Multiple sequence alignment - TraesCS5A01G328400

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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 TraesCS5A01G328400 chr5A 100.000 3143 0 0 1 3143 537614786 537617928 0.000000e+00 5805.0
1 TraesCS5A01G328400 chr5B 88.059 2730 175 70 201 2881 511851618 511854245 0.000000e+00 3096.0
2 TraesCS5A01G328400 chr5B 92.308 52 3 1 1242 1293 474968798 474968748 4.350000e-09 73.1
3 TraesCS5A01G328400 chr5D 90.146 1786 103 32 702 2442 423972871 423974628 0.000000e+00 2255.0
4 TraesCS5A01G328400 chr5D 90.832 709 30 17 2434 3122 423974666 423975359 0.000000e+00 917.0
5 TraesCS5A01G328400 chr5D 86.380 558 30 21 197 719 423972315 423972861 4.550000e-158 568.0
6 TraesCS5A01G328400 chr4B 74.251 668 122 40 1118 1766 474378599 474379235 5.240000e-58 235.0
7 TraesCS5A01G328400 chrUn 92.308 52 3 1 1242 1293 279044458 279044408 4.350000e-09 73.1
8 TraesCS5A01G328400 chr6D 100.000 31 0 0 1388 1418 84207062 84207092 1.220000e-04 58.4
9 TraesCS5A01G328400 chr6B 100.000 31 0 0 1388 1418 159952205 159952235 1.220000e-04 58.4
10 TraesCS5A01G328400 chr6A 100.000 31 0 0 1388 1418 101429011 101429041 1.220000e-04 58.4


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 TraesCS5A01G328400 chr5A 537614786 537617928 3142 False 5805.000000 5805 100.000000 1 3143 1 chr5A.!!$F1 3142
1 TraesCS5A01G328400 chr5B 511851618 511854245 2627 False 3096.000000 3096 88.059000 201 2881 1 chr5B.!!$F1 2680
2 TraesCS5A01G328400 chr5D 423972315 423975359 3044 False 1246.666667 2255 89.119333 197 3122 3 chr5D.!!$F1 2925
3 TraesCS5A01G328400 chr4B 474378599 474379235 636 False 235.000000 235 74.251000 1118 1766 1 chr4B.!!$F1 648

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
594 631 0.042013 GTACGAGATCGCAGAGACGG 60.042 60.0 1.39 0.0 43.63 4.79 F
978 1057 0.103026 CGATCGACCATCTTGCTCCA 59.897 55.0 10.26 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 1822 0.099082 CAGAAGACGACGAGGTAGGC 59.901 60.0 0.00 0.0 0.0 3.93 R
2335 2486 0.239879 GTGGCGGCTCGATTCAAAAA 59.760 50.0 11.43 0.0 0.0 1.94 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
20 21 3.354089 CAAGACCGCATGAAAACAACT 57.646 42.857 0.00 0.00 0.00 3.16
21 22 3.044986 CAAGACCGCATGAAAACAACTG 58.955 45.455 0.00 0.00 0.00 3.16
22 23 2.297701 AGACCGCATGAAAACAACTGT 58.702 42.857 0.00 0.00 0.00 3.55
23 24 2.687935 AGACCGCATGAAAACAACTGTT 59.312 40.909 0.00 0.00 40.50 3.16
35 36 3.812156 ACAACTGTTTTACCTTTGCCC 57.188 42.857 0.00 0.00 0.00 5.36
36 37 2.432874 ACAACTGTTTTACCTTTGCCCC 59.567 45.455 0.00 0.00 0.00 5.80
37 38 2.432510 CAACTGTTTTACCTTTGCCCCA 59.567 45.455 0.00 0.00 0.00 4.96
38 39 2.753247 ACTGTTTTACCTTTGCCCCAA 58.247 42.857 0.00 0.00 0.00 4.12
39 40 2.432874 ACTGTTTTACCTTTGCCCCAAC 59.567 45.455 0.00 0.00 0.00 3.77
40 41 2.432510 CTGTTTTACCTTTGCCCCAACA 59.567 45.455 0.00 0.00 0.00 3.33
41 42 2.432510 TGTTTTACCTTTGCCCCAACAG 59.567 45.455 0.00 0.00 0.00 3.16
42 43 1.710816 TTTACCTTTGCCCCAACAGG 58.289 50.000 0.00 0.00 32.25 4.00
43 44 0.558712 TTACCTTTGCCCCAACAGGT 59.441 50.000 12.80 12.80 37.96 4.00
44 45 0.178975 TACCTTTGCCCCAACAGGTG 60.179 55.000 15.61 0.00 36.41 4.00
45 46 1.457455 CCTTTGCCCCAACAGGTGT 60.457 57.895 0.00 0.00 0.00 4.16
46 47 1.463553 CCTTTGCCCCAACAGGTGTC 61.464 60.000 0.00 0.00 0.00 3.67
47 48 1.795170 CTTTGCCCCAACAGGTGTCG 61.795 60.000 0.00 0.00 0.00 4.35
48 49 2.559922 TTTGCCCCAACAGGTGTCGT 62.560 55.000 0.00 0.00 0.00 4.34
49 50 1.697082 TTGCCCCAACAGGTGTCGTA 61.697 55.000 0.00 0.00 0.00 3.43
50 51 1.071814 GCCCCAACAGGTGTCGTAA 59.928 57.895 0.00 0.00 0.00 3.18
51 52 0.535553 GCCCCAACAGGTGTCGTAAA 60.536 55.000 0.00 0.00 0.00 2.01
52 53 1.970092 CCCCAACAGGTGTCGTAAAA 58.030 50.000 0.00 0.00 0.00 1.52
53 54 2.510613 CCCCAACAGGTGTCGTAAAAT 58.489 47.619 0.00 0.00 0.00 1.82
54 55 2.227865 CCCCAACAGGTGTCGTAAAATG 59.772 50.000 0.00 0.00 0.00 2.32
55 56 2.227865 CCCAACAGGTGTCGTAAAATGG 59.772 50.000 0.00 0.00 0.00 3.16
56 57 3.142951 CCAACAGGTGTCGTAAAATGGA 58.857 45.455 0.00 0.00 0.00 3.41
57 58 3.058501 CCAACAGGTGTCGTAAAATGGAC 60.059 47.826 0.00 0.00 0.00 4.02
58 59 3.478857 ACAGGTGTCGTAAAATGGACA 57.521 42.857 0.00 0.00 40.63 4.02
64 65 4.061357 TGTCGTAAAATGGACACTCACA 57.939 40.909 0.00 0.00 38.19 3.58
65 66 4.443621 TGTCGTAAAATGGACACTCACAA 58.556 39.130 0.00 0.00 38.19 3.33
66 67 4.509970 TGTCGTAAAATGGACACTCACAAG 59.490 41.667 0.00 0.00 38.19 3.16
67 68 4.748102 GTCGTAAAATGGACACTCACAAGA 59.252 41.667 0.00 0.00 33.41 3.02
68 69 5.235616 GTCGTAAAATGGACACTCACAAGAA 59.764 40.000 0.00 0.00 33.41 2.52
69 70 5.465390 TCGTAAAATGGACACTCACAAGAAG 59.535 40.000 0.00 0.00 0.00 2.85
70 71 5.465390 CGTAAAATGGACACTCACAAGAAGA 59.535 40.000 0.00 0.00 0.00 2.87
71 72 6.147821 CGTAAAATGGACACTCACAAGAAGAT 59.852 38.462 0.00 0.00 0.00 2.40
72 73 7.330946 CGTAAAATGGACACTCACAAGAAGATA 59.669 37.037 0.00 0.00 0.00 1.98
73 74 8.999431 GTAAAATGGACACTCACAAGAAGATAA 58.001 33.333 0.00 0.00 0.00 1.75
74 75 7.440523 AAATGGACACTCACAAGAAGATAAC 57.559 36.000 0.00 0.00 0.00 1.89
75 76 4.894784 TGGACACTCACAAGAAGATAACC 58.105 43.478 0.00 0.00 0.00 2.85
76 77 3.927142 GGACACTCACAAGAAGATAACCG 59.073 47.826 0.00 0.00 0.00 4.44
77 78 4.557205 GACACTCACAAGAAGATAACCGT 58.443 43.478 0.00 0.00 0.00 4.83
78 79 4.307432 ACACTCACAAGAAGATAACCGTG 58.693 43.478 0.00 0.00 0.00 4.94
79 80 4.038763 ACACTCACAAGAAGATAACCGTGA 59.961 41.667 0.00 0.00 32.79 4.35
