Multiple sequence alignment - TraesCS5B01G312000

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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 TraesCS5B01G312000 chr5B 100.000 2645 0 0 1 2645 493632126 493629482 0.000000e+00 4885.0
1 TraesCS5B01G312000 chr5B 81.574 559 73 19 1000 1546 493160072 493159532 4.040000e-118 435.0
2 TraesCS5B01G312000 chr5B 80.000 370 59 7 1041 1395 493125319 493124950 2.610000e-65 259.0
3 TraesCS5B01G312000 chr5B 92.529 174 12 1 1934 2107 671350760 671350588 5.650000e-62 248.0
4 TraesCS5B01G312000 chr5B 76.433 157 20 9 1505 1645 493141067 493141222 4.720000e-08 69.4
5 TraesCS5B01G312000 chr5D 93.092 1549 58 22 194 1726 411171792 411170277 0.000000e+00 2222.0
6 TraesCS5B01G312000 chr5D 96.390 554 14 4 2098 2645 411165737 411165184 0.000000e+00 907.0
7 TraesCS5B01G312000 chr5D 81.932 559 71 18 1000 1546 410843290 410842750 1.870000e-121 446.0
8 TraesCS5B01G312000 chr5D 87.328 363 37 5 1037 1390 410539204 410539566 8.810000e-110 407.0
9 TraesCS5B01G312000 chr5D 96.262 214 7 1 1726 1939 411165948 411165736 1.510000e-92 350.0
10 TraesCS5B01G312000 chr5D 80.811 370 56 8 1041 1395 410638161 410637792 2.590000e-70 276.0
11 TraesCS5B01G312000 chr5D 84.564 149 23 0 52 200 450373180 450373328 5.900000e-32 148.0
12 TraesCS5B01G312000 chr5D 86.207 116 16 0 87 202 450372101 450371986 2.760000e-25 126.0
13 TraesCS5B01G312000 chr5A 93.546 1379 55 20 572 1937 523016530 523015173 0.000000e+00 2023.0
14 TraesCS5B01G312000 chr5A 95.183 519 22 3 2099 2615 523015171 523014654 0.000000e+00 817.0
15 TraesCS5B01G312000 chr5A 87.397 365 37 5 1037 1392 522104295 522104659 6.810000e-111 411.0
16 TraesCS5B01G312000 chr5A 80.969 557 68 26 999 1542 522605563 522605032 8.810000e-110 407.0
17 TraesCS5B01G312000 chr5A 86.872 358 38 5 1034 1382 522082786 522083143 2.470000e-105 392.0
18 TraesCS5B01G312000 chr5A 85.833 360 40 7 1034 1383 522425284 522425642 3.220000e-99 372.0
19 TraesCS5B01G312000 chr5A 97.674 129 3 0 387 515 523016680 523016552 3.430000e-54 222.0
20 TraesCS5B01G312000 chr2D 93.182 176 11 1 1931 2106 56541162 56540988 9.390000e-65 257.0
21 TraesCS5B01G312000 chr2D 84.211 152 22 2 52 202 56870926 56870776 2.120000e-31 147.0
22 TraesCS5B01G312000 chr2D 86.400 125 17 0 78 202 99118655 99118531 1.280000e-28 137.0
23 TraesCS5B01G312000 chr2B 93.939 165 10 0 1938 2102 23888592 23888756 1.570000e-62 250.0
24 TraesCS5B01G312000 chr2B 87.069 116 15 0 87 202 245302373 245302258 5.940000e-27 132.0
25 TraesCS5B01G312000 chr3D 92.486 173 12 1 1927 2099 410670053 410670224 2.030000e-61 246.0
26 TraesCS5B01G312000 chr3D 90.323 186 12 6 1935 2117 520636987 520636805 3.400000e-59 239.0
27 TraesCS5B01G312000 chr7A 92.045 176 11 3 1938 2112 206712118 206711945 7.310000e-61 244.0
28 TraesCS5B01G312000 chr7A 84.375 128 19 1 84 210 722767355 722767482 9.940000e-25 124.0
29 TraesCS5B01G312000 chr4B 91.209 182 13 3 1935 2114 352835563 352835383 7.310000e-61 244.0
30 TraesCS5B01G312000 chr4B 90.960 177 16 0 1936 2112 483266542 483266366 3.400000e-59 239.0
31 TraesCS5B01G312000 chr1B 91.209 182 13 3 1935 2114 543805939 543806119 7.310000e-61 244.0
32 TraesCS5B01G312000 chr4D 88.119 202 14 3 1 202 437244194 437244003 5.690000e-57 231.0
33 TraesCS5B01G312000 chr4D 88.079 151 18 0 52 202 487346441 487346291 2.090000e-41 180.0
34 TraesCS5B01G312000 chr7B 86.232 138 19 0 65 202 72078068 72077931 1.640000e-32 150.0
35 TraesCS5B01G312000 chr3B 88.000 125 15 0 78 202 684415795 684415671 5.900000e-32 148.0


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 TraesCS5B01G312000 chr5B 493629482 493632126 2644 True 4885.000000 4885 100.000000 1 2645 1 chr5B.!!$R3 2644
1 TraesCS5B01G312000 chr5B 493159532 493160072 540 True 435.000000 435 81.574000 1000 1546 1 chr5B.!!$R2 546
2 TraesCS5B01G312000 chr5D 411170277 411171792 1515 True 2222.000000 2222 93.092000 194 1726 1 chr5D.!!$R3 1532
3 TraesCS5B01G312000 chr5D 411165184 411165948 764 True 628.500000 907 96.326000 1726 2645 2 chr5D.!!$R5 919
4 TraesCS5B01G312000 chr5D 410842750 410843290 540 True 446.000000 446 81.932000 1000 1546 1 chr5D.!!$R2 546
5 TraesCS5B01G312000 chr5A 523014654 523016680 2026 True 1020.666667 2023 95.467667 387 2615 3 chr5A.!!$R2 2228
6 TraesCS5B01G312000 chr5A 522605032 522605563 531 True 407.000000 407 80.969000 999 1542 1 chr5A.!!$R1 543

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
568 577 0.034616 GCCTGCTTCCTCGATGCTAT 59.965 55.0 0.0 0.0 34.46 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2208 0.666577 GCTGTGACGCCGTAAGTTCT 60.667 55.0 0.0 0.0 0.0 3.01 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 3.839432 CGGCCCCTCTCCGTCTTC 61.839 72.222 0.00 0.00 41.85 2.87
24 25 3.471806 GGCCCCTCTCCGTCTTCC 61.472 72.222 0.00 0.00 0.00 3.46
25 26 3.839432 GCCCCTCTCCGTCTTCCG 61.839 72.222 0.00 0.00 0.00 4.30
35 36 4.373116 GTCTTCCGGGCGCTGACA 62.373 66.667 7.64 0.00 0.00 3.58
36 37 4.069232 TCTTCCGGGCGCTGACAG 62.069 66.667 7.64 0.00 0.00 3.51
46 47 2.512515 GCTGACAGCGGGATCCAC 60.513 66.667 15.23 4.84 0.00 4.02
47 48 2.202797 CTGACAGCGGGATCCACG 60.203 66.667 15.23 15.55 0.00 4.94
48 49 3.723235 CTGACAGCGGGATCCACGG 62.723 68.421 15.23 8.32 0.00 4.94
49 50 3.771160 GACAGCGGGATCCACGGT 61.771 66.667 15.23 16.86 43.47 4.83
50 51 2.363276 ACAGCGGGATCCACGGTA 60.363 61.111 21.55 0.00 40.39 4.02
