCTGAGTATATGTTCATTGAC 57.460 33.333 0.00 0.00 32.94 3.18
342 343 9.317936 GACATTCTGAGTATATGTTCATTGACA 57.682 33.333 0.00 0.00 32.94 3.58
343 344 9.322773 ACATTCTGAGTATATGTTCATTGACAG 57.677 33.333 0.00 0.00 32.19 3.51
344 345 9.538508 CATTCTGAGTATATGTTCATTGACAGA 57.461 33.333 0.00 0.00 32.19 3.41
357 358 8.950210 TGTTCATTGACAGAATTATTCTTCTCC 58.050 33.333 4.51 0.00 38.11 3.71
358 359 8.950210 GTTCATTGACAGAATTATTCTTCTCCA 58.050 33.333 4.51 0.00 38.11 3.86
359 360 9.690913 TTCATTGACAGAATTATTCTTCTCCAT 57.309 29.630 4.51 0.00 38.11 3.41
360 361 9.690913 TCATTGACAGAATTATTCTTCTCCATT 57.309 29.630 4.51 0.00 38.11 3.16
364 365 8.246180 TGACAGAATTATTCTTCTCCATTTTGC 58.754 33.333 4.51 0.00 38.11 3.68
365 366 8.125978 ACAGAATTATTCTTCTCCATTTTGCA 57.874 30.769 4.51 0.00 38.11 4.08
366 367 8.248945 ACAGAATTATTCTTCTCCATTTTGCAG 58.751 33.333 4.51 0.00 38.11 4.41
367 368 7.222224 CAGAATTATTCTTCTCCATTTTGCAGC 59.778 37.037 4.51 0.00 38.11 5.25
368 369 6.786967 ATTATTCTTCTCCATTTTGCAGCT 57.213 33.333 0.00 0.00 0.00 4.24
369 370 7.886629 ATTATTCTTCTCCATTTTGCAGCTA 57.113 32.000 0.00 0.00 0.00 3.32
370 371 7.886629 TTATTCTTCTCCATTTTGCAGCTAT 57.113 32.000 0.00 0.00 0.00 2.97
371 372 8.978874 TTATTCTTCTCCATTTTGCAGCTATA 57.021 30.769 0.00 0.00 0.00 1.31
506 508 4.941609 CTGCCGGCAGAAGTGTAT 57.058 55.556 46.72 0.00 46.30 2.29
557 559 6.622549 ACGATTTTTGTTTGTAAGGACACAA 58.377 32.000 0.00 0.00 36.65 3.33
936 993 3.133767 GATCCGTCGATGTCGCCCA 62.134 63.158 3.52 0.00 39.60 5.36
1185 1242 0.176680 CTGTGCCCGCTCTTCACTAT 59.823 55.000 0.00 0.00 0.00 2.12
2356 2731 2.814336 GCTCTTCCGGTGAAATTCAACT 59.186 45.455 9.53 0.00 30.24 3.16
2534 2910 3.902261 TCATGCTAGCACACAGTTTTG 57.098 42.857 22.07 11.99 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.840635 GAAGCCCAAGTCTGGACCTAT 59.159 52.381 0.00 0.00 46.92 2.57
2 3 1.203313 AGAAGCCCAAGTCTGGACCTA 60.203 52.381 0.00 0.00 46.92 3.08
3 4 0.474660 AGAAGCCCAAGTCTGGACCT 60.475 55.000 0.00 0.00 46.92 3.85
4 5 0.402121 AAGAAGCCCAAGTCTGGACC 59.598 55.000 0.00 0.00 46.92 4.46
5 6 1.072331 TGAAGAAGCCCAAGTCTGGAC 59.928 52.381 0.00 0.00 46.92 4.02
6 7 1.072331 GTGAAGAAGCCCAAGTCTGGA 59.928 52.381 0.00 0.00 46.92 3.86
7 8 1.072965 AGTGAAGAAGCCCAAGTCTGG 59.927 52.381 0.00 0.00 43.10 3.86
8 9 2.551459 CAAGTGAAGAAGCCCAAGTCTG 59.449 50.000 0.00 0.00 0.00 3.51
9 10 2.439507 TCAAGTGAAGAAGCCCAAGTCT 59.560 45.455 0.00 0.00 0.00 3.24
10 11 2.810852 CTCAAGTGAAGAAGCCCAAGTC 59.189 50.000 0.00 0.00 0.00 3.01
11 12 2.856222 CTCAAGTGAAGAAGCCCAAGT 58.144 47.619 0.00 0.00 0.00 3.16
12 13 1.538950 GCTCAAGTGAAGAAGCCCAAG 59.461 52.381 0.00 0.00 0.00 3.61
13 14 1.133823 TGCTCAAGTGAAGAAGCCCAA 60.134 47.619 0.00 0.00 0.00 4.12
