Multiple sequence alignment - TraesCS2A01G051100

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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 TraesCS2A01G051100 chr2A 100.000 2603 0 0 1 2603 19927775 19930377 0.000000e+00 4807.0
1 TraesCS2A01G051100 chr2A 87.691 1048 92 18 761 1793 19913695 19914720 0.000000e+00 1186.0
2 TraesCS2A01G051100 chr2A 87.803 1033 98 18 763 1793 19917982 19918988 0.000000e+00 1184.0
3 TraesCS2A01G051100 chr2A 82.327 894 129 20 720 1603 98456083 98456957 0.000000e+00 749.0
4 TraesCS2A01G051100 chr2A 82.509 869 109 32 734 1597 98578529 98579359 0.000000e+00 723.0
5 TraesCS2A01G051100 chr2A 83.841 656 56 22 1955 2582 19919304 19919937 1.740000e-161 579.0
6 TraesCS2A01G051100 chr2A 86.340 388 32 13 299 668 19912972 19913356 1.120000e-108 403.0
7 TraesCS2A01G051100 chr2A 80.711 197 14 11 483 666 19917730 19917915 5.850000e-27 132.0
8 TraesCS2A01G051100 chrUn 92.955 1320 67 9 854 2150 24365687 24364371 0.000000e+00 1899.0
9 TraesCS2A01G051100 chrUn 89.028 1039 82 19 761 1793 24369733 24368721 0.000000e+00 1258.0
10 TraesCS2A01G051100 chrUn 88.526 950 82 15 772 1707 24377627 24376691 0.000000e+00 1125.0
11 TraesCS2A01G051100 chrUn 96.239 452 15 2 2154 2603 24364334 24363883 0.000000e+00 739.0
12 TraesCS2A01G051100 chrUn 88.265 392 25 10 326 697 24378081 24377691 1.420000e-122 449.0
13 TraesCS2A01G051100 chrUn 78.960 404 44 24 310 697 24366316 24365938 1.200000e-58 237.0
14 TraesCS2A01G051100 chrUn 80.203 197 15 16 483 666 24369983 24369798 2.720000e-25 126.0
15 TraesCS2A01G051100 chrUn 94.737 57 3 0 761 817 24365887 24365831 3.570000e-14 89.8
16 TraesCS2A01G051100 chr2B 90.866 1259 77 13 385 1623 30637667 30636427 0.000000e+00 1653.0
17 TraesCS2A01G051100 chr2B 79.245 371 42 20 318 675 30633591 30633243 2.610000e-55 226.0
18 TraesCS2A01G051100 chr2B 94.915 118 6 0 2147 2264 30626530 30626413 4.420000e-43 185.0
19 TraesCS2A01G051100 chr2B 100.000 34 0 0 761 794 30633187 30633154 2.160000e-06 63.9
20 TraesCS2A01G051100 chr2D 82.759 870 106 33 734 1597 99561079 99561910 0.000000e+00 736.0
21 TraesCS2A01G051100 chr6D 84.667 150 20 2 1965 2114 89515861 89515715 2.090000e-31 147.0
22 TraesCS2A01G051100 chr4B 97.500 40 1 0 2046 2085 400851819 400851858 4.650000e-08 69.4
23 TraesCS2A01G051100 chr4D 100.000 34 0 0 202 235 503749891 503749924 2.160000e-06 63.9