80 81 5.171476 CACTCACAAGAAGATAACCGTGAT 58.829 41.667 0.00 0.00 33.30 3.06
81 82 5.062683 CACTCACAAGAAGATAACCGTGATG 59.937 44.000 0.00 0.00 33.30 3.07
82 83 5.147330 TCACAAGAAGATAACCGTGATGT 57.853 39.130 0.00 0.00 0.00 3.06
83 84 6.071560 ACTCACAAGAAGATAACCGTGATGTA 60.072 38.462 0.00 0.00 33.30 2.29
84 85 6.873997 TCACAAGAAGATAACCGTGATGTAT 58.126 36.000 0.00 0.00 0.00 2.29
85 86 7.327975 TCACAAGAAGATAACCGTGATGTATT 58.672 34.615 0.00 0.00 0.00 1.89
86 87 7.822334 TCACAAGAAGATAACCGTGATGTATTT 59.178 33.333 0.00 0.00 0.00 1.40
87 88 8.450964 CACAAGAAGATAACCGTGATGTATTTT 58.549 33.333 0.00 0.00 0.00 1.82
88 89 9.661563 ACAAGAAGATAACCGTGATGTATTTTA 57.338 29.630 0.00 0.00 0.00 1.52
90 91 8.888579 AGAAGATAACCGTGATGTATTTTAGG 57.111 34.615 0.00 0.00 0.00 2.69
91 92 8.701895 AGAAGATAACCGTGATGTATTTTAGGA 58.298 33.333 0.00 0.00 0.00 2.94
92 93 8.658499 AAGATAACCGTGATGTATTTTAGGAC 57.342 34.615 0.00 0.00 0.00 3.85
93 94 8.019656 AGATAACCGTGATGTATTTTAGGACT 57.980 34.615 0.00 0.00 0.00 3.85
94 95 9.139734 AGATAACCGTGATGTATTTTAGGACTA 57.860 33.333 0.00 0.00 0.00 2.59
95 96 9.189723 GATAACCGTGATGTATTTTAGGACTAC 57.810 37.037 0.00 0.00 0.00 2.73
96 97 5.585390 ACCGTGATGTATTTTAGGACTACG 58.415 41.667 0.00 0.00 0.00 3.51
97 98 4.980434 CCGTGATGTATTTTAGGACTACGG 59.020 45.833 0.00 0.00 40.84 4.02
98 99 5.450965 CCGTGATGTATTTTAGGACTACGGT 60.451 44.000 0.00 0.00 41.53 4.83
99 100 6.038356 CGTGATGTATTTTAGGACTACGGTT 58.962 40.000 0.00 0.00 0.00 4.44
100 101 6.020121 CGTGATGTATTTTAGGACTACGGTTG 60.020 42.308 0.00 0.00 0.00 3.77
101 102 7.037438 GTGATGTATTTTAGGACTACGGTTGA 58.963 38.462 0.00 0.00 0.00 3.18
102 103 7.546667 GTGATGTATTTTAGGACTACGGTTGAA 59.453 37.037 0.00 0.00 0.00 2.69
103 104 7.546667 TGATGTATTTTAGGACTACGGTTGAAC 59.453 37.037 0.00 0.00 0.00 3.18
104 105 6.757237 TGTATTTTAGGACTACGGTTGAACA 58.243 36.000 0.00 0.00 0.00 3.18
105 106 7.388437 TGTATTTTAGGACTACGGTTGAACAT 58.612 34.615 0.00 0.00 0.00 2.71
106 107 6.737254 ATTTTAGGACTACGGTTGAACATG 57.263 37.500 0.00 0.00 0.00 3.21
107 108 5.471556 TTTAGGACTACGGTTGAACATGA 57.528 39.130 0.00 0.00 0.00 3.07
108 109 5.471556 TTAGGACTACGGTTGAACATGAA 57.528 39.130 0.00 0.00 0.00 2.57
109 110 3.660865 AGGACTACGGTTGAACATGAAC 58.339 45.455 0.00 0.00 0.00 3.18
110 111 3.070446 AGGACTACGGTTGAACATGAACA 59.930 43.478 0.00 0.00 0.00 3.18
111 112 4.000988 GGACTACGGTTGAACATGAACAT 58.999 43.478 0.00 0.00 0.00 2.71
112 113 4.454504 GGACTACGGTTGAACATGAACATT 59.545 41.667 0.00 0.00 0.00 2.71
113 114 5.048991 GGACTACGGTTGAACATGAACATTT 60.049 40.000 0.00 0.00 0.00 2.32
114 115 6.385649 ACTACGGTTGAACATGAACATTTT 57.614 33.333 0.00 0.00 0.00 1.82
115 116 6.205784 ACTACGGTTGAACATGAACATTTTG 58.794 36.000 0.00 0.00 0.00 2.44
116 117 4.367450 ACGGTTGAACATGAACATTTTGG 58.633 39.130 0.00 0.00 0.00 3.28
117 118 4.142049 ACGGTTGAACATGAACATTTTGGT 60.142 37.500 0.00 0.00 0.00 3.67
118 119 4.208873 CGGTTGAACATGAACATTTTGGTG 59.791 41.667 0.00 0.00 0.00 4.17
119 120 5.115480 GGTTGAACATGAACATTTTGGTGT 58.885 37.500 0.00 0.00 0.00 4.16
120 121 5.584251 GGTTGAACATGAACATTTTGGTGTT 59.416 36.000 0.00 0.00 44.53 3.32
121 122 6.456718 GGTTGAACATGAACATTTTGGTGTTG 60.457 38.462 0.00 0.00 42.08 3.33
122 123 4.569966 TGAACATGAACATTTTGGTGTTGC 59.430 37.500 0.00 0.00 42.08 4.17
123 124 4.134379 ACATGAACATTTTGGTGTTGCA 57.866 36.364 0.00 0.00 42.08 4.08
124 125 4.511527 ACATGAACATTTTGGTGTTGCAA 58.488 34.783 0.00 0.00 42.08 4.08
125 126 4.940046 ACATGAACATTTTGGTGTTGCAAA 59.060 33.333 0.00 0.00 42.08 3.68
126 127 5.589452 ACATGAACATTTTGGTGTTGCAAAT 59.411 32.000 0.00 0.00 42.08 2.32
127 128 6.095160 ACATGAACATTTTGGTGTTGCAAATT 59.905 30.769 0.00 0.00 42.08 1.82
128 129 6.506500 TGAACATTTTGGTGTTGCAAATTT 57.493 29.167 0.00 0.00 42.08 1.82
129 130 6.549952 TGAACATTTTGGTGTTGCAAATTTC 58.450 32.000 0.00 0.00 42.08 2.17
130 131 5.154215 ACATTTTGGTGTTGCAAATTTCG 57.846 34.783 0.00 0.00 0.00 3.46
131 132 4.034975 ACATTTTGGTGTTGCAAATTTCGG 59.965 37.500 0.00 0.00 0.00 4.30
132 133 1.576356 TTGGTGTTGCAAATTTCGGC 58.424 45.000 0.00 0.00 0.00 5.54
133 134 0.461548 TGGTGTTGCAAATTTCGGCA 59.538 45.000 0.00 0.00 38.46 5.69
134 135 1.134699 TGGTGTTGCAAATTTCGGCAA 60.135 42.857 10.87 10.87 46.84 4.52
139 140 3.784883 TTGCAAATTTCGGCAATTTCG 57.215 38.095 10.87 0.00 44.41 3.46
140 141 3.018598 TGCAAATTTCGGCAATTTCGA 57.981 38.095 0.96 0.00 42.28 3.71
141 142 3.583806 TGCAAATTTCGGCAATTTCGAT 58.416 36.364 0.96 0.00 42.28 3.59
142 143 3.367327 TGCAAATTTCGGCAATTTCGATG 59.633 39.130 0.96 0.04 42.28 3.84
143 144 3.367630 GCAAATTTCGGCAATTTCGATGT 59.632 39.130 0.00 0.00 42.28 3.06
144 145 4.143137 GCAAATTTCGGCAATTTCGATGTT 60.143 37.500 0.00 0.00 42.28 2.71
145 146 5.307368 CAAATTTCGGCAATTTCGATGTTG 58.693 37.500 6.06 6.06 42.28 3.33
146 147 3.634568 TTTCGGCAATTTCGATGTTGT 57.365 38.095 10.72 0.00 36.49 3.32
147 148 4.750952 TTTCGGCAATTTCGATGTTGTA 57.249 36.364 10.72 0.00 36.49 2.41
148 149 4.750952 TTCGGCAATTTCGATGTTGTAA 57.249 36.364 10.72 3.08 36.49 2.41
149 150 4.750952 TCGGCAATTTCGATGTTGTAAA 57.249 36.364 10.72 0.00 0.00 2.01
150 151 5.303747 TCGGCAATTTCGATGTTGTAAAT 57.696 34.783 10.72 0.00 0.00 1.40
151 152 5.704888 TCGGCAATTTCGATGTTGTAAATT 58.295 33.333 10.72 0.00 34.09 1.82
152 153 6.153067 TCGGCAATTTCGATGTTGTAAATTT 58.847 32.000 10.72 0.00 32.05 1.82
153 154 6.642950 TCGGCAATTTCGATGTTGTAAATTTT 59.357 30.769 0.00 0.00 32.05 1.82