14 15 0.473755 TGCTCAAGTGAAGAAGCCCA 59.526 50.000 0.00 0.00 0.00 5.36
15 16 1.163554 CTGCTCAAGTGAAGAAGCCC 58.836 55.000 0.00 0.00 0.00 5.19
16 17 0.520847 GCTGCTCAAGTGAAGAAGCC 59.479 55.000 0.00 0.00 0.00 4.35
17 18 1.233019 TGCTGCTCAAGTGAAGAAGC 58.767 50.000 0.00 0.00 0.00 3.86
18 19 4.500603 AATTGCTGCTCAAGTGAAGAAG 57.499 40.909 0.00 0.00 38.22 2.85
19 20 4.098349 ACAAATTGCTGCTCAAGTGAAGAA 59.902 37.500 0.00 0.00 38.22 2.52
20 21 3.633525 ACAAATTGCTGCTCAAGTGAAGA 59.366 39.130 0.00 0.00 38.22 2.87
21 22 3.973657 ACAAATTGCTGCTCAAGTGAAG 58.026 40.909 0.00 0.00 38.22 3.02
22 23 4.389890 AACAAATTGCTGCTCAAGTGAA 57.610 36.364 0.00 0.00 38.22 3.18
23 24 4.114073 CAAACAAATTGCTGCTCAAGTGA 58.886 39.130 0.00 0.00 38.22 3.41
24 25 4.446857 CAAACAAATTGCTGCTCAAGTG 57.553 40.909 0.00 0.00 38.22 3.16
35 36 4.803088 TCAAGAAGAACGGCAAACAAATTG 59.197 37.500 0.00 0.00 42.21 2.32
36 37 5.004922 TCAAGAAGAACGGCAAACAAATT 57.995 34.783 0.00 0.00 0.00 1.82
37 38 4.647424 TCAAGAAGAACGGCAAACAAAT 57.353 36.364 0.00 0.00 0.00 2.32
38 39 4.082463 ACTTCAAGAAGAACGGCAAACAAA 60.082 37.500 16.16 0.00 40.79 2.83
39 40 3.442273 ACTTCAAGAAGAACGGCAAACAA 59.558 39.130 16.16 0.00 40.79 2.83
40 41 3.013921 ACTTCAAGAAGAACGGCAAACA 58.986 40.909 16.16 0.00 40.79 2.83
41 42 3.692791 ACTTCAAGAAGAACGGCAAAC 57.307 42.857 16.16 0.00 40.79 2.93
42 43 3.066203 GGAACTTCAAGAAGAACGGCAAA 59.934 43.478 16.16 0.00 40.79 3.68
43 44 2.616842 GGAACTTCAAGAAGAACGGCAA 59.383 45.455 16.16 0.00 40.79 4.52
44 45 2.158813 AGGAACTTCAAGAAGAACGGCA 60.159 45.455 16.16 0.00 40.79 5.69
45 46 2.480802 GAGGAACTTCAAGAAGAACGGC 59.519 50.000 16.16 0.15 41.55 5.68
46 47 3.996480 AGAGGAACTTCAAGAAGAACGG 58.004 45.455 16.16 0.00 41.55 4.44
58 59 4.043059 GGGTAAAGGGAAGAAGAGGAACTT 59.957 45.833 0.00 0.00 41.55 2.66
60 61 3.587951 AGGGTAAAGGGAAGAAGAGGAAC 59.412 47.826 0.00 0.00 0.00 3.62
61 62 3.883135 AGGGTAAAGGGAAGAAGAGGAA 58.117 45.455 0.00 0.00 0.00 3.36
62 63 3.579742 AGGGTAAAGGGAAGAAGAGGA 57.420 47.619 0.00 0.00 0.00 3.71
63 64 4.659529 AAAGGGTAAAGGGAAGAAGAGG 57.340 45.455 0.00 0.00 0.00 3.69
64 65 6.307776 AGAAAAAGGGTAAAGGGAAGAAGAG 58.692 40.000 0.00 0.00 0.00 2.85
65 66 6.275692 AGAAAAAGGGTAAAGGGAAGAAGA 57.724 37.500 0.00 0.00 0.00 2.87
66 67 6.549736 TCAAGAAAAAGGGTAAAGGGAAGAAG 59.450 38.462 0.00 0.00 0.00 2.85
67 68 6.436890 TCAAGAAAAAGGGTAAAGGGAAGAA 58.563 36.000 0.00 0.00 0.00 2.52
68 69 6.020881 TCAAGAAAAAGGGTAAAGGGAAGA 57.979 37.500 0.00 0.00 0.00 2.87
69 70 6.724893 TTCAAGAAAAAGGGTAAAGGGAAG 57.275 37.500 0.00 0.00 0.00 3.46
70 71 6.670464 AGTTTCAAGAAAAAGGGTAAAGGGAA 59.330 34.615 0.00 0.00 31.33 3.97
71 72 6.097696 CAGTTTCAAGAAAAAGGGTAAAGGGA 59.902 38.462 0.00 0.00 31.33 4.20