24 TraesCS2A01G051100 chr6A 100.000 33 0 0 203 235 571704944 571704912 7.780000e-06 62.1
25 TraesCS2A01G051100 chr7D 92.683 41 2 1 193 232 451897620 451897660 1.010000e-04 58.4
26 TraesCS2A01G051100 chr5D 88.000 50 4 2 183 231 388431137 388431089 1.010000e-04 58.4
27 TraesCS2A01G051100 chr4A 92.105 38 2 1 193 229 682760219 682760182 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 TraesCS2A01G051100 chr2A 19927775 19930377 2602 False 4807.000000 4807 100.0000 1 2603 1 chr2A.!!$F1 2602
1 TraesCS2A01G051100 chr2A 98456083 98456957 874 False 749.000000 749 82.3270 720 1603 1 chr2A.!!$F2 883
2 TraesCS2A01G051100 chr2A 98578529 98579359 830 False 723.000000 723 82.5090 734 1597 1 chr2A.!!$F3 863
3 TraesCS2A01G051100 chr2A 19912972 19919937 6965 False 696.800000 1186 85.2772 299 2582 5 chr2A.!!$F4 2283
4 TraesCS2A01G051100 chrUn 24376691 24378081 1390 True 787.000000 1125 88.3955 326 1707 2 chrUn.!!$R2 1381
5 TraesCS2A01G051100 chrUn 24363883 24369983 6100 True 724.800000 1899 88.6870 310 2603 6 chrUn.!!$R1 2293
6 TraesCS2A01G051100 chr2B 30633154 30637667 4513 True 647.633333 1653 90.0370 318 1623 3 chr2B.!!$R2 1305
7 TraesCS2A01G051100 chr2D 99561079 99561910 831 False 736.000000 736 82.7590 734 1597 1 chr2D.!!$F1 863

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
603 633 0.039437 CACCTAACACGAGTCGCTGT 60.039 55.0 13.59 13.15 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 11607 0.030101 CAAAACGGGCACGACACATT 59.97 50.0 19.19 0.0 44.6 2.71 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
26 27 9.581099 GGACATTTGAAAAGAAAACAGAAGTAA 57.419 29.630 0.00 0.00 0.00 2.24
28 29 9.072294 ACATTTGAAAAGAAAACAGAAGTAACG 57.928 29.630 0.00 0.00 0.00 3.18
29 30 8.531530 CATTTGAAAAGAAAACAGAAGTAACGG 58.468 33.333 0.00 0.00 0.00 4.44
31 32 7.846644 TGAAAAGAAAACAGAAGTAACGGTA 57.153 32.000 0.00 0.00 0.00 4.02
32 33 7.687445 TGAAAAGAAAACAGAAGTAACGGTAC 58.313 34.615 1.22 1.22 0.00 3.34
58 59 6.892310 GCCTTTGGCTATAAGATTTTTGTG 57.108 37.500 0.73 0.00 46.69 3.33
59 60 5.291858 GCCTTTGGCTATAAGATTTTTGTGC 59.708 40.000 0.73 0.00 46.69 4.57
60 61 6.397272 CCTTTGGCTATAAGATTTTTGTGCA 58.603 36.000 0.00 0.00 0.00 4.57
61 62 7.043565 CCTTTGGCTATAAGATTTTTGTGCAT 58.956 34.615 0.00 0.00 0.00 3.96
62 63 7.010738 CCTTTGGCTATAAGATTTTTGTGCATG 59.989 37.037 0.00 0.00 0.00 4.06
63 64 6.528537 TGGCTATAAGATTTTTGTGCATGT 57.471 33.333 0.00 0.00 0.00 3.21
64 65 6.331845 TGGCTATAAGATTTTTGTGCATGTG 58.668 36.000 0.00 0.00 0.00 3.21