51 52 2.106332 CAGCGGGATCCACGGTAC 59.894 66.667 21.55 8.25 40.39 3.34
52 53 2.043248 AGCGGGATCCACGGTACT 60.043 61.111 20.93 9.49 40.59 2.73
53 54 1.105167 CAGCGGGATCCACGGTACTA 61.105 60.000 21.55 0.00 40.39 1.82
54 55 0.822532 AGCGGGATCCACGGTACTAG 60.823 60.000 20.93 0.00 40.59 2.57
55 56 1.105759 GCGGGATCCACGGTACTAGT 61.106 60.000 15.23 0.00 0.00 2.57
56 57 0.950116 CGGGATCCACGGTACTAGTC 59.050 60.000 15.23 0.00 0.00 2.59
57 58 1.748244 CGGGATCCACGGTACTAGTCA 60.748 57.143 15.23 0.00 0.00 3.41
58 59 1.955080 GGGATCCACGGTACTAGTCAG 59.045 57.143 15.23 0.00 0.00 3.51
59 60 2.652590 GGATCCACGGTACTAGTCAGT 58.347 52.381 6.95 0.00 38.91 3.41
60 61 2.358267 GGATCCACGGTACTAGTCAGTG 59.642 54.545 6.95 8.40 36.14 3.66
61 62 1.830279 TCCACGGTACTAGTCAGTGG 58.170 55.000 26.01 26.01 46.82 4.00
62 63 0.172803 CCACGGTACTAGTCAGTGGC 59.827 60.000 22.85 0.00 42.10 5.01
63 64 1.174783 CACGGTACTAGTCAGTGGCT 58.825 55.000 1.28 1.28 36.14 4.75
64 65 1.132643 CACGGTACTAGTCAGTGGCTC 59.867 57.143 0.00 0.00 36.14 4.70
65 66 1.271762 ACGGTACTAGTCAGTGGCTCA 60.272 52.381 0.00 0.00 36.14 4.26
66 67 1.402259 CGGTACTAGTCAGTGGCTCAG 59.598 57.143 0.00 0.00 36.14 3.35
67 68 1.751924 GGTACTAGTCAGTGGCTCAGG 59.248 57.143 0.00 0.00 36.14 3.86
68 69 2.448453 GTACTAGTCAGTGGCTCAGGT 58.552 52.381 0.00 1.72 36.14 4.00
69 70 1.261480 ACTAGTCAGTGGCTCAGGTG 58.739 55.000 0.00 0.00 32.25 4.00
70 71 1.261480 CTAGTCAGTGGCTCAGGTGT 58.739 55.000 0.00 0.00 0.00 4.16
71 72 2.225041 ACTAGTCAGTGGCTCAGGTGTA 60.225 50.000 0.00 0.00 32.25 2.90
72 73 0.969894 AGTCAGTGGCTCAGGTGTAC 59.030 55.000 0.00 0.00 0.00 2.90
73 74 0.679505 GTCAGTGGCTCAGGTGTACA 59.320 55.000 0.00 0.00 0.00 2.90
74 75 0.679505 TCAGTGGCTCAGGTGTACAC 59.320 55.000 18.01 18.01 0.00 2.90
75 76 0.392706 CAGTGGCTCAGGTGTACACA 59.607 55.000 26.51 6.34 34.65 3.72
76 77 1.128200 AGTGGCTCAGGTGTACACAA 58.872 50.000 26.51 10.99 34.65 3.33
77 78 1.488812 AGTGGCTCAGGTGTACACAAA 59.511 47.619 26.51 10.65 34.65 2.83
78 79 1.602377 GTGGCTCAGGTGTACACAAAC 59.398 52.381 26.51 10.26 32.58 2.93
79 80 0.865769 GGCTCAGGTGTACACAAACG 59.134 55.000 26.51 13.07 0.00 3.60
80 81 1.578583 GCTCAGGTGTACACAAACGT 58.421 50.000 26.51 3.51 0.00 3.99
81 82 1.260561 GCTCAGGTGTACACAAACGTG 59.739 52.381 26.51 14.74 40.42 4.49
82 83 2.816689 CTCAGGTGTACACAAACGTGA 58.183 47.619 26.51 17.61 38.48 4.35
83 84 3.390135 CTCAGGTGTACACAAACGTGAT 58.610 45.455 26.51 0.08 39.62 3.06
84 85 3.799366 TCAGGTGTACACAAACGTGATT 58.201 40.909 26.51 0.00 36.55 2.57
85 86 4.193090 TCAGGTGTACACAAACGTGATTT 58.807 39.130 26.51 0.00 36.55 2.17
92 93 3.542825 CAAACGTGATTTGCACCGT 57.457 47.368 0.00 0.00 44.85 4.83
93 94 2.672188 CAAACGTGATTTGCACCGTA 57.328 45.000 0.00 0.00 44.85 4.02
94 95 3.196007 CAAACGTGATTTGCACCGTAT 57.804 42.857 0.00 0.00 44.85 3.06
95 96 3.560503 CAAACGTGATTTGCACCGTATT 58.439 40.909 0.00 0.00 44.85 1.89
96 97 3.907894 AACGTGATTTGCACCGTATTT 57.092 38.095 0.00 0.00 44.85 1.40
97 98 3.196007 ACGTGATTTGCACCGTATTTG 57.804 42.857 0.00 0.00 44.85 2.32
98 99 1.910819 CGTGATTTGCACCGTATTTGC 59.089 47.619 0.00 0.00 44.85 3.68
104 105 0.808125 TGCACCGTATTTGCACATCC 59.192 50.000 0.00 0.00 45.06 3.51
105 106 0.248054 GCACCGTATTTGCACATCCG 60.248 55.000 0.00 0.00 39.93 4.18
106 107 1.364721 CACCGTATTTGCACATCCGA 58.635 50.000 0.00 0.00 0.00 4.55
107 108 1.327460 CACCGTATTTGCACATCCGAG 59.673 52.381 0.00 0.00 0.00 4.63
108 109 0.304705 CCGTATTTGCACATCCGAGC 59.695 55.000 0.00 0.00 0.00 5.03
109 110 0.304705 CGTATTTGCACATCCGAGCC 59.695 55.000 0.00 0.00 0.00 4.70
110 111 1.378531 GTATTTGCACATCCGAGCCA 58.621 50.000 0.00 0.00 0.00 4.75
111 112 1.742831 GTATTTGCACATCCGAGCCAA 59.257 47.619 0.00 0.00 0.00 4.52
112 113 0.527565 ATTTGCACATCCGAGCCAAC 59.472 50.000 0.00 0.00 0.00 3.77
113 114 0.537143 TTTGCACATCCGAGCCAACT 60.537 50.000 0.00 0.00 0.00 3.16
114 115 0.537143 TTGCACATCCGAGCCAACTT 60.537 50.000 0.00 0.00 0.00 2.66
115 116 0.323302 TGCACATCCGAGCCAACTTA 59.677 50.000 0.00 0.00 0.00 2.24
116 117 1.065491 TGCACATCCGAGCCAACTTAT 60.065 47.619 0.00 0.00 0.00 1.73
117 118 2.017049 GCACATCCGAGCCAACTTATT 58.983 47.619 0.00 0.00 0.00 1.40
118 119 2.223340 GCACATCCGAGCCAACTTATTG 60.223 50.000 0.00 0.00 35.40 1.90
119 120 3.009723 CACATCCGAGCCAACTTATTGT 58.990 45.455 0.00 0.00 33.60 2.71
120 121 4.188462 CACATCCGAGCCAACTTATTGTA 58.812 43.478 0.00 0.00 33.60 2.41
121 122 4.816385 CACATCCGAGCCAACTTATTGTAT 59.184 41.667 0.00 0.00 33.60 2.29
122 123 5.050091 CACATCCGAGCCAACTTATTGTATC 60.050 44.000 0.00 0.00 33.60 2.24
123 124 4.746535 TCCGAGCCAACTTATTGTATCA 57.253 40.909 0.00 0.00 33.60 2.15
124 125 4.693283 TCCGAGCCAACTTATTGTATCAG 58.307 43.478 0.00 0.00 33.60 2.90
125 126 4.161565 TCCGAGCCAACTTATTGTATCAGT 59.838 41.667 0.00 0.00 33.60 3.41
126 127 4.876107 CCGAGCCAACTTATTGTATCAGTT 59.124 41.667 0.00 0.00 33.60 3.16
127 128 6.046593 CCGAGCCAACTTATTGTATCAGTTA 58.953 40.000 0.00 0.00 33.60 2.24
128 129 6.537301 CCGAGCCAACTTATTGTATCAGTTAA 59.463 38.462 0.00 0.00 33.60 2.01
129 130 7.065324 CCGAGCCAACTTATTGTATCAGTTAAA 59.935 37.037 0.00 0.00 33.60 1.52
130 131 8.612619 CGAGCCAACTTATTGTATCAGTTAAAT 58.387 33.333 0.00 0.00 33.60 1.40
131 132 9.722056 GAGCCAACTTATTGTATCAGTTAAATG 57.278 33.333 0.00 0.00 33.60 2.32
132 133 9.243105 AGCCAACTTATTGTATCAGTTAAATGT 57.757 29.630 2.43 0.00 33.60 2.71
140 141 7.929941 TTGTATCAGTTAAATGTATGCCACA 57.070 32.000 2.43 0.00 42.69 4.17
141 142 7.929941 TGTATCAGTTAAATGTATGCCACAA 57.070 32.000 2.43 0.00 41.55 3.33
