Multiple sequence alignment - TraesCS5A01G403500

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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 TraesCS5A01G403500 chr5A 100.000 2912 0 0 1 2912 595898971 595896060 0.000000e+00 5378.0
1 TraesCS5A01G403500 chr5A 91.204 216 11 4 1 208 673865591 673865806 1.320000e-73 287.0
2 TraesCS5A01G403500 chr5A 76.834 259 48 9 247 498 298230960 298231213 5.060000e-28 135.0
3 TraesCS5A01G403500 chr5D 91.602 2179 96 20 807 2912 476464562 476462398 0.000000e+00 2929.0
4 TraesCS5A01G403500 chr5D 78.475 446 52 20 173 579 476466284 476465844 4.820000e-63 252.0
5 TraesCS5A01G403500 chr5D 84.659 176 25 2 2617 2791 458632796 458632622 1.070000e-39 174.0
6 TraesCS5A01G403500 chr5B 93.095 1984 85 25 970 2912 583915190 583913218 0.000000e+00 2857.0
7 TraesCS5A01G403500 chr5B 85.227 176 24 2 2617 2791 562048493 562048319 2.310000e-41 180.0
8 TraesCS5A01G403500 chr5B 77.154 267 45 9 247 499 684481218 684481482 1.090000e-29 141.0
9 TraesCS5A01G403500 chr7A 93.607 219 6 4 1 211 667979420 667979638 1.300000e-83 320.0
10 TraesCS5A01G403500 chr7A 92.118 203 9 4 1 196 619570449 619570651 2.210000e-71 279.0
11 TraesCS5A01G403500 chr7A 81.188 202 32 6 247 445 234851408 234851606 1.080000e-34 158.0
12 TraesCS5A01G403500 chrUn 94.472 199 4 3 1 192 13762028 13762226 1.700000e-77 300.0
13 TraesCS5A01G403500 chr2A 94.472 199 4 3 1 192 177850291 177850489 1.700000e-77 300.0
14 TraesCS5A01G403500 chr2A 91.781 219 10 4 1 211 443992085 443991867 6.100000e-77 298.0
15 TraesCS5A01G403500 chr2A 90.741 216 10 5 1 208 78471664 78471877 2.210000e-71 279.0
16 TraesCS5A01G403500 chr2A 92.118 203 9 3 1 196 106586207 106586005 2.210000e-71 279.0
17 TraesCS5A01G403500 chr4A 91.324 219 11 4 1 211 140701305 140701087 2.840000e-75 292.0
18 TraesCS5A01G403500 chr4A 84.091 176 26 2 2617 2791 532162172 532161998 4.990000e-38 169.0
19 TraesCS5A01G403500 chr7B 93.467 199 6 4 1 192 660060509 660060707 3.670000e-74 289.0
20 TraesCS5A01G403500 chr7B 78.218 101 16 5 663 760 742475271 742475368 3.130000e-05 60.2
21 TraesCS5A01G403500 chr7B 94.444 36 2 0 730 765 4232722 4232757 4.050000e-04 56.5
22 TraesCS5A01G403500 chr3B 88.889 216 16 5 1 208 593967253 593967038 2.880000e-65 259.0
23 TraesCS5A01G403500 chr3B 94.444 36 2 0 730 765 571791668 571791633 4.050000e-04 56.5
24 TraesCS5A01G403500 chr1B 81.071 280 51 2 1634 1912 678259787 678259509 3.780000e-54 222.0
25 TraesCS5A01G403500 chr1B 81.818 176 30 2 2617 2791 520245489 520245315 2.340000e-31 147.0
26 TraesCS5A01G403500 chr1B 78.367 245 37 10 248 480 670526022 670526262 8.410000e-31 145.0
27 TraesCS5A01G403500 chr1B 78.531 177 26 9 332 498 659900716 659900890 3.970000e-19 106.0
28 TraesCS5A01G403500 chr1D 80.714 280 52 2 1634 1912 487168799 487168521 1.760000e-52 217.0
29 TraesCS5A01G403500 chr1D 90.566 53 1 4 453 503 261093238 261093188 1.870000e-07 67.6
30 TraesCS5A01G403500 chr1D 78.261 115 15 7 654 765 116008521 116008628 6.740000e-07 65.8
31 TraesCS5A01G403500 chr1A 80.714 280 52 2 1634 1912 584676321 584676043 1.760000e-52 217.0
32 TraesCS5A01G403500 chr1A 81.818 176 30 2 2617 2791 64844844 64844670 2.340000e-31 147.0
33 TraesCS5A01G403500 chr3D 79.468 263 39 9 249 498 596656984 596657244 3.860000e-39 172.0
34 TraesCS5A01G403500 chr3D 79.487 117 15 7 655 765 579560887 579560774 1.120000e-09 75.0
35 TraesCS5A01G403500 chr7D 83.523 176 27 2 2617 2791 332692924 332692750 2.320000e-36 163.0
36 TraesCS5A01G403500 chr7D 83.429 175 19 6 332 497 362361407 362361234 1.400000e-33 154.0
37 TraesCS5A01G403500 chr7D 83.929 56 7 1 733 788 86290858 86290805 5.000000e-03 52.8
38 TraesCS5A01G403500 chr6A 78.927 261 40 9 249 498 101542116 101542372 2.320000e-36 163.0
39 TraesCS5A01G403500 chr6A 73.333 300 49 22 512 788 39489152 39488861 6.690000e-12 82.4
40 TraesCS5A01G403500 chr2D 83.815 173 26 2 2617 2788 601056086 601056257 2.320000e-36 163.0
41 TraesCS5A01G403500 chr2B 78.491 265 43 8 247 499 777988704 777988442 8.350000e-36 161.0
42 TraesCS5A01G403500 chr2B 78.491 265 43 8 247 499 778069910 778069648 8.350000e-36 161.0
43 TraesCS5A01G403500 chr2B 74.005 377 61 20 248 589 794570177 794569803 5.100000e-23 119.0
44 TraesCS5A01G403500 chr4D 94.444 36 2 0 730 765 6677238 6677273 4.050000e-04 56.5
45 TraesCS5A01G403500 chr3A 94.444 36 2 0 730 765 63031955 63031990 4.050000e-04 56.5
46 TraesCS5A01G403500 chr3A 83.607 61 5 3 702 760 645733210 645733267 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G403500 chr5A 595896060 595898971 2911 True 5378.0 5378 100.0000 1 2912 1 chr5A.!!$R1 2911
1 TraesCS5A01G403500 chr5D 476462398 476466284 3886 True 1590.5 2929 85.0385 173 2912 2 chr5D.!!$R2 2739
2 TraesCS5A01G403500 chr5B 583913218 583915190 1972 True 2857.0 2857 93.0950 970 2912 1 chr5B.!!$R2 1942

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
53 54 0.036388 ACATTCCATTGCTCCGACGT 60.036 50.0 0.0 0.0 0.00 4.34 F
67 68 0.110688 CGACGTGGCTTTGTGACATG 60.111 55.0 0.0 0.0 46.03 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 2828 0.807667 GCTCGCTGTGGTACATGAGG 60.808 60.000 0.00 0.0 44.52 3.86 R
