Multiple sequence alignment - TraesCS3A01G035400

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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 TraesCS3A01G035400 chr3A 100.000 2498 0 0 1 2498 19558672 19561169 0.000000e+00 4614.0
1 TraesCS3A01G035400 chr3A 84.725 1198 92 39 323 1504 19609953 19608831 0.000000e+00 1114.0
2 TraesCS3A01G035400 chr3A 88.757 338 25 11 268 598 19632521 19632190 3.870000e-108 401.0
3 TraesCS3A01G035400 chr3A 90.426 94 9 0 170 263 19610152 19610059 9.380000e-25 124.0
4 TraesCS3A01G035400 chr3A 84.848 66 8 1 2215 2278 31681432 31681367 5.770000e-07 65.8
5 TraesCS3A01G035400 chr3B 86.997 1915 149 43 617 2498 24789289 24787442 0.000000e+00 2065.0
6 TraesCS3A01G035400 chr3B 90.528 739 51 11 782 1505 24749504 24750238 0.000000e+00 959.0
7 TraesCS3A01G035400 chr3B 87.500 336 27 11 260 586 24747357 24747686 8.440000e-100 374.0
8 TraesCS3A01G035400 chr3B 80.682 352 19 26 268 613 24789627 24789319 6.950000e-56 228.0
9 TraesCS3A01G035400 chr3B 90.722 97 6 2 170 263 24748919 24749015 2.610000e-25 126.0
10 TraesCS3A01G035400 chr3B 87.234 94 9 2 173 263 24789782 24789689 1.220000e-18 104.0
11 TraesCS3A01G035400 chr3B 84.058 69 10 1 2207 2274 676204970 676205038 5.770000e-07 65.8
12 TraesCS3A01G035400 chr4D 75.806 186 42 3 2315 2498 327374713 327374897 9.510000e-15 91.6
13 TraesCS3A01G035400 chr4D 83.333 84 12 1 2215 2296 127101066 127100983 2.660000e-10 76.8
14 TraesCS3A01G035400 chr7D 93.333 60 4 0 2213 2272 635663381 635663322 3.420000e-14 89.8
15 TraesCS3A01G035400 chr3D 90.000 60 6 0 2213 2272 83677301 83677360 7.410000e-11 78.7
16 TraesCS3A01G035400 chr2B 89.655 58 6 0 2215 2272 39792424 39792481 9.580000e-10 75.0
17 TraesCS3A01G035400 chr7A 90.566 53 4 1 2221 2272 515221774 515221826 4.460000e-08 69.4
18 TraesCS3A01G035400 chr4A 81.395 86 14 1 2213 2296 181642323 181642238 4.460000e-08 69.4
19 TraesCS3A01G035400 chr2A 94.444 36 2 0 2463 2498 771344773 771344808 3.470000e-04 56.5


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 TraesCS3A01G035400 chr3A 19558672 19561169 2497 False 4614.000000 4614 100.000000 1 2498 1 chr3A.!!$F1 2497
1 TraesCS3A01G035400 chr3A 19608831 19610152 1321 True 619.000000 1114 87.575500 170 1504 2 chr3A.!!$R3 1334
2 TraesCS3A01G035400 chr3B 24787442 24789782 2340 True 799.000000 2065 84.971000 173 2498 3 chr3B.!!$R1 2325
3 TraesCS3A01G035400 chr3B 24747357 24750238 2881 False 486.333333 959 89.583333 170 1505 3 chr3B.!!$F2 1335

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
992 2556 0.106894 GCAGGGCTAGCTAAACCGAT 59.893 55.0 15.72 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 3876 0.099968 CCGAGGCGTGTCTTCGATAA 59.9 55.0 0.0 0.0 0.0 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
23 24 4.029418 CGCACAAGCTTTGAATTTGATACG 59.971 41.667 0.00 0.00 39.10 3.06
24 25 4.324402 GCACAAGCTTTGAATTTGATACGG 59.676 41.667 0.00 0.00 37.91 4.02
25 26 4.324402 CACAAGCTTTGAATTTGATACGGC 59.676 41.667 0.00 0.00 0.00 5.68
27 28 1.846175 GCTTTGAATTTGATACGGCGC 59.154 47.619 6.90 0.00 0.00 6.53
29 30 3.497118 CTTTGAATTTGATACGGCGCAA 58.503 40.909 10.83 0.00 0.00 4.85
31 32 3.129852 TGAATTTGATACGGCGCAAAG 57.870 42.857 10.83 1.82 37.41 2.77
32 33 2.744741 TGAATTTGATACGGCGCAAAGA 59.255 40.909 10.83 0.00 37.41 2.52
34 35 4.142491 TGAATTTGATACGGCGCAAAGAAT 60.142 37.500 10.83 0.00 37.41 2.40
35 36 3.840890 TTTGATACGGCGCAAAGAATT 57.159 38.095 10.83 0.00 31.07 2.17
36 37 4.948608 TTTGATACGGCGCAAAGAATTA 57.051 36.364 10.83 0.00 31.07 1.40
37 38 4.948608 TTGATACGGCGCAAAGAATTAA 57.051 36.364 10.83 0.00 0.00 1.40
38 39 5.493133 TTGATACGGCGCAAAGAATTAAT 57.507 34.783 10.83 0.00 0.00 1.40
41 42 3.405170 ACGGCGCAAAGAATTAATGAG 57.595 42.857 10.83 0.00 0.00 2.90
42 43 3.006940 ACGGCGCAAAGAATTAATGAGA 58.993 40.909 10.83 0.00 0.00 3.27
43 44 3.438781 ACGGCGCAAAGAATTAATGAGAA 59.561 39.130 10.83 0.00 0.00 2.87
47 48 4.354587 CGCAAAGAATTAATGAGAAGCCC 58.645 43.478 0.00 0.00 0.00 5.19
48 49 4.096984 CGCAAAGAATTAATGAGAAGCCCT 59.903 41.667 0.00 0.00 0.00 5.19
49 50 5.586339 GCAAAGAATTAATGAGAAGCCCTC 58.414 41.667 0.00 0.00 42.30 4.30
51 52 4.445557 AGAATTAATGAGAAGCCCTCCC 57.554 45.455 0.00 0.00 41.25 4.30
52 53 4.050757 AGAATTAATGAGAAGCCCTCCCT 58.949 43.478 0.00 0.00 41.25 4.20
54 55 4.888626 ATTAATGAGAAGCCCTCCCTTT 57.111 40.909 1.79 0.00 41.25 3.11
55 56 4.675063 TTAATGAGAAGCCCTCCCTTTT 57.325 40.909 1.79 0.00 41.25 2.27
57 58 0.698818 TGAGAAGCCCTCCCTTTTCC 59.301 55.000 1.79 0.00 41.25 3.13
58 59 0.698818 GAGAAGCCCTCCCTTTTCCA 59.301 55.000 0.00 0.00 35.87 3.53
60 61 1.503347 AGAAGCCCTCCCTTTTCCAAA 59.497 47.619 0.00 0.00 0.00 3.28
62 63 0.539669 AGCCCTCCCTTTTCCAAACG 60.540 55.000 0.00 0.00 0.00 3.60
63 64 0.826256 GCCCTCCCTTTTCCAAACGT 60.826 55.000 0.00 0.00 0.00 3.99
64 65 1.546099 GCCCTCCCTTTTCCAAACGTA 60.546 52.381 0.00 0.00 0.00 3.57
66 67 2.555325 CCCTCCCTTTTCCAAACGTAAC 59.445 50.000 0.00 0.00 0.00 2.50
67 68 3.215975 CCTCCCTTTTCCAAACGTAACA 58.784 45.455 0.00 0.00 0.00 2.41
68 69 3.633065 CCTCCCTTTTCCAAACGTAACAA 59.367 43.478 0.00 0.00 0.00 2.83