142 143 7.984391 TGTATCAGTTAAATGTATGCCACAAG 58.016 34.615 2.43 0.00 41.55 3.16
143 144 7.609918 TGTATCAGTTAAATGTATGCCACAAGT 59.390 33.333 2.43 0.00 41.55 3.16
144 145 6.892658 TCAGTTAAATGTATGCCACAAGTT 57.107 33.333 2.43 0.00 41.55 2.66
145 146 6.908825 TCAGTTAAATGTATGCCACAAGTTC 58.091 36.000 2.43 0.00 41.55 3.01
146 147 6.714810 TCAGTTAAATGTATGCCACAAGTTCT 59.285 34.615 2.43 0.00 41.55 3.01
147 148 7.880713 TCAGTTAAATGTATGCCACAAGTTCTA 59.119 33.333 2.43 0.00 41.55 2.10
148 149 8.177663 CAGTTAAATGTATGCCACAAGTTCTAG 58.822 37.037 0.00 0.00 41.55 2.43
149 150 5.567138 AAATGTATGCCACAAGTTCTAGC 57.433 39.130 0.00 0.00 41.55 3.42
150 151 3.694043 TGTATGCCACAAGTTCTAGCA 57.306 42.857 0.00 0.00 37.94 3.49
151 152 4.220693 TGTATGCCACAAGTTCTAGCAT 57.779 40.909 7.83 7.83 45.58 3.79
152 153 4.191544 TGTATGCCACAAGTTCTAGCATC 58.808 43.478 6.35 1.75 42.86 3.91
153 154 2.857186 TGCCACAAGTTCTAGCATCA 57.143 45.000 0.00 0.00 0.00 3.07
154 155 3.138884 TGCCACAAGTTCTAGCATCAA 57.861 42.857 0.00 0.00 0.00 2.57
155 156 3.485394 TGCCACAAGTTCTAGCATCAAA 58.515 40.909 0.00 0.00 0.00 2.69
156 157 3.888323 TGCCACAAGTTCTAGCATCAAAA 59.112 39.130 0.00 0.00 0.00 2.44
157 158 4.523943 TGCCACAAGTTCTAGCATCAAAAT 59.476 37.500 0.00 0.00 0.00 1.82
158 159 4.860907 GCCACAAGTTCTAGCATCAAAATG 59.139 41.667 0.00 0.00 35.87 2.32
159 160 5.404946 CCACAAGTTCTAGCATCAAAATGG 58.595 41.667 0.00 0.00 33.19 3.16
160 161 4.860907 CACAAGTTCTAGCATCAAAATGGC 59.139 41.667 0.00 0.00 33.19 4.40
161 162 4.082026 ACAAGTTCTAGCATCAAAATGGCC 60.082 41.667 0.00 0.00 33.19 5.36
162 163 2.684881 AGTTCTAGCATCAAAATGGCCG 59.315 45.455 0.00 0.00 33.19 6.13
163 164 2.418368 TCTAGCATCAAAATGGCCGT 57.582 45.000 0.00 0.00 33.19 5.68
164 165 2.722094 TCTAGCATCAAAATGGCCGTT 58.278 42.857 3.71 3.71 33.19 4.44
165 166 3.088532 TCTAGCATCAAAATGGCCGTTT 58.911 40.909 17.53 17.53 33.19 3.60
166 167 2.083167 AGCATCAAAATGGCCGTTTG 57.917 45.000 23.51 21.80 37.32 2.93
167 168 1.344114 AGCATCAAAATGGCCGTTTGT 59.656 42.857 23.51 10.91 37.28 2.83
168 169 1.460359 GCATCAAAATGGCCGTTTGTG 59.540 47.619 23.51 20.80 37.28 3.33
169 170 2.067766 CATCAAAATGGCCGTTTGTGG 58.932 47.619 23.51 15.52 37.28 4.17
179 180 2.969443 CCGTTTGTGGCAAGTTCTAG 57.031 50.000 0.00 0.00 0.00 2.43
180 181 1.069227 CCGTTTGTGGCAAGTTCTAGC 60.069 52.381 0.00 0.00 0.00 3.42
181 182 1.601903 CGTTTGTGGCAAGTTCTAGCA 59.398 47.619 0.00 0.00 0.00 3.49
182 183 2.602217 CGTTTGTGGCAAGTTCTAGCAC 60.602 50.000 0.00 0.00 0.00 4.40
183 184 1.604604 TTGTGGCAAGTTCTAGCACC 58.395 50.000 0.00 0.00 0.00 5.01
184 185 0.472044 TGTGGCAAGTTCTAGCACCA 59.528 50.000 0.00 0.00 0.00 4.17
185 186 0.875059 GTGGCAAGTTCTAGCACCAC 59.125 55.000 0.00 0.00 40.64 4.16
186 187 0.602638 TGGCAAGTTCTAGCACCACG 60.603 55.000 0.00 0.00 0.00 4.94
187 188 1.298859 GGCAAGTTCTAGCACCACGG 61.299 60.000 0.00 0.00 0.00 4.94
188 189 1.298859 GCAAGTTCTAGCACCACGGG 61.299 60.000 0.00 0.00 0.00 5.28
189 190 0.034896 CAAGTTCTAGCACCACGGGT 59.965 55.000 0.00 0.00 35.62 5.28
200 201 2.467566 ACCACGGGTGTAATTGACTC 57.532 50.000 0.00 0.00 32.98 3.36
201 202 1.975680 ACCACGGGTGTAATTGACTCT 59.024 47.619 0.00 0.00 32.98 3.24
202 203 2.028385 ACCACGGGTGTAATTGACTCTC 60.028 50.000 0.00 0.00 32.98 3.20
213 214 7.955864 GGTGTAATTGACTCTCGAAAAATACAC 59.044 37.037 12.90 12.90 0.00 2.90
226 227 6.264744 TCGAAAAATACACCCCAACAAACATA 59.735 34.615 0.00 0.00 0.00 2.29
232 233 4.027437 ACACCCCAACAAACATAACAGTT 58.973 39.130 0.00 0.00 0.00 3.16
296 299 1.065358 AACAGGCGTAATCGTTCACG 58.935 50.000 0.00 0.00 41.04 4.35
320 323 3.021695 TGGTGAGACTAGAACGGGTATG 58.978 50.000 0.00 0.00 0.00 2.39
345 348 2.158726 TCCGTTGCTTGGTCTAAAAGGT 60.159 45.455 0.00 0.00 0.00 3.50
382 385 5.220491 CGCTAATCCAGAAGCTTTGAACTAC 60.220 44.000 0.00 0.00 36.56 2.73
438 441 4.947388 ACAAAAATCCTTGCCGCTATAAGA 59.053 37.500 0.00 0.00 0.00 2.10
544 553 3.399770 GCACAGTTACGTCGCGCA 61.400 61.111 8.75 0.00 0.00 6.09
559 568 4.357279 GCACTGGGCCTGCTTCCT 62.357 66.667 10.71 0.00 36.11 3.36
560 569 2.045536 CACTGGGCCTGCTTCCTC 60.046 66.667 10.71 0.00 0.00 3.71
561 570 3.710722 ACTGGGCCTGCTTCCTCG 61.711 66.667 10.71 0.00 0.00 4.63
562 571 3.393970 CTGGGCCTGCTTCCTCGA 61.394 66.667 4.53 0.00 0.00 4.04
563 572 2.688666 TGGGCCTGCTTCCTCGAT 60.689 61.111 4.53 0.00 0.00 3.59
564 573 2.203126 GGGCCTGCTTCCTCGATG 60.203 66.667 0.84 0.00 0.00 3.84
565 574 2.899339 GGCCTGCTTCCTCGATGC 60.899 66.667 0.00 0.00 34.04 3.91
566 575 2.188994 GCCTGCTTCCTCGATGCT 59.811 61.111 0.00 0.00 34.46 3.79
567 576 1.443407 GCCTGCTTCCTCGATGCTA 59.557 57.895 0.00 0.00 34.46 3.49
568 577 0.034616 GCCTGCTTCCTCGATGCTAT 59.965 55.000 0.00 0.00 34.46 2.97
569 578 1.793258 CCTGCTTCCTCGATGCTATG 58.207 55.000 0.00 0.00 34.46 2.23
570 579 1.607509 CCTGCTTCCTCGATGCTATGG 60.608 57.143 0.00 0.00 34.46 2.74
578 587 0.829990 TCGATGCTATGGCCAACAGA 59.170 50.000 10.96 0.37 37.74 3.41
598 607 3.072184 AGAGCTCCGAAAGATATGCCAAT 59.928 43.478 10.93 0.00 0.00 3.16
653 662 4.558226 AGATGCTTGGATGTGAAGTGTA 57.442 40.909 0.00 0.00 0.00 2.90
707 716 8.785329 AGAAAAGAAAAAGATCTAGTGCTAGG 57.215 34.615 0.00 0.00 34.06 3.02
708 717 8.598041 AGAAAAGAAAAAGATCTAGTGCTAGGA 58.402 33.333 0.00 0.00 34.06 2.94
709 718 8.785329 AAAAGAAAAAGATCTAGTGCTAGGAG 57.215 34.615 0.00 0.00 34.06 3.69
710 719 5.912892 AGAAAAAGATCTAGTGCTAGGAGC 58.087 41.667 0.00 0.00 42.82 4.70