72 73 6.280643 CAGTTTCAAGAAAAAGGGTAAAGGG 58.719 40.000 0.00 0.00 31.33 3.95
73 74 6.127168 ACCAGTTTCAAGAAAAAGGGTAAAGG 60.127 38.462 14.92 0.00 35.10 3.11
74 75 6.756542 CACCAGTTTCAAGAAAAAGGGTAAAG 59.243 38.462 14.92 3.12 35.10 1.85
75 76 6.437793 TCACCAGTTTCAAGAAAAAGGGTAAA 59.562 34.615 14.92 5.97 35.10 2.01
76 77 5.952947 TCACCAGTTTCAAGAAAAAGGGTAA 59.047 36.000 14.92 1.74 35.10 2.85
77 78 5.511363 TCACCAGTTTCAAGAAAAAGGGTA 58.489 37.500 14.92 4.39 35.10 3.69
78 79 4.349365 TCACCAGTTTCAAGAAAAAGGGT 58.651 39.130 14.92 11.43 36.48 4.34
79 80 5.302823 AGATCACCAGTTTCAAGAAAAAGGG 59.697 40.000 14.92 10.96 33.40 3.95
80 81 6.396829 AGATCACCAGTTTCAAGAAAAAGG 57.603 37.500 10.99 10.99 34.54 3.11
81 82 7.260603 ACAAGATCACCAGTTTCAAGAAAAAG 58.739 34.615 0.00 0.00 31.33 2.27
82 83 7.169158 ACAAGATCACCAGTTTCAAGAAAAA 57.831 32.000 0.00 0.00 31.33 1.94
83 84 6.773976 ACAAGATCACCAGTTTCAAGAAAA 57.226 33.333 0.00 0.00 31.33 2.29
84 85 6.376864 TCAACAAGATCACCAGTTTCAAGAAA 59.623 34.615 0.00 0.00 0.00 2.52
85 86 5.885352 TCAACAAGATCACCAGTTTCAAGAA 59.115 36.000 0.00 0.00 0.00 2.52
86 87 5.296780 GTCAACAAGATCACCAGTTTCAAGA 59.703 40.000 0.00 0.00 0.00 3.02
87 88 5.506317 GGTCAACAAGATCACCAGTTTCAAG 60.506 44.000 0.00 0.00 0.00 3.02
88 89 4.338118 GGTCAACAAGATCACCAGTTTCAA 59.662 41.667 0.00 0.00 0.00 2.69
89 90 3.882888 GGTCAACAAGATCACCAGTTTCA 59.117 43.478 0.00 0.00 0.00 2.69
90 91 3.882888 TGGTCAACAAGATCACCAGTTTC 59.117 43.478 0.00 0.00 33.83 2.78
91 92 3.897239 TGGTCAACAAGATCACCAGTTT 58.103 40.909 0.00 0.00 33.83 2.66
92 93 3.576078 TGGTCAACAAGATCACCAGTT 57.424 42.857 0.00 0.00 33.83 3.16
93 94 3.072915 TGATGGTCAACAAGATCACCAGT 59.927 43.478 6.51 0.00 40.95 4.00
94 95 3.678289 TGATGGTCAACAAGATCACCAG 58.322 45.455 6.51 0.00 40.95 4.00
95 96 3.786368 TGATGGTCAACAAGATCACCA 57.214 42.857 3.07 3.07 40.95 4.17
121 122 9.838339 GGAGGTAGAAATCAAGAAAGAATATCA 57.162 33.333 0.00 0.00 0.00 2.15
122 123 8.983724 CGGAGGTAGAAATCAAGAAAGAATATC 58.016 37.037 0.00 0.00 0.00 1.63
123 124 7.442666 GCGGAGGTAGAAATCAAGAAAGAATAT 59.557 37.037 0.00 0.00 0.00 1.28
124 125 6.761714 GCGGAGGTAGAAATCAAGAAAGAATA 59.238 38.462 0.00 0.00 0.00 1.75
125 126 5.586643 GCGGAGGTAGAAATCAAGAAAGAAT 59.413 40.000 0.00 0.00 0.00 2.40
126 127 4.935808 GCGGAGGTAGAAATCAAGAAAGAA 59.064 41.667 0.00 0.00 0.00 2.52
127 128 4.020573 TGCGGAGGTAGAAATCAAGAAAGA 60.021 41.667 0.00 0.00 0.00 2.52
128 129 4.253685 TGCGGAGGTAGAAATCAAGAAAG 58.746 43.478 0.00 0.00 0.00 2.62
129 130 4.253685 CTGCGGAGGTAGAAATCAAGAAA 58.746 43.478 0.00 0.00 0.00 2.52
130 131 3.260884 ACTGCGGAGGTAGAAATCAAGAA 59.739 43.478 9.36 0.00 0.00 2.52
131 132 2.832129 ACTGCGGAGGTAGAAATCAAGA 59.168 45.455 9.36 0.00 0.00 3.02