69 70 4.261447 CCTCCCTTTTCCAAACGTAACAAG 60.261 45.833 0.00 0.00 0.00 3.16
70 71 4.525024 TCCCTTTTCCAAACGTAACAAGA 58.475 39.130 0.00 0.00 0.00 3.02
71 72 4.948621 TCCCTTTTCCAAACGTAACAAGAA 59.051 37.500 0.00 0.00 0.00 2.52
72 73 5.038683 CCCTTTTCCAAACGTAACAAGAAC 58.961 41.667 0.00 0.00 0.00 3.01
73 74 5.393243 CCCTTTTCCAAACGTAACAAGAACA 60.393 40.000 0.00 0.00 0.00 3.18
74 75 6.270064 CCTTTTCCAAACGTAACAAGAACAT 58.730 36.000 0.00 0.00 0.00 2.71
75 76 6.198216 CCTTTTCCAAACGTAACAAGAACATG 59.802 38.462 0.00 0.00 0.00 3.21
78 79 4.273969 TCCAAACGTAACAAGAACATGGAC 59.726 41.667 0.00 0.00 29.93 4.02
79 80 4.208355 CAAACGTAACAAGAACATGGACG 58.792 43.478 0.00 0.00 38.76 4.79
82 83 3.243636 ACGTAACAAGAACATGGACGACT 60.244 43.478 0.00 0.00 37.28 4.18
83 84 3.364023 CGTAACAAGAACATGGACGACTC 59.636 47.826 0.00 0.00 36.47 3.36
84 85 3.469008 AACAAGAACATGGACGACTCA 57.531 42.857 0.00 0.00 0.00 3.41
85 86 2.755650 ACAAGAACATGGACGACTCAC 58.244 47.619 0.00 0.00 0.00 3.51
86 87 2.069273 CAAGAACATGGACGACTCACC 58.931 52.381 0.00 0.00 0.00 4.02
87 88 1.338107 AGAACATGGACGACTCACCA 58.662 50.000 0.00 0.00 40.57 4.17
88 89 1.691976 AGAACATGGACGACTCACCAA 59.308 47.619 0.00 0.00 39.69 3.67
90 91 2.859165 ACATGGACGACTCACCAAAT 57.141 45.000 0.00 0.00 39.69 2.32
91 92 2.426522 ACATGGACGACTCACCAAATG 58.573 47.619 0.00 0.00 39.69 2.32
92 93 2.224523 ACATGGACGACTCACCAAATGT 60.225 45.455 0.00 0.00 39.69 2.71
93 94 3.007506 ACATGGACGACTCACCAAATGTA 59.992 43.478 0.00 0.00 39.69 2.29
95 96 3.395639 TGGACGACTCACCAAATGTAAC 58.604 45.455 0.00 0.00 32.93 2.50
96 97 3.181464 TGGACGACTCACCAAATGTAACA 60.181 43.478 0.00 0.00 32.93 2.41
98 99 3.399330 ACGACTCACCAAATGTAACAGG 58.601 45.455 0.00 0.00 0.00 4.00
99 100 3.070446 ACGACTCACCAAATGTAACAGGA 59.930 43.478 0.00 0.00 0.00 3.86
100 101 4.062293 CGACTCACCAAATGTAACAGGAA 58.938 43.478 0.00 0.00 0.00 3.36
101 102 4.152402 CGACTCACCAAATGTAACAGGAAG 59.848 45.833 0.00 0.00 0.00 3.46
103 104 3.820467 CTCACCAAATGTAACAGGAAGCA 59.180 43.478 0.00 0.00 0.00 3.91
106 107 4.278170 CACCAAATGTAACAGGAAGCAAGA 59.722 41.667 0.00 0.00 0.00 3.02
107 108 5.047802 CACCAAATGTAACAGGAAGCAAGAT 60.048 40.000 0.00 0.00 0.00 2.40
108 109 5.539955 ACCAAATGTAACAGGAAGCAAGATT 59.460 36.000 0.00 0.00 0.00 2.40
109 110 6.719370 ACCAAATGTAACAGGAAGCAAGATTA 59.281 34.615 0.00 0.00 0.00 1.75
110 111 7.232534 ACCAAATGTAACAGGAAGCAAGATTAA 59.767 33.333 0.00 0.00 0.00 1.40
111 112 7.756722 CCAAATGTAACAGGAAGCAAGATTAAG 59.243 37.037 0.00 0.00 0.00 1.85
112 113 5.880054 TGTAACAGGAAGCAAGATTAAGC 57.120 39.130 0.00 0.00 0.00 3.09
113 114 5.560724 TGTAACAGGAAGCAAGATTAAGCT 58.439 37.500 0.00 0.00 44.31 3.74
114 115 6.707290 TGTAACAGGAAGCAAGATTAAGCTA 58.293 36.000 0.00 0.00 40.90 3.32
115 116 7.338710 TGTAACAGGAAGCAAGATTAAGCTAT 58.661 34.615 0.00 0.00 40.90 2.97
117 118 5.749462 ACAGGAAGCAAGATTAAGCTATGT 58.251 37.500 0.00 0.00 40.90 2.29
118 119 5.587844 ACAGGAAGCAAGATTAAGCTATGTG 59.412 40.000 0.00 0.00 40.90 3.21
119 120 5.819379 CAGGAAGCAAGATTAAGCTATGTGA 59.181 40.000 0.00 0.00 40.90 3.58
120 121 5.819901 AGGAAGCAAGATTAAGCTATGTGAC 59.180 40.000 0.00 0.00 40.90 3.67
122 123 5.365021 AGCAAGATTAAGCTATGTGACCT 57.635 39.130 0.00 0.00 39.78 3.85
123 124 5.121811 AGCAAGATTAAGCTATGTGACCTG 58.878 41.667 0.00 0.00 39.78 4.00
124 125 4.878397 GCAAGATTAAGCTATGTGACCTGT 59.122 41.667 0.00 0.00 0.00 4.00
126 127 4.446371 AGATTAAGCTATGTGACCTGTGC 58.554 43.478 0.00 0.00 0.00 4.57
127 128 2.293677 TAAGCTATGTGACCTGTGCG 57.706 50.000 0.00 0.00 0.00 5.34
128 129 0.321671 AAGCTATGTGACCTGTGCGT 59.678 50.000 0.00 0.00 0.00 5.24
129 130 1.182667 AGCTATGTGACCTGTGCGTA 58.817 50.000 0.00 0.00 0.00 4.42
132 133 2.738643 GCTATGTGACCTGTGCGTATGT 60.739 50.000 0.00 0.00 0.00 2.29
133 134 3.490249 GCTATGTGACCTGTGCGTATGTA 60.490 47.826 0.00 0.00 0.00 2.29
137 138 3.259064 GTGACCTGTGCGTATGTAACAT 58.741 45.455 0.00 0.00 0.00 2.71
138 139 3.306166 GTGACCTGTGCGTATGTAACATC 59.694 47.826 0.00 0.00 0.00 3.06
139 140 3.056465 TGACCTGTGCGTATGTAACATCA 60.056 43.478 0.00 0.00 0.00 3.07
140 141 3.259064 ACCTGTGCGTATGTAACATCAC 58.741 45.455 0.00 0.00 33.92 3.06
141 142 3.056107 ACCTGTGCGTATGTAACATCACT 60.056 43.478 0.00 0.00 34.25 3.41
142 143 4.158949 ACCTGTGCGTATGTAACATCACTA 59.841 41.667 0.00 0.00 34.25 2.74
143 144 4.740205 CCTGTGCGTATGTAACATCACTAG 59.260 45.833 0.00 0.00 34.25 2.57
145 146 4.142249 TGTGCGTATGTAACATCACTAGCT 60.142 41.667 0.00 0.00 34.25 3.32
147 148 5.975344 GTGCGTATGTAACATCACTAGCTAA 59.025 40.000 0.00 0.00 31.87 3.09
149 150 7.009815 GTGCGTATGTAACATCACTAGCTAAAA 59.990 37.037 0.00 0.00 31.87 1.52
150 151 7.222031 TGCGTATGTAACATCACTAGCTAAAAG 59.778 37.037 0.00 0.00 0.00 2.27
151 152 7.434307 GCGTATGTAACATCACTAGCTAAAAGA 59.566 37.037 0.00 0.00 0.00 2.52
152 153 9.297586 CGTATGTAACATCACTAGCTAAAAGAA 57.702 33.333 0.00 0.00 0.00 2.52
155 156 7.974675 TGTAACATCACTAGCTAAAAGAATGC 58.025 34.615 0.00 0.00 0.00 3.56
156 157 7.824289 TGTAACATCACTAGCTAAAAGAATGCT 59.176 33.333 0.00 0.00 40.43 3.79
157 158 7.693969 AACATCACTAGCTAAAAGAATGCTT 57.306 32.000 0.00 0.00 38.15 3.91
158 159 7.081526 ACATCACTAGCTAAAAGAATGCTTG 57.918 36.000 0.00 0.00 38.15 4.01