873 885 4.095932 TCAGCTATATATACTCCGCCGTTG 59.904 45.833 0.00 0.00 0.00 4.10
909 939 0.455410 CTCACCGCTCCTCTCTCAAG 59.545 60.000 0.00 0.00 0.00 3.02
911 941 0.108898 CACCGCTCCTCTCTCAAGTG 60.109 60.000 0.00 0.00 0.00 3.16
931 961 1.136224 GTCTCAACGCAGCAGCTAAAC 60.136 52.381 0.00 0.00 39.10 2.01
932 962 0.867746 CTCAACGCAGCAGCTAAACA 59.132 50.000 0.00 0.00 39.10 2.83
933 963 0.586319 TCAACGCAGCAGCTAAACAC 59.414 50.000 0.00 0.00 39.10 3.32
934 964 0.722469 CAACGCAGCAGCTAAACACG 60.722 55.000 0.00 0.00 39.10 4.49
935 965 2.202222 CGCAGCAGCTAAACACGC 60.202 61.111 0.00 0.00 39.10 5.34
936 966 2.671177 CGCAGCAGCTAAACACGCT 61.671 57.895 0.00 0.00 39.10 5.07
937 967 1.351430 CGCAGCAGCTAAACACGCTA 61.351 55.000 0.00 0.00 39.10 4.26
938 968 0.796312 GCAGCAGCTAAACACGCTAA 59.204 50.000 0.00 0.00 35.63 3.09
939 969 1.201965 GCAGCAGCTAAACACGCTAAG 60.202 52.381 0.00 0.00 35.63 2.18
940 970 1.079503 AGCAGCTAAACACGCTAAGC 58.920 50.000 0.00 0.00 35.63 3.09
941 971 1.079503 GCAGCTAAACACGCTAAGCT 58.920 50.000 0.00 0.00 45.94 3.74
942 972 2.094182 AGCAGCTAAACACGCTAAGCTA 60.094 45.455 0.00 0.00 43.26 3.32
943 973 2.029365 GCAGCTAAACACGCTAAGCTAC 59.971 50.000 0.00 0.00 43.26 3.58
1215 1245 4.643387 GGCACCTTCACCACCGCT 62.643 66.667 0.00 0.00 0.00 5.52
1260 1290 4.484258 GCCGTTCTCGCGCTCTCT 62.484 66.667 5.56 0.00 35.54 3.10
1263 1293 2.202676 GTTCTCGCGCTCTCTGGG 60.203 66.667 5.56 0.00 0.00 4.45
1394 1439 2.644992 GTTCCAAAGGCAGCACCG 59.355 61.111 0.00 0.00 46.52 4.94
1538 1583 4.462394 CATGGATGCCGGATCGTT 57.538 55.556 5.05 0.00 30.87 3.85
1603 1648 1.751162 CGGGAAGACCTCGAGCTCT 60.751 63.158 12.85 5.53 36.97 4.09
1647 1692 3.613299 GGAGCTACTTGTTCGACTAAAGC 59.387 47.826 0.00 0.00 0.00 3.51
1660 1705 9.048446 TGTTCGACTAAAGCAGTTAAGTTAAAT 57.952 29.630 0.00 0.00 37.72 1.40
1779 1825 2.789409 AGCCTCCGCTGTCTATTTTT 57.211 45.000 0.00 0.00 46.19 1.94
1923 1969 1.677217 GGACCTCAAGCACTCCATGAC 60.677 57.143 0.00 0.00 0.00 3.06
1937 1983 6.459066 CACTCCATGACCGACATAAGATATT 58.541 40.000 0.00 0.00 37.46 1.28
1938 1984 7.602753 CACTCCATGACCGACATAAGATATTA 58.397 38.462 0.00 0.00 37.46 0.98
1939 1985 7.542477 CACTCCATGACCGACATAAGATATTAC 59.458 40.741 0.00 0.00 37.46 1.89
1940 1986 7.451877 ACTCCATGACCGACATAAGATATTACT 59.548 37.037 0.00 0.00 37.46 2.24
1941 1987 7.827701 TCCATGACCGACATAAGATATTACTC 58.172 38.462 0.00 0.00 37.46 2.59
1942 1988 7.036220 CCATGACCGACATAAGATATTACTCC 58.964 42.308 0.00 0.00 37.46 3.85
1943 1989 7.093727 CCATGACCGACATAAGATATTACTCCT 60.094 40.741 0.00 0.00 37.46 3.69
1944 1990 7.834881 TGACCGACATAAGATATTACTCCTT 57.165 36.000 0.00 0.00 0.00 3.36
1945 1991 7.883217 TGACCGACATAAGATATTACTCCTTC 58.117 38.462 0.00 0.00 0.00 3.46
1946 1992 7.039923 TGACCGACATAAGATATTACTCCTTCC 60.040 40.741 0.00 0.00 0.00 3.46
1947 1993 6.072064 ACCGACATAAGATATTACTCCTTCCG 60.072 42.308 0.00 0.00 0.00 4.30
1948 1994 6.072064 CCGACATAAGATATTACTCCTTCCGT 60.072 42.308 0.00 0.00 0.00 4.69
1949 1995 7.368833 CGACATAAGATATTACTCCTTCCGTT 58.631 38.462 0.00 0.00 0.00 4.44
1950 1996 7.866393 CGACATAAGATATTACTCCTTCCGTTT 59.134 37.037 0.00 0.00 0.00 3.60
1951 1997 9.194271 GACATAAGATATTACTCCTTCCGTTTC 57.806 37.037 0.00 0.00 0.00 2.78
1952 1998 8.925338 ACATAAGATATTACTCCTTCCGTTTCT 58.075 33.333 0.00 0.00 0.00 2.52
1964 2010 8.979534 ACTCCTTCCGTTTCTAAATATAAGTCT 58.020 33.333 0.00 0.00 0.00 3.24
1965 2011 9.819267 CTCCTTCCGTTTCTAAATATAAGTCTT 57.181 33.333 0.00 0.00 0.00 3.01
1994 2040 8.873215 AGAGATTTCACTATAAACCACATACG 57.127 34.615 0.00 0.00 0.00 3.06
1995 2041 7.926555 AGAGATTTCACTATAAACCACATACGG 59.073 37.037 0.00 0.00 0.00 4.02
1996 2042 7.788026 AGATTTCACTATAAACCACATACGGA 58.212 34.615 0.00 0.00 0.00 4.69
1997 2043 8.429641 AGATTTCACTATAAACCACATACGGAT 58.570 33.333 0.00 0.00 0.00 4.18
1998 2044 7.780008 TTTCACTATAAACCACATACGGATG 57.220 36.000 5.94 5.94 39.16 3.51
2000 2046 7.585579 TCACTATAAACCACATACGGATGTA 57.414 36.000 14.23 0.00 44.82 2.29
2001 2047 8.185506 TCACTATAAACCACATACGGATGTAT 57.814 34.615 14.23 5.54 44.82 2.29
2002 2048 9.299465 TCACTATAAACCACATACGGATGTATA 57.701 33.333 14.23 6.48 44.82 1.47
2009 2055 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
2010 2056 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
2011 2057 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
2012 2058 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
2013 2059 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
2014 2060 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
2018 2064 9.809096 ACGGATGTATATAGATGCATTTTAGAG 57.191 33.333 11.19 0.00 38.38 2.43
2019 2065 9.809096 CGGATGTATATAGATGCATTTTAGAGT 57.191 33.333 11.19 0.00 38.38 3.24
2040 2086 8.885494 AGAGTATAGATTCACTCAATTTGCTC 57.115 34.615 4.70 0.00 42.99 4.26
2041 2087 7.930865 AGAGTATAGATTCACTCAATTTGCTCC 59.069 37.037 4.70 0.00 42.99 4.70
2042 2088 5.998454 ATAGATTCACTCAATTTGCTCCG 57.002 39.130 0.00 0.00 0.00 4.63
2043 2089 3.679389 AGATTCACTCAATTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2044 2090 4.832248 AGATTCACTCAATTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2045 2091 5.431765 AGATTCACTCAATTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2046 2092 4.944962 TTCACTCAATTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2047 2093 3.937814 TCACTCAATTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2048 2094 5.079689 TCACTCAATTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2049 2095 5.670485 TCACTCAATTTGCTCCGTATGTAT 58.330 37.500 0.00 0.00 0.00 2.29