154 155 6.731505 CGGCAATTTCGATGTTGTAAATTTTG 59.268 34.615 0.00 0.00 32.05 2.44
155 156 6.519419 GGCAATTTCGATGTTGTAAATTTTGC 59.481 34.615 0.00 0.00 32.05 3.68
156 157 7.290118 GCAATTTCGATGTTGTAAATTTTGCT 58.710 30.769 0.00 0.00 32.05 3.91
157 158 7.475256 GCAATTTCGATGTTGTAAATTTTGCTC 59.525 33.333 0.00 0.00 32.05 4.26
158 159 7.581011 ATTTCGATGTTGTAAATTTTGCTCC 57.419 32.000 0.00 0.00 0.00 4.70
159 160 5.697473 TCGATGTTGTAAATTTTGCTCCA 57.303 34.783 0.00 0.00 0.00 3.86
160 161 6.078202 TCGATGTTGTAAATTTTGCTCCAA 57.922 33.333 0.00 0.00 0.00 3.53
161 162 6.148948 TCGATGTTGTAAATTTTGCTCCAAG 58.851 36.000 0.00 0.00 0.00 3.61
162 163 5.164061 CGATGTTGTAAATTTTGCTCCAAGC 60.164 40.000 0.00 0.00 42.82 4.01
163 164 4.376146 TGTTGTAAATTTTGCTCCAAGCC 58.624 39.130 0.00 0.00 41.51 4.35
164 165 4.141846 TGTTGTAAATTTTGCTCCAAGCCA 60.142 37.500 0.00 0.00 41.51 4.75
165 166 4.679373 TGTAAATTTTGCTCCAAGCCAA 57.321 36.364 0.00 0.00 41.51 4.52
166 167 4.376146 TGTAAATTTTGCTCCAAGCCAAC 58.624 39.130 0.00 0.00 41.51 3.77
167 168 3.557228 AAATTTTGCTCCAAGCCAACA 57.443 38.095 0.00 0.00 41.51 3.33
168 169 3.775261 AATTTTGCTCCAAGCCAACAT 57.225 38.095 0.00 0.00 41.51 2.71
169 170 3.775261 ATTTTGCTCCAAGCCAACATT 57.225 38.095 0.00 0.00 41.51 2.71
170 171 2.529780 TTTGCTCCAAGCCAACATTG 57.470 45.000 0.00 0.00 41.51 2.82
171 172 1.702182 TTGCTCCAAGCCAACATTGA 58.298 45.000 0.00 0.00 41.51 2.57
172 173 1.927487 TGCTCCAAGCCAACATTGAT 58.073 45.000 0.00 0.00 41.51 2.57
173 174 1.546923 TGCTCCAAGCCAACATTGATG 59.453 47.619 0.00 0.00 41.51 3.07
174 175 1.738030 GCTCCAAGCCAACATTGATGC 60.738 52.381 0.00 0.00 34.48 3.91
175 176 0.896923 TCCAAGCCAACATTGATGCC 59.103 50.000 0.00 0.00 0.00 4.40
176 177 0.108041 CCAAGCCAACATTGATGCCC 60.108 55.000 0.00 0.00 0.00 5.36
177 178 0.899720 CAAGCCAACATTGATGCCCT 59.100 50.000 0.00 0.00 0.00 5.19
178 179 2.101783 CAAGCCAACATTGATGCCCTA 58.898 47.619 0.00 0.00 0.00 3.53
179 180 2.496871 CAAGCCAACATTGATGCCCTAA 59.503 45.455 0.00 0.00 0.00 2.69
180 181 2.818921 AGCCAACATTGATGCCCTAAA 58.181 42.857 0.00 0.00 0.00 1.85
181 182 3.172339 AGCCAACATTGATGCCCTAAAA 58.828 40.909 0.00 0.00 0.00 1.52
182 183 3.776417 AGCCAACATTGATGCCCTAAAAT 59.224 39.130 0.00 0.00 0.00 1.82
183 184 4.961730 AGCCAACATTGATGCCCTAAAATA 59.038 37.500 0.00 0.00 0.00 1.40
184 185 5.069516 AGCCAACATTGATGCCCTAAAATAG 59.930 40.000 0.00 0.00 0.00 1.73
185 186 5.068987 GCCAACATTGATGCCCTAAAATAGA 59.931 40.000 0.00 0.00 0.00 1.98
186 187 6.736794 GCCAACATTGATGCCCTAAAATAGAG 60.737 42.308 0.00 0.00 0.00 2.43
187 188 6.211515 CAACATTGATGCCCTAAAATAGAGC 58.788 40.000 0.00 0.00 0.00 4.09
188 189 5.448654 ACATTGATGCCCTAAAATAGAGCA 58.551 37.500 0.00 0.00 43.78 4.26
212 213 7.283127 GCATCTATTGGATCAGGTTTTGAACTA 59.717 37.037 0.00 0.00 39.77 2.24
218 219 5.183713 TGGATCAGGTTTTGAACTAAGCATG 59.816 40.000 0.00 0.00 39.77 4.06
220 221 3.058293 TCAGGTTTTGAACTAAGCATGCG 60.058 43.478 13.01 0.00 31.34 4.73
237 238 4.580044 GTGATGATGCACGCGCGG 62.580 66.667 35.22 23.25 42.97 6.46
259 260 1.771565 TACAGATACAGGTCACGGGG 58.228 55.000 0.00 0.00 0.00 5.73
260 261 0.976073 ACAGATACAGGTCACGGGGG 60.976 60.000 0.00 0.00 0.00 5.40
270 271 4.838152 CACGGGGGATGTCGGCAG 62.838 72.222 0.00 0.00 0.00 4.85
295 302 1.746220 CTCATCGGAGAGAAAGGACGT 59.254 52.381 0.00 0.00 44.26 4.34
322 329 1.543614 CGCTCGTCAGTGAGATTCTG 58.456 55.000 0.00 0.00 38.28 3.02
393 400 2.432628 GACGACGAACCCTGGCAG 60.433 66.667 7.75 7.75 0.00 4.85
394 401 2.915659 ACGACGAACCCTGGCAGA 60.916 61.111 17.94 0.00 0.00 4.26
395 402 2.125912 CGACGAACCCTGGCAGAG 60.126 66.667 17.94 4.90 0.00 3.35
396 403 2.266055 GACGAACCCTGGCAGAGG 59.734 66.667 17.94 17.54 42.38 3.69
397 404 3.959991 GACGAACCCTGGCAGAGGC 62.960 68.421 17.94 0.00 41.19 4.70
398 405 4.020617 CGAACCCTGGCAGAGGCA 62.021 66.667 17.94 0.00 41.19 4.75
420 427 3.028921 GCAGACTGGCTCCCCTGAG 62.029 68.421 4.26 0.00 41.84 3.35
423 449 0.043940 AGACTGGCTCCCCTGAGATT 59.956 55.000 0.00 0.00 41.42 2.40
426 452 1.138568 CTGGCTCCCCTGAGATTCAT 58.861 55.000 0.00 0.00 41.42 2.57
436 462 4.155709 CCCTGAGATTCATCTAGCTACCA 58.844 47.826 0.00 0.00 37.25 3.25
437 463 4.590647 CCCTGAGATTCATCTAGCTACCAA 59.409 45.833 0.00 0.00 37.25 3.67
438 464 5.248020 CCCTGAGATTCATCTAGCTACCAAT 59.752 44.000 0.00 0.00 37.25 3.16
445 471 0.527600 TCTAGCTACCAATGCGCGTG 60.528 55.000 8.43 2.84 35.28 5.34
558 591 7.801547 AACAAATCATCATTTTAGTCGCTTG 57.198 32.000 0.00 0.00 28.97 4.01
562 599 6.992063 ATCATCATTTTAGTCGCTTGAAGT 57.008 33.333 0.00 0.00 0.00 3.01
563 600 6.801539 TCATCATTTTAGTCGCTTGAAGTT 57.198 33.333 0.00 0.00 0.00 2.66
594 631 0.042013 GTACGAGATCGCAGAGACGG 60.042 60.000 1.39 0.00 43.63 4.79
653 693 5.804639 TGAGTAATCACTTAGCATGTGGTT 58.195 37.500 7.27 7.27 41.11 3.67
818 893 4.699522 GTCCACCACTGTCCCCGC 62.700 72.222 0.00 0.00 0.00 6.13
819 894 4.954118 TCCACCACTGTCCCCGCT 62.954 66.667 0.00 0.00 0.00 5.52
820 895 4.394712 CCACCACTGTCCCCGCTC 62.395 72.222 0.00 0.00 0.00 5.03
821 896 3.314331 CACCACTGTCCCCGCTCT 61.314 66.667 0.00 0.00 0.00 4.09
892 971 3.572539 ATTGCGCGCATACCACCG 61.573 61.111 36.83 0.00 0.00 4.94
903 982 3.944250 TACCACCGTCCCGACCTCC 62.944 68.421 0.00 0.00 0.00 4.30
917 996 1.456518 CCTCCATCGAGCTCCTCCA 60.457 63.158 8.47 0.00 34.49 3.86
918 997 1.739049 CTCCATCGAGCTCCTCCAC 59.261 63.158 8.47 0.00 0.00 4.02
922 1001 1.039785 CATCGAGCTCCTCCACTCCA 61.040 60.000 8.47 0.00 0.00 3.86