159 160 5.551760 TCACTAGCTAAAAGAATGCTTGC 57.448 39.130 0.00 0.00 38.15 4.01
160 161 4.396166 TCACTAGCTAAAAGAATGCTTGCC 59.604 41.667 0.00 0.00 38.15 4.52
161 162 4.397417 CACTAGCTAAAAGAATGCTTGCCT 59.603 41.667 0.00 0.00 38.15 4.75
162 163 5.012893 ACTAGCTAAAAGAATGCTTGCCTT 58.987 37.500 0.00 0.00 38.15 4.35
163 164 4.446994 AGCTAAAAGAATGCTTGCCTTC 57.553 40.909 3.06 3.06 33.79 3.46
164 165 3.828451 AGCTAAAAGAATGCTTGCCTTCA 59.172 39.130 11.86 0.00 33.79 3.02
166 167 4.559300 GCTAAAAGAATGCTTGCCTTCACA 60.559 41.667 11.86 0.00 33.79 3.58
167 168 4.405116 AAAAGAATGCTTGCCTTCACAA 57.595 36.364 11.86 0.00 33.79 3.33
168 169 4.612264 AAAGAATGCTTGCCTTCACAAT 57.388 36.364 11.86 0.00 33.79 2.71
170 171 2.494870 AGAATGCTTGCCTTCACAATCC 59.505 45.455 11.86 0.00 0.00 3.01
171 172 2.226962 ATGCTTGCCTTCACAATCCT 57.773 45.000 0.00 0.00 0.00 3.24
195 1589 2.593346 AGAGGCTAGAATCTTGCGTG 57.407 50.000 15.64 0.00 33.37 5.34
217 1611 3.621715 GGAACCACTAAAGAATACGCAGG 59.378 47.826 0.00 0.00 0.00 4.85
229 1626 2.449031 TACGCAGGCCACACCAAGAG 62.449 60.000 5.01 0.00 43.14 2.85
310 1764 1.194896 GACGCGATCTTTCTCGTCGG 61.195 60.000 15.93 0.00 46.34 4.79
349 1833 2.917971 GAGAAAGAGTGTGAACGGATCG 59.082 50.000 0.00 0.00 0.00 3.69
351 1835 0.732880 AAGAGTGTGAACGGATCGCG 60.733 55.000 0.00 0.00 41.64 5.87
404 1892 4.054825 GCATGTTGCCCCACACCG 62.055 66.667 0.00 0.00 37.42 4.94
405 1893 2.597217 CATGTTGCCCCACACCGT 60.597 61.111 0.00 0.00 0.00 4.83
406 1894 2.597217 ATGTTGCCCCACACCGTG 60.597 61.111 0.00 0.00 0.00 4.94
416 1904 4.373116 ACACCGTGGCGAGCGAAT 62.373 61.111 3.03 0.00 0.00 3.34
417 1905 3.554692 CACCGTGGCGAGCGAATC 61.555 66.667 0.00 0.00 0.00 2.52
418 1906 4.814294 ACCGTGGCGAGCGAATCC 62.814 66.667 0.00 0.00 0.00 3.01
419 1907 4.514577 CCGTGGCGAGCGAATCCT 62.515 66.667 0.00 0.00 0.00 3.24
420 1908 3.257561 CGTGGCGAGCGAATCCTG 61.258 66.667 0.00 0.00 0.00 3.86
467 1966 3.505808 CGAAGCCTAGCTAGCATCC 57.494 57.895 18.83 1.95 38.25 3.51
468 1967 0.387878 CGAAGCCTAGCTAGCATCCG 60.388 60.000 18.83 11.46 38.25 4.18
540 2040 2.338620 GCCCGGAAAAGTTGTGCC 59.661 61.111 0.73 0.00 0.00 5.01
541 2041 2.642700 CCCGGAAAAGTTGTGCCG 59.357 61.111 0.73 0.00 43.20 5.69
543 2043 2.050442 CGGAAAAGTTGTGCCGGC 60.050 61.111 22.73 22.73 40.08 6.13
544 2044 2.551912 CGGAAAAGTTGTGCCGGCT 61.552 57.895 29.70 3.54 40.08 5.52
545 2045 1.007387 GGAAAAGTTGTGCCGGCTG 60.007 57.895 29.70 0.00 0.00 4.85
546 2046 1.661509 GAAAAGTTGTGCCGGCTGC 60.662 57.895 29.70 20.57 41.77 5.25
547 2047 3.150647 AAAAGTTGTGCCGGCTGCC 62.151 57.895 29.70 15.93 40.16 4.85
613 2117 6.304683 GCGATATATTTTGGCGTAAAATGGTC 59.695 38.462 17.22 12.51 45.90 4.02
625 2156 5.640783 GCGTAAAATGGTCCTGTAAAGTAGT 59.359 40.000 0.00 0.00 0.00 2.73
671 2202 1.444836 TTTTTAGGTGCATCGGGTCG 58.555 50.000 0.00 0.00 0.00 4.79
698 2229 2.738147 CGTTGCTCGGATTTCTCGT 58.262 52.632 0.00 0.00 35.71 4.18
739 2283 2.287188 CCATATGAGTCCATGCGCAAAC 60.287 50.000 17.11 13.67 34.31 2.93
751 2295 1.206115 GCGCAAACCAACGAAACTGG 61.206 55.000 0.30 0.00 40.05 4.00
754 2298 0.593773 CAAACCAACGAAACTGGCCG 60.594 55.000 0.00 0.00 37.48 6.13
756 2300 4.038080 CCAACGAAACTGGCCGGC 62.038 66.667 21.18 21.18 0.00 6.13
809 2354 2.992543 CAACTCAAGCTACAGAGACAGC 59.007 50.000 15.27 0.00 38.09 4.40
813 2358 1.510383 AGCTACAGAGACAGCTGCG 59.490 57.895 15.27 0.00 46.21 5.18
815 2360 1.140589 CTACAGAGACAGCTGCGGG 59.859 63.158 15.27 1.56 39.51 6.13
846 2391 3.994853 GCAAGGCAGGTTGGTGGC 61.995 66.667 0.00 0.00 43.28 5.01
851 2401 3.297620 GCAGGTTGGTGGCTGGTG 61.298 66.667 0.00 0.00 0.00 4.17
879 2429 1.399440 TCGTCGTCCATATATAGCCGC 59.601 52.381 0.00 0.00 0.00 6.53
916 2466 3.054878 CAGCTCCAAGCATTCACAAAAC 58.945 45.455 1.29 0.00 45.56 2.43
977 2541 3.795688 ACATACATATCCCCAAGCAGG 57.204 47.619 0.00 0.00 37.03 4.85
989 2553 1.383523 CAAGCAGGGCTAGCTAAACC 58.616 55.000 15.72 7.18 42.53 3.27
990 2554 0.107654 AAGCAGGGCTAGCTAAACCG 60.108 55.000 15.72 5.16 42.53 4.44
991 2555 0.976073 AGCAGGGCTAGCTAAACCGA 60.976 55.000 15.72 0.00 41.32 4.69
992 2556 0.106894 GCAGGGCTAGCTAAACCGAT 59.893 55.000 15.72 0.00 0.00 4.18
993 2557 1.874320 GCAGGGCTAGCTAAACCGATC 60.874 57.143 15.72 0.00 0.00 3.69
994 2558 1.689273 CAGGGCTAGCTAAACCGATCT 59.311 52.381 15.72 0.00 0.00 2.75
1504 3069 4.166011 GCCCGTGCTGATTGCGAC 62.166 66.667 0.00 0.00 46.63 5.19
1505 3070 3.853330 CCCGTGCTGATTGCGACG 61.853 66.667 0.00 0.00 46.63 5.12
1507 3072 1.803922 CCGTGCTGATTGCGACGTA 60.804 57.895 0.00 0.00 46.63 3.57
1508 3073 1.145759 CCGTGCTGATTGCGACGTAT 61.146 55.000 0.00 0.00 46.63 3.06
1509 3074 0.043907 CGTGCTGATTGCGACGTATG 60.044 55.000 0.00 0.00 46.63 2.39
1510 3075 0.315382 GTGCTGATTGCGACGTATGC 60.315 55.000 5.36 5.36 46.63 3.14
1511 3076 1.276844 GCTGATTGCGACGTATGCC 59.723 57.895 9.51 0.00 0.00 4.40
1512 3077 1.559814 CTGATTGCGACGTATGCCG 59.440 57.895 9.51 0.00 44.03 5.69
1535 3126 2.126580 GACGTGCGAGCGGTAAGT 60.127 61.111 0.00 0.00 35.98 2.24
1536 3127 1.731969 GACGTGCGAGCGGTAAGTT 60.732 57.895 0.00 0.00 35.98 2.66
1537 3128 1.941476 GACGTGCGAGCGGTAAGTTG 61.941 60.000 0.00 0.00 35.98 3.16