132 133 3.118956 AGACTGCGGAGGTAGAAATCAAG 60.119 47.826 9.36 0.00 0.00 3.02
133 134 2.832129 AGACTGCGGAGGTAGAAATCAA 59.168 45.455 9.36 0.00 0.00 2.57
134 135 2.457598 AGACTGCGGAGGTAGAAATCA 58.542 47.619 9.36 0.00 0.00 2.57
135 136 3.528597 AAGACTGCGGAGGTAGAAATC 57.471 47.619 9.36 0.00 0.00 2.17
136 137 3.983044 AAAGACTGCGGAGGTAGAAAT 57.017 42.857 9.36 0.00 0.00 2.17
137 138 3.368116 GCTAAAGACTGCGGAGGTAGAAA 60.368 47.826 9.36 0.00 0.00 2.52
138 139 2.165845 GCTAAAGACTGCGGAGGTAGAA 59.834 50.000 9.36 0.00 0.00 2.10
139 140 1.749634 GCTAAAGACTGCGGAGGTAGA 59.250 52.381 9.36 0.00 0.00 2.59
140 141 1.476891 TGCTAAAGACTGCGGAGGTAG 59.523 52.381 9.36 5.47 0.00 3.18
141 142 1.552578 TGCTAAAGACTGCGGAGGTA 58.447 50.000 9.36 0.00 0.00 3.08
142 143 0.905357 ATGCTAAAGACTGCGGAGGT 59.095 50.000 9.36 0.00 0.00 3.85
143 144 1.667724 CAATGCTAAAGACTGCGGAGG 59.332 52.381 9.36 0.00 0.00 4.30
144 145 1.063174 GCAATGCTAAAGACTGCGGAG 59.937 52.381 0.85 0.85 0.00 4.63
145 146 1.086696 GCAATGCTAAAGACTGCGGA 58.913 50.000 0.00 0.00 0.00 5.54
146 147 3.611433 GCAATGCTAAAGACTGCGG 57.389 52.632 0.00 0.00 0.00 5.69
148 149 2.416547 TCTTCGCAATGCTAAAGACTGC 59.583 45.455 13.50 0.00 0.00 4.40
149 150 3.484886 GCTCTTCGCAATGCTAAAGACTG 60.485 47.826 13.50 8.25 38.92 3.51
150 151 2.675348 GCTCTTCGCAATGCTAAAGACT 59.325 45.455 13.50 0.00 38.92 3.24
151 152 2.675348 AGCTCTTCGCAATGCTAAAGAC 59.325 45.455 13.50 11.19 42.61 3.01
152 153 2.932614 GAGCTCTTCGCAATGCTAAAGA 59.067 45.455 15.68 15.68 42.61 2.52
153 154 2.285486 CGAGCTCTTCGCAATGCTAAAG 60.285 50.000 12.85 7.24 43.22 1.85
154 155 1.660607 CGAGCTCTTCGCAATGCTAAA 59.339 47.619 12.85 0.00 43.22 1.85
155 156 1.280982 CGAGCTCTTCGCAATGCTAA 58.719 50.000 12.85 0.00 43.22 3.09
156 157 2.963499 CGAGCTCTTCGCAATGCTA 58.037 52.632 12.85 0.00 43.22 3.49
157 158 3.791539 CGAGCTCTTCGCAATGCT 58.208 55.556 12.85 0.00 43.22 3.79
165 166 3.467374 AAGATGATTCCCGAGCTCTTC 57.533 47.619 12.85 1.74 0.00 2.87
166 167 4.020662 GGATAAGATGATTCCCGAGCTCTT 60.021 45.833 12.85 0.00 0.00 2.85
167 168 3.513515 GGATAAGATGATTCCCGAGCTCT 59.486 47.826 12.85 0.00 0.00 4.09
168 169 3.259374 TGGATAAGATGATTCCCGAGCTC 59.741 47.826 2.73 2.73 0.00 4.09
169 170 3.242867 TGGATAAGATGATTCCCGAGCT 58.757 45.455 0.00 0.00 0.00 4.09
170 171 3.685139 TGGATAAGATGATTCCCGAGC 57.315 47.619 0.00 0.00 0.00 5.03
171 172 4.383552 GGGATGGATAAGATGATTCCCGAG 60.384 50.000 0.00 0.00 32.61 4.63
172 173 3.519510 GGGATGGATAAGATGATTCCCGA 59.480 47.826 0.00 0.00 32.61 5.14
173 174 3.521126 AGGGATGGATAAGATGATTCCCG 59.479 47.826 0.00 0.00 44.91 5.14
174 175 5.259632 CAAGGGATGGATAAGATGATTCCC 58.740 45.833 0.00 0.00 41.39 3.97