2050 2096 6.112734 TCACTCAATTTGCTCCGTATGTATT 58.887 36.000 0.00 0.00 0.00 1.89
2051 2097 6.257849 TCACTCAATTTGCTCCGTATGTATTC 59.742 38.462 0.00 0.00 0.00 1.75
2052 2098 5.527582 ACTCAATTTGCTCCGTATGTATTCC 59.472 40.000 0.00 0.00 0.00 3.01
2053 2099 5.432645 TCAATTTGCTCCGTATGTATTCCA 58.567 37.500 0.00 0.00 0.00 3.53
2054 2100 6.061441 TCAATTTGCTCCGTATGTATTCCAT 58.939 36.000 0.00 0.00 37.58 3.41
2055 2101 7.220740 TCAATTTGCTCCGTATGTATTCCATA 58.779 34.615 0.00 0.00 34.86 2.74
2056 2102 7.387673 TCAATTTGCTCCGTATGTATTCCATAG 59.612 37.037 0.00 0.00 36.71 2.23
2057 2103 5.801531 TTGCTCCGTATGTATTCCATAGT 57.198 39.130 0.00 0.00 36.71 2.12
2058 2104 5.134202 TGCTCCGTATGTATTCCATAGTG 57.866 43.478 0.00 0.00 36.71 2.74
2059 2105 4.830600 TGCTCCGTATGTATTCCATAGTGA 59.169 41.667 0.00 0.00 36.71 3.41
2060 2106 5.303333 TGCTCCGTATGTATTCCATAGTGAA 59.697 40.000 0.00 0.00 36.71 3.18
2061 2107 6.183360 TGCTCCGTATGTATTCCATAGTGAAA 60.183 38.462 0.00 0.00 36.71 2.69
2062 2108 6.874134 GCTCCGTATGTATTCCATAGTGAAAT 59.126 38.462 0.00 0.00 36.71 2.17
2063 2109 7.063544 GCTCCGTATGTATTCCATAGTGAAATC 59.936 40.741 0.00 0.00 36.71 2.17
2064 2110 8.190326 TCCGTATGTATTCCATAGTGAAATCT 57.810 34.615 0.00 0.00 36.71 2.40
2065 2111 8.304596 TCCGTATGTATTCCATAGTGAAATCTC 58.695 37.037 0.00 0.00 36.71 2.75
2066 2112 8.307483 CCGTATGTATTCCATAGTGAAATCTCT 58.693 37.037 0.00 0.00 36.71 3.10
2074 2120 9.606631 ATTCCATAGTGAAATCTCTACAAAGAC 57.393 33.333 0.00 0.00 0.00 3.01
2075 2121 8.367660 TCCATAGTGAAATCTCTACAAAGACT 57.632 34.615 0.00 0.00 0.00 3.24
2076 2122 8.816894 TCCATAGTGAAATCTCTACAAAGACTT 58.183 33.333 0.00 0.00 0.00 3.01
2093 2139 9.853177 ACAAAGACTTATATTTAGGAATGGAGG 57.147 33.333 0.00 0.00 0.00 4.30
2141 2187 6.754193 ACCAGAAAAGACACTTCAAAAACAA 58.246 32.000 0.00 0.00 0.00 2.83
2143 2189 6.311200 CCAGAAAAGACACTTCAAAAACAAGG 59.689 38.462 0.00 0.00 0.00 3.61
2255 2302 3.587797 TCGTTCAGATGAGGTTACCAC 57.412 47.619 3.51 0.00 0.00 4.16
2350 2397 2.228822 CCTCCGCAATTATTATGGGCAC 59.771 50.000 0.00 0.00 0.00 5.01
2562 2615 2.102588 TCTTAAGATCAGGGGTAAGCGC 59.897 50.000 0.00 0.00 0.00 5.92
2582 2635 8.578308 AAGCGCGTAACAACTATATATAAACA 57.422 30.769 8.43 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.616721 CGGAGAGGGGCCGTATGG 61.617 72.222 0.00 0.00 43.66 2.74
7 8 3.471806 GGAAGACGGAGAGGGGCC 61.472 72.222 0.00 0.00 0.00 5.80
8 9 3.839432 CGGAAGACGGAGAGGGGC 61.839 72.222 0.00 0.00 39.42 5.80
18 19 4.373116 TGTCAGCGCCCGGAAGAC 62.373 66.667 0.73 3.82 0.00 3.01
19 20 4.069232 CTGTCAGCGCCCGGAAGA 62.069 66.667 0.73 0.00 0.00 2.87
29 30 2.512515 GTGGATCCCGCTGTCAGC 60.513 66.667 15.22 15.22 38.02 4.26
30 31 2.202797 CGTGGATCCCGCTGTCAG 60.203 66.667 9.90 0.00 0.00 3.51
31 32 3.770040 CCGTGGATCCCGCTGTCA 61.770 66.667 9.90 0.00 0.00 3.58
32 33 2.420568 TACCGTGGATCCCGCTGTC 61.421 63.158 9.90 0.00 33.75 3.51
33 34 2.363276 TACCGTGGATCCCGCTGT 60.363 61.111 9.90 7.44 35.73 4.40
34 35 1.105167 TAGTACCGTGGATCCCGCTG 61.105 60.000 9.90 1.28 0.00 5.18
35 36 0.822532 CTAGTACCGTGGATCCCGCT 60.823 60.000 9.90 7.70 0.00 5.52
36 37 1.105759 ACTAGTACCGTGGATCCCGC 61.106 60.000 9.90 0.91 0.00 6.13
37 38 0.950116 GACTAGTACCGTGGATCCCG 59.050 60.000 9.90 12.26 0.00 5.14
38 39 1.955080 CTGACTAGTACCGTGGATCCC 59.045 57.143 9.90 0.00 0.00 3.85
39 40 2.358267 CACTGACTAGTACCGTGGATCC 59.642 54.545 4.20 4.20 34.74 3.36
40 41 2.358267 CCACTGACTAGTACCGTGGATC 59.642 54.545 23.41 0.00 46.11 3.36
41 42 2.376109 CCACTGACTAGTACCGTGGAT 58.624 52.381 23.41 0.00 46.11 3.41
42 43 1.830279 CCACTGACTAGTACCGTGGA 58.170 55.000 23.41 0.00 46.11 4.02
43 44 0.172803 GCCACTGACTAGTACCGTGG 59.827 60.000 23.44 23.44 45.99 4.94
44 45 1.132643 GAGCCACTGACTAGTACCGTG 59.867 57.143 0.00 3.58 34.74 4.94
45 46 1.271762 TGAGCCACTGACTAGTACCGT 60.272 52.381 0.00 0.00 34.74 4.83
46 47 1.402259 CTGAGCCACTGACTAGTACCG 59.598 57.143 0.00 0.00 34.74 4.02
47 48 1.751924 CCTGAGCCACTGACTAGTACC 59.248 57.143 0.00 0.00 34.74 3.34
48 49 2.164624 CACCTGAGCCACTGACTAGTAC 59.835 54.545 0.00 0.00 34.74 2.73
49 50 2.225041 ACACCTGAGCCACTGACTAGTA 60.225 50.000 0.00 0.00 34.74 1.82
50 51 1.261480 CACCTGAGCCACTGACTAGT 58.739 55.000 0.00 0.00 37.75 2.57
51 52 1.261480 ACACCTGAGCCACTGACTAG 58.739 55.000 0.00 0.00 0.00 2.57
52 53 2.168496 GTACACCTGAGCCACTGACTA 58.832 52.381 0.00 0.00 0.00 2.59
53 54 0.969894 GTACACCTGAGCCACTGACT 59.030 55.000 0.00 0.00 0.00 3.41
54 55 0.679505 TGTACACCTGAGCCACTGAC 59.320 55.000 0.00 0.00 0.00 3.51
55 56 0.679505 GTGTACACCTGAGCCACTGA 59.320 55.000 15.42 0.00 0.00 3.41
56 57 0.392706 TGTGTACACCTGAGCCACTG 59.607 55.000 22.91 0.00 0.00 3.66
57 58 1.128200 TTGTGTACACCTGAGCCACT 58.872 50.000 22.91 0.00 0.00 4.00
58 59 1.602377 GTTTGTGTACACCTGAGCCAC 59.398 52.381 22.91 5.69 0.00 5.01
59 60 1.808512 CGTTTGTGTACACCTGAGCCA 60.809 52.381 22.91 0.00 0.00 4.75
60 61 0.865769 CGTTTGTGTACACCTGAGCC 59.134 55.000 22.91 4.63 0.00 4.70
61 62 1.260561 CACGTTTGTGTACACCTGAGC 59.739 52.381 22.91 10.08 41.34 4.26
62 63 2.816689 TCACGTTTGTGTACACCTGAG 58.183 47.619 22.91 13.93 46.49 3.35
63 64 2.963548 TCACGTTTGTGTACACCTGA 57.036 45.000 22.91 12.15 46.49 3.86
64 65 4.278858 CAAATCACGTTTGTGTACACCTG 58.721 43.478 22.91 12.04 46.49 4.00
65 66 4.545823 CAAATCACGTTTGTGTACACCT 57.454 40.909 22.91 0.00 46.49 4.00
75 76 3.907894 AATACGGTGCAAATCACGTTT 57.092 38.095 6.90 0.00 46.56 3.60