930 1009 1.484240 CTCCTCCACTCCACCTGAATC 59.516 57.143 0.00 0.00 0.00 2.52
935 1014 1.561076 CCACTCCACCTGAATCCATCA 59.439 52.381 0.00 0.00 36.38 3.07
936 1015 2.025981 CCACTCCACCTGAATCCATCAA 60.026 50.000 0.00 0.00 37.67 2.57
943 1022 1.753073 CCTGAATCCATCAAGCAACCC 59.247 52.381 0.00 0.00 37.67 4.11
950 1029 2.846206 TCCATCAAGCAACCCTACTCAT 59.154 45.455 0.00 0.00 0.00 2.90
954 1033 2.501723 TCAAGCAACCCTACTCATCTCC 59.498 50.000 0.00 0.00 0.00 3.71
955 1034 2.503356 CAAGCAACCCTACTCATCTCCT 59.497 50.000 0.00 0.00 0.00 3.69
956 1035 2.114616 AGCAACCCTACTCATCTCCTG 58.885 52.381 0.00 0.00 0.00 3.86
957 1036 2.111384 GCAACCCTACTCATCTCCTGA 58.889 52.381 0.00 0.00 0.00 3.86
958 1037 2.703007 GCAACCCTACTCATCTCCTGAT 59.297 50.000 0.00 0.00 32.10 2.90
960 1039 2.870175 ACCCTACTCATCTCCTGATCG 58.130 52.381 0.00 0.00 32.10 3.69
961 1040 2.443632 ACCCTACTCATCTCCTGATCGA 59.556 50.000 0.00 0.00 32.10 3.59
962 1041 3.075283 ACCCTACTCATCTCCTGATCGAT 59.925 47.826 0.00 0.00 32.10 3.59
963 1042 3.694072 CCCTACTCATCTCCTGATCGATC 59.306 52.174 18.72 18.72 32.10 3.69
964 1043 3.373748 CCTACTCATCTCCTGATCGATCG 59.626 52.174 20.03 9.36 32.10 3.69
968 1047 1.882623 CATCTCCTGATCGATCGACCA 59.117 52.381 22.06 17.22 0.00 4.02
969 1048 2.278332 TCTCCTGATCGATCGACCAT 57.722 50.000 22.06 4.32 0.00 3.55
972 1051 2.556189 CTCCTGATCGATCGACCATCTT 59.444 50.000 22.06 2.53 0.00 2.40
973 1052 2.294512 TCCTGATCGATCGACCATCTTG 59.705 50.000 22.06 4.57 0.00 3.02
974 1053 2.057316 CTGATCGATCGACCATCTTGC 58.943 52.381 22.06 3.35 0.00 4.01
975 1054 1.683385 TGATCGATCGACCATCTTGCT 59.317 47.619 22.06 0.00 0.00 3.91
976 1055 2.287849 TGATCGATCGACCATCTTGCTC 60.288 50.000 22.06 11.14 0.00 4.26
977 1056 0.385751 TCGATCGACCATCTTGCTCC 59.614 55.000 15.15 0.00 0.00 4.70
978 1057 0.103026 CGATCGACCATCTTGCTCCA 59.897 55.000 10.26 0.00 0.00 3.86
1042 1123 3.491208 ATGCTCAACATCTCCTGCC 57.509 52.632 0.00 0.00 31.52 4.85
1086 1167 2.034066 CCGGGTGCATTGTCCACT 59.966 61.111 0.00 0.00 33.78 4.00
1429 1510 1.067582 GACGGCTCTAACATCCCCG 59.932 63.158 0.00 0.00 44.19 5.73
1716 1803 2.883828 CGCCACCTCCACCTTCACT 61.884 63.158 0.00 0.00 0.00 3.41
1799 1886 1.735018 CGTCCATAAACCATTCGTGCA 59.265 47.619 0.00 0.00 0.00 4.57
1920 2044 3.281395 TCGTCCGTCGTGAGCACA 61.281 61.111 1.20 0.00 40.80 4.57
1933 2063 3.279116 GCACAAGCACGAGCACCA 61.279 61.111 7.77 0.00 45.49 4.17
1980 2110 2.363925 GTCTCCTACCTGGGCCGT 60.364 66.667 0.00 0.00 36.20 5.68
2046 2188 3.282745 GAGCCAGGCGTCGTCTTCA 62.283 63.158 5.55 0.00 0.00 3.02
2218 2365 1.300080 AATGCAACGCAACAGCCAC 60.300 52.632 0.00 0.00 43.62 5.01
2219 2366 2.014064 AATGCAACGCAACAGCCACA 62.014 50.000 0.00 0.00 43.62 4.17
2223 2370 2.488403 AACGCAACAGCCACATGCA 61.488 52.632 0.00 0.00 44.83 3.96
2252 2399 1.006102 ACAGTTTGACCTCGCCTCG 60.006 57.895 0.00 0.00 0.00 4.63
2309 2460 2.275318 AGCGAGTCTGATTTAGCAAGC 58.725 47.619 0.00 0.00 0.00 4.01
2310 2461 2.002586 GCGAGTCTGATTTAGCAAGCA 58.997 47.619 0.00 0.00 0.00 3.91
2311 2462 2.416547 GCGAGTCTGATTTAGCAAGCAA 59.583 45.455 0.00 0.00 0.00 3.91
2312 2463 3.484886 GCGAGTCTGATTTAGCAAGCAAG 60.485 47.826 0.00 0.00 0.00 4.01
2320 2471 2.138596 TTAGCAAGCAAGCAAGCAAC 57.861 45.000 10.52 0.00 36.85 4.17
2333 2484 0.889186 AAGCAACGCGGTGGAGAAAT 60.889 50.000 27.78 0.00 0.00 2.17
2334 2485 0.889186 AGCAACGCGGTGGAGAAATT 60.889 50.000 27.78 0.00 0.00 1.82
2335 2486 0.039527 GCAACGCGGTGGAGAAATTT 60.040 50.000 27.78 0.00 0.00 1.82
2424 2577 1.767681 CAGATTGGAGGAGAGAAGGGG 59.232 57.143 0.00 0.00 0.00 4.79
2450 2649 3.327404 CAGGTGGGCCGGTACCTT 61.327 66.667 20.12 7.36 44.72 3.50
2478 2682 1.216444 GTCGACCATGAGCTCTGCA 59.784 57.895 16.19 0.00 0.00 4.41
2479 2683 0.805322 GTCGACCATGAGCTCTGCAG 60.805 60.000 16.19 7.63 0.00 4.41
2480 2684 1.521010 CGACCATGAGCTCTGCAGG 60.521 63.158 15.13 13.17 0.00 4.85
2481 2685 1.818785 GACCATGAGCTCTGCAGGC 60.819 63.158 15.13 16.01 0.00 4.85
2504 2708 0.767375 ACACTGCAGAACCCAGATGT 59.233 50.000 23.35 8.73 34.47 3.06
2540 2744 1.732809 TCTCGAGACAGACGTGACATC 59.267 52.381 12.08 0.00 0.00 3.06
2757 2972 1.648116 ATCTTGGCCCAAAGTTGCAT 58.352 45.000 0.00 0.00 0.00 3.96
2767 2982 2.289195 CCAAAGTTGCATGTTGCTCCAT 60.289 45.455 0.75 0.00 45.31 3.41
2769 2984 2.211250 AGTTGCATGTTGCTCCATCT 57.789 45.000 0.75 0.00 45.31 2.90
2881 3096 1.973281 CGGCTCCAAATGTGGCACT 60.973 57.895 19.83 1.19 45.54 4.40
2882 3097 1.885871 GGCTCCAAATGTGGCACTC 59.114 57.895 19.83 0.00 45.54 3.51
2924 3139 1.005037 CGCTACCTCCACAGCAACA 60.005 57.895 0.00 0.00 37.66 3.33
2935 3154 5.247507 TCCACAGCAACATTATAATGCAC 57.752 39.130 22.66 13.36 42.45 4.57
2939 3158 6.267070 CACAGCAACATTATAATGCACATGA 58.733 36.000 22.66 0.00 42.45 3.07
2961 3180 1.974543 CCATGTGGCCCCTTTTGTC 59.025 57.895 0.00 0.00 0.00 3.18
2962 3181 0.831288 CCATGTGGCCCCTTTTGTCA 60.831 55.000 0.00 0.00 0.00 3.58
3076 3295 7.227512 AGTTATATCACCATTACTTGCTTGCTC 59.772 37.037 0.00 0.00 0.00 4.26
3118 3337 3.706373 CCAGTGGGTGTCGAGGGG 61.706 72.222 0.00 0.00 0.00 4.79
3122 3341 4.954118 TGGGTGTCGAGGGGTGCT 62.954 66.667 0.00 0.00 0.00 4.40
3123 3342 3.637273 GGGTGTCGAGGGGTGCTT 61.637 66.667 0.00 0.00 0.00 3.91
3124 3343 2.047179 GGTGTCGAGGGGTGCTTC 60.047 66.667 0.00 0.00 0.00 3.86
3125 3344 2.584391 GGTGTCGAGGGGTGCTTCT 61.584 63.158 0.00 0.00 0.00 2.85
3126 3345 1.255667 GGTGTCGAGGGGTGCTTCTA 61.256 60.000 0.00 0.00 0.00 2.10