175 176 4.704057 GCAAGGGATGGATAAGATGATTCC 59.296 45.833 0.00 0.00 0.00 3.01
176 177 5.319453 TGCAAGGGATGGATAAGATGATTC 58.681 41.667 0.00 0.00 0.00 2.52
177 178 5.329191 TGCAAGGGATGGATAAGATGATT 57.671 39.130 0.00 0.00 0.00 2.57
178 179 5.531753 ATGCAAGGGATGGATAAGATGAT 57.468 39.130 0.00 0.00 38.47 2.45
179 180 6.647461 ATATGCAAGGGATGGATAAGATGA 57.353 37.500 0.00 0.00 44.29 2.92
180 181 8.991783 ATAATATGCAAGGGATGGATAAGATG 57.008 34.615 0.00 0.00 44.29 2.90
182 183 9.284131 ACTATAATATGCAAGGGATGGATAAGA 57.716 33.333 0.00 0.00 44.29 2.10
183 184 9.911788 AACTATAATATGCAAGGGATGGATAAG 57.088 33.333 0.00 0.00 44.29 1.73
184 185 9.905713 GAACTATAATATGCAAGGGATGGATAA 57.094 33.333 0.00 0.00 44.29 1.75
185 186 9.056799 TGAACTATAATATGCAAGGGATGGATA 57.943 33.333 0.00 0.00 45.05 2.59
186 187 7.932134 TGAACTATAATATGCAAGGGATGGAT 58.068 34.615 0.00 0.00 43.28 3.41
187 188 7.328404 TGAACTATAATATGCAAGGGATGGA 57.672 36.000 0.00 0.00 0.00 3.41
188 189 7.830697 TGATGAACTATAATATGCAAGGGATGG 59.169 37.037 0.00 0.00 0.00 3.51
189 190 8.797350 TGATGAACTATAATATGCAAGGGATG 57.203 34.615 0.00 0.00 0.00 3.51
190 191 9.404848 CATGATGAACTATAATATGCAAGGGAT 57.595 33.333 0.00 0.00 0.00 3.85
191 192 8.605065 TCATGATGAACTATAATATGCAAGGGA 58.395 33.333 0.00 0.00 0.00 4.20
192 193 8.797350 TCATGATGAACTATAATATGCAAGGG 57.203 34.615 0.00 0.00 0.00 3.95
194 195 9.770503 GCTTCATGATGAACTATAATATGCAAG 57.229 33.333 12.54 0.00 32.21 4.01
195 196 9.511272 AGCTTCATGATGAACTATAATATGCAA 57.489 29.630 12.54 0.00 32.21 4.08
196 197 9.159364 GAGCTTCATGATGAACTATAATATGCA 57.841 33.333 12.54 0.00 32.21 3.96
197 198 9.381033 AGAGCTTCATGATGAACTATAATATGC 57.619 33.333 12.54 3.17 32.21 3.14
202 203 9.755804 CTACAAGAGCTTCATGATGAACTATAA 57.244 33.333 12.54 0.00 32.21 0.98
220 221 1.271054 ACTGCCACCAAGCTACAAGAG 60.271 52.381 0.00 0.00 0.00 2.85
221 222 0.764890 ACTGCCACCAAGCTACAAGA 59.235 50.000 0.00 0.00 0.00 3.02
222 223 0.877071 CACTGCCACCAAGCTACAAG 59.123 55.000 0.00 0.00 0.00 3.16
223 224 0.472044 TCACTGCCACCAAGCTACAA 59.528 50.000 0.00 0.00 0.00 2.41
224 225 0.692476 ATCACTGCCACCAAGCTACA 59.308 50.000 0.00 0.00 0.00 2.74
225 226 1.470098 CAATCACTGCCACCAAGCTAC 59.530 52.381 0.00 0.00 0.00 3.58
226 227 1.350684 TCAATCACTGCCACCAAGCTA 59.649 47.619 0.00 0.00 0.00 3.32
227 228 0.111061 TCAATCACTGCCACCAAGCT 59.889 50.000 0.00 0.00 0.00 3.74
228 229 0.961019 TTCAATCACTGCCACCAAGC 59.039 50.000 0.00 0.00 0.00 4.01
229 230 2.507484 TCTTCAATCACTGCCACCAAG 58.493 47.619 0.00 0.00 0.00 3.61
230 231 2.622942 GTTCTTCAATCACTGCCACCAA 59.377 45.455 0.00 0.00 0.00 3.67
231 232 2.158623 AGTTCTTCAATCACTGCCACCA 60.159 45.455 0.00 0.00 0.00 4.17
232 233 2.485814 GAGTTCTTCAATCACTGCCACC 59.514 50.000 0.00 0.00 0.00 4.61