76 77 3.560503 CAAATACGGTGCAAATCACGTT 58.439 40.909 6.90 0.00 46.56 3.99
77 78 2.667171 GCAAATACGGTGCAAATCACGT 60.667 45.455 0.00 0.00 46.56 4.49
78 79 1.910819 GCAAATACGGTGCAAATCACG 59.089 47.619 0.00 0.00 46.56 4.35
86 87 0.248054 CGGATGTGCAAATACGGTGC 60.248 55.000 14.15 0.00 42.55 5.01
87 88 1.327460 CTCGGATGTGCAAATACGGTG 59.673 52.381 21.38 10.85 34.50 4.94
88 89 1.651987 CTCGGATGTGCAAATACGGT 58.348 50.000 21.38 0.00 34.50 4.83
89 90 0.304705 GCTCGGATGTGCAAATACGG 59.695 55.000 21.38 12.84 34.50 4.02
90 91 0.304705 GGCTCGGATGTGCAAATACG 59.695 55.000 15.86 15.86 36.33 3.06
91 92 1.378531 TGGCTCGGATGTGCAAATAC 58.621 50.000 0.00 0.00 36.33 1.89
92 93 1.742831 GTTGGCTCGGATGTGCAAATA 59.257 47.619 0.00 0.00 36.33 1.40
93 94 0.527565 GTTGGCTCGGATGTGCAAAT 59.472 50.000 0.00 0.00 36.33 2.32
94 95 0.537143 AGTTGGCTCGGATGTGCAAA 60.537 50.000 0.00 0.00 36.33 3.68
95 96 0.537143 AAGTTGGCTCGGATGTGCAA 60.537 50.000 0.00 0.00 36.33 4.08
96 97 0.323302 TAAGTTGGCTCGGATGTGCA 59.677 50.000 0.00 0.00 36.33 4.57
97 98 1.668419 ATAAGTTGGCTCGGATGTGC 58.332 50.000 0.00 0.00 0.00 4.57
98 99 3.009723 ACAATAAGTTGGCTCGGATGTG 58.990 45.455 0.00 0.00 39.70 3.21
99 100 3.350219 ACAATAAGTTGGCTCGGATGT 57.650 42.857 0.00 0.00 39.70 3.06
100 101 5.056480 TGATACAATAAGTTGGCTCGGATG 58.944 41.667 0.00 0.00 39.70 3.51
101 102 5.163301 ACTGATACAATAAGTTGGCTCGGAT 60.163 40.000 7.57 0.00 39.70 4.18
102 103 4.161565 ACTGATACAATAAGTTGGCTCGGA 59.838 41.667 7.57 0.00 39.70 4.55
103 104 4.442706 ACTGATACAATAAGTTGGCTCGG 58.557 43.478 0.00 0.00 39.70 4.63
104 105 7.534085 TTAACTGATACAATAAGTTGGCTCG 57.466 36.000 0.64 0.00 39.70 5.03
105 106 9.722056 CATTTAACTGATACAATAAGTTGGCTC 57.278 33.333 0.64 0.00 39.70 4.70
106 107 9.243105 ACATTTAACTGATACAATAAGTTGGCT 57.757 29.630 0.00 0.00 39.70 4.75
114 115 9.620259 TGTGGCATACATTTAACTGATACAATA 57.380 29.630 0.00 0.00 33.42 1.90
115 116 8.518430 TGTGGCATACATTTAACTGATACAAT 57.482 30.769 0.00 0.00 33.42 2.71
116 117 7.929941 TGTGGCATACATTTAACTGATACAA 57.070 32.000 0.00 0.00 33.42 2.41
117 118 7.609918 ACTTGTGGCATACATTTAACTGATACA 59.390 33.333 0.00 0.00 39.48 2.29
118 119 7.985476 ACTTGTGGCATACATTTAACTGATAC 58.015 34.615 0.00 0.00 39.48 2.24
119 120 8.574251 AACTTGTGGCATACATTTAACTGATA 57.426 30.769 0.00 0.00 39.48 2.15
120 121 7.394359 AGAACTTGTGGCATACATTTAACTGAT 59.606 33.333 0.00 0.00 39.48 2.90
121 122 6.714810 AGAACTTGTGGCATACATTTAACTGA 59.285 34.615 0.00 0.00 39.48 3.41
122 123 6.913170 AGAACTTGTGGCATACATTTAACTG 58.087 36.000 0.00 0.00 39.48 3.16
123 124 7.148239 GCTAGAACTTGTGGCATACATTTAACT 60.148 37.037 0.00 0.00 39.48 2.24
124 125 6.967199 GCTAGAACTTGTGGCATACATTTAAC 59.033 38.462 0.00 0.00 39.48 2.01
125 126 6.657117 TGCTAGAACTTGTGGCATACATTTAA 59.343 34.615 0.00 0.00 39.48 1.52
126 127 6.176896 TGCTAGAACTTGTGGCATACATTTA 58.823 36.000 0.00 0.00 39.48 1.40
127 128 5.009631 TGCTAGAACTTGTGGCATACATTT 58.990 37.500 0.00 0.00 39.48 2.32
128 129 4.588899 TGCTAGAACTTGTGGCATACATT 58.411 39.130 0.00 0.00 39.48 2.71
129 130 4.220693 TGCTAGAACTTGTGGCATACAT 57.779 40.909 0.00 0.00 39.48 2.29
130 131 3.694043 TGCTAGAACTTGTGGCATACA 57.306 42.857 0.00 0.00 37.56 2.29
131 132 4.191544 TGATGCTAGAACTTGTGGCATAC 58.808 43.478 9.39 5.22 42.57 2.39
132 133 4.486125 TGATGCTAGAACTTGTGGCATA 57.514 40.909 9.39 0.00 42.57 3.14
133 134 3.354948 TGATGCTAGAACTTGTGGCAT 57.645 42.857 9.21 9.21 44.73 4.40
134 135 2.857186 TGATGCTAGAACTTGTGGCA 57.143 45.000 0.00 0.00 37.32 4.92
135 136 4.503741 TTTTGATGCTAGAACTTGTGGC 57.496 40.909 0.00 0.00 0.00 5.01
136 137 5.404946 CCATTTTGATGCTAGAACTTGTGG 58.595 41.667 0.00 0.00 0.00 4.17
137 138 4.860907 GCCATTTTGATGCTAGAACTTGTG 59.139 41.667 0.00 0.00 0.00 3.33
138 139 4.082026 GGCCATTTTGATGCTAGAACTTGT 60.082 41.667 0.00 0.00 0.00 3.16
139 140 4.427312 GGCCATTTTGATGCTAGAACTTG 58.573 43.478 0.00 0.00 0.00 3.16
140 141 3.129287 CGGCCATTTTGATGCTAGAACTT 59.871 43.478 2.24 0.00 0.00 2.66
141 142 2.684881 CGGCCATTTTGATGCTAGAACT 59.315 45.455 2.24 0.00 0.00 3.01
142 143 2.423538 ACGGCCATTTTGATGCTAGAAC 59.576 45.455 2.24 0.00 0.00 3.01
143 144 2.722094 ACGGCCATTTTGATGCTAGAA 58.278 42.857 2.24 0.00 0.00 2.10
144 145 2.418368 ACGGCCATTTTGATGCTAGA 57.582 45.000 2.24 0.00 0.00 2.43
145 146 3.181397 CAAACGGCCATTTTGATGCTAG 58.819 45.455 18.18 0.00 36.24 3.42
146 147 2.560542 ACAAACGGCCATTTTGATGCTA 59.439 40.909 26.23 0.00 37.39 3.49
147 148 1.344114 ACAAACGGCCATTTTGATGCT 59.656 42.857 26.23 7.56 37.39 3.79
148 149 1.460359 CACAAACGGCCATTTTGATGC 59.540 47.619 26.23 0.00 37.39 3.91
149 150 2.067766 CCACAAACGGCCATTTTGATG 58.932 47.619 26.23 20.03 37.39 3.07
150 151 2.453983 CCACAAACGGCCATTTTGAT 57.546 45.000 26.23 12.48 37.39 2.57
151 152 3.976339 CCACAAACGGCCATTTTGA 57.024 47.368 26.23 0.00 37.39 2.69
160 161 1.069227 GCTAGAACTTGCCACAAACGG 60.069 52.381 0.00 0.00 0.00 4.44
161 162 1.601903 TGCTAGAACTTGCCACAAACG 59.398 47.619 0.00 0.00 0.00 3.60
162 163 2.287608 GGTGCTAGAACTTGCCACAAAC 60.288 50.000 0.00 0.00 0.00 2.93
163 164 1.953686 GGTGCTAGAACTTGCCACAAA 59.046 47.619 0.00 0.00 0.00 2.83
164 165 1.133945 TGGTGCTAGAACTTGCCACAA 60.134 47.619 0.00 0.00 0.00 3.33
165 166 0.472044 TGGTGCTAGAACTTGCCACA 59.528 50.000 0.00 2.83 0.00 4.17
166 167 0.875059 GTGGTGCTAGAACTTGCCAC 59.125 55.000 0.00 0.00 39.38 5.01
167 168 0.602638 CGTGGTGCTAGAACTTGCCA 60.603 55.000 0.00 0.00 0.00 4.92