2002 3145 2.955660 TCCACTTACACAAGGCCAAAAG 59.044 45.455 5.01 1.3 35.97 2.27 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
28 29 9.503399 AGTTCGATGAGGTTAGAATTTTAAAGT 57.497 29.630 0.00 0.00 0.00 2.66
48 49 7.728847 AAAGTTTTAAACATTCCATTGCTCC 57.271 32.000 10.60 0.00 0.00 4.70
49 50 5.469479 AGTTTTAAACATTCCATTGCTCCG 58.531 37.500 10.60 0.00 0.00 4.63
50 51 5.242838 AGTTTTAAACATTCCATTGCTCCGA 59.757 36.000 10.60 0.00 0.00 4.55
51 52 4.695217 TTAAACATTCCATTGCTCCGAC 57.305 40.909 0.00 0.00 0.00 4.79
52 53 1.086696 AACATTCCATTGCTCCGACG 58.913 50.000 0.00 0.00 0.00 5.12
53 54 0.036388 ACATTCCATTGCTCCGACGT 60.036 50.000 0.00 0.00 0.00 4.34
54 55 0.374758 CATTCCATTGCTCCGACGTG 59.625 55.000 0.00 0.00 0.00 4.49
55 56 0.744414 ATTCCATTGCTCCGACGTGG 60.744 55.000 0.00 0.00 40.09 4.94
56 57 3.499737 CCATTGCTCCGACGTGGC 61.500 66.667 0.00 0.00 37.80 5.01
57 58 2.434884 CATTGCTCCGACGTGGCT 60.435 61.111 0.00 0.00 37.80 4.75
58 59 2.034879 CATTGCTCCGACGTGGCTT 61.035 57.895 0.00 0.00 37.80 4.35
59 60 1.302511 ATTGCTCCGACGTGGCTTT 60.303 52.632 0.00 0.00 37.80 3.51
60 61 1.577328 ATTGCTCCGACGTGGCTTTG 61.577 55.000 0.00 0.00 37.80 2.77
61 62 2.665185 GCTCCGACGTGGCTTTGT 60.665 61.111 0.00 0.00 37.80 2.83
62 63 2.954753 GCTCCGACGTGGCTTTGTG 61.955 63.158 0.00 0.00 37.80 3.33
63 64 1.300620 CTCCGACGTGGCTTTGTGA 60.301 57.895 0.00 0.00 37.80 3.58
64 65 1.557443 CTCCGACGTGGCTTTGTGAC 61.557 60.000 0.00 0.00 37.80 3.67
65 66 1.885388 CCGACGTGGCTTTGTGACA 60.885 57.895 0.00 0.00 0.00 3.58
66 67 1.227999 CCGACGTGGCTTTGTGACAT 61.228 55.000 0.00 0.00 35.31 3.06
67 68 0.110688 CGACGTGGCTTTGTGACATG 60.111 55.000 0.00 0.00 46.03 3.21
69 70 3.460114 CGTGGCTTTGTGACATGTG 57.540 52.632 1.15 0.00 35.98 3.21
70 71 0.662619 CGTGGCTTTGTGACATGTGT 59.337 50.000 1.15 0.00 35.98 3.72
71 72 1.597690 CGTGGCTTTGTGACATGTGTG 60.598 52.381 1.15 0.00 35.98 3.82
72 73 1.405105 GTGGCTTTGTGACATGTGTGT 59.595 47.619 1.15 0.00 42.49 3.72
81 82 2.861763 GACATGTGTGTCGTGTGATG 57.138 50.000 1.15 0.00 45.10 3.07
82 83 1.460743 GACATGTGTGTCGTGTGATGG 59.539 52.381 1.15 0.00 45.10 3.51
83 84 0.166597 CATGTGTGTCGTGTGATGGC 59.833 55.000 0.00 0.00 0.00 4.40
84 85 0.955428 ATGTGTGTCGTGTGATGGCC 60.955 55.000 0.00 0.00 0.00 5.36
85 86 2.356913 TGTGTCGTGTGATGGCCG 60.357 61.111 0.00 0.00 0.00 6.13
86 87 2.048597 GTGTCGTGTGATGGCCGA 60.049 61.111 0.00 0.00 0.00 5.54
87 88 2.094659 GTGTCGTGTGATGGCCGAG 61.095 63.158 0.00 0.00 0.00 4.63
88 89 3.188786 GTCGTGTGATGGCCGAGC 61.189 66.667 0.00 0.00 0.00 5.03
89 90 3.381983 TCGTGTGATGGCCGAGCT 61.382 61.111 0.00 0.00 0.00 4.09
90 91 3.190849 CGTGTGATGGCCGAGCTG 61.191 66.667 0.00 0.00 0.00 4.24
91 92 2.265739 GTGTGATGGCCGAGCTGA 59.734 61.111 0.00 0.00 0.00 4.26
92 93 1.153289 GTGTGATGGCCGAGCTGAT 60.153 57.895 0.00 0.00 0.00 2.90
93 94 1.144716 TGTGATGGCCGAGCTGATC 59.855 57.895 0.00 0.00 0.00 2.92
107 108 2.979299 GCTGATCGCTAAGCAATGTTC 58.021 47.619 0.00 0.00 39.31 3.18
108 109 2.352651 GCTGATCGCTAAGCAATGTTCA 59.647 45.455 0.00 0.00 39.31 3.18
109 110 3.786818 GCTGATCGCTAAGCAATGTTCAC 60.787 47.826 0.00 0.00 39.31 3.18
110 111 3.333804 TGATCGCTAAGCAATGTTCACA 58.666 40.909 0.00 0.00 0.00 3.58
111 112 3.125146 TGATCGCTAAGCAATGTTCACAC 59.875 43.478 0.00 0.00 0.00 3.82
112 113 1.804151 TCGCTAAGCAATGTTCACACC 59.196 47.619 0.00 0.00 0.00 4.16
113 114 1.135689 CGCTAAGCAATGTTCACACCC 60.136 52.381 0.00 0.00 0.00 4.61
114 115 1.885887 GCTAAGCAATGTTCACACCCA 59.114 47.619 0.00 0.00 0.00 4.51
115 116 2.493278 GCTAAGCAATGTTCACACCCAT 59.507 45.455 0.00 0.00 0.00 4.00
116 117 3.056607 GCTAAGCAATGTTCACACCCATT 60.057 43.478 0.00 0.00 0.00 3.16
117 118 4.157656 GCTAAGCAATGTTCACACCCATTA 59.842 41.667 0.00 0.00 30.41 1.90
118 119 4.519540 AAGCAATGTTCACACCCATTAC 57.480 40.909 0.00 0.00 30.41 1.89
119 120 2.487762 AGCAATGTTCACACCCATTACG 59.512 45.455 0.00 0.00 30.41 3.18
120 121 2.486203 GCAATGTTCACACCCATTACGA 59.514 45.455 0.00 0.00 30.41 3.43
121 122 3.128589 GCAATGTTCACACCCATTACGAT 59.871 43.478 0.00 0.00 30.41 3.73
122 123 4.380444 GCAATGTTCACACCCATTACGATT 60.380 41.667 0.00 0.00 30.41 3.34
123 124 5.163703 GCAATGTTCACACCCATTACGATTA 60.164 40.000 0.00 0.00 30.41 1.75
124 125 6.486248 CAATGTTCACACCCATTACGATTAG 58.514 40.000 0.00 0.00 30.41 1.73
125 126 5.408880 TGTTCACACCCATTACGATTAGA 57.591 39.130 0.00 0.00 0.00 2.10
126 127 5.984725 TGTTCACACCCATTACGATTAGAT 58.015 37.500 0.00 0.00 0.00 1.98
127 128 5.815222 TGTTCACACCCATTACGATTAGATG 59.185 40.000 0.00 0.00 0.00 2.90
128 129 4.956085 TCACACCCATTACGATTAGATGG 58.044 43.478 0.00 0.00 39.99 3.51
129 130 4.651962 TCACACCCATTACGATTAGATGGA 59.348 41.667 3.28 0.00 42.31 3.41
130 131 4.750098 CACACCCATTACGATTAGATGGAC 59.250 45.833 3.28 0.00 42.31 4.02
131 132 4.407621 ACACCCATTACGATTAGATGGACA 59.592 41.667 3.28 0.00 42.31 4.02
132 133 5.071788 ACACCCATTACGATTAGATGGACAT 59.928 40.000 3.28 0.00 42.31 3.06
133 134 5.639506 CACCCATTACGATTAGATGGACATC 59.360 44.000 4.15 4.15 42.31 3.06
134 135 5.306937 ACCCATTACGATTAGATGGACATCA 59.693 40.000 14.16 0.00 42.31 3.07
135 136 6.013379 ACCCATTACGATTAGATGGACATCAT 60.013 38.462 14.16 0.49 42.31 2.45
136 137 6.314648 CCCATTACGATTAGATGGACATCATG 59.685 42.308 14.16 6.56 42.31 3.07