1538 3129 2.474712 GTGCGAGCGGTAAGTTGC 59.525 61.111 0.00 0.00 0.00 4.17
1539 3130 2.740826 TGCGAGCGGTAAGTTGCC 60.741 61.111 0.00 0.00 0.00 4.52
1548 3139 1.524008 GGTAAGTTGCCTTGCCGCTT 61.524 55.000 2.22 0.00 42.50 4.68
1572 3163 0.319125 GATCTGCTCGATCGGTTCCC 60.319 60.000 16.41 0.11 39.22 3.97
1573 3164 1.749334 ATCTGCTCGATCGGTTCCCC 61.749 60.000 16.41 0.00 0.00 4.81
1615 3206 3.004629 TGTGGTGTTCGATGTACGTAACT 59.995 43.478 0.00 0.00 43.13 2.24
1616 3207 4.215185 TGTGGTGTTCGATGTACGTAACTA 59.785 41.667 0.00 0.00 43.13 2.24
1617 3208 4.554973 GTGGTGTTCGATGTACGTAACTAC 59.445 45.833 0.00 0.00 43.13 2.73
1618 3209 4.215185 TGGTGTTCGATGTACGTAACTACA 59.785 41.667 0.00 0.00 43.13 2.74
1619 3210 4.790140 GGTGTTCGATGTACGTAACTACAG 59.210 45.833 0.00 0.00 43.13 2.74
1634 3225 6.090088 CGTAACTACAGTACGTACTTGAGTCT 59.910 42.308 27.45 21.42 33.46 3.24
1637 3228 4.745837 ACAGTACGTACTTGAGTCTGTC 57.254 45.455 25.35 0.00 33.46 3.51
1639 3230 5.545588 ACAGTACGTACTTGAGTCTGTCTA 58.454 41.667 25.35 0.00 33.46 2.59
1650 3241 1.012841 GTCTGTCTATGGCTTGCTGC 58.987 55.000 0.00 0.00 41.94 5.25
1652 3243 1.015109 CTGTCTATGGCTTGCTGCTG 58.985 55.000 0.00 0.00 42.39 4.41
1653 3244 0.325933 TGTCTATGGCTTGCTGCTGT 59.674 50.000 0.00 0.00 42.39 4.40
1654 3245 0.731417 GTCTATGGCTTGCTGCTGTG 59.269 55.000 0.00 0.00 42.39 3.66
1682 3273 0.109153 TGAGTGAGGTGCTTGCATGT 59.891 50.000 0.00 0.00 0.00 3.21
1710 3301 6.145696 GCCTGTACTGTTACTTGTTAGTTCTG 59.854 42.308 0.00 0.00 35.78 3.02
1742 3333 6.142139 CGCTCAAATTAATGAAGTGTTCACA 58.858 36.000 5.74 0.00 43.48 3.58
1775 3366 6.946584 CGCTAATTAACTGTACTCGTTGAAAC 59.053 38.462 10.19 0.00 0.00 2.78
1788 3379 2.480419 CGTTGAAACATGAGACCACCTC 59.520 50.000 0.00 0.00 42.30 3.85
1790 3381 3.407424 TGAAACATGAGACCACCTCTG 57.593 47.619 0.00 0.00 42.44 3.35
1854 3445 9.022915 TCAAGCGCATGATTTATTTTATTTCTG 57.977 29.630 11.93 0.00 0.00 3.02
1868 3459 1.885560 TTTCTGTCGATTCGCCCAAA 58.114 45.000 0.00 0.00 0.00 3.28
1871 3462 1.966493 CTGTCGATTCGCCCAAACCG 61.966 60.000 0.00 0.00 0.00 4.44
1873 3464 0.737019 GTCGATTCGCCCAAACCGTA 60.737 55.000 0.00 0.00 0.00 4.02
1875 3466 0.738412 CGATTCGCCCAAACCGTACT 60.738 55.000 0.00 0.00 0.00 2.73
1880 3471 2.620242 TCGCCCAAACCGTACTATTTC 58.380 47.619 0.00 0.00 0.00 2.17
1981 3572 3.695830 GTCATGGACCACCTAGAAACA 57.304 47.619 0.00 0.00 37.04 2.83
1991 3582 5.374071 ACCACCTAGAAACAACTAAACCAG 58.626 41.667 0.00 0.00 0.00 4.00
1993 3584 5.238650 CCACCTAGAAACAACTAAACCAGTG 59.761 44.000 0.00 0.00 37.63 3.66
1998 3589 1.878953 ACAACTAAACCAGTGGAGCG 58.121 50.000 18.40 3.58 37.63 5.03
2006 3597 0.034059 ACCAGTGGAGCGAGTCAAAG 59.966 55.000 18.40 0.00 0.00 2.77
2011 3602 0.674581 TGGAGCGAGTCAAAGGCATG 60.675 55.000 0.00 0.00 0.00 4.06
2012 3603 0.391661 GGAGCGAGTCAAAGGCATGA 60.392 55.000 0.00 0.00 0.00 3.07
2029 3622 1.275666 TGACATCGTCATCACCCCTT 58.724 50.000 0.00 0.00 37.67 3.95
2037 3630 1.351017 GTCATCACCCCTTCTTCACCA 59.649 52.381 0.00 0.00 0.00 4.17
2041 3634 0.322008 CACCCCTTCTTCACCAGAGC 60.322 60.000 0.00 0.00 31.12 4.09
2056 3649 2.280628 CAGAGCCGACCAAACCTTATC 58.719 52.381 0.00 0.00 0.00 1.75
2059 3652 2.872858 GAGCCGACCAAACCTTATCATC 59.127 50.000 0.00 0.00 0.00 2.92
2075 3668 8.303156 ACCTTATCATCATAGACAATCGAGAAG 58.697 37.037 0.00 0.00 0.00 2.85
2090 3683 9.449719 ACAATCGAGAAGTTTTCATATTAAGGT 57.550 29.630 0.00 0.00 0.00 3.50
2091 3684 9.922305 CAATCGAGAAGTTTTCATATTAAGGTC 57.078 33.333 0.00 0.00 0.00 3.85
2093 3686 8.928270 TCGAGAAGTTTTCATATTAAGGTCTC 57.072 34.615 0.00 0.00 0.00 3.36
2111 3704 5.449107 GTCTCATAGGACCAGCGTATTAA 57.551 43.478 0.00 0.00 0.00 1.40
2116 3709 6.408035 TCATAGGACCAGCGTATTAAAACAA 58.592 36.000 0.00 0.00 0.00 2.83
2124 3717 4.381566 CAGCGTATTAAAACAACAGCCAAC 59.618 41.667 0.00 0.00 0.00 3.77
2125 3718 4.036971 AGCGTATTAAAACAACAGCCAACA 59.963 37.500 0.00 0.00 0.00 3.33
2131 3724 0.678366 AACAACAGCCAACACCGACA 60.678 50.000 0.00 0.00 0.00 4.35
2139 3732 1.673920 GCCAACACCGACAAAGAGAAA 59.326 47.619 0.00 0.00 0.00 2.52
2180 3778 9.897744 ATCAAACATATAGACACACAAACAAAG 57.102 29.630 0.00 0.00 0.00 2.77
2190 3788 3.064682 CACACAAACAAAGACGATGGACA 59.935 43.478 0.00 0.00 0.00 4.02
2205 3803 1.303309 GGACAGCCGAATCAAGATGG 58.697 55.000 0.00 0.00 0.00 3.51
2221 3819 1.136305 GATGGATCCACCGAAGACGAA 59.864 52.381 18.99 0.00 42.61 3.85
2231 3829 1.792949 CCGAAGACGAACAAAGACTGG 59.207 52.381 0.00 0.00 42.66 4.00
2255 3853 3.486383 TCAAACAGATCCACCAAAGACC 58.514 45.455 0.00 0.00 0.00 3.85
2272 3870 0.110486 ACCAGCACCGAACAAATCCT 59.890 50.000 0.00 0.00 0.00 3.24
2277 3875 2.026822 AGCACCGAACAAATCCTGAGAT 60.027 45.455 0.00 0.00 0.00 2.75
2278 3876 2.749621 GCACCGAACAAATCCTGAGATT 59.250 45.455 0.00 0.00 44.86 2.40
2296 3894 1.904144 TTTATCGAAGACACGCCTCG 58.096 50.000 0.00 0.00 42.51 4.63
2297 3895 0.099968 TTATCGAAGACACGCCTCGG 59.900 55.000 0.00 0.00 42.51 4.63
2310 3908 2.044555 CCTCGGTGGTGCTAGACGA 61.045 63.158 0.00 0.00 0.00 4.20
2345 3943 3.577415 GGGCTAGGACGTAAGGACATTAT 59.423 47.826 0.00 0.00 46.39 1.28
2368 3966 1.556911 CATCTACAGGGAGGTGTTGCT 59.443 52.381 0.00 0.00 31.46 3.91