3127 3346 0.173708 GTGTCGAGGGGTGCTTCTAG 59.826 60.000 0.00 0.00 0.00 2.43
3128 3347 0.251653 TGTCGAGGGGTGCTTCTAGT 60.252 55.000 0.00 0.00 0.00 2.57
3129 3348 0.896226 GTCGAGGGGTGCTTCTAGTT 59.104 55.000 0.00 0.00 0.00 2.24
3130 3349 1.135053 GTCGAGGGGTGCTTCTAGTTC 60.135 57.143 0.00 0.00 0.00 3.01
3131 3350 1.187087 CGAGGGGTGCTTCTAGTTCT 58.813 55.000 0.00 0.00 0.00 3.01
3132 3351 1.135333 CGAGGGGTGCTTCTAGTTCTC 59.865 57.143 0.00 0.00 0.00 2.87
3133 3352 1.135333 GAGGGGTGCTTCTAGTTCTCG 59.865 57.143 0.00 0.00 0.00 4.04
3134 3353 0.175989 GGGGTGCTTCTAGTTCTCGG 59.824 60.000 0.00 0.00 0.00 4.63
3135 3354 0.460459 GGGTGCTTCTAGTTCTCGGC 60.460 60.000 0.00 0.00 0.00 5.54
3136 3355 0.460459 GGTGCTTCTAGTTCTCGGCC 60.460 60.000 0.00 0.00 0.00 6.13
3137 3356 0.802607 GTGCTTCTAGTTCTCGGCCG 60.803 60.000 22.12 22.12 0.00 6.13
3138 3357 1.248785 TGCTTCTAGTTCTCGGCCGT 61.249 55.000 27.15 7.91 0.00 5.68
3139 3358 0.108756 GCTTCTAGTTCTCGGCCGTT 60.109 55.000 27.15 9.41 0.00 4.44
3140 3359 1.672145 GCTTCTAGTTCTCGGCCGTTT 60.672 52.381 27.15 9.77 0.00 3.60
3141 3360 1.993370 CTTCTAGTTCTCGGCCGTTTG 59.007 52.381 27.15 16.50 0.00 2.93
3142 3361 0.389426 TCTAGTTCTCGGCCGTTTGC 60.389 55.000 27.15 14.24 40.16 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.044986 CAGTTGTTTTCATGCGGTCTTG 58.955 45.455 0.00 0.00 0.00 3.02
2 3 2.297701 ACAGTTGTTTTCATGCGGTCT 58.702 42.857 0.00 0.00 0.00 3.85
3 4 2.774439 ACAGTTGTTTTCATGCGGTC 57.226 45.000 0.00 0.00 0.00 4.79
14 15 3.118555 GGGGCAAAGGTAAAACAGTTGTT 60.119 43.478 0.00 0.00 40.50 2.83
15 16 2.432874 GGGGCAAAGGTAAAACAGTTGT 59.567 45.455 0.00 0.00 0.00 3.32
16 17 2.432510 TGGGGCAAAGGTAAAACAGTTG 59.567 45.455 0.00 0.00 0.00 3.16
17 18 2.753247 TGGGGCAAAGGTAAAACAGTT 58.247 42.857 0.00 0.00 0.00 3.16
18 19 2.432874 GTTGGGGCAAAGGTAAAACAGT 59.567 45.455 0.00 0.00 0.00 3.55
19 20 2.432510 TGTTGGGGCAAAGGTAAAACAG 59.567 45.455 0.00 0.00 0.00 3.16
20 21 2.432510 CTGTTGGGGCAAAGGTAAAACA 59.567 45.455 0.00 0.00 0.00 2.83
21 22 2.224185 CCTGTTGGGGCAAAGGTAAAAC 60.224 50.000 0.00 0.00 0.00 2.43
22 23 2.043227 CCTGTTGGGGCAAAGGTAAAA 58.957 47.619 0.00 0.00 0.00 1.52
23 24 1.062810 ACCTGTTGGGGCAAAGGTAAA 60.063 47.619 0.00 0.00 41.28 2.01
24 25 0.558712 ACCTGTTGGGGCAAAGGTAA 59.441 50.000 0.00 0.00 41.28 2.85
25 26 0.178975 CACCTGTTGGGGCAAAGGTA 60.179 55.000 0.00 0.00 41.14 3.08
26 27 1.457455 CACCTGTTGGGGCAAAGGT 60.457 57.895 0.00 0.00 43.92 3.50
27 28 1.457455 ACACCTGTTGGGGCAAAGG 60.457 57.895 0.00 0.00 41.53 3.11
28 29 1.795170 CGACACCTGTTGGGGCAAAG 61.795 60.000 0.00 0.00 41.53 2.77
29 30 1.826054 CGACACCTGTTGGGGCAAA 60.826 57.895 0.00 0.00 41.53 3.68
30 31 1.697082 TACGACACCTGTTGGGGCAA 61.697 55.000 0.00 0.00 41.53 4.52
31 32 1.697082 TTACGACACCTGTTGGGGCA 61.697 55.000 0.00 0.00 41.53 5.36
32 33 0.535553 TTTACGACACCTGTTGGGGC 60.536 55.000 0.00 0.00 41.53 5.80
33 34 1.970092 TTTTACGACACCTGTTGGGG 58.030 50.000 0.00 0.00 44.04 4.96
34 35 2.227865 CCATTTTACGACACCTGTTGGG 59.772 50.000 0.00 0.00 41.89 4.12
35 36 3.058501 GTCCATTTTACGACACCTGTTGG 60.059 47.826 0.00 0.00 39.83 3.77
36 37 3.562141 TGTCCATTTTACGACACCTGTTG 59.438 43.478 0.00 0.00 34.14 3.33
37 38 3.811083 TGTCCATTTTACGACACCTGTT 58.189 40.909 0.00 0.00 34.14 3.16
38 39 3.478857 TGTCCATTTTACGACACCTGT 57.521 42.857 0.00 0.00 34.14 4.00
43 44 4.061357 TGTGAGTGTCCATTTTACGACA 57.939 40.909 0.00 0.00 36.67 4.35
44 45 4.748102 TCTTGTGAGTGTCCATTTTACGAC 59.252 41.667 0.00 0.00 0.00 4.34
45 46 4.951254 TCTTGTGAGTGTCCATTTTACGA 58.049 39.130 0.00 0.00 0.00 3.43
46 47 5.465390 TCTTCTTGTGAGTGTCCATTTTACG 59.535 40.000 0.00 0.00 0.00 3.18
47 48 6.861065 TCTTCTTGTGAGTGTCCATTTTAC 57.139 37.500 0.00 0.00 0.00 2.01
48 49 8.999431 GTTATCTTCTTGTGAGTGTCCATTTTA 58.001 33.333 0.00 0.00 0.00 1.52
49 50 7.040409 GGTTATCTTCTTGTGAGTGTCCATTTT 60.040 37.037 0.00 0.00 0.00 1.82
50 51 6.431234 GGTTATCTTCTTGTGAGTGTCCATTT 59.569 38.462 0.00 0.00 0.00 2.32
51 52 5.940470 GGTTATCTTCTTGTGAGTGTCCATT 59.060 40.000 0.00 0.00 0.00 3.16
52 53 5.491982 GGTTATCTTCTTGTGAGTGTCCAT 58.508 41.667 0.00 0.00 0.00 3.41
53 54 4.560716 CGGTTATCTTCTTGTGAGTGTCCA 60.561 45.833 0.00 0.00 0.00 4.02
54 55 3.927142 CGGTTATCTTCTTGTGAGTGTCC 59.073 47.826 0.00 0.00 0.00 4.02
55 56 4.386049 CACGGTTATCTTCTTGTGAGTGTC 59.614 45.833 0.00 0.00 0.00 3.67
56 57 4.038763 TCACGGTTATCTTCTTGTGAGTGT 59.961 41.667 0.00 0.00 32.96 3.55
57 58 4.556233 TCACGGTTATCTTCTTGTGAGTG 58.444 43.478 0.00 0.00 32.96 3.51
58 59 4.866508 TCACGGTTATCTTCTTGTGAGT 57.133 40.909 0.00 0.00 32.96 3.41
59 60 5.171476 ACATCACGGTTATCTTCTTGTGAG 58.829 41.667 0.00 0.00 39.43 3.51
60 61 5.147330 ACATCACGGTTATCTTCTTGTGA 57.853 39.130 0.00 0.00 40.24 3.58
61 62 7.539712 AATACATCACGGTTATCTTCTTGTG 57.460 36.000 0.00 0.00 0.00 3.33
62 63 8.561738 AAAATACATCACGGTTATCTTCTTGT 57.438 30.769 0.00 0.00 0.00 3.16
64 65 9.326413 CCTAAAATACATCACGGTTATCTTCTT 57.674 33.333 0.00 0.00 0.00 2.52
65 66 8.701895 TCCTAAAATACATCACGGTTATCTTCT 58.298 33.333 0.00 0.00 0.00 2.85
66 67 8.762426 GTCCTAAAATACATCACGGTTATCTTC 58.238 37.037 0.00 0.00 0.00 2.87
67 68 8.483758 AGTCCTAAAATACATCACGGTTATCTT 58.516 33.333 0.00 0.00 0.00 2.40
68 69 8.019656 AGTCCTAAAATACATCACGGTTATCT 57.980 34.615 0.00 0.00 0.00 1.98
69 70 9.189723 GTAGTCCTAAAATACATCACGGTTATC 57.810 37.037 0.00 0.00 0.00 1.75
70 71 7.864379 CGTAGTCCTAAAATACATCACGGTTAT 59.136 37.037 0.00 0.00 0.00 1.89