233 234 3.188048 CAGAGTTCTTCAATCACTGCCAC 59.812 47.826 0.00 0.00 0.00 5.01
234 235 3.181451 ACAGAGTTCTTCAATCACTGCCA 60.181 43.478 0.00 0.00 0.00 4.92
235 236 3.406764 ACAGAGTTCTTCAATCACTGCC 58.593 45.455 0.00 0.00 0.00 4.85
236 237 4.060900 TGACAGAGTTCTTCAATCACTGC 58.939 43.478 0.00 0.00 0.00 4.40
237 238 6.426025 TCATTGACAGAGTTCTTCAATCACTG 59.574 38.462 12.47 0.00 37.78 3.66
238 239 6.426328 GTCATTGACAGAGTTCTTCAATCACT 59.574 38.462 11.93 0.00 37.78 3.41
239 240 6.203530 TGTCATTGACAGAGTTCTTCAATCAC 59.796 38.462 15.41 11.62 37.78 3.06
240 241 6.203530 GTGTCATTGACAGAGTTCTTCAATCA 59.796 38.462 19.53 8.74 43.57 2.57
241 242 6.426328 AGTGTCATTGACAGAGTTCTTCAATC 59.574 38.462 19.53 3.74 43.57 2.67
242 243 6.294473 AGTGTCATTGACAGAGTTCTTCAAT 58.706 36.000 19.53 10.82 43.57 2.57
243 244 5.674525 AGTGTCATTGACAGAGTTCTTCAA 58.325 37.500 19.53 8.26 43.57 2.69
244 245 5.282055 AGTGTCATTGACAGAGTTCTTCA 57.718 39.130 19.53 0.00 43.57 3.02
245 246 7.093354 TGATAGTGTCATTGACAGAGTTCTTC 58.907 38.462 19.53 12.15 43.57 2.87
246 247 6.997655 TGATAGTGTCATTGACAGAGTTCTT 58.002 36.000 19.53 4.76 43.57 2.52
247 248 6.596309 TGATAGTGTCATTGACAGAGTTCT 57.404 37.500 19.53 14.35 43.57 3.01
260 261 8.311395 AGTTAATCTTCCTGATGATAGTGTCA 57.689 34.615 0.00 0.00 42.06 3.58
261 262 7.870445 GGAGTTAATCTTCCTGATGATAGTGTC 59.130 40.741 0.00 0.00 35.21 3.67
262 263 7.202047 GGGAGTTAATCTTCCTGATGATAGTGT 60.202 40.741 4.32 0.00 38.77 3.55
263 264 7.158021 GGGAGTTAATCTTCCTGATGATAGTG 58.842 42.308 4.32 0.00 38.77 2.74
264 265 6.846505 TGGGAGTTAATCTTCCTGATGATAGT 59.153 38.462 4.61 0.00 42.32 2.12
265 266 7.308450 TGGGAGTTAATCTTCCTGATGATAG 57.692 40.000 4.61 0.00 42.32 2.08
266 267 6.239714 GCTGGGAGTTAATCTTCCTGATGATA 60.240 42.308 11.13 0.00 42.32 2.15
267 268 5.455899 GCTGGGAGTTAATCTTCCTGATGAT 60.456 44.000 11.13 0.00 42.32 2.45
268 269 4.141620 GCTGGGAGTTAATCTTCCTGATGA 60.142 45.833 11.13 0.00 42.32 2.92
269 270 4.133078 GCTGGGAGTTAATCTTCCTGATG 58.867 47.826 11.13 0.61 42.32 3.07
270 271 4.043596 AGCTGGGAGTTAATCTTCCTGAT 58.956 43.478 11.13 4.66 42.32 2.90
271 272 3.198635 CAGCTGGGAGTTAATCTTCCTGA 59.801 47.826 5.57 0.00 42.32 3.86
272 273 3.198635 TCAGCTGGGAGTTAATCTTCCTG 59.801 47.826 15.13 5.05 42.32 3.86
273 274 3.454082 CTCAGCTGGGAGTTAATCTTCCT 59.546 47.826 8.28 0.00 42.32 3.36
274 275 3.198853 ACTCAGCTGGGAGTTAATCTTCC 59.801 47.826 23.49 0.00 45.59 3.46
275 276 4.479786 ACTCAGCTGGGAGTTAATCTTC 57.520 45.455 23.49 0.00 45.59 2.87
284 285 0.036577 CCACTTGACTCAGCTGGGAG 60.037 60.000 23.49 10.20 40.79 4.30
285 286 0.764369 ACCACTTGACTCAGCTGGGA 60.764 55.000 23.49 0.00 0.00 4.37
286 287 0.109342 AACCACTTGACTCAGCTGGG 59.891 55.000 13.44 13.44 0.00 4.45