2375 3973 2.031163 GAGGTGTTGCTGCCTCGT 59.969 61.111 0.00 0.00 41.40 4.18
2379 3977 1.569479 GGTGTTGCTGCCTCGTCTTC 61.569 60.000 0.00 0.00 0.00 2.87
2384 3982 0.973632 TGCTGCCTCGTCTTCCTAAA 59.026 50.000 0.00 0.00 0.00 1.85
2415 4013 6.920758 CACAAATCCTAACCGAAATCAAAACA 59.079 34.615 0.00 0.00 0.00 2.83
2416 4014 7.598493 CACAAATCCTAACCGAAATCAAAACAT 59.402 33.333 0.00 0.00 0.00 2.71
2447 4046 1.596934 GAGCACGATCCTTCCCACA 59.403 57.895 0.00 0.00 0.00 4.17
2448 4047 0.460987 GAGCACGATCCTTCCCACAG 60.461 60.000 0.00 0.00 0.00 3.66
2450 4049 0.179000 GCACGATCCTTCCCACAGAT 59.821 55.000 0.00 0.00 0.00 2.90
2455 4054 2.037772 CGATCCTTCCCACAGATAAGGG 59.962 54.545 0.00 0.00 46.90 3.95
2456 4055 1.213296 TCCTTCCCACAGATAAGGGC 58.787 55.000 0.00 0.00 45.07 5.19
2469 4068 1.204146 TAAGGGCTGGAGTCCATCAC 58.796 55.000 13.56 10.20 43.78 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.324402 GCCGTATCAAATTCAAAGCTTGTG 59.676 41.667 0.00 0.74 0.00 3.33
5 6 3.758300 CGCCGTATCAAATTCAAAGCTT 58.242 40.909 0.00 0.00 0.00 3.74
7 8 1.846175 GCGCCGTATCAAATTCAAAGC 59.154 47.619 0.00 0.00 0.00 3.51
8 9 3.129852 TGCGCCGTATCAAATTCAAAG 57.870 42.857 4.18 0.00 0.00 2.77
9 10 3.560902 TTGCGCCGTATCAAATTCAAA 57.439 38.095 4.18 0.00 0.00 2.69
10 11 3.189495 TCTTTGCGCCGTATCAAATTCAA 59.811 39.130 4.18 0.00 32.51 2.69
12 13 3.398954 TCTTTGCGCCGTATCAAATTC 57.601 42.857 4.18 0.00 32.51 2.17
13 14 3.840890 TTCTTTGCGCCGTATCAAATT 57.159 38.095 4.18 0.00 32.51 1.82
14 15 4.370364 AATTCTTTGCGCCGTATCAAAT 57.630 36.364 4.18 0.00 32.51 2.32
16 17 4.948608 TTAATTCTTTGCGCCGTATCAA 57.051 36.364 4.18 0.00 0.00 2.57
17 18 4.572795 TCATTAATTCTTTGCGCCGTATCA 59.427 37.500 4.18 0.00 0.00 2.15
18 19 5.050363 TCTCATTAATTCTTTGCGCCGTATC 60.050 40.000 4.18 0.00 0.00 2.24
19 20 4.814234 TCTCATTAATTCTTTGCGCCGTAT 59.186 37.500 4.18 0.00 0.00 3.06
20 21 4.185394 TCTCATTAATTCTTTGCGCCGTA 58.815 39.130 4.18 0.00 0.00 4.02
21 22 3.006940 TCTCATTAATTCTTTGCGCCGT 58.993 40.909 4.18 0.00 0.00 5.68
23 24 3.793492 GCTTCTCATTAATTCTTTGCGCC 59.207 43.478 4.18 0.00 0.00 6.53
24 25 3.793492 GGCTTCTCATTAATTCTTTGCGC 59.207 43.478 0.00 0.00 0.00 6.09
25 26 4.096984 AGGGCTTCTCATTAATTCTTTGCG 59.903 41.667 0.00 0.00 0.00 4.85
27 28 5.068329 GGGAGGGCTTCTCATTAATTCTTTG 59.932 44.000 9.20 0.00 44.19 2.77
29 30 4.480166 AGGGAGGGCTTCTCATTAATTCTT 59.520 41.667 0.00 0.00 44.19 2.52
31 32 4.445557 AGGGAGGGCTTCTCATTAATTC 57.554 45.455 0.00 0.00 44.19 2.17
32 33 4.888626 AAGGGAGGGCTTCTCATTAATT 57.111 40.909 0.00 0.00 44.19 1.40
34 35 4.569865 GGAAAAGGGAGGGCTTCTCATTAA 60.570 45.833 0.00 0.00 44.19 1.40
35 36 3.053619 GGAAAAGGGAGGGCTTCTCATTA 60.054 47.826 0.00 0.00 44.19 1.90
36 37 2.291865 GGAAAAGGGAGGGCTTCTCATT 60.292 50.000 0.00 0.00 44.19 2.57
37 38 1.286257 GGAAAAGGGAGGGCTTCTCAT 59.714 52.381 0.00 0.00 44.19 2.90
38 39 0.698818 GGAAAAGGGAGGGCTTCTCA 59.301 55.000 0.00 0.00 44.19 3.27
41 42 1.618837 GTTTGGAAAAGGGAGGGCTTC 59.381 52.381 0.00 0.00 0.00 3.86
42 43 1.717032 GTTTGGAAAAGGGAGGGCTT 58.283 50.000 0.00 0.00 0.00 4.35
43 44 0.539669 CGTTTGGAAAAGGGAGGGCT 60.540 55.000 0.00 0.00 0.00 5.19
47 48 4.577283 TCTTGTTACGTTTGGAAAAGGGAG 59.423 41.667 0.00 0.00 0.00 4.30
48 49 4.525024 TCTTGTTACGTTTGGAAAAGGGA 58.475 39.130 0.00 0.00 0.00 4.20
49 50 4.904253 TCTTGTTACGTTTGGAAAAGGG 57.096 40.909 0.00 0.00 0.00 3.95
51 52 6.198216 CCATGTTCTTGTTACGTTTGGAAAAG 59.802 38.462 0.00 0.00 0.00 2.27
52 53 6.037098 CCATGTTCTTGTTACGTTTGGAAAA 58.963 36.000 0.00 0.00 0.00 2.29
54 55 4.882427 TCCATGTTCTTGTTACGTTTGGAA 59.118 37.500 0.00 0.00 0.00 3.53
55 56 4.273969 GTCCATGTTCTTGTTACGTTTGGA 59.726 41.667 0.00 0.00 0.00 3.53
57 58 4.025563 TCGTCCATGTTCTTGTTACGTTTG 60.026 41.667 0.00 0.00 0.00 2.93
58 59 4.025480 GTCGTCCATGTTCTTGTTACGTTT 60.025 41.667 0.00 0.00 0.00 3.60
60 61 3.054878 GTCGTCCATGTTCTTGTTACGT 58.945 45.455 0.00 0.00 0.00 3.57
62 63 4.150098 GTGAGTCGTCCATGTTCTTGTTAC 59.850 45.833 0.00 0.00 0.00 2.50
63 64 4.304110 GTGAGTCGTCCATGTTCTTGTTA 58.696 43.478 0.00 0.00 0.00 2.41
64 65 3.131396 GTGAGTCGTCCATGTTCTTGTT 58.869 45.455 0.00 0.00 0.00 2.83
66 67 2.069273 GGTGAGTCGTCCATGTTCTTG 58.931 52.381 0.00 0.00 0.00 3.02
67 68 1.691976 TGGTGAGTCGTCCATGTTCTT 59.308 47.619 3.20 0.00 0.00 2.52
68 69 1.338107 TGGTGAGTCGTCCATGTTCT 58.662 50.000 3.20 0.00 0.00 3.01
69 70 2.163818 TTGGTGAGTCGTCCATGTTC 57.836 50.000 7.53 0.00 33.50 3.18
70 71 2.631160 TTTGGTGAGTCGTCCATGTT 57.369 45.000 7.53 0.00 33.50 2.71
71 72 2.224523 ACATTTGGTGAGTCGTCCATGT 60.225 45.455 7.53 7.39 33.50 3.21
72 73 2.426522 ACATTTGGTGAGTCGTCCATG 58.573 47.619 7.53 6.87 33.50 3.66
73 74 2.859165 ACATTTGGTGAGTCGTCCAT 57.141 45.000 7.53 0.00 33.50 3.41
74 75 3.181464 TGTTACATTTGGTGAGTCGTCCA 60.181 43.478 3.20 3.20 0.00 4.02
75 76 3.395639 TGTTACATTTGGTGAGTCGTCC 58.604 45.455 0.00 0.00 0.00 4.79
78 79 3.659786 TCCTGTTACATTTGGTGAGTCG 58.340 45.455 0.00 0.00 0.00 4.18
79 80 4.083271 GCTTCCTGTTACATTTGGTGAGTC 60.083 45.833 0.00 0.00 0.00 3.36
82 83 3.826524 TGCTTCCTGTTACATTTGGTGA 58.173 40.909 0.00 0.00 0.00 4.02
83 84 4.278170 TCTTGCTTCCTGTTACATTTGGTG 59.722 41.667 0.00 0.00 0.00 4.17