71 72 7.195646 CGTAGTCCTAAAATACATCACGGTTA 58.804 38.462 0.00 0.00 0.00 2.85
72 73 6.038356 CGTAGTCCTAAAATACATCACGGTT 58.962 40.000 0.00 0.00 0.00 4.44
73 74 5.450965 CCGTAGTCCTAAAATACATCACGGT 60.451 44.000 0.00 0.00 40.11 4.83
74 75 4.980434 CCGTAGTCCTAAAATACATCACGG 59.020 45.833 0.00 0.00 39.18 4.94
75 76 5.585390 ACCGTAGTCCTAAAATACATCACG 58.415 41.667 0.00 0.00 0.00 4.35
76 77 7.037438 TCAACCGTAGTCCTAAAATACATCAC 58.963 38.462 0.00 0.00 0.00 3.06
77 78 7.172868 TCAACCGTAGTCCTAAAATACATCA 57.827 36.000 0.00 0.00 0.00 3.07
78 79 7.546667 TGTTCAACCGTAGTCCTAAAATACATC 59.453 37.037 0.00 0.00 0.00 3.06
79 80 7.388437 TGTTCAACCGTAGTCCTAAAATACAT 58.612 34.615 0.00 0.00 0.00 2.29
80 81 6.757237 TGTTCAACCGTAGTCCTAAAATACA 58.243 36.000 0.00 0.00 0.00 2.29
81 82 7.546667 TCATGTTCAACCGTAGTCCTAAAATAC 59.453 37.037 0.00 0.00 0.00 1.89
82 83 7.613585 TCATGTTCAACCGTAGTCCTAAAATA 58.386 34.615 0.00 0.00 0.00 1.40
83 84 6.469410 TCATGTTCAACCGTAGTCCTAAAAT 58.531 36.000 0.00 0.00 0.00 1.82
84 85 5.856156 TCATGTTCAACCGTAGTCCTAAAA 58.144 37.500 0.00 0.00 0.00 1.52
85 86 5.471556 TCATGTTCAACCGTAGTCCTAAA 57.528 39.130 0.00 0.00 0.00 1.85
86 87 5.221481 TGTTCATGTTCAACCGTAGTCCTAA 60.221 40.000 0.00 0.00 0.00 2.69
87 88 4.281435 TGTTCATGTTCAACCGTAGTCCTA 59.719 41.667 0.00 0.00 0.00 2.94
88 89 3.070446 TGTTCATGTTCAACCGTAGTCCT 59.930 43.478 0.00 0.00 0.00 3.85
89 90 3.395639 TGTTCATGTTCAACCGTAGTCC 58.604 45.455 0.00 0.00 0.00 3.85
90 91 5.607119 AATGTTCATGTTCAACCGTAGTC 57.393 39.130 0.00 0.00 0.00 2.59
91 92 6.205784 CAAAATGTTCATGTTCAACCGTAGT 58.794 36.000 0.00 0.00 0.00 2.73
92 93 5.629020 CCAAAATGTTCATGTTCAACCGTAG 59.371 40.000 0.00 0.00 0.00 3.51
93 94 5.067936 ACCAAAATGTTCATGTTCAACCGTA 59.932 36.000 0.00 0.00 0.00 4.02
94 95 4.142049 ACCAAAATGTTCATGTTCAACCGT 60.142 37.500 0.00 0.00 0.00 4.83
95 96 4.208873 CACCAAAATGTTCATGTTCAACCG 59.791 41.667 0.00 0.00 0.00 4.44
96 97 5.115480 ACACCAAAATGTTCATGTTCAACC 58.885 37.500 0.00 0.00 0.00 3.77
97 98 6.476896 CAACACCAAAATGTTCATGTTCAAC 58.523 36.000 0.00 0.00 40.89 3.18
98 99 5.064452 GCAACACCAAAATGTTCATGTTCAA 59.936 36.000 0.00 0.00 40.89 2.69
99 100 4.569966 GCAACACCAAAATGTTCATGTTCA 59.430 37.500 0.00 0.00 40.89 3.18
100 101 4.569966 TGCAACACCAAAATGTTCATGTTC 59.430 37.500 0.00 0.00 40.89 3.18
101 102 4.511527 TGCAACACCAAAATGTTCATGTT 58.488 34.783 0.00 0.00 40.89 2.71
102 103 4.134379 TGCAACACCAAAATGTTCATGT 57.866 36.364 0.00 0.00 40.89 3.21
103 104 5.481200 TTTGCAACACCAAAATGTTCATG 57.519 34.783 0.00 0.00 40.89 3.07
104 105 6.696441 AATTTGCAACACCAAAATGTTCAT 57.304 29.167 0.00 0.00 40.89 2.57
105 106 6.506500 AAATTTGCAACACCAAAATGTTCA 57.493 29.167 0.00 0.00 40.89 3.18
106 107 5.676310 CGAAATTTGCAACACCAAAATGTTC 59.324 36.000 0.00 0.00 40.89 3.18
107 108 5.448360 CCGAAATTTGCAACACCAAAATGTT 60.448 36.000 0.00 0.00 43.67 2.71
108 109 4.034975 CCGAAATTTGCAACACCAAAATGT 59.965 37.500 0.00 0.00 38.12 2.71
109 110 4.525686 CCGAAATTTGCAACACCAAAATG 58.474 39.130 0.00 0.00 38.12 2.32
110 111 3.003171 GCCGAAATTTGCAACACCAAAAT 59.997 39.130 0.00 0.00 38.12 1.82
111 112 2.352960 GCCGAAATTTGCAACACCAAAA 59.647 40.909 0.00 0.00 38.12 2.44
112 113 1.936547 GCCGAAATTTGCAACACCAAA 59.063 42.857 0.00 0.00 38.87 3.28
113 114 1.134699 TGCCGAAATTTGCAACACCAA 60.135 42.857 0.00 0.00 33.87 3.67
114 115 0.461548 TGCCGAAATTTGCAACACCA 59.538 45.000 0.00 0.00 33.87 4.17
115 116 1.576356 TTGCCGAAATTTGCAACACC 58.424 45.000 10.87 0.00 42.19 4.16
119 120 3.384668 TCGAAATTGCCGAAATTTGCAA 58.615 36.364 15.74 15.74 46.29 4.08
120 121 3.018598 TCGAAATTGCCGAAATTTGCA 57.981 38.095 11.88 0.00 46.29 4.08
121 122 3.367630 ACATCGAAATTGCCGAAATTTGC 59.632 39.130 11.88 0.00 46.29 3.68
122 123 5.107530 ACAACATCGAAATTGCCGAAATTTG 60.108 36.000 11.88 11.37 46.29 2.32
124 125 4.555262 ACAACATCGAAATTGCCGAAATT 58.445 34.783 10.94 3.18 40.32 1.82
125 126 4.173036 ACAACATCGAAATTGCCGAAAT 57.827 36.364 10.94 0.00 39.62 2.17
126 127 3.634568 ACAACATCGAAATTGCCGAAA 57.365 38.095 10.94 0.00 39.62 3.46
127 128 4.750952 TTACAACATCGAAATTGCCGAA 57.249 36.364 10.94 2.56 39.62 4.30
128 129 4.750952 TTTACAACATCGAAATTGCCGA 57.249 36.364 10.94 5.79 40.53 5.54
129 130 6.388259 AAATTTACAACATCGAAATTGCCG 57.612 33.333 10.94 0.00 34.01 5.69
130 131 6.519419 GCAAAATTTACAACATCGAAATTGCC 59.481 34.615 10.94 0.00 34.01 4.52
131 132 7.290118 AGCAAAATTTACAACATCGAAATTGC 58.710 30.769 10.94 0.00 34.01 3.56
132 133 7.951565 GGAGCAAAATTTACAACATCGAAATTG 59.048 33.333 9.75 9.75 34.01 2.32
133 134 7.655328 TGGAGCAAAATTTACAACATCGAAATT 59.345 29.630 0.00 0.00 34.94 1.82
134 135 7.151308 TGGAGCAAAATTTACAACATCGAAAT 58.849 30.769 0.00 0.00 0.00 2.17
135 136 6.507900 TGGAGCAAAATTTACAACATCGAAA 58.492 32.000 0.00 0.00 0.00 3.46
136 137 6.078202 TGGAGCAAAATTTACAACATCGAA 57.922 33.333 0.00 0.00 0.00 3.71
137 138 5.697473 TGGAGCAAAATTTACAACATCGA 57.303 34.783 0.00 0.00 0.00 3.59
138 139 5.164061 GCTTGGAGCAAAATTTACAACATCG 60.164 40.000 0.00 0.00 41.89 3.84
139 140 5.120674 GGCTTGGAGCAAAATTTACAACATC 59.879 40.000 2.04 0.00 44.75 3.06
140 141 4.996758 GGCTTGGAGCAAAATTTACAACAT 59.003 37.500 2.04 0.00 44.75 2.71
141 142 4.141846 TGGCTTGGAGCAAAATTTACAACA 60.142 37.500 2.04 0.00 44.75 3.33
142 143 4.376146 TGGCTTGGAGCAAAATTTACAAC 58.624 39.130 2.04 0.00 44.75 3.32
143 144 4.679373 TGGCTTGGAGCAAAATTTACAA 57.321 36.364 2.04 0.00 44.75 2.41