65 66 6.071447 TGGCTATAAGATTTTTGTGCATGTGT 60.071 34.615 0.00 0.00 0.00 3.72
66 67 6.254157 GGCTATAAGATTTTTGTGCATGTGTG 59.746 38.462 0.00 0.00 0.00 3.82
67 68 6.808212 GCTATAAGATTTTTGTGCATGTGTGT 59.192 34.615 0.00 0.00 0.00 3.72
68 69 7.967854 GCTATAAGATTTTTGTGCATGTGTGTA 59.032 33.333 0.00 0.00 0.00 2.90
70 71 8.692110 ATAAGATTTTTGTGCATGTGTGTATG 57.308 30.769 0.00 0.00 0.00 2.39
71 72 6.088016 AGATTTTTGTGCATGTGTGTATGT 57.912 33.333 0.00 0.00 0.00 2.29
72 73 6.514947 AGATTTTTGTGCATGTGTGTATGTT 58.485 32.000 0.00 0.00 0.00 2.71
73 74 5.963140 TTTTTGTGCATGTGTGTATGTTG 57.037 34.783 0.00 0.00 0.00 3.33
74 75 4.645762 TTTGTGCATGTGTGTATGTTGT 57.354 36.364 0.00 0.00 0.00 3.32
75 76 4.645762 TTGTGCATGTGTGTATGTTGTT 57.354 36.364 0.00 0.00 0.00 2.83
76 77 4.645762 TGTGCATGTGTGTATGTTGTTT 57.354 36.364 0.00 0.00 0.00 2.83
77 78 5.003692 TGTGCATGTGTGTATGTTGTTTT 57.996 34.783 0.00 0.00 0.00 2.43
78 79 5.414360 TGTGCATGTGTGTATGTTGTTTTT 58.586 33.333 0.00 0.00 0.00 1.94
99 100 5.961395 TTTATGTTATCGAAACCGAGAGC 57.039 39.130 0.00 0.00 39.64 4.09
100 101 3.520290 ATGTTATCGAAACCGAGAGCA 57.480 42.857 2.00 2.00 41.27 4.26
101 102 3.306917 TGTTATCGAAACCGAGAGCAA 57.693 42.857 0.00 0.00 36.02 3.91
102 103 3.655486 TGTTATCGAAACCGAGAGCAAA 58.345 40.909 0.00 0.00 36.02 3.68
103 104 4.059511 TGTTATCGAAACCGAGAGCAAAA 58.940 39.130 0.00 0.00 36.02 2.44
104 105 4.693566 TGTTATCGAAACCGAGAGCAAAAT 59.306 37.500 0.00 0.00 36.02 1.82
105 106 5.163893 TGTTATCGAAACCGAGAGCAAAATC 60.164 40.000 0.00 0.00 36.02 2.17
106 107 2.073816 TCGAAACCGAGAGCAAAATCC 58.926 47.619 0.00 0.00 0.00 3.01
107 108 1.130561 CGAAACCGAGAGCAAAATCCC 59.869 52.381 0.00 0.00 0.00 3.85
108 109 2.159382 GAAACCGAGAGCAAAATCCCA 58.841 47.619 0.00 0.00 0.00 4.37
109 110 2.286365 AACCGAGAGCAAAATCCCAA 57.714 45.000 0.00 0.00 0.00 4.12
110 111 1.534729 ACCGAGAGCAAAATCCCAAC 58.465 50.000 0.00 0.00 0.00 3.77
111 112 1.202879 ACCGAGAGCAAAATCCCAACA 60.203 47.619 0.00 0.00 0.00 3.33
112 113 1.470098 CCGAGAGCAAAATCCCAACAG 59.530 52.381 0.00 0.00 0.00 3.16
113 114 2.154462 CGAGAGCAAAATCCCAACAGT 58.846 47.619 0.00 0.00 0.00 3.55
114 115 3.334691 CGAGAGCAAAATCCCAACAGTA 58.665 45.455 0.00 0.00 0.00 2.74
115 116 3.372206 CGAGAGCAAAATCCCAACAGTAG 59.628 47.826 0.00 0.00 0.00 2.57
116 117 4.579869 GAGAGCAAAATCCCAACAGTAGA 58.420 43.478 0.00 0.00 0.00 2.59