84 85 4.469657 TCTTGCTTCCTGTTACATTTGGT 58.530 39.130 0.00 0.00 0.00 3.67
85 86 5.649782 ATCTTGCTTCCTGTTACATTTGG 57.350 39.130 0.00 0.00 0.00 3.28
86 87 7.274250 GCTTAATCTTGCTTCCTGTTACATTTG 59.726 37.037 0.00 0.00 0.00 2.32
87 88 7.177392 AGCTTAATCTTGCTTCCTGTTACATTT 59.823 33.333 0.00 0.00 35.86 2.32
88 89 6.660949 AGCTTAATCTTGCTTCCTGTTACATT 59.339 34.615 0.00 0.00 35.86 2.71
90 91 5.560724 AGCTTAATCTTGCTTCCTGTTACA 58.439 37.500 0.00 0.00 35.86 2.41
91 92 7.281100 ACATAGCTTAATCTTGCTTCCTGTTAC 59.719 37.037 0.00 0.00 40.35 2.50
92 93 7.280876 CACATAGCTTAATCTTGCTTCCTGTTA 59.719 37.037 0.00 0.00 40.35 2.41
93 94 6.094603 CACATAGCTTAATCTTGCTTCCTGTT 59.905 38.462 0.00 0.00 40.35 3.16
95 96 5.819379 TCACATAGCTTAATCTTGCTTCCTG 59.181 40.000 0.00 0.00 40.35 3.86
96 97 5.819901 GTCACATAGCTTAATCTTGCTTCCT 59.180 40.000 0.00 0.00 40.35 3.36
98 99 5.819901 AGGTCACATAGCTTAATCTTGCTTC 59.180 40.000 0.00 0.00 40.35 3.86
99 100 5.587844 CAGGTCACATAGCTTAATCTTGCTT 59.412 40.000 0.00 0.00 40.35 3.91
100 101 5.121811 CAGGTCACATAGCTTAATCTTGCT 58.878 41.667 0.00 0.00 42.67 3.91
101 102 4.878397 ACAGGTCACATAGCTTAATCTTGC 59.122 41.667 0.00 0.00 32.16 4.01
103 104 4.878397 GCACAGGTCACATAGCTTAATCTT 59.122 41.667 0.00 0.00 32.16 2.40
106 107 3.198068 CGCACAGGTCACATAGCTTAAT 58.802 45.455 0.00 0.00 32.16 1.40
107 108 2.028476 ACGCACAGGTCACATAGCTTAA 60.028 45.455 0.00 0.00 32.16 1.85
108 109 1.548719 ACGCACAGGTCACATAGCTTA 59.451 47.619 0.00 0.00 32.16 3.09
109 110 0.321671 ACGCACAGGTCACATAGCTT 59.678 50.000 0.00 0.00 32.16 3.74
110 111 1.182667 TACGCACAGGTCACATAGCT 58.817 50.000 0.00 0.00 35.94 3.32
111 112 1.860950 CATACGCACAGGTCACATAGC 59.139 52.381 0.00 0.00 0.00 2.97
112 113 3.165058 ACATACGCACAGGTCACATAG 57.835 47.619 0.00 0.00 0.00 2.23
113 114 4.082136 TGTTACATACGCACAGGTCACATA 60.082 41.667 0.00 0.00 0.00 2.29
114 115 3.259064 GTTACATACGCACAGGTCACAT 58.741 45.455 0.00 0.00 0.00 3.21
115 116 2.036089 TGTTACATACGCACAGGTCACA 59.964 45.455 0.00 0.00 0.00 3.58
117 118 3.056465 TGATGTTACATACGCACAGGTCA 60.056 43.478 0.00 0.00 0.00 4.02
118 119 3.306166 GTGATGTTACATACGCACAGGTC 59.694 47.826 9.75 0.00 35.76 3.85
119 120 3.056107 AGTGATGTTACATACGCACAGGT 60.056 43.478 14.96 0.00 37.22 4.00
120 121 3.521560 AGTGATGTTACATACGCACAGG 58.478 45.455 14.96 0.00 37.22 4.00
122 123 4.109766 GCTAGTGATGTTACATACGCACA 58.890 43.478 14.96 0.15 37.22 4.57
123 124 4.360563 AGCTAGTGATGTTACATACGCAC 58.639 43.478 0.00 2.73 35.87 5.34
124 125 4.649088 AGCTAGTGATGTTACATACGCA 57.351 40.909 0.00 0.00 0.00 5.24
126 127 8.851960 TCTTTTAGCTAGTGATGTTACATACG 57.148 34.615 0.00 0.00 0.00 3.06
129 130 8.616076 GCATTCTTTTAGCTAGTGATGTTACAT 58.384 33.333 0.00 0.00 0.00 2.29
132 133 8.668353 CAAGCATTCTTTTAGCTAGTGATGTTA 58.332 33.333 0.00 0.00 37.70 2.41
133 134 7.533426 CAAGCATTCTTTTAGCTAGTGATGTT 58.467 34.615 0.00 0.00 37.70 2.71
137 138 4.396166 GGCAAGCATTCTTTTAGCTAGTGA 59.604 41.667 0.00 0.00 37.70 3.41
138 139 4.397417 AGGCAAGCATTCTTTTAGCTAGTG 59.603 41.667 0.00 0.00 37.70 2.74
139 140 4.593956 AGGCAAGCATTCTTTTAGCTAGT 58.406 39.130 0.00 0.00 37.70 2.57
140 141 5.124457 TGAAGGCAAGCATTCTTTTAGCTAG 59.876 40.000 18.52 0.00 37.70 3.42
141 142 5.009631 TGAAGGCAAGCATTCTTTTAGCTA 58.990 37.500 18.52 0.00 37.70 3.32
142 143 3.828451 TGAAGGCAAGCATTCTTTTAGCT 59.172 39.130 18.52 0.00 41.03 3.32
143 144 3.922850 GTGAAGGCAAGCATTCTTTTAGC 59.077 43.478 18.52 1.56 37.58 3.09
145 146 5.528043 TTGTGAAGGCAAGCATTCTTTTA 57.472 34.783 18.52 0.00 37.58 1.52
147 148 4.562143 GGATTGTGAAGGCAAGCATTCTTT 60.562 41.667 18.52 3.17 37.58 2.52
149 150 2.494870 GGATTGTGAAGGCAAGCATTCT 59.505 45.455 18.52 0.33 37.58 2.40
150 151 2.494870 AGGATTGTGAAGGCAAGCATTC 59.505 45.455 12.06 12.06 36.58 2.67
151 152 2.532843 AGGATTGTGAAGGCAAGCATT 58.467 42.857 0.00 0.00 36.58 3.56
152 153 2.226962 AGGATTGTGAAGGCAAGCAT 57.773 45.000 0.00 0.00 36.58 3.79
155 156 2.996631 AGCTAGGATTGTGAAGGCAAG 58.003 47.619 0.00 0.00 0.00 4.01
156 157 3.774766 TCTAGCTAGGATTGTGAAGGCAA 59.225 43.478 20.58 0.00 0.00 4.52
157 158 3.374764 TCTAGCTAGGATTGTGAAGGCA 58.625 45.455 20.58 0.00 0.00 4.75
158 159 3.244044 CCTCTAGCTAGGATTGTGAAGGC 60.244 52.174 20.58 0.00 39.15 4.35
159 160 3.244044 GCCTCTAGCTAGGATTGTGAAGG 60.244 52.174 20.58 16.73 39.15 3.46
160 161 3.988819 GCCTCTAGCTAGGATTGTGAAG 58.011 50.000 20.58 7.76 39.15 3.02
195 1589 3.621715 CCTGCGTATTCTTTAGTGGTTCC 59.378 47.826 0.00 0.00 0.00 3.62
229 1626 1.739067 GATGGCTCAACAGTGGTACC 58.261 55.000 4.43 4.43 0.00 3.34
234 1631 1.732259 GGTAACGATGGCTCAACAGTG 59.268 52.381 0.00 0.00 0.00 3.66
266 1720 3.969250 AAGGCCGGCCACGTATGTG 62.969 63.158 45.13 8.18 46.00 3.21
287 1741 1.626388 GAGAAAGATCGCGTCGTGC 59.374 57.895 5.77 0.00 41.47 5.34
310 1764 1.143373 TCACTCACACGTTGTGTCGC 61.143 55.000 14.79 0.00 43.92 5.19
387 1871 4.054825 CGGTGTGGGGCAACATGC 62.055 66.667 0.00 0.00 44.08 4.06
404 1892 2.125512 ACAGGATTCGCTCGCCAC 60.126 61.111 0.00 0.00 0.00 5.01
405 1893 2.125552 CACAGGATTCGCTCGCCA 60.126 61.111 0.00 0.00 0.00 5.69
406 1894 3.567797 GCACAGGATTCGCTCGCC 61.568 66.667 0.00 0.00 0.00 5.54