137 138 6.183360 CCATTACGATTAGATGGACATCATGC 60.183 42.308 14.16 0.98 42.31 4.06
138 139 3.668447 ACGATTAGATGGACATCATGCC 58.332 45.455 14.16 0.00 40.22 4.40
139 140 3.071457 ACGATTAGATGGACATCATGCCA 59.929 43.478 14.16 3.61 40.22 4.92
140 141 3.434641 CGATTAGATGGACATCATGCCAC 59.565 47.826 14.16 0.00 40.22 5.01
141 142 2.936919 TAGATGGACATCATGCCACC 57.063 50.000 14.16 0.00 40.22 4.61
142 143 0.179037 AGATGGACATCATGCCACCG 60.179 55.000 14.16 0.00 40.22 4.94
143 144 0.464373 GATGGACATCATGCCACCGT 60.464 55.000 7.40 0.00 36.92 4.83
144 145 0.464373 ATGGACATCATGCCACCGTC 60.464 55.000 3.24 0.00 36.92 4.79
145 146 1.078497 GGACATCATGCCACCGTCA 60.078 57.895 0.00 0.00 0.00 4.35
146 147 0.676466 GGACATCATGCCACCGTCAA 60.676 55.000 0.00 0.00 0.00 3.18
147 148 0.447801 GACATCATGCCACCGTCAAC 59.552 55.000 0.00 0.00 0.00 3.18
148 149 0.250684 ACATCATGCCACCGTCAACA 60.251 50.000 0.00 0.00 0.00 3.33
149 150 0.880441 CATCATGCCACCGTCAACAA 59.120 50.000 0.00 0.00 0.00 2.83
150 151 1.473677 CATCATGCCACCGTCAACAAT 59.526 47.619 0.00 0.00 0.00 2.71
151 152 0.880441 TCATGCCACCGTCAACAATG 59.120 50.000 0.00 0.00 0.00 2.82
152 153 0.880441 CATGCCACCGTCAACAATGA 59.120 50.000 0.00 0.00 0.00 2.57
153 154 1.135603 CATGCCACCGTCAACAATGAG 60.136 52.381 0.00 0.00 35.88 2.90
154 155 0.888736 TGCCACCGTCAACAATGAGG 60.889 55.000 0.00 0.00 40.35 3.86
155 156 0.605319 GCCACCGTCAACAATGAGGA 60.605 55.000 0.46 0.00 42.66 3.71
156 157 1.156736 CCACCGTCAACAATGAGGAC 58.843 55.000 0.46 0.00 42.66 3.85
157 158 1.542328 CCACCGTCAACAATGAGGACA 60.542 52.381 8.98 0.00 42.66 4.02
158 159 2.217750 CACCGTCAACAATGAGGACAA 58.782 47.619 8.98 0.00 42.66 3.18
159 160 2.224079 CACCGTCAACAATGAGGACAAG 59.776 50.000 8.98 3.51 42.66 3.16
160 161 2.104111 ACCGTCAACAATGAGGACAAGA 59.896 45.455 8.98 0.00 42.66 3.02
161 162 3.138304 CCGTCAACAATGAGGACAAGAA 58.862 45.455 8.98 0.00 42.66 2.52
162 163 3.753272 CCGTCAACAATGAGGACAAGAAT 59.247 43.478 8.98 0.00 42.66 2.40
163 164 4.378770 CCGTCAACAATGAGGACAAGAATG 60.379 45.833 8.98 0.00 42.66 2.67
164 165 4.452114 CGTCAACAATGAGGACAAGAATGA 59.548 41.667 8.98 0.00 42.66 2.57
165 166 5.390251 CGTCAACAATGAGGACAAGAATGAG 60.390 44.000 8.98 0.00 42.66 2.90
166 167 5.471456 GTCAACAATGAGGACAAGAATGAGT 59.529 40.000 4.69 0.00 35.88 3.41
167 168 6.650807 GTCAACAATGAGGACAAGAATGAGTA 59.349 38.462 4.69 0.00 35.88 2.59
168 169 7.173218 GTCAACAATGAGGACAAGAATGAGTAA 59.827 37.037 4.69 0.00 35.88 2.24
169 170 7.884877 TCAACAATGAGGACAAGAATGAGTAAT 59.115 33.333 0.00 0.00 0.00 1.89
170 171 9.166173 CAACAATGAGGACAAGAATGAGTAATA 57.834 33.333 0.00 0.00 0.00 0.98
171 172 8.723942 ACAATGAGGACAAGAATGAGTAATAC 57.276 34.615 0.00 0.00 0.00 1.89
172 173 8.543774 ACAATGAGGACAAGAATGAGTAATACT 58.456 33.333 0.00 0.00 0.00 2.12
173 174 9.388506 CAATGAGGACAAGAATGAGTAATACTT 57.611 33.333 0.00 0.00 0.00 2.24
174 175 9.965902 AATGAGGACAAGAATGAGTAATACTTT 57.034 29.630 0.00 0.00 0.00 2.66
175 176 9.965902 ATGAGGACAAGAATGAGTAATACTTTT 57.034 29.630 0.00 0.00 0.00 2.27
197 198 2.126888 CGTTGCAACGCATGGGTC 60.127 61.111 35.89 5.27 46.06 4.46
198 199 2.902419 CGTTGCAACGCATGGGTCA 61.902 57.895 35.89 8.02 46.06 4.02
199 200 1.586028 GTTGCAACGCATGGGTCAT 59.414 52.632 16.57 0.00 38.76 3.06
200 201 0.808125 GTTGCAACGCATGGGTCATA 59.192 50.000 16.57 2.51 38.76 2.15
238 240 0.436913 CGACAAAACGTGCTATCGCA 59.563 50.000 0.00 0.00 45.60 5.10
256 258 2.159920 CGCACTTCAGACGAAATCACTG 60.160 50.000 0.00 0.00 0.00 3.66
257 259 2.158449 GCACTTCAGACGAAATCACTGG 59.842 50.000 0.00 0.00 33.19 4.00
263 265 4.566004 TCAGACGAAATCACTGGTTAAGG 58.434 43.478 0.00 0.00 33.19 2.69
268 270 3.941483 CGAAATCACTGGTTAAGGAGCAT 59.059 43.478 0.00 0.00 34.78 3.79
270 272 5.447818 CGAAATCACTGGTTAAGGAGCATTC 60.448 44.000 0.00 0.00 34.78 2.67
271 273 3.350219 TCACTGGTTAAGGAGCATTCC 57.650 47.619 0.00 0.00 44.39 3.01
281 283 1.168714 GGAGCATTCCTCGCAAAAGT 58.831 50.000 0.00 0.00 41.71 2.66
286 288 2.413371 GCATTCCTCGCAAAAGTCACTC 60.413 50.000 0.00 0.00 0.00 3.51
287 289 2.910688 TTCCTCGCAAAAGTCACTCT 57.089 45.000 0.00 0.00 0.00 3.24
293 295 3.993081 CTCGCAAAAGTCACTCTCATCTT 59.007 43.478 0.00 0.00 0.00 2.40
298 300 5.642919 GCAAAAGTCACTCTCATCTTCTCAT 59.357 40.000 0.00 0.00 0.00 2.90
300 302 5.999205 AAGTCACTCTCATCTTCTCATGT 57.001 39.130 0.00 0.00 0.00 3.21
301 303 5.581126 AGTCACTCTCATCTTCTCATGTC 57.419 43.478 0.00 0.00 0.00 3.06
302 304 4.096231 AGTCACTCTCATCTTCTCATGTCG 59.904 45.833 0.00 0.00 0.00 4.35
303 305 4.095632 GTCACTCTCATCTTCTCATGTCGA 59.904 45.833 0.00 0.00 0.00 4.20
323 325 4.567959 TCGAGACAAATGATGCACTGTATG 59.432 41.667 0.00 0.00 0.00 2.39
337 339 0.510790 TGTATGTGCGTTGCTTGTCG 59.489 50.000 0.00 0.00 0.00 4.35
404 424 9.270576 CAAAGATTTGATCTCTTAAATCGTGTG 57.729 33.333 9.40 6.55 44.17 3.82
411 431 6.878923 TGATCTCTTAAATCGTGTGTCCAAAT 59.121 34.615 0.00 0.00 0.00 2.32
418 438 3.313012 TCGTGTGTCCAAATCTCGAAT 57.687 42.857 0.00 0.00 0.00 3.34
425 445 5.080068 GTGTCCAAATCTCGAATCGTTTTC 58.920 41.667 1.52 0.00 0.00 2.29
429 449 4.083537 CCAAATCTCGAATCGTTTTCACCA 60.084 41.667 1.52 0.00 0.00 4.17
451 471 4.545208 TTGGATTCCTCGTGTTGACATA 57.455 40.909 3.95 0.00 0.00 2.29
457 485 7.155328 GGATTCCTCGTGTTGACATATAGATT 58.845 38.462 0.00 0.00 0.00 2.40