168 169 1.298859 CCGTGGTGCTAGAACTTGCC 61.299 60.000 0.00 0.00 0.00 4.52
169 170 1.298859 CCCGTGGTGCTAGAACTTGC 61.299 60.000 0.00 1.72 0.00 4.01
170 171 0.034896 ACCCGTGGTGCTAGAACTTG 59.965 55.000 0.00 0.00 32.98 3.16
171 172 2.448749 ACCCGTGGTGCTAGAACTT 58.551 52.632 0.00 0.00 32.98 2.66
172 173 4.210158 ACCCGTGGTGCTAGAACT 57.790 55.556 0.00 0.00 32.98 3.01
181 182 1.975680 AGAGTCAATTACACCCGTGGT 59.024 47.619 0.00 0.00 35.62 4.16
182 183 2.618053 GAGAGTCAATTACACCCGTGG 58.382 52.381 0.00 0.00 34.19 4.94
183 184 2.094906 TCGAGAGTCAATTACACCCGTG 60.095 50.000 0.00 0.00 0.00 4.94
184 185 2.165167 TCGAGAGTCAATTACACCCGT 58.835 47.619 0.00 0.00 0.00 5.28
185 186 2.933495 TCGAGAGTCAATTACACCCG 57.067 50.000 0.00 0.00 0.00 5.28
186 187 5.934935 TTTTTCGAGAGTCAATTACACCC 57.065 39.130 0.00 0.00 0.00 4.61
187 188 7.955864 GTGTATTTTTCGAGAGTCAATTACACC 59.044 37.037 10.97 0.00 36.43 4.16
188 189 7.955864 GGTGTATTTTTCGAGAGTCAATTACAC 59.044 37.037 12.45 12.45 38.46 2.90
189 190 7.118680 GGGTGTATTTTTCGAGAGTCAATTACA 59.881 37.037 0.00 0.00 0.00 2.41
190 191 7.413767 GGGGTGTATTTTTCGAGAGTCAATTAC 60.414 40.741 0.00 0.00 0.00 1.89
191 192 6.596497 GGGGTGTATTTTTCGAGAGTCAATTA 59.404 38.462 0.00 0.00 0.00 1.40
192 193 5.414765 GGGGTGTATTTTTCGAGAGTCAATT 59.585 40.000 0.00 0.00 0.00 2.32
193 194 4.941873 GGGGTGTATTTTTCGAGAGTCAAT 59.058 41.667 0.00 0.00 0.00 2.57
194 195 4.202377 TGGGGTGTATTTTTCGAGAGTCAA 60.202 41.667 0.00 0.00 0.00 3.18
195 196 3.325425 TGGGGTGTATTTTTCGAGAGTCA 59.675 43.478 0.00 0.00 0.00 3.41
196 197 3.934068 TGGGGTGTATTTTTCGAGAGTC 58.066 45.455 0.00 0.00 0.00 3.36
197 198 4.070009 GTTGGGGTGTATTTTTCGAGAGT 58.930 43.478 0.00 0.00 0.00 3.24
198 199 4.069304 TGTTGGGGTGTATTTTTCGAGAG 58.931 43.478 0.00 0.00 0.00 3.20
199 200 4.088056 TGTTGGGGTGTATTTTTCGAGA 57.912 40.909 0.00 0.00 0.00 4.04
200 201 4.839668 TTGTTGGGGTGTATTTTTCGAG 57.160 40.909 0.00 0.00 0.00 4.04
201 202 4.401519 TGTTTGTTGGGGTGTATTTTTCGA 59.598 37.500 0.00 0.00 0.00 3.71
202 203 4.683832 TGTTTGTTGGGGTGTATTTTTCG 58.316 39.130 0.00 0.00 0.00 3.46
226 227 5.776208 ACCCCGTTATTTTTATCCAACTGTT 59.224 36.000 0.00 0.00 0.00 3.16
232 233 6.095720 GTCATCAACCCCGTTATTTTTATCCA 59.904 38.462 0.00 0.00 0.00 3.41
235 236 6.037830 CGAGTCATCAACCCCGTTATTTTTAT 59.962 38.462 0.00 0.00 0.00 1.40
242 243 0.108520 GCGAGTCATCAACCCCGTTA 60.109 55.000 0.00 0.00 0.00 3.18
245 246 0.953471 TTTGCGAGTCATCAACCCCG 60.953 55.000 0.00 0.00 0.00 5.73
296 299 1.067776 CCCGTTCTAGTCTCACCACAC 60.068 57.143 0.00 0.00 0.00 3.82
310 313 4.120085 CGGAAGGCATACCCGTTC 57.880 61.111 4.24 0.00 38.55 3.95
320 323 0.321298 TAGACCAAGCAACGGAAGGC 60.321 55.000 0.00 0.00 0.00 4.35
345 348 2.093869 GGATTAGCGTACTTGACCACCA 60.094 50.000 0.00 0.00 0.00 4.17
382 385 1.954927 GAAAAGATCCAGGGCTACGG 58.045 55.000 0.00 0.00 0.00 4.02
438 441 3.494332 AGCAAATGAAAAGGACAGCTCT 58.506 40.909 0.00 0.00 0.00 4.09
521 530 1.554042 CGACGTAACTGTGCCACCAC 61.554 60.000 0.00 0.00 42.40 4.16
523 532 2.664436 GCGACGTAACTGTGCCACC 61.664 63.158 0.00 0.00 0.00 4.61
544 553 3.710722 CGAGGAAGCAGGCCCAGT 61.711 66.667 0.00 0.00 0.00 4.00
553 562 0.952984 GGCCATAGCATCGAGGAAGC 60.953 60.000 0.00 0.00 42.56 3.86
554 563 0.394192 TGGCCATAGCATCGAGGAAG 59.606 55.000 0.00 0.00 42.56 3.46
555 564 0.836606 TTGGCCATAGCATCGAGGAA 59.163 50.000 6.09 0.00 42.56 3.36
556 565 0.106708 GTTGGCCATAGCATCGAGGA 59.893 55.000 6.09 0.00 42.56 3.71
557 566 0.179048 TGTTGGCCATAGCATCGAGG 60.179 55.000 6.09 0.00 42.56 4.63
558 567 1.202568 TCTGTTGGCCATAGCATCGAG 60.203 52.381 6.09 0.00 42.56 4.04
559 568 0.829990 TCTGTTGGCCATAGCATCGA 59.170 50.000 6.09 0.00 42.56 3.59
560 569 1.224075 CTCTGTTGGCCATAGCATCG 58.776 55.000 6.09 0.00 42.56 3.84
561 570 0.950116 GCTCTGTTGGCCATAGCATC 59.050 55.000 19.40 6.45 41.59 3.91
562 571 0.549950 AGCTCTGTTGGCCATAGCAT 59.450 50.000 23.71 11.67 43.73 3.79
563 572 0.107508 GAGCTCTGTTGGCCATAGCA 60.108 55.000 23.71 15.53 43.73 3.49
564 573 0.817229 GGAGCTCTGTTGGCCATAGC 60.817 60.000 14.64 13.90 42.12 2.97
565 574 0.531532 CGGAGCTCTGTTGGCCATAG 60.532 60.000 14.84 8.93 0.00 2.23
566 575 0.975556 TCGGAGCTCTGTTGGCCATA 60.976 55.000 21.88 0.00 0.00 2.74
567 576 1.841302 TTCGGAGCTCTGTTGGCCAT 61.841 55.000 21.88 0.00 0.00 4.40
568 577 2.050836 TTTCGGAGCTCTGTTGGCCA 62.051 55.000 21.88 0.00 0.00 5.36
569 578 1.301677 CTTTCGGAGCTCTGTTGGCC 61.302 60.000 21.88 0.00 0.00 5.36
570 579 0.320771 TCTTTCGGAGCTCTGTTGGC 60.321 55.000 21.88 0.00 0.00 4.52
578 587 3.498774 ATTGGCATATCTTTCGGAGCT 57.501 42.857 0.00 0.00 0.00 4.09
653 662 5.185249 TCGAACAAGTATCTTAGTTGAGGCT 59.815 40.000 8.65 0.00 40.68 4.58
709 718 1.167851 TGCAAGGACAAGCATACTGC 58.832 50.000 0.00 0.00 45.46 4.40
772 782 3.181490 ACGCGCTCAGTGACATTATCTTA 60.181 43.478 5.73 0.00 0.00 2.10
776 786 1.135112 TCACGCGCTCAGTGACATTAT 60.135 47.619 5.73 0.00 42.91 1.28
835 845 1.669115 CTGAGTGGTGGTTGCTCGG 60.669 63.158 0.00 0.00 32.32 4.63
873 885 1.000396 AGGCTTGGTTGGATGAGGC 60.000 57.895 0.00 0.00 35.17 4.70
909 939 0.667487 TAGCTGCTGCGTTGAGACAC 60.667 55.000 13.43 0.00 45.42 3.67
911 941 1.136224 GTTTAGCTGCTGCGTTGAGAC 60.136 52.381 13.43 0.00 45.42 3.36
931 961 0.867753 CAGCGAGGTAGCTTAGCGTG 60.868 60.000 14.67 10.81 46.80 5.34
932 962 1.433879 CAGCGAGGTAGCTTAGCGT 59.566 57.895 14.67 4.46 46.80 5.07
933 963 1.946650 GCAGCGAGGTAGCTTAGCG 60.947 63.158 14.67 7.28 46.80 4.26