410 1898 2.434884 CCGTGCACAGGATTCGCT 60.435 61.111 18.64 0.00 0.00 4.93
411 1899 4.166011 GCCGTGCACAGGATTCGC 62.166 66.667 25.37 10.27 0.00 4.70
455 1954 1.129624 CTCGCTACGGATGCTAGCTAG 59.870 57.143 16.84 16.84 35.41 3.42
456 1955 1.157585 CTCGCTACGGATGCTAGCTA 58.842 55.000 17.23 2.58 35.41 3.32
457 1956 1.519751 CCTCGCTACGGATGCTAGCT 61.520 60.000 17.23 0.83 35.41 3.32
458 1957 1.081108 CCTCGCTACGGATGCTAGC 60.081 63.158 8.10 8.10 34.39 3.42
459 1958 0.039978 CACCTCGCTACGGATGCTAG 60.040 60.000 0.00 0.00 0.00 3.42
460 1959 0.464916 TCACCTCGCTACGGATGCTA 60.465 55.000 0.00 0.00 0.00 3.49
461 1960 1.753078 TCACCTCGCTACGGATGCT 60.753 57.895 0.00 0.00 0.00 3.79
462 1961 1.589196 GTCACCTCGCTACGGATGC 60.589 63.158 0.00 0.00 0.00 3.91
463 1962 1.298413 CGTCACCTCGCTACGGATG 60.298 63.158 0.00 0.00 33.13 3.51
464 1963 1.437772 CTCGTCACCTCGCTACGGAT 61.438 60.000 0.00 0.00 37.24 4.18
465 1964 2.046988 TCGTCACCTCGCTACGGA 60.047 61.111 0.00 0.00 37.24 4.69
466 1965 2.403987 CTCGTCACCTCGCTACGG 59.596 66.667 0.00 0.00 37.24 4.02
467 1966 1.437772 ATCCTCGTCACCTCGCTACG 61.438 60.000 0.00 0.00 37.96 3.51
468 1967 1.590932 TATCCTCGTCACCTCGCTAC 58.409 55.000 0.00 0.00 0.00 3.58
524 2023 2.642700 CGGCACAACTTTTCCGGG 59.357 61.111 0.00 0.00 38.35 5.73
548 2048 0.321919 GTTACAAACGGTCCCTCCCC 60.322 60.000 0.00 0.00 0.00 4.81
580 2083 4.593157 GCCAAAATATATCGCACGTGAAA 58.407 39.130 22.23 6.21 0.00 2.69
671 2202 2.556287 CGAGCAACGGTGAAAGCC 59.444 61.111 3.55 0.00 38.46 4.35
698 2229 1.136690 GACGATCACGAAAGCACACA 58.863 50.000 0.00 0.00 42.66 3.72
739 2283 4.038080 GCCGGCCAGTTTCGTTGG 62.038 66.667 18.11 0.00 38.78 3.77
751 2295 0.727398 GTAATGTGAAGTGAGCCGGC 59.273 55.000 21.89 21.89 0.00 6.13
754 2298 2.633488 GGGAGTAATGTGAAGTGAGCC 58.367 52.381 0.00 0.00 0.00 4.70
756 2300 2.271800 GCGGGAGTAATGTGAAGTGAG 58.728 52.381 0.00 0.00 0.00 3.51
838 2383 2.781681 AGTATACACCAGCCACCAAC 57.218 50.000 5.50 0.00 0.00 3.77
839 2384 3.681593 GAAAGTATACACCAGCCACCAA 58.318 45.455 5.50 0.00 0.00 3.67
840 2385 2.354303 CGAAAGTATACACCAGCCACCA 60.354 50.000 5.50 0.00 0.00 4.17
842 2387 2.968675 ACGAAAGTATACACCAGCCAC 58.031 47.619 5.50 0.00 46.88 5.01
879 2429 2.190313 TGGCTAATGGCGAGGCAG 59.810 61.111 5.43 0.00 43.87 4.85
934 2485 3.753272 AGCTTGTGTACTACCAAATGCTG 59.247 43.478 0.00 0.00 33.24 4.41
946 2510 6.164176 GGGGATATGTATGTAGCTTGTGTAC 58.836 44.000 0.00 0.00 0.00 2.90
947 2511 5.841783 TGGGGATATGTATGTAGCTTGTGTA 59.158 40.000 0.00 0.00 0.00 2.90
948 2512 4.658435 TGGGGATATGTATGTAGCTTGTGT 59.342 41.667 0.00 0.00 0.00 3.72
949 2513 5.227569 TGGGGATATGTATGTAGCTTGTG 57.772 43.478 0.00 0.00 0.00 3.33
950 2514 5.746065 GCTTGGGGATATGTATGTAGCTTGT 60.746 44.000 0.00 0.00 0.00 3.16
951 2515 4.697352 GCTTGGGGATATGTATGTAGCTTG 59.303 45.833 0.00 0.00 0.00 4.01
952 2516 4.350816 TGCTTGGGGATATGTATGTAGCTT 59.649 41.667 0.00 0.00 0.00 3.74
977 2541 3.191791 CCTCTAGATCGGTTTAGCTAGCC 59.808 52.174 12.13 6.41 35.82 3.93
983 2547 4.515944 ACGACATCCTCTAGATCGGTTTAG 59.484 45.833 15.12 0.00 30.59 1.85
989 2553 2.619177 ACCAACGACATCCTCTAGATCG 59.381 50.000 10.38 10.38 30.59 3.69
990 2554 3.632604 TCACCAACGACATCCTCTAGATC 59.367 47.826 0.00 0.00 30.59 2.75
991 2555 3.632333 TCACCAACGACATCCTCTAGAT 58.368 45.455 0.00 0.00 34.66 1.98
992 2556 3.017442 CTCACCAACGACATCCTCTAGA 58.983 50.000 0.00 0.00 0.00 2.43
993 2557 2.099921 CCTCACCAACGACATCCTCTAG 59.900 54.545 0.00 0.00 0.00 2.43
994 2558 2.100197 CCTCACCAACGACATCCTCTA 58.900 52.381 0.00 0.00 0.00 2.43
1191 2756 1.185618 TGACCTCCTCCTTGGTGACG 61.186 60.000 0.00 0.00 36.59 4.35
1403 2968 3.625897 CCCTGGGCACTGTGACGA 61.626 66.667 12.86 4.82 0.00 4.20
1521 3112 2.474712 GCAACTTACCGCTCGCAC 59.525 61.111 0.00 0.00 0.00 5.34
1535 3126 0.607762 TCATACAAGCGGCAAGGCAA 60.608 50.000 1.45 0.00 34.64 4.52
1536 3127 0.394216 ATCATACAAGCGGCAAGGCA 60.394 50.000 1.45 0.00 34.64 4.75
1537 3128 0.308993 GATCATACAAGCGGCAAGGC 59.691 55.000 1.45 0.00 0.00 4.35
1538 3129 1.600957 CAGATCATACAAGCGGCAAGG 59.399 52.381 1.45 0.00 0.00 3.61
1539 3130 1.003116 GCAGATCATACAAGCGGCAAG 60.003 52.381 1.45 0.00 0.00 4.01
1568 3159 0.774096 TGGAATCACACCCAGGGGAA 60.774 55.000 11.37 0.00 38.96 3.97
1615 3206 5.545588 AGACAGACTCAAGTACGTACTGTA 58.454 41.667 28.00 17.57 37.27 2.74
1616 3207 4.387598 AGACAGACTCAAGTACGTACTGT 58.612 43.478 28.00 20.91 39.32 3.55
1617 3208 6.457122 CCATAGACAGACTCAAGTACGTACTG 60.457 46.154 28.00 20.44 36.50 2.74
1618 3209 5.585445 CCATAGACAGACTCAAGTACGTACT 59.415 44.000 22.45 22.45 38.39 2.73
1619 3210 5.730010 GCCATAGACAGACTCAAGTACGTAC 60.730 48.000 18.10 18.10 0.00 3.67
1650 3241 2.477825 CTCACTCACAAGTCACCACAG 58.522 52.381 0.00 0.00 31.71 3.66
1652 3243 1.139058 ACCTCACTCACAAGTCACCAC 59.861 52.381 0.00 0.00 31.71 4.16
1653 3244 1.138859 CACCTCACTCACAAGTCACCA 59.861 52.381 0.00 0.00 31.71 4.17
1654 3245 1.871080 CACCTCACTCACAAGTCACC 58.129 55.000 0.00 0.00 31.71 4.02
1682 3273 6.350906 ACTAACAAGTAACAGTACAGGCAAA 58.649 36.000 0.00 0.00 32.12 3.68
1710 3301 5.041951 TCATTAATTTGAGCGTGAACACC 57.958 39.130 0.00 0.00 0.00 4.16
1742 3333 9.017669 CGAGTACAGTTAATTAGCGAATACTTT 57.982 33.333 11.55 0.00 0.00 2.66