458 486 7.329717 GGATTCCTCGTGTTGACATATAGATTC 59.670 40.741 0.00 0.00 0.00 2.52
465 493 8.417884 TCGTGTTGACATATAGATTCCATGTTA 58.582 33.333 0.00 0.00 33.16 2.41
478 506 7.985476 AGATTCCATGTTAATAGGTTTTGACG 58.015 34.615 0.00 0.00 0.00 4.35
481 510 6.469410 TCCATGTTAATAGGTTTTGACGACT 58.531 36.000 0.00 0.00 0.00 4.18
556 590 1.066908 CGGCCTCTCACAAAAGCAAAA 59.933 47.619 0.00 0.00 0.00 2.44
570 604 2.184385 GCAAAATCATGCCTCTGACG 57.816 50.000 0.00 0.00 40.49 4.35
573 813 2.749076 CAAAATCATGCCTCTGACGGAA 59.251 45.455 0.00 0.00 0.00 4.30
579 819 2.631160 TGCCTCTGACGGAAGAAAAA 57.369 45.000 0.00 0.00 0.00 1.94
640 880 7.754851 TTTTGTCCAAAGGTTAAGATAGACC 57.245 36.000 0.00 0.00 36.15 3.85
641 881 5.080969 TGTCCAAAGGTTAAGATAGACCG 57.919 43.478 0.00 0.00 40.89 4.79
643 883 5.107824 GTCCAAAGGTTAAGATAGACCGAC 58.892 45.833 0.00 0.00 40.89 4.79
648 888 3.194116 AGGTTAAGATAGACCGACGCAAA 59.806 43.478 0.00 0.00 40.89 3.68
650 890 1.641577 AAGATAGACCGACGCAAAGC 58.358 50.000 0.00 0.00 0.00 3.51
651 891 0.179108 AGATAGACCGACGCAAAGCC 60.179 55.000 0.00 0.00 0.00 4.35
652 892 1.480219 GATAGACCGACGCAAAGCCG 61.480 60.000 0.00 0.00 0.00 5.52
653 893 1.940883 ATAGACCGACGCAAAGCCGA 61.941 55.000 0.00 0.00 0.00 5.54
654 894 2.144833 TAGACCGACGCAAAGCCGAA 62.145 55.000 0.00 0.00 0.00 4.30
655 895 2.589442 ACCGACGCAAAGCCGAAA 60.589 55.556 0.00 0.00 0.00 3.46
656 896 2.108344 GACCGACGCAAAGCCGAAAA 62.108 55.000 0.00 0.00 0.00 2.29
657 897 1.440353 CCGACGCAAAGCCGAAAAG 60.440 57.895 0.00 0.00 0.00 2.27
659 899 1.729484 GACGCAAAGCCGAAAAGCC 60.729 57.895 0.00 0.00 0.00 4.35
661 901 2.642700 GCAAAGCCGAAAAGCCGA 59.357 55.556 0.00 0.00 0.00 5.54
662 902 1.007849 GCAAAGCCGAAAAGCCGAA 60.008 52.632 0.00 0.00 0.00 4.30
726 1053 4.609018 ATCCGGATCAAGCGCCCG 62.609 66.667 12.38 14.15 42.64 6.13
770 1109 2.186384 GAGAGCGTGCCATCAGCT 59.814 61.111 0.00 0.00 44.23 4.24
788 1127 4.041567 TCAGCTCACTTCAAATGACCCTTA 59.958 41.667 0.00 0.00 0.00 2.69
789 1128 4.154918 CAGCTCACTTCAAATGACCCTTAC 59.845 45.833 0.00 0.00 0.00 2.34
790 1129 3.125316 GCTCACTTCAAATGACCCTTACG 59.875 47.826 0.00 0.00 0.00 3.18
792 1131 4.963373 TCACTTCAAATGACCCTTACGAA 58.037 39.130 0.00 0.00 0.00 3.85
797 1136 4.963373 TCAAATGACCCTTACGAAGTTCA 58.037 39.130 3.32 0.00 37.78 3.18
799 1138 5.411361 TCAAATGACCCTTACGAAGTTCATG 59.589 40.000 3.32 0.00 37.78 3.07
800 1139 4.819105 ATGACCCTTACGAAGTTCATGA 57.181 40.909 3.32 0.00 37.78 3.07
801 1140 4.188247 TGACCCTTACGAAGTTCATGAG 57.812 45.455 3.32 0.00 37.78 2.90
802 1141 2.930682 GACCCTTACGAAGTTCATGAGC 59.069 50.000 0.50 0.50 37.78 4.26
803 1142 1.927174 CCCTTACGAAGTTCATGAGCG 59.073 52.381 3.72 5.95 37.78 5.03
815 1905 1.281867 TCATGAGCGTTTCCCCTTCAT 59.718 47.619 0.00 0.00 0.00 2.57
831 1922 3.137360 CCTTCATAAGCTAGAAAGGCCCT 59.863 47.826 0.00 0.00 0.00 5.19
843 1934 4.307259 AGAAAGGCCCTTGTATCTATGGA 58.693 43.478 0.00 0.00 0.00 3.41
848 1939 5.224441 AGGCCCTTGTATCTATGGACTTAA 58.776 41.667 0.00 0.00 26.72 1.85
859 1950 3.994931 ATGGACTTAAACTTACCGGCT 57.005 42.857 0.00 0.00 0.00 5.52
873 1964 0.165944 CCGGCTCAACACGAATTGAC 59.834 55.000 0.00 0.00 34.84 3.18
884 1992 2.651703 CACGAATTGACACACGAATTGC 59.348 45.455 0.00 0.00 0.00 3.56
885 1993 2.548057 ACGAATTGACACACGAATTGCT 59.452 40.909 0.00 0.00 0.00 3.91
890 1998 2.135139 TGACACACGAATTGCTGTCTC 58.865 47.619 0.00 0.00 37.25 3.36
899 2007 1.016130 ATTGCTGTCTCGTCCGCAAG 61.016 55.000 0.00 0.00 44.42 4.01
915 2023 3.222354 AAGTGTGCCCTCGTCGTCC 62.222 63.158 0.00 0.00 0.00 4.79
916 2024 3.681835 GTGTGCCCTCGTCGTCCT 61.682 66.667 0.00 0.00 0.00 3.85
918 2026 4.131088 GTGCCCTCGTCGTCCTCC 62.131 72.222 0.00 0.00 0.00 4.30
921 2029 2.829458 CCCTCGTCGTCCTCCCTC 60.829 72.222 0.00 0.00 0.00 4.30
923 2031 3.203412 CTCGTCGTCCTCCCTCCG 61.203 72.222 0.00 0.00 0.00 4.63
927 2035 3.654143 TCGTCCTCCCTCCGTCCA 61.654 66.667 0.00 0.00 0.00 4.02
960 2069 0.392595 GCGGTTACCCCTTCTCCTTG 60.393 60.000 0.00 0.00 0.00 3.61
1057 2181 3.001406 ACCCGTCCCCTTTCCTCG 61.001 66.667 0.00 0.00 0.00 4.63
1092 2216 3.518998 GACCGCGCTGCTCTAGGA 61.519 66.667 5.56 0.00 0.00 2.94
1101 2225 1.452145 CTGCTCTAGGAGGCCTCGTC 61.452 65.000 30.38 15.88 34.61 4.20
1104 2228 0.821711 CTCTAGGAGGCCTCGTCCAG 60.822 65.000 30.38 22.45 40.46 3.86
1211 2347 2.109463 CGTATCGACCAATGACACTCG 58.891 52.381 0.00 0.00 0.00 4.18
1275 2411 2.344203 CGACCTCGAGGGAGCAGTT 61.344 63.158 34.04 12.49 43.02 3.16
1297 2433 1.067142 ACCTGCTCGACGAAATGCTTA 60.067 47.619 8.74 0.00 0.00 3.09
1298 2434 1.324736 CCTGCTCGACGAAATGCTTAC 59.675 52.381 8.74 0.00 0.00 2.34
1371 2507 1.874345 CGGTCCTCCAGTGCTACGTT 61.874 60.000 0.00 0.00 0.00 3.99
1411 2547 2.282251 TCAGACGAGGTCACCGCT 60.282 61.111 0.00 0.00 34.60 5.52
1451 2587 2.207924 GGTACTCCGGGATCGCCAT 61.208 63.158 0.00 0.00 35.15 4.40
1683 2819 4.077184 ATCGACGAGGCCGCCAAA 62.077 61.111 13.15 0.00 39.95 3.28
1740 2876 4.681978 GCGTTCGGGCTGGTGAGT 62.682 66.667 0.00 0.00 0.00 3.41
1924 3061 4.436998 GGTGAGACGCCTCCACCG 62.437 72.222 0.00 0.00 38.66 4.94
1933 3074 2.350895 CCTCCACCGCACCATTGA 59.649 61.111 0.00 0.00 0.00 2.57
1942 3083 1.477700 CCGCACCATTGACATCCATTT 59.522 47.619 0.00 0.00 0.00 2.32