144 145 4.141846 TGTTGGCTTGGAGCAAAATTTACA 60.142 37.500 2.04 0.00 44.75 2.41
145 146 4.376146 TGTTGGCTTGGAGCAAAATTTAC 58.624 39.130 2.04 0.00 44.75 2.01
146 147 4.679373 TGTTGGCTTGGAGCAAAATTTA 57.321 36.364 2.04 0.00 44.75 1.40
147 148 3.557228 TGTTGGCTTGGAGCAAAATTT 57.443 38.095 2.04 0.00 44.75 1.82
148 149 3.775261 ATGTTGGCTTGGAGCAAAATT 57.225 38.095 2.04 0.00 44.75 1.82
149 150 3.071312 TCAATGTTGGCTTGGAGCAAAAT 59.929 39.130 2.04 0.00 44.75 1.82
150 151 2.433604 TCAATGTTGGCTTGGAGCAAAA 59.566 40.909 2.04 0.00 44.75 2.44
151 152 2.037901 TCAATGTTGGCTTGGAGCAAA 58.962 42.857 2.04 0.00 44.75 3.68
152 153 1.702182 TCAATGTTGGCTTGGAGCAA 58.298 45.000 2.04 0.00 44.75 3.91
153 154 1.546923 CATCAATGTTGGCTTGGAGCA 59.453 47.619 2.04 0.00 44.75 4.26
154 155 1.738030 GCATCAATGTTGGCTTGGAGC 60.738 52.381 0.00 0.00 41.46 4.70
155 156 1.134907 GGCATCAATGTTGGCTTGGAG 60.135 52.381 10.15 0.00 36.76 3.86
156 157 0.896923 GGCATCAATGTTGGCTTGGA 59.103 50.000 10.15 0.00 36.76 3.53
157 158 0.108041 GGGCATCAATGTTGGCTTGG 60.108 55.000 15.78 0.00 39.44 3.61
158 159 0.899720 AGGGCATCAATGTTGGCTTG 59.100 50.000 15.78 0.00 39.44 4.01
159 160 2.530460 TAGGGCATCAATGTTGGCTT 57.470 45.000 15.78 11.74 39.44 4.35
160 161 2.530460 TTAGGGCATCAATGTTGGCT 57.470 45.000 15.78 6.48 39.44 4.75
161 162 3.608316 TTTTAGGGCATCAATGTTGGC 57.392 42.857 9.08 9.08 38.82 4.52
162 163 6.713762 TCTATTTTAGGGCATCAATGTTGG 57.286 37.500 0.00 0.00 0.00 3.77
174 175 8.324306 TGATCCAATAGATGCTCTATTTTAGGG 58.676 37.037 12.82 11.54 44.77 3.53
175 176 9.381033 CTGATCCAATAGATGCTCTATTTTAGG 57.619 37.037 12.82 11.78 44.77 2.69
176 177 9.381033 CCTGATCCAATAGATGCTCTATTTTAG 57.619 37.037 12.82 7.63 44.77 1.85
177 178 8.884323 ACCTGATCCAATAGATGCTCTATTTTA 58.116 33.333 12.82 7.21 44.77 1.52
178 179 7.753630 ACCTGATCCAATAGATGCTCTATTTT 58.246 34.615 12.82 4.99 44.77 1.82
179 180 7.327064 ACCTGATCCAATAGATGCTCTATTT 57.673 36.000 12.82 3.44 44.77 1.40
181 182 6.949117 AACCTGATCCAATAGATGCTCTAT 57.051 37.500 0.00 1.26 41.19 1.98
182 183 6.753913 AAACCTGATCCAATAGATGCTCTA 57.246 37.500 0.00 0.00 34.42 2.43
183 184 5.643421 AAACCTGATCCAATAGATGCTCT 57.357 39.130 0.00 0.00 34.42 4.09
184 185 5.824624 TCAAAACCTGATCCAATAGATGCTC 59.175 40.000 0.00 0.00 34.42 4.26
185 186 5.759059 TCAAAACCTGATCCAATAGATGCT 58.241 37.500 0.00 0.00 34.42 3.79
186 187 6.096001 AGTTCAAAACCTGATCCAATAGATGC 59.904 38.462 0.00 0.00 34.42 3.91
187 188 7.636150 AGTTCAAAACCTGATCCAATAGATG 57.364 36.000 0.00 0.00 34.42 2.90
188 189 9.401058 CTTAGTTCAAAACCTGATCCAATAGAT 57.599 33.333 0.00 0.00 38.17 1.98
189 190 7.336931 GCTTAGTTCAAAACCTGATCCAATAGA 59.663 37.037 0.00 0.00 32.78 1.98
190 191 7.121168 TGCTTAGTTCAAAACCTGATCCAATAG 59.879 37.037 0.00 0.00 32.78 1.73
191 192 6.945435 TGCTTAGTTCAAAACCTGATCCAATA 59.055 34.615 0.00 0.00 32.78 1.90
192 193 5.774690 TGCTTAGTTCAAAACCTGATCCAAT 59.225 36.000 0.00 0.00 32.78 3.16
193 194 5.136828 TGCTTAGTTCAAAACCTGATCCAA 58.863 37.500 0.00 0.00 32.78 3.53
194 195 4.724399 TGCTTAGTTCAAAACCTGATCCA 58.276 39.130 0.00 0.00 32.78 3.41
195 196 5.644644 CATGCTTAGTTCAAAACCTGATCC 58.355 41.667 0.00 0.00 32.78 3.36
196 197 5.098211 GCATGCTTAGTTCAAAACCTGATC 58.902 41.667 11.37 0.00 32.78 2.92
197 198 4.379813 CGCATGCTTAGTTCAAAACCTGAT 60.380 41.667 17.13 0.00 32.78 2.90
198 199 3.058293 CGCATGCTTAGTTCAAAACCTGA 60.058 43.478 17.13 0.00 0.00 3.86
199 200 3.236816 CGCATGCTTAGTTCAAAACCTG 58.763 45.455 17.13 0.00 0.00 4.00
212 213 0.099968 GTGCATCATCACGCATGCTT 59.900 50.000 17.13 2.67 44.90 3.91
220 221 4.580044 CCGCGCGTGCATCATCAC 62.580 66.667 29.95 0.00 42.97 3.06
237 238 2.545952 CCCGTGACCTGTATCTGTATGC 60.546 54.545 0.00 0.00 0.00 3.14
259 260 4.521062 AGCTCGCTGCCGACATCC 62.521 66.667 0.00 0.00 44.23 3.51
260 261 2.959071 GAGCTCGCTGCCGACATC 60.959 66.667 0.00 0.00 44.23 3.06
270 271 0.101399 TTTCTCTCCGATGAGCTCGC 59.899 55.000 9.64 2.58 46.25 5.03
393 400 2.583520 CCAGTCTGCCTCTGCCTC 59.416 66.667 0.00 0.00 36.33 4.70
394 401 3.715097 GCCAGTCTGCCTCTGCCT 61.715 66.667 0.00 0.00 36.33 4.75
395 402 3.678951 GAGCCAGTCTGCCTCTGCC 62.679 68.421 3.56 0.00 36.33 4.85
396 403 2.125188 GAGCCAGTCTGCCTCTGC 60.125 66.667 3.56 0.00 38.26 4.26
397 404 2.583520 GGAGCCAGTCTGCCTCTG 59.416 66.667 10.46 0.00 0.00 3.35
420 427 3.124297 GCGCATTGGTAGCTAGATGAATC 59.876 47.826 0.30 0.00 0.00 2.52
423 449 1.602920 CGCGCATTGGTAGCTAGATGA 60.603 52.381 8.75 0.00 0.00 2.92
426 452 0.527600 CACGCGCATTGGTAGCTAGA 60.528 55.000 5.73 0.00 0.00 2.43
445 471 2.630592 GAATCTCGGTGGACGGCTCC 62.631 65.000 0.00 0.00 44.45 4.70
558 591 3.976942 TCGTACGTCTTTGCAGTAACTTC 59.023 43.478 16.05 0.00 0.00 3.01
562 599 3.902261 TCTCGTACGTCTTTGCAGTAA 57.098 42.857 16.05 0.00 0.00 2.24
563 600 3.484721 CGATCTCGTACGTCTTTGCAGTA 60.485 47.826 16.05 0.00 34.11 2.74
594 631 6.139638 CGGTTTTTACTCTGTTTTCTTTACGC 59.860 38.462 0.00 0.00 0.00 4.42
653 693 1.250328 CCTGCCAGATTCTTTGTGCA 58.750 50.000 0.00 0.00 0.00 4.57
818 893 1.867233 GAGAGCTAGCGTGAGAGAGAG 59.133 57.143 9.55 0.00 0.00 3.20
819 894 1.484653 AGAGAGCTAGCGTGAGAGAGA 59.515 52.381 9.55 0.00 0.00 3.10
820 895 1.953559 AGAGAGCTAGCGTGAGAGAG 58.046 55.000 9.55 0.00 0.00 3.20
821 896 2.093181 AGAAGAGAGCTAGCGTGAGAGA 60.093 50.000 9.55 0.00 0.00 3.10
892 971 3.121019 CTCGATGGAGGTCGGGAC 58.879 66.667 0.00 0.00 44.72 4.46
903 982 1.039785 TGGAGTGGAGGAGCTCGATG 61.040 60.000 7.83 0.00 32.83 3.84