1748 3339 6.380995 TCAACGAGTACAGTTAATTAGCGAA 58.619 36.000 6.45 0.00 0.00 4.70
1775 3366 1.208776 TGATGCAGAGGTGGTCTCATG 59.791 52.381 0.00 0.00 44.81 3.07
1788 3379 1.466856 TTTAGGCAGGCTTGATGCAG 58.533 50.000 0.00 0.00 45.68 4.41
1818 3409 1.731093 TGCGCTTGATGGCATGATG 59.269 52.632 9.73 0.00 33.52 3.07
1819 3410 4.246053 TGCGCTTGATGGCATGAT 57.754 50.000 9.73 0.00 33.52 2.45
1823 3414 0.818938 AAATCATGCGCTTGATGGCA 59.181 45.000 31.95 11.17 44.29 4.92
1824 3415 2.780065 TAAATCATGCGCTTGATGGC 57.220 45.000 31.95 0.00 36.48 4.40
1825 3416 7.878477 ATAAAATAAATCATGCGCTTGATGG 57.122 32.000 31.95 5.84 36.48 3.51
1854 3445 0.737019 TACGGTTTGGGCGAATCGAC 60.737 55.000 6.91 2.09 36.66 4.20
1906 3497 9.188588 CTAATGCATTTTTAACTGCCATGATAG 57.811 33.333 18.75 0.00 37.59 2.08
1908 3499 7.784037 TCTAATGCATTTTTAACTGCCATGAT 58.216 30.769 18.75 0.00 37.59 2.45
1914 3505 7.594758 TGTCACTTCTAATGCATTTTTAACTGC 59.405 33.333 18.75 4.23 38.87 4.40
1981 3572 1.692519 ACTCGCTCCACTGGTTTAGTT 59.307 47.619 0.00 0.00 37.60 2.24
1991 3582 0.674895 ATGCCTTTGACTCGCTCCAC 60.675 55.000 0.00 0.00 0.00 4.02
1993 3584 0.391661 TCATGCCTTTGACTCGCTCC 60.392 55.000 0.00 0.00 0.00 4.70
1998 3589 2.349886 GACGATGTCATGCCTTTGACTC 59.650 50.000 11.39 6.87 45.07 3.36
2011 3602 1.482593 AGAAGGGGTGATGACGATGTC 59.517 52.381 0.00 0.00 0.00 3.06
2012 3603 1.573108 AGAAGGGGTGATGACGATGT 58.427 50.000 0.00 0.00 0.00 3.06
2013 3604 2.093500 TGAAGAAGGGGTGATGACGATG 60.093 50.000 0.00 0.00 0.00 3.84
2014 3605 2.093447 GTGAAGAAGGGGTGATGACGAT 60.093 50.000 0.00 0.00 0.00 3.73
2015 3606 1.275291 GTGAAGAAGGGGTGATGACGA 59.725 52.381 0.00 0.00 0.00 4.20
2016 3607 1.676014 GGTGAAGAAGGGGTGATGACG 60.676 57.143 0.00 0.00 0.00 4.35
2017 3608 1.351017 TGGTGAAGAAGGGGTGATGAC 59.649 52.381 0.00 0.00 0.00 3.06
2018 3609 1.630369 CTGGTGAAGAAGGGGTGATGA 59.370 52.381 0.00 0.00 0.00 2.92
2029 3622 1.118965 TTGGTCGGCTCTGGTGAAGA 61.119 55.000 0.00 0.00 0.00 2.87
2037 3630 1.906574 TGATAAGGTTTGGTCGGCTCT 59.093 47.619 0.00 0.00 0.00 4.09
2041 3634 5.696724 GTCTATGATGATAAGGTTTGGTCGG 59.303 44.000 0.00 0.00 0.00 4.79
2056 3649 8.189709 TGAAAACTTCTCGATTGTCTATGATG 57.810 34.615 0.00 0.00 0.00 3.07
2090 3683 6.127281 TGTTTTAATACGCTGGTCCTATGAGA 60.127 38.462 0.00 0.00 0.00 3.27
2091 3684 6.046593 TGTTTTAATACGCTGGTCCTATGAG 58.953 40.000 0.00 0.00 0.00 2.90
2093 3686 6.092944 TGTTGTTTTAATACGCTGGTCCTATG 59.907 38.462 0.00 0.00 0.00 2.23
2106 3699 4.579340 TCGGTGTTGGCTGTTGTTTTAATA 59.421 37.500 0.00 0.00 0.00 0.98
2108 3701 2.753452 TCGGTGTTGGCTGTTGTTTTAA 59.247 40.909 0.00 0.00 0.00 1.52
2111 3704 0.454196 GTCGGTGTTGGCTGTTGTTT 59.546 50.000 0.00 0.00 0.00 2.83
2116 3709 0.107410 TCTTTGTCGGTGTTGGCTGT 60.107 50.000 0.00 0.00 0.00 4.40
2124 3717 7.806690 TCAATCTATTTTTCTCTTTGTCGGTG 58.193 34.615 0.00 0.00 0.00 4.94
2125 3718 7.979444 TCAATCTATTTTTCTCTTTGTCGGT 57.021 32.000 0.00 0.00 0.00 4.69
2161 3754 7.064609 CCATCGTCTTTGTTTGTGTGTCTATAT 59.935 37.037 0.00 0.00 0.00 0.86
2163 3756 5.179368 CCATCGTCTTTGTTTGTGTGTCTAT 59.821 40.000 0.00 0.00 0.00 1.98
2170 3763 3.849645 GCTGTCCATCGTCTTTGTTTGTG 60.850 47.826 0.00 0.00 0.00 3.33
2180 3778 0.179111 TGATTCGGCTGTCCATCGTC 60.179 55.000 0.00 0.00 0.00 4.20
2190 3788 1.770658 TGGATCCATCTTGATTCGGCT 59.229 47.619 11.44 0.00 0.00 5.52
2205 3803 2.074547 TTGTTCGTCTTCGGTGGATC 57.925 50.000 0.00 0.00 37.69 3.36
2221 3819 5.474876 GGATCTGTTTGAATCCAGTCTTTGT 59.525 40.000 0.00 0.00 33.55 2.83
2231 3829 5.335976 GGTCTTTGGTGGATCTGTTTGAATC 60.336 44.000 0.00 0.00 0.00 2.52
2255 3853 1.466167 CTCAGGATTTGTTCGGTGCTG 59.534 52.381 0.00 0.00 33.27 4.41
2272 3870 3.130516 AGGCGTGTCTTCGATAAATCTCA 59.869 43.478 0.00 0.00 0.00 3.27
2277 3875 1.468565 CCGAGGCGTGTCTTCGATAAA 60.469 52.381 0.00 0.00 0.00 1.40
2278 3876 0.099968 CCGAGGCGTGTCTTCGATAA 59.900 55.000 0.00 0.00 0.00 1.75
2282 3880 2.805353 CACCGAGGCGTGTCTTCG 60.805 66.667 0.00 0.00 0.00 3.79
2284 3882 3.231736 ACCACCGAGGCGTGTCTT 61.232 61.111 0.00 0.00 43.14 3.01
2296 3894 2.577593 GGGTCGTCTAGCACCACC 59.422 66.667 7.43 4.73 33.91 4.61
2297 3895 2.181021 CGGGTCGTCTAGCACCAC 59.819 66.667 7.43 0.00 33.91 4.16
2345 3943 2.571653 CAACACCTCCCTGTAGATGGAA 59.428 50.000 0.00 0.00 0.00 3.53
2368 3966 2.743636 CTGTTTAGGAAGACGAGGCA 57.256 50.000 0.00 0.00 0.00 4.75
2434 4033 2.037772 CCCTTATCTGTGGGAAGGATCG 59.962 54.545 1.42 0.00 46.15 3.69
2436 4035 1.777272 GCCCTTATCTGTGGGAAGGAT 59.223 52.381 1.75 0.00 46.15 3.24
2440 4039 0.918983 CCAGCCCTTATCTGTGGGAA 59.081 55.000 1.75 0.00 46.15 3.97
2442 4041 0.471617 CTCCAGCCCTTATCTGTGGG 59.528 60.000 0.00 0.00 46.00 4.61
2447 4046 2.334023 GATGGACTCCAGCCCTTATCT 58.666 52.381 1.44 0.00 36.75 1.98
2448 4047 2.050144 TGATGGACTCCAGCCCTTATC 58.950 52.381 10.88 0.00 39.46 1.75
2450 4049 1.204146 GTGATGGACTCCAGCCCTTA 58.796 55.000 10.88 0.00 39.46 2.69
2455 4054 2.512515 GGCGTGATGGACTCCAGC 60.513 66.667 6.37 6.37 40.77 4.85
2456 4055 0.460987 GAAGGCGTGATGGACTCCAG 60.461 60.000 3.62 0.00 36.75 3.86


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

AutoCloner maintained by Alex Coulton.