934 964 0.179097 AAGCAGCGAGGTAGCTTAGC 60.179 55.000 13.31 13.31 46.80 3.09
936 966 4.402056 AATTAAGCAGCGAGGTAGCTTA 57.598 40.909 0.00 0.00 46.80 3.09
937 967 2.990066 ATTAAGCAGCGAGGTAGCTT 57.010 45.000 0.00 13.28 46.80 3.74
939 969 3.718815 AGTAATTAAGCAGCGAGGTAGC 58.281 45.455 0.00 0.00 37.41 3.58
940 970 4.202121 TGGAGTAATTAAGCAGCGAGGTAG 60.202 45.833 0.00 0.00 0.00 3.18
941 971 3.702548 TGGAGTAATTAAGCAGCGAGGTA 59.297 43.478 0.00 0.00 0.00 3.08
942 972 2.500098 TGGAGTAATTAAGCAGCGAGGT 59.500 45.455 0.00 0.00 0.00 3.85
943 973 2.866762 GTGGAGTAATTAAGCAGCGAGG 59.133 50.000 0.00 0.00 0.00 4.63
1538 1583 0.683504 GAACAGGCCCTCCGAGTAGA 60.684 60.000 0.00 0.00 37.47 2.59
1673 1718 3.711704 TGGTGGAACAGAAGAGAGAAACT 59.288 43.478 0.00 0.00 41.80 2.66
1738 1784 4.661993 TTCACAATGAACGAGCACATAC 57.338 40.909 0.00 0.00 30.26 2.39
1779 1825 2.143575 TACAAATGCGCCCTCCCCAA 62.144 55.000 4.18 0.00 0.00 4.12
1923 1969 6.072064 ACGGAAGGAGTAATATCTTATGTCGG 60.072 42.308 0.00 0.00 0.00 4.79
1938 1984 8.979534 AGACTTATATTTAGAAACGGAAGGAGT 58.020 33.333 0.00 0.00 0.00 3.85
1939 1985 9.819267 AAGACTTATATTTAGAAACGGAAGGAG 57.181 33.333 0.00 0.00 0.00 3.69
1968 2014 9.961265 CGTATGTGGTTTATAGTGAAATCTCTA 57.039 33.333 0.00 0.00 0.00 2.43
1969 2015 7.926555 CCGTATGTGGTTTATAGTGAAATCTCT 59.073 37.037 0.00 0.00 0.00 3.10
1970 2016 7.924412 TCCGTATGTGGTTTATAGTGAAATCTC 59.076 37.037 0.00 0.00 0.00 2.75
1971 2017 7.788026 TCCGTATGTGGTTTATAGTGAAATCT 58.212 34.615 0.00 0.00 0.00 2.40
1972 2018 8.495949 CATCCGTATGTGGTTTATAGTGAAATC 58.504 37.037 0.00 0.00 0.00 2.17
1973 2019 7.990886 ACATCCGTATGTGGTTTATAGTGAAAT 59.009 33.333 0.00 0.00 44.79 2.17
1974 2020 7.332557 ACATCCGTATGTGGTTTATAGTGAAA 58.667 34.615 0.00 0.00 44.79 2.69
1975 2021 6.880484 ACATCCGTATGTGGTTTATAGTGAA 58.120 36.000 0.00 0.00 44.79 3.18
1976 2022 6.474140 ACATCCGTATGTGGTTTATAGTGA 57.526 37.500 0.00 0.00 44.79 3.41
1983 2029 7.764443 GCATCTATATACATCCGTATGTGGTTT 59.236 37.037 3.56 0.00 45.99 3.27
1984 2030 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
1985 2031 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
1986 2032 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
1987 2033 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
1992 2038 9.809096 CTCTAAAATGCATCTATATACATCCGT 57.191 33.333 0.00 0.00 0.00 4.69
1993 2039 9.809096 ACTCTAAAATGCATCTATATACATCCG 57.191 33.333 0.00 0.00 0.00 4.18
2014 2060 9.973450 GAGCAAATTGAGTGAATCTATACTCTA 57.027 33.333 0.00 0.00 42.86 2.43
2015 2061 7.930865 GGAGCAAATTGAGTGAATCTATACTCT 59.069 37.037 0.00 0.00 42.86 3.24
2016 2062 7.095857 CGGAGCAAATTGAGTGAATCTATACTC 60.096 40.741 0.00 0.00 42.77 2.59
2017 2063 6.703607 CGGAGCAAATTGAGTGAATCTATACT 59.296 38.462 0.00 0.00 0.00 2.12
2018 2064 6.480320 ACGGAGCAAATTGAGTGAATCTATAC 59.520 38.462 0.00 0.00 0.00 1.47
2019 2065 6.582636 ACGGAGCAAATTGAGTGAATCTATA 58.417 36.000 0.00 0.00 0.00 1.31
2020 2066 5.431765 ACGGAGCAAATTGAGTGAATCTAT 58.568 37.500 0.00 0.00 0.00 1.98
2021 2067 4.832248 ACGGAGCAAATTGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2022 2068 3.679389 ACGGAGCAAATTGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2023 2069 5.065218 ACATACGGAGCAAATTGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2024 2070 4.943705 ACATACGGAGCAAATTGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2025 2071 4.323417 ACATACGGAGCAAATTGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2026 2072 3.937814 ACATACGGAGCAAATTGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2027 2073 5.991328 ATACATACGGAGCAAATTGAGTG 57.009 39.130 0.00 0.00 0.00 3.51
2028 2074 5.527582 GGAATACATACGGAGCAAATTGAGT 59.472 40.000 0.00 0.00 0.00 3.41
2029 2075 5.527214 TGGAATACATACGGAGCAAATTGAG 59.473 40.000 0.00 0.00 0.00 3.02
2030 2076 5.432645 TGGAATACATACGGAGCAAATTGA 58.567 37.500 0.00 0.00 0.00 2.57
2031 2077 5.749596 TGGAATACATACGGAGCAAATTG 57.250 39.130 0.00 0.00 0.00 2.32
2032 2078 7.173218 CACTATGGAATACATACGGAGCAAATT 59.827 37.037 0.00 0.00 41.03 1.82
2033 2079 6.650807 CACTATGGAATACATACGGAGCAAAT 59.349 38.462 0.00 0.00 41.03 2.32
2034 2080 5.989168 CACTATGGAATACATACGGAGCAAA 59.011 40.000 0.00 0.00 41.03 3.68
2035 2081 5.303333 TCACTATGGAATACATACGGAGCAA 59.697 40.000 0.00 0.00 41.03 3.91
2036 2082 4.830600 TCACTATGGAATACATACGGAGCA 59.169 41.667 0.00 0.00 41.03 4.26
2037 2083 5.386958 TCACTATGGAATACATACGGAGC 57.613 43.478 0.00 0.00 41.03 4.70
2038 2084 8.307483 AGATTTCACTATGGAATACATACGGAG 58.693 37.037 0.00 0.00 41.03 4.63
2039 2085 8.190326 AGATTTCACTATGGAATACATACGGA 57.810 34.615 0.00 0.00 41.03 4.69
2040 2086 8.307483 AGAGATTTCACTATGGAATACATACGG 58.693 37.037 0.00 0.00 41.03 4.02
2048 2094 9.606631 GTCTTTGTAGAGATTTCACTATGGAAT 57.393 33.333 0.00 0.00 0.00 3.01
2049 2095 8.816894 AGTCTTTGTAGAGATTTCACTATGGAA 58.183 33.333 0.00 0.00 0.00 3.53
2050 2096 8.367660 AGTCTTTGTAGAGATTTCACTATGGA 57.632 34.615 0.00 0.00 0.00 3.41
2067 2113 9.853177 CCTCCATTCCTAAATATAAGTCTTTGT 57.147 33.333 0.00 0.00 0.00 2.83
2071 2117 9.453830 ACTTCCTCCATTCCTAAATATAAGTCT 57.546 33.333 0.00 0.00 0.00 3.24
2084 2130 9.793259 TGACATAAATTATACTTCCTCCATTCC 57.207 33.333 0.00 0.00 0.00 3.01
2105 2151 6.980397 GTGTCTTTTCTGGTTTCAATTGACAT 59.020 34.615 7.89 0.00 34.10 3.06
2113 2159 6.582677 TTTGAAGTGTCTTTTCTGGTTTCA 57.417 33.333 0.00 0.00 0.00 2.69
2161 2208 0.666577 GCTGTGACGCCGTAAGTTCT 60.667 55.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.