117 118 4.985538 AGAGCAAAATCCCAACAGTAGAA 58.014 39.130 0.00 0.00 0.00 2.10
118 119 5.574188 AGAGCAAAATCCCAACAGTAGAAT 58.426 37.500 0.00 0.00 0.00 2.40
119 120 6.721318 AGAGCAAAATCCCAACAGTAGAATA 58.279 36.000 0.00 0.00 0.00 1.75
120 121 6.825721 AGAGCAAAATCCCAACAGTAGAATAG 59.174 38.462 0.00 0.00 0.00 1.73
121 122 6.721318 AGCAAAATCCCAACAGTAGAATAGA 58.279 36.000 0.00 0.00 0.00 1.98
122 123 7.175104 AGCAAAATCCCAACAGTAGAATAGAA 58.825 34.615 0.00 0.00 0.00 2.10
123 124 7.836183 AGCAAAATCCCAACAGTAGAATAGAAT 59.164 33.333 0.00 0.00 0.00 2.40
124 125 7.917505 GCAAAATCCCAACAGTAGAATAGAATG 59.082 37.037 0.00 0.00 0.00 2.67
125 126 8.408601 CAAAATCCCAACAGTAGAATAGAATGG 58.591 37.037 0.00 0.00 0.00 3.16
126 127 7.451731 AATCCCAACAGTAGAATAGAATGGA 57.548 36.000 0.00 0.00 0.00 3.41
127 128 6.884472 TCCCAACAGTAGAATAGAATGGAA 57.116 37.500 0.00 0.00 0.00 3.53
128 129 7.265599 TCCCAACAGTAGAATAGAATGGAAA 57.734 36.000 0.00 0.00 0.00 3.13
129 130 7.110155 TCCCAACAGTAGAATAGAATGGAAAC 58.890 38.462 0.00 0.00 0.00 2.78
130 131 6.037172 CCCAACAGTAGAATAGAATGGAAACG 59.963 42.308 0.00 0.00 0.00 3.60
131 132 6.037172 CCAACAGTAGAATAGAATGGAAACGG 59.963 42.308 0.00 0.00 0.00 4.44
132 133 6.295719 ACAGTAGAATAGAATGGAAACGGT 57.704 37.500 0.00 0.00 0.00 4.83
133 134 6.338937 ACAGTAGAATAGAATGGAAACGGTC 58.661 40.000 0.00 0.00 0.00 4.79
134 135 6.154706 ACAGTAGAATAGAATGGAAACGGTCT 59.845 38.462 0.00 0.00 0.00 3.85
135 136 7.341256 ACAGTAGAATAGAATGGAAACGGTCTA 59.659 37.037 0.00 0.00 34.14 2.59
136 137 7.863375 CAGTAGAATAGAATGGAAACGGTCTAG 59.137 40.741 0.00 0.00 33.41 2.43
137 138 5.602628 AGAATAGAATGGAAACGGTCTAGC 58.397 41.667 0.00 0.00 33.41 3.42
138 139 2.295253 AGAATGGAAACGGTCTAGCG 57.705 50.000 0.00 0.00 0.00 4.26
139 140 1.549170 AGAATGGAAACGGTCTAGCGT 59.451 47.619 0.65 0.65 0.00 5.07
140 141 1.925185 GAATGGAAACGGTCTAGCGTC 59.075 52.381 7.75 0.00 0.00 5.19
141 142 1.183549 ATGGAAACGGTCTAGCGTCT 58.816 50.000 7.75 0.00 0.00 4.18
142 143 0.242825 TGGAAACGGTCTAGCGTCTG 59.757 55.000 7.75 0.00 0.00 3.51
143 144 0.243095 GGAAACGGTCTAGCGTCTGT 59.757 55.000 7.75 0.00 0.00 3.41
144 145 1.615502 GAAACGGTCTAGCGTCTGTC 58.384 55.000 7.75 2.97 0.00 3.51
145 146 0.956633 AAACGGTCTAGCGTCTGTCA 59.043 50.000 7.75 0.00 0.00 3.58
146 147 1.174783 AACGGTCTAGCGTCTGTCAT 58.825 50.000 7.75 0.00 0.00 3.06
147 148 0.452184 ACGGTCTAGCGTCTGTCATG 59.548 55.000 0.65 0.00 0.00 3.07
148 149 0.867753 CGGTCTAGCGTCTGTCATGC 60.868 60.000 0.00 0.00 37.27 4.06