1951 3092 6.825721 ACCATTGACATCCATTTCTCTCTTAC 59.174 38.462 0.00 0.00 0.00 2.34
1952 3093 7.052873 CCATTGACATCCATTTCTCTCTTACT 58.947 38.462 0.00 0.00 0.00 2.24
1953 3094 7.012138 CCATTGACATCCATTTCTCTCTTACTG 59.988 40.741 0.00 0.00 0.00 2.74
1954 3095 6.857437 TGACATCCATTTCTCTCTTACTGA 57.143 37.500 0.00 0.00 0.00 3.41
1955 3096 7.429374 TGACATCCATTTCTCTCTTACTGAT 57.571 36.000 0.00 0.00 0.00 2.90
1957 3098 8.981659 TGACATCCATTTCTCTCTTACTGATTA 58.018 33.333 0.00 0.00 0.00 1.75
1958 3099 9.255304 GACATCCATTTCTCTCTTACTGATTAC 57.745 37.037 0.00 0.00 0.00 1.89
1959 3100 8.986991 ACATCCATTTCTCTCTTACTGATTACT 58.013 33.333 0.00 0.00 0.00 2.24
1960 3101 9.258826 CATCCATTTCTCTCTTACTGATTACTG 57.741 37.037 0.00 0.00 0.00 2.74
1961 3102 7.786030 TCCATTTCTCTCTTACTGATTACTGG 58.214 38.462 0.00 0.00 0.00 4.00
1962 3103 6.989169 CCATTTCTCTCTTACTGATTACTGGG 59.011 42.308 0.00 0.00 0.00 4.45
1965 3106 8.660295 TTTCTCTCTTACTGATTACTGGGTAA 57.340 34.615 0.00 0.00 32.36 2.85
1977 3118 6.440647 TGATTACTGGGTAATTCAGTGTCTCT 59.559 38.462 8.20 0.00 44.24 3.10
1982 3123 4.841813 TGGGTAATTCAGTGTCTCTACCAA 59.158 41.667 12.35 2.79 0.00 3.67
2009 3152 1.608055 AATTTTGGCAGGCTTTTGGC 58.392 45.000 0.00 3.68 46.43 4.52
2082 3225 2.368439 TGATGCATTACCCAGCAAGAC 58.632 47.619 0.00 0.00 44.88 3.01
2195 3357 6.976925 AGCAAAGAATCAAGAGAACAAAACAG 59.023 34.615 0.00 0.00 0.00 3.16
2400 3565 2.524394 GCCGCTCCTCTATCCCCA 60.524 66.667 0.00 0.00 0.00 4.96
2403 3568 1.834378 CGCTCCTCTATCCCCAGCA 60.834 63.158 0.00 0.00 0.00 4.41
2613 3778 3.768185 ATTCGCCACGATCGTCCGG 62.768 63.158 27.29 23.11 35.23 5.14
2649 3814 0.671781 GCTGGAGCTGCTCGAAGAAA 60.672 55.000 26.04 8.65 38.21 2.52
2827 3992 0.674581 CTTCTGAGCACCGGCATTGA 60.675 55.000 0.00 0.00 44.61 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.503399 ACTTTAAAATTCTAACCTCATCGAACT 57.497 29.630 0.00 0.00 0.00 3.01
22 23 9.267084 GGAGCAATGGAATGTTTAAAACTTTAA 57.733 29.630 0.00 0.00 0.00 1.52
23 24 7.596995 CGGAGCAATGGAATGTTTAAAACTTTA 59.403 33.333 0.00 0.00 0.00 1.85
24 25 6.423604 CGGAGCAATGGAATGTTTAAAACTTT 59.576 34.615 0.00 0.00 0.00 2.66
25 26 5.925969 CGGAGCAATGGAATGTTTAAAACTT 59.074 36.000 0.00 0.00 0.00 2.66
26 27 5.242838 TCGGAGCAATGGAATGTTTAAAACT 59.757 36.000 0.00 0.00 0.00 2.66
27 28 5.344933 GTCGGAGCAATGGAATGTTTAAAAC 59.655 40.000 0.00 0.00 0.00 2.43
28 29 5.465935 GTCGGAGCAATGGAATGTTTAAAA 58.534 37.500 0.00 0.00 0.00 1.52
29 30 4.378978 CGTCGGAGCAATGGAATGTTTAAA 60.379 41.667 0.00 0.00 0.00 1.52
30 31 3.126171 CGTCGGAGCAATGGAATGTTTAA 59.874 43.478 0.00 0.00 0.00 1.52
31 32 2.675844 CGTCGGAGCAATGGAATGTTTA 59.324 45.455 0.00 0.00 0.00 2.01
32 33 1.468520 CGTCGGAGCAATGGAATGTTT 59.531 47.619 0.00 0.00 0.00 2.83
33 34 1.086696 CGTCGGAGCAATGGAATGTT 58.913 50.000 0.00 0.00 0.00 2.71
34 35 0.036388 ACGTCGGAGCAATGGAATGT 60.036 50.000 0.00 0.00 0.00 2.71
35 36 0.374758 CACGTCGGAGCAATGGAATG 59.625 55.000 0.00 0.00 0.00 2.67
36 37 0.744414 CCACGTCGGAGCAATGGAAT 60.744 55.000 0.00 0.00 36.56 3.01
37 38 1.375396 CCACGTCGGAGCAATGGAA 60.375 57.895 0.00 0.00 36.56 3.53
38 39 2.264480 CCACGTCGGAGCAATGGA 59.736 61.111 0.00 0.00 36.56 3.41
39 40 3.499737 GCCACGTCGGAGCAATGG 61.500 66.667 8.04 0.00 36.56 3.16
40 41 1.577328 AAAGCCACGTCGGAGCAATG 61.577 55.000 10.79 0.00 36.56 2.82
41 42 1.302511 AAAGCCACGTCGGAGCAAT 60.303 52.632 10.79 0.00 36.56 3.56
42 43 2.110213 AAAGCCACGTCGGAGCAA 59.890 55.556 10.79 0.00 36.56 3.91
43 44 2.664851 CAAAGCCACGTCGGAGCA 60.665 61.111 10.79 0.00 36.56 4.26
44 45 2.665185 ACAAAGCCACGTCGGAGC 60.665 61.111 8.04 0.00 36.56 4.70
45 46 1.300620 TCACAAAGCCACGTCGGAG 60.301 57.895 8.04 0.00 36.56 4.63
46 47 1.593209 GTCACAAAGCCACGTCGGA 60.593 57.895 8.04 0.00 36.56 4.55
47 48 1.227999 ATGTCACAAAGCCACGTCGG 61.228 55.000 0.00 0.00 38.11 4.79
48 49 0.110688 CATGTCACAAAGCCACGTCG 60.111 55.000 0.00 0.00 0.00 5.12
49 50 0.944386 ACATGTCACAAAGCCACGTC 59.056 50.000 0.00 0.00 0.00 4.34
50 51 0.662619 CACATGTCACAAAGCCACGT 59.337 50.000 0.00 0.00 0.00 4.49
51 52 0.662619 ACACATGTCACAAAGCCACG 59.337 50.000 0.00 0.00 0.00 4.94
52 53 1.405105 ACACACATGTCACAAAGCCAC 59.595 47.619 0.00 0.00 31.55 5.01
53 54 1.761449 ACACACATGTCACAAAGCCA 58.239 45.000 0.00 0.00 31.55 4.75
63 64 1.511850 CCATCACACGACACACATGT 58.488 50.000 0.00 0.00 43.71 3.21
64 65 0.166597 GCCATCACACGACACACATG 59.833 55.000 0.00 0.00 0.00 3.21
65 66 0.955428 GGCCATCACACGACACACAT 60.955 55.000 0.00 0.00 0.00 3.21
66 67 1.596752 GGCCATCACACGACACACA 60.597 57.895 0.00 0.00 0.00 3.72
67 68 2.667318 CGGCCATCACACGACACAC 61.667 63.158 2.24 0.00 0.00 3.82
68 69 2.356913 CGGCCATCACACGACACA 60.357 61.111 2.24 0.00 0.00 3.72
69 70 2.048597 TCGGCCATCACACGACAC 60.049 61.111 2.24 0.00 0.00 3.67
70 71 2.261361 CTCGGCCATCACACGACA 59.739 61.111 2.24 0.00 32.66 4.35
71 72 3.188786 GCTCGGCCATCACACGAC 61.189 66.667 2.24 0.00 32.66 4.34
72 73 3.381983 AGCTCGGCCATCACACGA 61.382 61.111 2.24 0.00 35.14 4.35
73 74 2.913054 ATCAGCTCGGCCATCACACG 62.913 60.000 2.24 0.00 0.00 4.49
74 75 1.153289 ATCAGCTCGGCCATCACAC 60.153 57.895 2.24 0.00 0.00 3.82
75 76 1.144716 GATCAGCTCGGCCATCACA 59.855 57.895 2.24 0.00 0.00 3.58