917 996 2.356535 GCTTGATGGATTCAGGTGGAGT 60.357 50.000 0.00 0.00 35.27 3.85
918 997 2.295885 GCTTGATGGATTCAGGTGGAG 58.704 52.381 0.00 0.00 35.27 3.86
922 1001 2.450476 GGTTGCTTGATGGATTCAGGT 58.550 47.619 0.00 0.00 35.27 4.00
930 1009 2.787473 TGAGTAGGGTTGCTTGATGG 57.213 50.000 0.00 0.00 0.00 3.51
935 1014 2.503356 CAGGAGATGAGTAGGGTTGCTT 59.497 50.000 0.00 0.00 0.00 3.91
936 1015 2.114616 CAGGAGATGAGTAGGGTTGCT 58.885 52.381 0.00 0.00 0.00 3.91
943 1022 4.092821 GTCGATCGATCAGGAGATGAGTAG 59.907 50.000 22.50 4.21 42.53 2.57
950 1029 2.155279 GATGGTCGATCGATCAGGAGA 58.845 52.381 32.26 12.19 38.77 3.71
954 1033 2.057316 GCAAGATGGTCGATCGATCAG 58.943 52.381 32.26 21.05 38.77 2.90
955 1034 1.683385 AGCAAGATGGTCGATCGATCA 59.317 47.619 31.49 31.49 39.80 2.92
956 1035 2.323959 GAGCAAGATGGTCGATCGATC 58.676 52.381 22.50 21.98 35.04 3.69
957 1036 1.000283 GGAGCAAGATGGTCGATCGAT 60.000 52.381 22.50 5.04 45.17 3.59
958 1037 0.385751 GGAGCAAGATGGTCGATCGA 59.614 55.000 15.15 15.15 45.17 3.59
960 1039 2.411904 GATGGAGCAAGATGGTCGATC 58.588 52.381 15.34 15.34 46.80 3.69
961 1040 1.269988 CGATGGAGCAAGATGGTCGAT 60.270 52.381 6.74 6.74 45.17 3.59
962 1041 0.103026 CGATGGAGCAAGATGGTCGA 59.897 55.000 3.75 0.48 45.17 4.20
963 1042 1.493950 GCGATGGAGCAAGATGGTCG 61.494 60.000 3.75 0.00 45.17 4.79
964 1043 1.162800 GGCGATGGAGCAAGATGGTC 61.163 60.000 1.06 1.06 43.63 4.02
968 1047 2.109799 CCGGCGATGGAGCAAGAT 59.890 61.111 9.30 0.00 39.27 2.40
969 1048 4.838152 GCCGGCGATGGAGCAAGA 62.838 66.667 12.58 0.00 39.27 3.02
996 1076 4.036804 GTCGTTGCCGCCATTGCA 62.037 61.111 0.00 0.00 37.32 4.08
997 1077 3.667429 GAGTCGTTGCCGCCATTGC 62.667 63.158 0.00 0.00 0.00 3.56
998 1078 2.480555 GAGTCGTTGCCGCCATTG 59.519 61.111 0.00 0.00 0.00 2.82
1040 1121 1.911471 CCCAGAAAGAGGAGGAGGC 59.089 63.158 0.00 0.00 0.00 4.70
1041 1122 0.620121 AGCCCAGAAAGAGGAGGAGG 60.620 60.000 0.00 0.00 0.00 4.30
1042 1123 0.829990 GAGCCCAGAAAGAGGAGGAG 59.170 60.000 0.00 0.00 0.00 3.69
1073 1154 2.096417 GTGAACGTAGTGGACAATGCAC 60.096 50.000 0.00 0.00 45.00 4.57
1086 1167 0.386476 AGTTGGTCAGCGTGAACGTA 59.614 50.000 4.59 0.00 36.73 3.57
1419 1500 3.004354 ACGGCCACGGGGATGTTA 61.004 61.111 8.67 0.00 46.48 2.41
1689 1776 2.202401 GAGGTGGCGTCGTCGTAC 60.202 66.667 3.66 3.77 39.49 3.67
1735 1822 0.099082 CAGAAGACGACGAGGTAGGC 59.901 60.000 0.00 0.00 0.00 3.93
1799 1886 1.934589 ACGTACGTATGCATGCACAT 58.065 45.000 25.37 11.24 0.00 3.21
1883 1998 1.339438 ACTTGAGGCTGCATCACGATT 60.339 47.619 24.32 3.25 0.00 3.34
1886 2010 1.690283 CGACTTGAGGCTGCATCACG 61.690 60.000 17.37 17.43 0.00 4.35
1892 2016 2.811317 CGGACGACTTGAGGCTGC 60.811 66.667 0.00 0.00 0.00 5.25
2127 2269 1.747898 GCTAGCTAGGACGGAGACAGT 60.748 57.143 22.10 0.00 0.00 3.55
2218 2365 1.153309 TGTCGGCTCCATCTGCATG 60.153 57.895 0.00 0.00 0.00 4.06
2219 2366 1.145598 CTGTCGGCTCCATCTGCAT 59.854 57.895 0.00 0.00 0.00 3.96
2223 2370 0.976641 TCAAACTGTCGGCTCCATCT 59.023 50.000 0.00 0.00 0.00 2.90
2252 2399 1.069258 GATGCTACCACTACGGCCC 59.931 63.158 0.00 0.00 39.03 5.80
2262 2409 8.314751 ACAATAATCTATACAGGTGATGCTACC 58.685 37.037 0.00 0.00 41.17 3.18
2309 2460 2.726912 CACCGCGTTGCTTGCTTG 60.727 61.111 4.92 0.00 0.00 4.01
2310 2461 3.964875 CCACCGCGTTGCTTGCTT 61.965 61.111 4.92 0.00 0.00 3.91
2311 2462 4.927782 TCCACCGCGTTGCTTGCT 62.928 61.111 4.92 0.00 0.00 3.91
2312 2463 4.389576 CTCCACCGCGTTGCTTGC 62.390 66.667 4.92 0.00 0.00 4.01
2335 2486 0.239879 GTGGCGGCTCGATTCAAAAA 59.760 50.000 11.43 0.00 0.00 1.94
2350 2501 4.783621 TGCTGCGATCTGGGTGGC 62.784 66.667 0.00 0.00 0.00 5.01
2397 2550 4.393834 TCTCTCCTCCAATCTGATACGAG 58.606 47.826 0.00 6.84 0.00 4.18
2398 2551 4.439253 TCTCTCCTCCAATCTGATACGA 57.561 45.455 0.00 0.00 0.00 3.43
2399 2552 4.022416 CCTTCTCTCCTCCAATCTGATACG 60.022 50.000 0.00 0.00 0.00 3.06
2446 2645 1.066143 GGTCGACCATGTGATGAAGGT 60.066 52.381 29.75 0.00 37.00 3.50
2481 2685 1.512996 CTGGGTTCTGCAGTGTGCTG 61.513 60.000 14.67 0.00 45.31 4.41
2540 2744 2.088674 GATCCCTCGTGACCCCGATG 62.089 65.000 0.00 0.00 36.08 3.84
2586 2790 0.603569 ACCTGACGGACAAGCAGTAG 59.396 55.000 0.00 0.00 0.00 2.57
2691 2905 3.458189 CGGAGGACACATATGGTTCTTC 58.542 50.000 7.80 8.29 0.00 2.87
2924 3139 4.116782 TGGCCCTCATGTGCATTATAAT 57.883 40.909 0.00 0.00 0.00 1.28
2973 3192 3.944650 TCATGCATGCACTATAACCGTTT 59.055 39.130 25.37 0.00 0.00 3.60
2974 3193 3.540617 TCATGCATGCACTATAACCGTT 58.459 40.909 25.37 0.00 0.00 4.44
2975 3194 3.192541 TCATGCATGCACTATAACCGT 57.807 42.857 25.37 0.00 0.00 4.83
2976 3195 4.550577 TTTCATGCATGCACTATAACCG 57.449 40.909 25.37 4.30 0.00 4.44
2977 3196 6.506147 TGATTTTCATGCATGCACTATAACC 58.494 36.000 25.37 11.16 0.00 2.85
3057 3276 2.076100 CGAGCAAGCAAGTAATGGTGA 58.924 47.619 0.00 0.00 40.33 4.02
3076 3295 4.566759 TGCTCAGTATAACTGCTTAAAGCG 59.433 41.667 10.98 0.00 46.26 4.68
3095 3314 1.961277 CGACACCCACTGGTTGCTC 60.961 63.158 0.00 0.00 44.75 4.26
3118 3337 0.802607 CGGCCGAGAACTAGAAGCAC 60.803 60.000 24.07 0.00 0.00 4.40
3122 3341 1.938016 GCAAACGGCCGAGAACTAGAA 60.938 52.381 35.90 0.00 36.11 2.10
3123 3342 0.389426 GCAAACGGCCGAGAACTAGA 60.389 55.000 35.90 0.00 36.11 2.43
3124 3343 2.079049 GCAAACGGCCGAGAACTAG 58.921 57.895 35.90 14.59 36.11 2.57
3125 3344 4.272100 GCAAACGGCCGAGAACTA 57.728 55.556 35.90 0.00 36.11 2.24


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

AutoCloner maintained by Alex Coulton.