149 150 0.173481 GGTCTAGCGTCTGTCATGCA 59.827 55.000 0.00 0.00 39.85 3.96
150 151 1.202463 GGTCTAGCGTCTGTCATGCAT 60.202 52.381 0.00 0.00 39.85 3.96
151 152 1.857217 GTCTAGCGTCTGTCATGCATG 59.143 52.381 21.07 21.07 39.85 4.06
152 153 1.750778 TCTAGCGTCTGTCATGCATGA 59.249 47.619 25.42 25.42 39.85 3.07
153 154 2.363359 TCTAGCGTCTGTCATGCATGAT 59.637 45.455 30.89 16.22 39.85 2.45
154 155 2.034104 AGCGTCTGTCATGCATGATT 57.966 45.000 30.89 9.35 39.85 2.57
155 156 3.183793 AGCGTCTGTCATGCATGATTA 57.816 42.857 30.89 21.28 39.85 1.75
156 157 3.736720 AGCGTCTGTCATGCATGATTAT 58.263 40.909 30.89 11.31 39.85 1.28
157 158 4.886579 AGCGTCTGTCATGCATGATTATA 58.113 39.130 30.89 16.74 39.85 0.98
158 159 5.485620 AGCGTCTGTCATGCATGATTATAT 58.514 37.500 30.89 12.29 39.85 0.86
159 160 5.350640 AGCGTCTGTCATGCATGATTATATG 59.649 40.000 30.89 20.95 39.85 1.78
160 161 5.121298 GCGTCTGTCATGCATGATTATATGT 59.879 40.000 30.89 0.00 39.30 2.29
161 162 6.347969 GCGTCTGTCATGCATGATTATATGTT 60.348 38.462 30.89 0.00 39.30 2.71
162 163 7.148590 GCGTCTGTCATGCATGATTATATGTTA 60.149 37.037 30.89 2.86 39.30 2.41
163 164 8.711457 CGTCTGTCATGCATGATTATATGTTAA 58.289 33.333 30.89 2.31 39.30 2.01
165 166 9.223099 TCTGTCATGCATGATTATATGTTAAGG 57.777 33.333 30.89 9.41 39.30 2.69
166 167 8.922931 TGTCATGCATGATTATATGTTAAGGT 57.077 30.769 30.89 0.00 39.30 3.50
167 168 8.785946 TGTCATGCATGATTATATGTTAAGGTG 58.214 33.333 30.89 0.00 39.30 4.00
168 169 9.002600 GTCATGCATGATTATATGTTAAGGTGA 57.997 33.333 30.89 1.02 39.30 4.02
169 170 9.002600 TCATGCATGATTATATGTTAAGGTGAC 57.997 33.333 25.42 0.00 0.00 3.67
170 171 8.785946 CATGCATGATTATATGTTAAGGTGACA 58.214 33.333 22.59 0.00 0.00 3.58
171 172 8.922931 TGCATGATTATATGTTAAGGTGACAT 57.077 30.769 0.00 0.00 40.59 3.06
172 173 8.785946 TGCATGATTATATGTTAAGGTGACATG 58.214 33.333 0.00 0.00 38.17 3.21
173 174 8.786898 GCATGATTATATGTTAAGGTGACATGT 58.213 33.333 0.00 0.00 38.17 3.21
175 176 8.587952 TGATTATATGTTAAGGTGACATGTCG 57.412 34.615 20.54 0.00 38.17 4.35
176 177 8.417884 TGATTATATGTTAAGGTGACATGTCGA 58.582 33.333 20.54 7.55 38.17 4.20
177 178 7.997107 TTATATGTTAAGGTGACATGTCGAC 57.003 36.000 20.54 17.78 38.17 4.20
178 179 4.537135 ATGTTAAGGTGACATGTCGACT 57.463 40.909 20.54 17.16 36.43 4.18
179 180 5.654603 ATGTTAAGGTGACATGTCGACTA 57.345 39.130 20.54 6.96 36.43 2.59
180 181 5.456548 TGTTAAGGTGACATGTCGACTAA 57.543 39.130 20.54 12.06 0.00 2.24