76 77 1.953138 CGATCAGCTCGGCCATCAC 60.953 63.158 2.24 0.00 43.82 3.06
77 78 2.418777 CGATCAGCTCGGCCATCA 59.581 61.111 2.24 0.00 43.82 3.07
88 89 3.371898 TGTGAACATTGCTTAGCGATCAG 59.628 43.478 3.58 0.00 28.96 2.90
89 90 3.125146 GTGTGAACATTGCTTAGCGATCA 59.875 43.478 3.58 0.00 28.96 2.92
90 91 3.485877 GGTGTGAACATTGCTTAGCGATC 60.486 47.826 3.58 0.00 28.96 3.69
91 92 2.420022 GGTGTGAACATTGCTTAGCGAT 59.580 45.455 0.22 0.22 32.09 4.58
92 93 1.804151 GGTGTGAACATTGCTTAGCGA 59.196 47.619 0.00 0.00 0.00 4.93
93 94 1.135689 GGGTGTGAACATTGCTTAGCG 60.136 52.381 0.00 0.00 0.00 4.26
94 95 1.885887 TGGGTGTGAACATTGCTTAGC 59.114 47.619 0.00 0.00 0.00 3.09
95 96 4.789012 AATGGGTGTGAACATTGCTTAG 57.211 40.909 0.00 0.00 36.07 2.18
96 97 4.155099 CGTAATGGGTGTGAACATTGCTTA 59.845 41.667 0.00 0.00 37.49 3.09
97 98 3.057596 CGTAATGGGTGTGAACATTGCTT 60.058 43.478 0.00 0.00 37.49 3.91
98 99 2.487762 CGTAATGGGTGTGAACATTGCT 59.512 45.455 0.00 0.00 37.49 3.91
99 100 2.486203 TCGTAATGGGTGTGAACATTGC 59.514 45.455 0.00 0.00 37.80 3.56
100 101 4.963276 ATCGTAATGGGTGTGAACATTG 57.037 40.909 0.00 0.00 37.80 2.82
101 102 6.411376 TCTAATCGTAATGGGTGTGAACATT 58.589 36.000 0.00 0.00 40.21 2.71
102 103 5.984725 TCTAATCGTAATGGGTGTGAACAT 58.015 37.500 0.00 0.00 0.00 2.71
103 104 5.408880 TCTAATCGTAATGGGTGTGAACA 57.591 39.130 0.00 0.00 0.00 3.18
104 105 5.236478 CCATCTAATCGTAATGGGTGTGAAC 59.764 44.000 0.00 0.00 36.99 3.18
105 106 5.129650 TCCATCTAATCGTAATGGGTGTGAA 59.870 40.000 0.00 0.00 40.34 3.18
106 107 4.651962 TCCATCTAATCGTAATGGGTGTGA 59.348 41.667 0.00 0.00 40.34 3.58
107 108 4.750098 GTCCATCTAATCGTAATGGGTGTG 59.250 45.833 0.00 0.00 40.34 3.82
108 109 4.407621 TGTCCATCTAATCGTAATGGGTGT 59.592 41.667 0.00 0.00 40.34 4.16
109 110 4.956085 TGTCCATCTAATCGTAATGGGTG 58.044 43.478 0.00 0.00 40.34 4.61
110 111 5.306937 TGATGTCCATCTAATCGTAATGGGT 59.693 40.000 8.61 0.00 40.34 4.51
111 112 5.793817 TGATGTCCATCTAATCGTAATGGG 58.206 41.667 8.61 0.00 40.34 4.00
112 113 6.183360 GCATGATGTCCATCTAATCGTAATGG 60.183 42.308 8.61 0.00 41.12 3.16
113 114 6.183360 GGCATGATGTCCATCTAATCGTAATG 60.183 42.308 8.61 3.13 38.60 1.90
114 115 5.877012 GGCATGATGTCCATCTAATCGTAAT 59.123 40.000 8.61 0.00 38.60 1.89
115 116 5.221621 TGGCATGATGTCCATCTAATCGTAA 60.222 40.000 8.61 0.00 38.60 3.18
116 117 4.283212 TGGCATGATGTCCATCTAATCGTA 59.717 41.667 8.61 0.00 38.60 3.43
117 118 3.071457 TGGCATGATGTCCATCTAATCGT 59.929 43.478 8.61 0.00 38.60 3.73
118 119 3.434641 GTGGCATGATGTCCATCTAATCG 59.565 47.826 10.84 0.00 38.60 3.34
119 120 3.755378 GGTGGCATGATGTCCATCTAATC 59.245 47.826 10.84 0.00 38.60 1.75
120 121 3.759581 GGTGGCATGATGTCCATCTAAT 58.240 45.455 10.84 0.00 38.60 1.73
121 122 2.485302 CGGTGGCATGATGTCCATCTAA 60.485 50.000 14.25 0.00 38.60 2.10
122 123 1.070601 CGGTGGCATGATGTCCATCTA 59.929 52.381 14.25 0.00 38.60 1.98
123 124 0.179037 CGGTGGCATGATGTCCATCT 60.179 55.000 14.25 0.00 38.60 2.90
124 125 0.464373 ACGGTGGCATGATGTCCATC 60.464 55.000 10.84 9.64 38.29 3.51
125 126 0.464373 GACGGTGGCATGATGTCCAT 60.464 55.000 10.84 0.00 34.47 3.41
126 127 1.078497 GACGGTGGCATGATGTCCA 60.078 57.895 0.00 4.79 0.00 4.02
127 128 0.676466 TTGACGGTGGCATGATGTCC 60.676 55.000 0.00 0.00 0.00 4.02
128 129 0.447801 GTTGACGGTGGCATGATGTC 59.552 55.000 0.00 0.00 0.00 3.06
129 130 0.250684 TGTTGACGGTGGCATGATGT 60.251 50.000 0.00 0.00 0.00 3.06
130 131 0.880441 TTGTTGACGGTGGCATGATG 59.120 50.000 0.00 0.00 0.00 3.07
131 132 1.473677 CATTGTTGACGGTGGCATGAT 59.526 47.619 0.00 0.00 0.00 2.45
132 133 0.880441 CATTGTTGACGGTGGCATGA 59.120 50.000 0.00 0.00 0.00 3.07
133 134 0.880441 TCATTGTTGACGGTGGCATG 59.120 50.000 0.00 0.00 0.00 4.06
134 135 1.167851 CTCATTGTTGACGGTGGCAT 58.832 50.000 0.00 0.00 0.00 4.40
135 136 0.888736 CCTCATTGTTGACGGTGGCA 60.889 55.000 0.00 0.00 0.00 4.92
136 137 0.605319 TCCTCATTGTTGACGGTGGC 60.605 55.000 0.00 0.00 0.00 5.01
137 138 1.156736 GTCCTCATTGTTGACGGTGG 58.843 55.000 0.00 0.00 0.00 4.61
138 139 1.877637 TGTCCTCATTGTTGACGGTG 58.122 50.000 0.00 0.00 0.00 4.94
139 140 2.104111 TCTTGTCCTCATTGTTGACGGT 59.896 45.455 0.00 0.00 0.00 4.83
140 141 2.766313 TCTTGTCCTCATTGTTGACGG 58.234 47.619 0.00 0.00 0.00 4.79
141 142 4.452114 TCATTCTTGTCCTCATTGTTGACG 59.548 41.667 0.00 0.00 0.00 4.35
142 143 5.471456 ACTCATTCTTGTCCTCATTGTTGAC 59.529 40.000 0.00 0.00 0.00 3.18
143 144 5.624159 ACTCATTCTTGTCCTCATTGTTGA 58.376 37.500 0.00 0.00 0.00 3.18
144 145 5.954296 ACTCATTCTTGTCCTCATTGTTG 57.046 39.130 0.00 0.00 0.00 3.33
145 146 9.167311 GTATTACTCATTCTTGTCCTCATTGTT 57.833 33.333 0.00 0.00 0.00 2.83
146 147 8.543774 AGTATTACTCATTCTTGTCCTCATTGT 58.456 33.333 0.00 0.00 0.00 2.71
147 148 8.954950 AGTATTACTCATTCTTGTCCTCATTG 57.045 34.615 0.00 0.00 0.00 2.82
148 149 9.965902 AAAGTATTACTCATTCTTGTCCTCATT 57.034 29.630 0.00 0.00 0.00 2.57
149 150 9.965902 AAAAGTATTACTCATTCTTGTCCTCAT 57.034 29.630 0.00 0.00 0.00 2.90
155 156 9.326413 CGGGATAAAAGTATTACTCATTCTTGT 57.674 33.333 0.00 0.00 0.00 3.16
156 157 9.326413 ACGGGATAAAAGTATTACTCATTCTTG 57.674 33.333 0.00 0.00 0.00 3.02
157 158 9.901172 AACGGGATAAAAGTATTACTCATTCTT 57.099 29.630 0.00 0.00 0.00 2.52
158 159 9.326413 CAACGGGATAAAAGTATTACTCATTCT 57.674 33.333 0.00 0.00 0.00 2.40