287 288 1.233019 CAACCACTTGACTCAGCTGG 58.767 55.000 15.13 7.28 0.00 4.85
288 289 1.959042 ACAACCACTTGACTCAGCTG 58.041 50.000 7.63 7.63 0.00 4.24
289 290 2.700897 ACTACAACCACTTGACTCAGCT 59.299 45.455 0.00 0.00 0.00 4.24
290 291 3.113260 ACTACAACCACTTGACTCAGC 57.887 47.619 0.00 0.00 0.00 4.26
291 292 4.982916 GTGTACTACAACCACTTGACTCAG 59.017 45.833 0.00 0.00 0.00 3.35
292 293 4.403113 TGTGTACTACAACCACTTGACTCA 59.597 41.667 0.00 0.00 36.06 3.41
293 294 4.940463 TGTGTACTACAACCACTTGACTC 58.060 43.478 0.00 0.00 36.06 3.36
294 295 4.647853 TCTGTGTACTACAACCACTTGACT 59.352 41.667 0.00 0.00 39.20 3.41
295 296 4.743644 GTCTGTGTACTACAACCACTTGAC 59.256 45.833 0.00 0.00 39.20 3.18
296 297 4.403113 TGTCTGTGTACTACAACCACTTGA 59.597 41.667 0.00 0.00 39.20 3.02
297 298 4.689071 TGTCTGTGTACTACAACCACTTG 58.311 43.478 0.00 0.00 39.20 3.16
298 299 5.546621 ATGTCTGTGTACTACAACCACTT 57.453 39.130 0.00 0.00 39.20 3.16
299 300 5.304614 AGAATGTCTGTGTACTACAACCACT 59.695 40.000 0.00 0.00 39.20 4.00
300 301 5.405571 CAGAATGTCTGTGTACTACAACCAC 59.594 44.000 0.00 0.00 39.58 4.16
301 302 5.303333 TCAGAATGTCTGTGTACTACAACCA 59.697 40.000 5.23 0.00 44.58 3.67
302 303 5.779922 TCAGAATGTCTGTGTACTACAACC 58.220 41.667 5.23 0.00 44.58 3.77
303 304 6.448006 ACTCAGAATGTCTGTGTACTACAAC 58.552 40.000 10.39 0.60 45.85 3.32
304 305 6.650427 ACTCAGAATGTCTGTGTACTACAA 57.350 37.500 10.39 0.00 45.85 2.41
312 313 8.883954 ATGAACATATACTCAGAATGTCTGTG 57.116 34.615 5.23 5.60 44.58 3.66
313 314 9.322773 CAATGAACATATACTCAGAATGTCTGT 57.677 33.333 5.23 0.00 44.58 3.41
314 315 9.538508 TCAATGAACATATACTCAGAATGTCTG 57.461 33.333 0.00 0.00 45.59 3.51
315 316 9.539825 GTCAATGAACATATACTCAGAATGTCT 57.460 33.333 0.00 0.00 37.40 3.41
316 317 9.317936 TGTCAATGAACATATACTCAGAATGTC 57.682 33.333 0.00 0.00 37.40 3.06
317 318 9.322773 CTGTCAATGAACATATACTCAGAATGT 57.677 33.333 0.00 0.00 37.40 2.71
318 319 9.538508 TCTGTCAATGAACATATACTCAGAATG 57.461 33.333 0.00 0.00 37.54 2.67
331 332 8.950210 GGAGAAGAATAATTCTGTCAATGAACA 58.050 33.333 0.00 0.00 39.63 3.18
332 333 8.950210 TGGAGAAGAATAATTCTGTCAATGAAC 58.050 33.333 0.00 0.00 39.63 3.18
333 334 9.690913 ATGGAGAAGAATAATTCTGTCAATGAA 57.309 29.630 0.00 0.00 39.63 2.57
334 335 9.690913 AATGGAGAAGAATAATTCTGTCAATGA 57.309 29.630 0.00 0.00 39.63 2.57
338 339 8.246180 GCAAAATGGAGAAGAATAATTCTGTCA 58.754 33.333 0.00 0.00 39.63 3.58
339 340 8.246180 TGCAAAATGGAGAAGAATAATTCTGTC 58.754 33.333 0.00 0.00 39.63 3.51
340 341 8.125978 TGCAAAATGGAGAAGAATAATTCTGT 57.874 30.769 0.00 0.00 39.63 3.41
341 342 7.222224 GCTGCAAAATGGAGAAGAATAATTCTG 59.778 37.037 2.86 0.00 38.14 3.02
342 343 7.123847 AGCTGCAAAATGGAGAAGAATAATTCT 59.876 33.333 1.02 0.00 38.14 2.40