181 182 5.845103 TGTTAAGGTGACATGTCGACTAAA 58.155 37.500 20.54 9.54 0.00 1.85
182 183 6.282167 TGTTAAGGTGACATGTCGACTAAAA 58.718 36.000 20.54 14.47 0.00 1.52
183 184 6.932400 TGTTAAGGTGACATGTCGACTAAAAT 59.068 34.615 20.54 8.60 0.00 1.82
184 185 8.089597 TGTTAAGGTGACATGTCGACTAAAATA 58.910 33.333 20.54 13.06 0.00 1.40
185 186 8.928733 GTTAAGGTGACATGTCGACTAAAATAA 58.071 33.333 20.54 12.42 0.00 1.40
186 187 6.963049 AGGTGACATGTCGACTAAAATAAC 57.037 37.500 20.54 8.92 0.00 1.89
187 188 6.460781 AGGTGACATGTCGACTAAAATAACA 58.539 36.000 20.54 3.02 0.00 2.41
188 189 6.367969 AGGTGACATGTCGACTAAAATAACAC 59.632 38.462 20.54 13.27 0.00 3.32
189 190 6.146510 GGTGACATGTCGACTAAAATAACACA 59.853 38.462 20.54 0.00 0.00 3.72
190 191 7.007697 GTGACATGTCGACTAAAATAACACAC 58.992 38.462 20.54 4.58 0.00 3.82
191 192 6.926826 TGACATGTCGACTAAAATAACACACT 59.073 34.615 20.54 0.00 0.00 3.55
192 193 7.439955 TGACATGTCGACTAAAATAACACACTT 59.560 33.333 20.54 0.00 0.00 3.16
193 194 7.793902 ACATGTCGACTAAAATAACACACTTC 58.206 34.615 17.92 0.00 0.00 3.01
194 195 6.774354 TGTCGACTAAAATAACACACTTCC 57.226 37.500 17.92 0.00 0.00 3.46
195 196 5.697633 TGTCGACTAAAATAACACACTTCCC 59.302 40.000 17.92 0.00 0.00 3.97
196 197 5.930569 GTCGACTAAAATAACACACTTCCCT 59.069 40.000 8.70 0.00 0.00 4.20
197 198 6.426025 GTCGACTAAAATAACACACTTCCCTT 59.574 38.462 8.70 0.00 0.00 3.95
198 199 7.599998 GTCGACTAAAATAACACACTTCCCTTA 59.400 37.037 8.70 0.00 0.00 2.69
199 200 8.316214 TCGACTAAAATAACACACTTCCCTTAT 58.684 33.333 0.00 0.00 0.00 1.73
200 201 8.943002 CGACTAAAATAACACACTTCCCTTATT 58.057 33.333 0.00 0.00 0.00 1.40
202 203 9.239551 ACTAAAATAACACACTTCCCTTATTCC 57.760 33.333 0.00 0.00 0.00 3.01
203 204 9.238368 CTAAAATAACACACTTCCCTTATTCCA 57.762 33.333 0.00 0.00 0.00 3.53
204 205 8.664669 AAAATAACACACTTCCCTTATTCCAT 57.335 30.769 0.00 0.00 0.00 3.41
205 206 9.762381 AAAATAACACACTTCCCTTATTCCATA 57.238 29.630 0.00 0.00 0.00 2.74
206 207 9.762381 AAATAACACACTTCCCTTATTCCATAA 57.238 29.630 0.00 0.00 0.00 1.90
207 208 9.936329 AATAACACACTTCCCTTATTCCATAAT 57.064 29.630 0.00 0.00 0.00 1.28
217 218 9.802039 TTCCCTTATTCCATAATATAAAAGCGT 57.198 29.630 0.00 0.00 0.00 5.07
218 219 9.802039 TCCCTTATTCCATAATATAAAAGCGTT 57.198 29.630 0.00 0.00 0.00 4.84
254 255 8.857098 AGTGTAGCTTTTATATTATGAGACGGA 58.143 33.333 0.00 0.00 0.00 4.69
255 256 9.130312 GTGTAGCTTTTATATTATGAGACGGAG 57.870 37.037 0.00 0.00 0.00 4.63