159 160 8.068380 GCAACGGGATAAAAGTATTACTCATTC 58.932 37.037 0.00 0.00 0.00 2.67
160 161 7.554835 TGCAACGGGATAAAAGTATTACTCATT 59.445 33.333 0.00 0.00 0.00 2.57
161 162 7.051623 TGCAACGGGATAAAAGTATTACTCAT 58.948 34.615 0.00 0.00 0.00 2.90
162 163 6.408035 TGCAACGGGATAAAAGTATTACTCA 58.592 36.000 0.00 0.00 0.00 3.41
163 164 6.913873 TGCAACGGGATAAAAGTATTACTC 57.086 37.500 0.00 0.00 0.00 2.59
164 165 7.080353 GTTGCAACGGGATAAAAGTATTACT 57.920 36.000 14.90 0.00 0.00 2.24
192 193 3.923648 ACCTACACTAGCATATGACCCA 58.076 45.455 6.97 0.00 0.00 4.51
196 197 7.703621 GTCGTTTTAACCTACACTAGCATATGA 59.296 37.037 6.97 0.00 0.00 2.15
197 198 7.490079 TGTCGTTTTAACCTACACTAGCATATG 59.510 37.037 0.00 0.00 0.00 1.78
198 199 7.549839 TGTCGTTTTAACCTACACTAGCATAT 58.450 34.615 0.00 0.00 0.00 1.78
199 200 6.923012 TGTCGTTTTAACCTACACTAGCATA 58.077 36.000 0.00 0.00 0.00 3.14
200 201 5.786311 TGTCGTTTTAACCTACACTAGCAT 58.214 37.500 0.00 0.00 0.00 3.79
238 240 3.753294 ACCAGTGATTTCGTCTGAAGT 57.247 42.857 0.00 0.00 35.06 3.01
263 265 1.806542 TGACTTTTGCGAGGAATGCTC 59.193 47.619 0.00 0.00 0.00 4.26
268 270 2.102420 TGAGAGTGACTTTTGCGAGGAA 59.898 45.455 0.00 0.00 0.00 3.36
270 272 2.154854 TGAGAGTGACTTTTGCGAGG 57.845 50.000 0.00 0.00 0.00 4.63
271 273 3.583806 AGATGAGAGTGACTTTTGCGAG 58.416 45.455 0.00 0.00 0.00 5.03
273 275 3.993081 AGAAGATGAGAGTGACTTTTGCG 59.007 43.478 0.00 0.00 0.00 4.85
281 283 4.265073 TCGACATGAGAAGATGAGAGTGA 58.735 43.478 0.00 0.00 0.00 3.41
298 300 2.738314 CAGTGCATCATTTGTCTCGACA 59.262 45.455 0.00 0.00 39.98 4.35
300 302 3.044235 ACAGTGCATCATTTGTCTCGA 57.956 42.857 0.00 0.00 0.00 4.04
301 303 4.330894 ACATACAGTGCATCATTTGTCTCG 59.669 41.667 0.00 0.00 0.00 4.04
302 304 5.566623 CACATACAGTGCATCATTTGTCTC 58.433 41.667 0.00 0.00 42.15 3.36
303 305 5.556355 CACATACAGTGCATCATTTGTCT 57.444 39.130 0.00 0.00 42.15 3.41
377 397 8.454106 ACACGATTTAAGAGATCAAATCTTTGG 58.546 33.333 12.05 2.83 40.38 3.28
378 398 9.270576 CACACGATTTAAGAGATCAAATCTTTG 57.729 33.333 12.05 11.06 40.38 2.77
382 402 7.064609 TGGACACACGATTTAAGAGATCAAATC 59.935 37.037 0.00 0.94 37.65 2.17
387 407 6.721571 TTTGGACACACGATTTAAGAGATC 57.278 37.500 0.00 0.00 0.00 2.75
404 424 5.080068 GTGAAAACGATTCGAGATTTGGAC 58.920 41.667 13.95 6.46 0.00 4.02
411 431 3.435327 CCAATGGTGAAAACGATTCGAGA 59.565 43.478 13.95 0.00 0.00 4.04
418 438 3.756434 GAGGAATCCAATGGTGAAAACGA 59.244 43.478 0.61 0.00 0.00 3.85
425 445 2.113860 ACACGAGGAATCCAATGGTG 57.886 50.000 0.61 6.29 0.00 4.17
429 449 3.417069 TGTCAACACGAGGAATCCAAT 57.583 42.857 0.61 0.00 0.00 3.16
457 485 6.469410 AGTCGTCAAAACCTATTAACATGGA 58.531 36.000 0.00 0.00 0.00 3.41
458 486 6.737254 AGTCGTCAAAACCTATTAACATGG 57.263 37.500 0.00 0.00 0.00 3.66
519 548 1.945819 GCCGTGCCTCTCAGAAATGAA 60.946 52.381 0.00 0.00 0.00 2.57
520 549 0.391661 GCCGTGCCTCTCAGAAATGA 60.392 55.000 0.00 0.00 0.00 2.57
521 550 1.372087 GGCCGTGCCTCTCAGAAATG 61.372 60.000 7.58 0.00 46.69 2.32
522 551 1.078143 GGCCGTGCCTCTCAGAAAT 60.078 57.895 7.58 0.00 46.69 2.17
545 579 4.039488 TCAGAGGCATGATTTTGCTTTTGT 59.961 37.500 0.00 0.00 42.38 2.83
547 581 4.563061 GTCAGAGGCATGATTTTGCTTTT 58.437 39.130 0.00 0.00 42.38 2.27
548 582 3.366679 CGTCAGAGGCATGATTTTGCTTT 60.367 43.478 0.00 0.00 42.38 3.51
556 590 1.489481 TCTTCCGTCAGAGGCATGAT 58.511 50.000 0.00 0.00 0.00 2.45
615 855 7.120726 CGGTCTATCTTAACCTTTGGACAAAAT 59.879 37.037 0.00 0.00 33.14 1.82
616 856 6.428771 CGGTCTATCTTAACCTTTGGACAAAA 59.571 38.462 0.00 0.00 33.14 2.44
617 857 5.935789 CGGTCTATCTTAACCTTTGGACAAA 59.064 40.000 0.00 0.00 33.14 2.83
618 858 5.246656 TCGGTCTATCTTAACCTTTGGACAA 59.753 40.000 0.00 0.00 33.14 3.18
619 859 4.773674 TCGGTCTATCTTAACCTTTGGACA 59.226 41.667 0.00 0.00 33.14 4.02
620 860 5.107824 GTCGGTCTATCTTAACCTTTGGAC 58.892 45.833 0.00 0.00 33.14 4.02
621 861 4.142315 CGTCGGTCTATCTTAACCTTTGGA 60.142 45.833 0.00 0.00 33.14 3.53
622 862 4.110482 CGTCGGTCTATCTTAACCTTTGG 58.890 47.826 0.00 0.00 33.14 3.28
623 863 3.550678 GCGTCGGTCTATCTTAACCTTTG 59.449 47.826 0.00 0.00 33.14 2.77
624 864 3.194116 TGCGTCGGTCTATCTTAACCTTT 59.806 43.478 0.00 0.00 33.14 3.11
625 865 2.756760 TGCGTCGGTCTATCTTAACCTT 59.243 45.455 0.00 0.00 33.14 3.50
626 866 2.372264 TGCGTCGGTCTATCTTAACCT 58.628 47.619 0.00 0.00 33.14 3.50
627 867 2.857592 TGCGTCGGTCTATCTTAACC 57.142 50.000 0.00 0.00 0.00 2.85
628 868 3.000022 GCTTTGCGTCGGTCTATCTTAAC 60.000 47.826 0.00 0.00 0.00 2.01
631 871 1.641577 GCTTTGCGTCGGTCTATCTT 58.358 50.000 0.00 0.00 0.00 2.40
632 872 0.179108 GGCTTTGCGTCGGTCTATCT 60.179 55.000 0.00 0.00 0.00 1.98
633 873 1.480219 CGGCTTTGCGTCGGTCTATC 61.480 60.000 0.00 0.00 0.00 2.08
634 874 1.518572 CGGCTTTGCGTCGGTCTAT 60.519 57.895 0.00 0.00 0.00 1.98
635 875 2.126228 CGGCTTTGCGTCGGTCTA 60.126 61.111 0.00 0.00 0.00 2.59
636 876 2.981977 TTTCGGCTTTGCGTCGGTCT 62.982 55.000 0.00 0.00 0.00 3.85
638 878 2.113131 CTTTTCGGCTTTGCGTCGGT 62.113 55.000 0.00 0.00 0.00 4.69
639 879 1.440353 CTTTTCGGCTTTGCGTCGG 60.440 57.895 0.00 0.00 0.00 4.79
640 880 2.074920 GCTTTTCGGCTTTGCGTCG 61.075 57.895 0.00 0.00 0.00 5.12
641 881 1.729484 GGCTTTTCGGCTTTGCGTC 60.729 57.895 0.00 0.00 34.85 5.19