343 344 7.263496 AGCTGCAAAATGGAGAAGAATAATTC 58.737 34.615 1.02 0.00 38.14 2.17
344 345 7.179076 AGCTGCAAAATGGAGAAGAATAATT 57.821 32.000 1.02 0.00 38.14 1.40
345 346 6.786967 AGCTGCAAAATGGAGAAGAATAAT 57.213 33.333 1.02 0.00 38.14 1.28
346 347 7.886629 ATAGCTGCAAAATGGAGAAGAATAA 57.113 32.000 1.02 0.00 38.14 1.40
347 348 7.992608 TGTATAGCTGCAAAATGGAGAAGAATA 59.007 33.333 1.02 0.00 38.14 1.75
348 349 6.830324 TGTATAGCTGCAAAATGGAGAAGAAT 59.170 34.615 1.02 0.00 38.14 2.40
349 350 6.094048 GTGTATAGCTGCAAAATGGAGAAGAA 59.906 38.462 1.02 0.00 38.14 2.52
350 351 5.586243 GTGTATAGCTGCAAAATGGAGAAGA 59.414 40.000 1.02 0.00 38.14 2.87
351 352 5.587844 AGTGTATAGCTGCAAAATGGAGAAG 59.412 40.000 1.02 0.00 38.14 2.85
352 353 5.500234 AGTGTATAGCTGCAAAATGGAGAA 58.500 37.500 1.02 0.00 38.14 2.87
353 354 5.102953 AGTGTATAGCTGCAAAATGGAGA 57.897 39.130 1.02 0.00 38.14 3.71
354 355 5.817296 TGTAGTGTATAGCTGCAAAATGGAG 59.183 40.000 1.02 0.00 38.97 3.86
355 356 5.584649 GTGTAGTGTATAGCTGCAAAATGGA 59.415 40.000 1.02 0.00 30.87 3.41
356 357 5.220854 GGTGTAGTGTATAGCTGCAAAATGG 60.221 44.000 1.02 0.00 30.87 3.16
357 358 5.353956 TGGTGTAGTGTATAGCTGCAAAATG 59.646 40.000 1.02 0.00 30.87 2.32
358 359 5.354234 GTGGTGTAGTGTATAGCTGCAAAAT 59.646 40.000 1.02 0.00 30.87 1.82
359 360 4.693566 GTGGTGTAGTGTATAGCTGCAAAA 59.306 41.667 1.02 0.00 30.87 2.44
360 361 4.250464 GTGGTGTAGTGTATAGCTGCAAA 58.750 43.478 1.02 0.00 30.87 3.68
361 362 3.259625 TGTGGTGTAGTGTATAGCTGCAA 59.740 43.478 1.02 0.00 30.87 4.08
362 363 2.829120 TGTGGTGTAGTGTATAGCTGCA 59.171 45.455 1.02 0.00 0.00 4.41
363 364 3.520290 TGTGGTGTAGTGTATAGCTGC 57.480 47.619 0.00 0.00 0.00 5.25
364 365 4.625742 GTGTTGTGGTGTAGTGTATAGCTG 59.374 45.833 0.00 0.00 0.00 4.24
365 366 4.527038 AGTGTTGTGGTGTAGTGTATAGCT 59.473 41.667 0.00 0.00 0.00 3.32
366 367 4.817517 AGTGTTGTGGTGTAGTGTATAGC 58.182 43.478 0.00 0.00 0.00 2.97
367 368 8.997621 ATTAAGTGTTGTGGTGTAGTGTATAG 57.002 34.615 0.00 0.00 0.00 1.31
369 370 9.781633 TTAATTAAGTGTTGTGGTGTAGTGTAT 57.218 29.630 0.00 0.00 0.00 2.29
370 371 9.263538 CTTAATTAAGTGTTGTGGTGTAGTGTA 57.736 33.333 15.81 0.00 0.00 2.90
371 372 7.227910 CCTTAATTAAGTGTTGTGGTGTAGTGT 59.772 37.037 20.99 0.00 0.00 3.55
506 508 2.203084 TTTGTGCGCCCTCGTTCA 60.203 55.556 4.18 0.00 38.14 3.18
557 559 2.806244 GTTTAGTTGTGACGGCAGACAT 59.194 45.455 0.00 0.00 0.00 3.06
650 654 2.047274 CTTTTCGCGGGCCTCTCA 60.047 61.111 6.13 0.00 0.00 3.27
936 993 2.997897 GTCTGGTGCGGGAGAGGT 60.998 66.667 0.00 0.00 0.00 3.85
1269 1326 2.818432 CCTCTGAGCAGCTGACAAATTT 59.182 45.455 20.43 0.00 0.00 1.82
1708 1840 8.717821 TCCTCTCAAATAAATCACTTGTTAACG 58.282 33.333 0.26 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.