256 257 8.304596 TGTAGCTTTTATATTATGAGACGGAGG 58.695 37.037 0.00 0.00 0.00 4.30
257 258 6.702329 AGCTTTTATATTATGAGACGGAGGG 58.298 40.000 0.00 0.00 0.00 4.30
258 259 6.497259 AGCTTTTATATTATGAGACGGAGGGA 59.503 38.462 0.00 0.00 0.00 4.20
259 260 6.590677 GCTTTTATATTATGAGACGGAGGGAC 59.409 42.308 0.00 0.00 0.00 4.46
261 262 8.945195 TTTTATATTATGAGACGGAGGGACTA 57.055 34.615 0.00 0.00 41.55 2.59
262 263 9.543231 TTTTATATTATGAGACGGAGGGACTAT 57.457 33.333 0.00 0.00 41.55 2.12
263 264 9.543231 TTTATATTATGAGACGGAGGGACTATT 57.457 33.333 0.00 0.00 41.55 1.73
264 265 9.543231 TTATATTATGAGACGGAGGGACTATTT 57.457 33.333 0.00 0.00 41.55 1.40
266 267 9.716556 ATATTATGAGACGGAGGGACTATTTAT 57.283 33.333 0.00 0.00 41.55 1.40
267 268 5.986501 ATGAGACGGAGGGACTATTTATC 57.013 43.478 0.00 0.00 41.55 1.75
268 269 4.800023 TGAGACGGAGGGACTATTTATCA 58.200 43.478 0.00 0.00 41.55 2.15
269 270 5.394738 TGAGACGGAGGGACTATTTATCAT 58.605 41.667 0.00 0.00 41.55 2.45
270 271 5.243954 TGAGACGGAGGGACTATTTATCATG 59.756 44.000 0.00 0.00 41.55 3.07
271 272 5.148502 AGACGGAGGGACTATTTATCATGT 58.851 41.667 0.00 0.00 41.55 3.21
272 273 5.244178 AGACGGAGGGACTATTTATCATGTC 59.756 44.000 0.00 0.00 41.55 3.06
273 274 4.022242 ACGGAGGGACTATTTATCATGTCG 60.022 45.833 0.00 0.00 41.55 4.35
274 275 4.217767 CGGAGGGACTATTTATCATGTCGA 59.782 45.833 0.00 0.00 41.55 4.20
275 276 5.620205 CGGAGGGACTATTTATCATGTCGAG 60.620 48.000 0.00 0.00 41.55 4.04
276 277 5.140747 AGGGACTATTTATCATGTCGAGC 57.859 43.478 0.00 0.00 36.02 5.03
277 278 3.921021 GGGACTATTTATCATGTCGAGCG 59.079 47.826 0.00 0.00 0.00 5.03
278 279 4.321008 GGGACTATTTATCATGTCGAGCGA 60.321 45.833 0.00 0.00 0.00 4.93
279 280 5.220381 GGACTATTTATCATGTCGAGCGAA 58.780 41.667 0.00 0.00 0.00 4.70
280 281 5.690409 GGACTATTTATCATGTCGAGCGAAA 59.310 40.000 0.00 0.00 0.00 3.46
281 282 6.366332 GGACTATTTATCATGTCGAGCGAAAT 59.634 38.462 0.00 0.00 0.00 2.17
282 283 7.541091 GGACTATTTATCATGTCGAGCGAAATA 59.459 37.037 0.00 0.00 0.00 1.40
283 284 8.454293 ACTATTTATCATGTCGAGCGAAATAG 57.546 34.615 12.80 12.80 38.78 1.73
284 285 8.082852 ACTATTTATCATGTCGAGCGAAATAGT 58.917 33.333 13.67 13.67 39.79 2.12
285 286 7.715265 ATTTATCATGTCGAGCGAAATAGTT 57.285 32.000 0.00 0.00 0.00 2.24
286 287 7.534085 TTTATCATGTCGAGCGAAATAGTTT 57.466 32.000 0.00 0.00 0.00 2.66
287 288 8.637281 TTTATCATGTCGAGCGAAATAGTTTA 57.363 30.769 0.00 0.00 0.00 2.01