643 883 2.725275 TTCGGCTTTTCGGCTTTGCG 62.725 55.000 0.00 0.00 35.72 4.85
705 1032 0.455815 GGCGCTTGATCCGGATTTTT 59.544 50.000 20.22 0.00 0.00 1.94
713 1040 4.918201 CTCCCGGGCGCTTGATCC 62.918 72.222 18.49 0.00 0.00 3.36
755 1082 2.849120 AGTGAGCTGATGGCACGCTC 62.849 60.000 21.47 21.47 46.29 5.03
760 1087 2.275134 TTTGAAGTGAGCTGATGGCA 57.725 45.000 0.00 0.00 44.79 4.92
770 1109 4.610605 TCGTAAGGGTCATTTGAAGTGA 57.389 40.909 0.00 0.00 38.47 3.41
788 1127 1.798813 GGAAACGCTCATGAACTTCGT 59.201 47.619 0.00 1.60 34.63 3.85
789 1128 1.128692 GGGAAACGCTCATGAACTTCG 59.871 52.381 0.00 0.95 0.00 3.79
790 1129 1.468914 GGGGAAACGCTCATGAACTTC 59.531 52.381 0.00 0.00 40.76 3.01
792 1131 3.249687 GGGGAAACGCTCATGAACT 57.750 52.632 0.00 0.00 40.76 3.01
801 1140 1.751437 AGCTTATGAAGGGGAAACGC 58.249 50.000 0.00 0.00 45.13 4.84
802 1141 4.402056 TCTAGCTTATGAAGGGGAAACG 57.598 45.455 0.00 0.00 0.00 3.60
803 1142 5.590663 CCTTTCTAGCTTATGAAGGGGAAAC 59.409 44.000 13.45 0.00 36.27 2.78
815 1905 4.969359 AGATACAAGGGCCTTTCTAGCTTA 59.031 41.667 18.16 0.00 0.00 3.09
831 1922 8.199449 CCGGTAAGTTTAAGTCCATAGATACAA 58.801 37.037 0.00 0.00 0.00 2.41
843 1934 3.811497 GTGTTGAGCCGGTAAGTTTAAGT 59.189 43.478 1.90 0.00 0.00 2.24
848 1939 0.390124 TCGTGTTGAGCCGGTAAGTT 59.610 50.000 1.90 0.00 0.00 2.66
859 1950 2.541556 TCGTGTGTCAATTCGTGTTGA 58.458 42.857 1.99 1.99 35.84 3.18
873 1964 1.125021 GACGAGACAGCAATTCGTGTG 59.875 52.381 9.69 0.00 46.38 3.82
884 1992 1.007271 ACACTTGCGGACGAGACAG 60.007 57.895 0.00 0.00 0.00 3.51
885 1993 1.299850 CACACTTGCGGACGAGACA 60.300 57.895 0.00 0.00 0.00 3.41
899 2007 3.628280 GAGGACGACGAGGGCACAC 62.628 68.421 0.00 0.00 0.00 3.82
904 2012 2.829458 GAGGGAGGACGACGAGGG 60.829 72.222 0.00 0.00 0.00 4.30
915 2023 3.147595 TGCGATGGACGGAGGGAG 61.148 66.667 0.00 0.00 42.83 4.30
916 2024 3.458163 GTGCGATGGACGGAGGGA 61.458 66.667 0.00 0.00 43.91 4.20
918 2026 2.105128 GAGTGCGATGGACGGAGG 59.895 66.667 0.00 0.00 43.91 4.30
920 2028 2.885113 CAGAGTGCGATGGACGGA 59.115 61.111 0.00 0.00 42.83 4.69
921 2029 2.887568 GCAGAGTGCGATGGACGG 60.888 66.667 0.00 0.00 42.83 4.79
960 2069 1.376812 CAGGGGAACTTGGTACGCC 60.377 63.158 0.00 0.00 32.95 5.68
1035 2159 1.597461 GAAAGGGGACGGGTGAGAG 59.403 63.158 0.00 0.00 0.00 3.20
1084 2208 2.197605 GGACGAGGCCTCCTAGAGC 61.198 68.421 27.20 9.55 31.76 4.09
1275 2411 1.067142 AGCATTTCGTCGAGCAGGTTA 60.067 47.619 7.58 0.00 0.00 2.85
1404 2540 4.617520 TTGGCGAGCAAGCGGTGA 62.618 61.111 0.00 0.00 38.18 4.02
1411 2547 2.664851 CGTGGACTTGGCGAGCAA 60.665 61.111 0.37 0.00 0.00 3.91
1451 2587 2.874648 GATCCTGTGCACGATGGGCA 62.875 60.000 13.13 0.00 39.32 5.36
1683 2819 3.147595 TACATGAGGGCGCGCTCT 61.148 61.111 41.95 37.66 0.00 4.09
1692 2828 0.807667 GCTCGCTGTGGTACATGAGG 60.808 60.000 0.00 0.00 44.52 3.86
1802 2938 3.257561 CGATGAGCTTGACGGCGG 61.258 66.667 13.24 0.00 37.29 6.13
1924 3061 3.698040 AGAGAAATGGATGTCAATGGTGC 59.302 43.478 0.00 0.00 0.00 5.01
1933 3074 8.986991 AGTAATCAGTAAGAGAGAAATGGATGT 58.013 33.333 0.00 0.00 0.00 3.06
1942 3083 8.840200 AATTACCCAGTAATCAGTAAGAGAGA 57.160 34.615 0.72 0.00 37.69 3.10
1951 3092 6.644347 AGACACTGAATTACCCAGTAATCAG 58.356 40.000 16.63 16.63 42.44 2.90
1952 3093 6.440647 AGAGACACTGAATTACCCAGTAATCA 59.559 38.462 0.72 1.57 42.44 2.57
1953 3094 6.879400 AGAGACACTGAATTACCCAGTAATC 58.121 40.000 0.72 0.00 42.44 1.75
1954 3095 6.875972 AGAGACACTGAATTACCCAGTAAT 57.124 37.500 0.00 0.00 42.44 1.89
1955 3096 6.154021 GGTAGAGACACTGAATTACCCAGTAA 59.846 42.308 0.00 0.00 42.44 2.24
1957 3098 4.466726 GGTAGAGACACTGAATTACCCAGT 59.533 45.833 0.00 0.00 44.92 4.00
1958 3099 4.466370 TGGTAGAGACACTGAATTACCCAG 59.534 45.833 0.00 0.00 37.64 4.45
1959 3100 4.422057 TGGTAGAGACACTGAATTACCCA 58.578 43.478 0.00 0.00 31.68 4.51
1960 3101 5.416271 TTGGTAGAGACACTGAATTACCC 57.584 43.478 0.00 0.00 31.68 3.69
1961 3102 4.870991 GCTTGGTAGAGACACTGAATTACC 59.129 45.833 0.00 0.00 0.00 2.85
1962 3103 4.870991 GGCTTGGTAGAGACACTGAATTAC 59.129 45.833 0.00 0.00 0.00 1.89
1965 3106 3.055530 CAGGCTTGGTAGAGACACTGAAT 60.056 47.826 0.00 0.00 0.00 2.57
1977 3118 4.529109 GCCAAAATTTACAGGCTTGGTA 57.471 40.909 17.34 0.00 43.70 3.25
2002 3145 2.955660 TCCACTTACACAAGGCCAAAAG 59.044 45.455 5.01 1.30 35.97 2.27
2009 3152 4.336889 TGTTCTCTCCACTTACACAAGG 57.663 45.455 0.00 0.00 35.97 3.61
2082 3225 2.987149 AGATTTCGTTGTAGCAGTGTCG 59.013 45.455 0.00 0.00 0.00 4.35
2385 3547 1.814772 CTGCTGGGGATAGAGGAGCG 61.815 65.000 0.00 0.00 32.05 5.03
2386 3548 2.056985 CTGCTGGGGATAGAGGAGC 58.943 63.158 0.00 0.00 0.00 4.70
2387 3549 1.814772 CGCTGCTGGGGATAGAGGAG 61.815 65.000 0.00 0.00 0.00 3.69
2556 3721 1.134848 CAAGGAGAGGAAGAAGGCGAG 60.135 57.143 0.00 0.00 0.00 5.03
2562 3727 0.987294 CAGGCCAAGGAGAGGAAGAA 59.013 55.000 5.01 0.00 0.00 2.52
2649 3814 4.189580 ACGGTGGTGCAGGTGCTT 62.190 61.111 3.18 0.00 42.66 3.91
2811 3976 2.758089 GCTCAATGCCGGTGCTCAG 61.758 63.158 1.90 0.00 38.71 3.35
2827 3992 1.434622 CTTGATCGATGCTTGCGGCT 61.435 55.000 0.54 0.00 42.39 5.52
2830 3995 1.070108 CCATCTTGATCGATGCTTGCG 60.070 52.381 0.54 0.00 39.51 4.85


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

AutoCloner maintained by Alex Coulton.