288 289 8.812147 TTATCATGTCGAGCGAAATAGTTTAT 57.188 30.769 0.00 0.00 0.00 1.40
289 290 6.510746 TCATGTCGAGCGAAATAGTTTATG 57.489 37.500 0.00 0.00 0.00 1.90
290 291 5.462068 TCATGTCGAGCGAAATAGTTTATGG 59.538 40.000 0.00 0.00 0.00 2.74
291 292 3.554324 TGTCGAGCGAAATAGTTTATGGC 59.446 43.478 0.00 0.00 0.00 4.40
292 293 3.554324 GTCGAGCGAAATAGTTTATGGCA 59.446 43.478 0.00 0.00 0.00 4.92
293 294 3.802139 TCGAGCGAAATAGTTTATGGCAG 59.198 43.478 0.00 0.00 0.00 4.85
294 295 3.059597 CGAGCGAAATAGTTTATGGCAGG 60.060 47.826 0.00 0.00 0.00 4.85
295 296 3.877508 GAGCGAAATAGTTTATGGCAGGT 59.122 43.478 0.00 0.00 0.00 4.00
296 297 5.031066 AGCGAAATAGTTTATGGCAGGTA 57.969 39.130 0.00 0.00 0.00 3.08
297 298 5.621193 AGCGAAATAGTTTATGGCAGGTAT 58.379 37.500 0.00 0.00 0.00 2.73
298 299 6.765403 AGCGAAATAGTTTATGGCAGGTATA 58.235 36.000 0.00 0.00 0.00 1.47
299 300 6.649557 AGCGAAATAGTTTATGGCAGGTATAC 59.350 38.462 0.00 0.00 0.00 1.47
300 301 6.425721 GCGAAATAGTTTATGGCAGGTATACA 59.574 38.462 5.01 0.00 0.00 2.29
301 302 7.360101 GCGAAATAGTTTATGGCAGGTATACAG 60.360 40.741 5.01 0.00 0.00 2.74
302 303 7.870954 CGAAATAGTTTATGGCAGGTATACAGA 59.129 37.037 5.01 0.00 0.00 3.41
303 304 9.726438 GAAATAGTTTATGGCAGGTATACAGAT 57.274 33.333 5.01 0.00 0.00 2.90
304 305 9.507329 AAATAGTTTATGGCAGGTATACAGATG 57.493 33.333 5.01 1.65 0.00 2.90
305 306 5.308825 AGTTTATGGCAGGTATACAGATGC 58.691 41.667 15.02 15.02 37.95 3.91
306 307 5.072329 AGTTTATGGCAGGTATACAGATGCT 59.928 40.000 19.88 9.17 38.71 3.79
307 308 3.692257 ATGGCAGGTATACAGATGCTC 57.308 47.619 19.88 13.45 38.71 4.26
308 309 2.682594 TGGCAGGTATACAGATGCTCT 58.317 47.619 19.88 0.00 38.71 4.09
319 320 2.937469 AGATGCTCTGTCGTCTGAAG 57.063 50.000 0.00 0.00 31.54 3.02
320 321 2.166829 AGATGCTCTGTCGTCTGAAGT 58.833 47.619 0.00 0.00 31.54 3.01
321 322 3.348119 AGATGCTCTGTCGTCTGAAGTA 58.652 45.455 0.00 0.00 31.54 2.24
322 323 3.951037 AGATGCTCTGTCGTCTGAAGTAT 59.049 43.478 0.00 0.00 31.54 2.12
323 324 4.400884 AGATGCTCTGTCGTCTGAAGTATT 59.599 41.667 0.00 0.00 31.54 1.89
324 325 5.590663 AGATGCTCTGTCGTCTGAAGTATTA 59.409 40.000 0.00 0.00 31.54 0.98
325 326 5.836821 TGCTCTGTCGTCTGAAGTATTAT 57.163 39.130 0.00 0.00 0.00 1.28
326 327 6.208988 TGCTCTGTCGTCTGAAGTATTATT 57.791 37.500 0.00 0.00 0.00 1.40
327 328 6.631016 TGCTCTGTCGTCTGAAGTATTATTT 58.369 36.000 0.00 0.00 0.00 1.40
328 329 6.531594 TGCTCTGTCGTCTGAAGTATTATTTG 59.468 38.462 0.00 0.00 0.00 2.32
333 334 3.247648 CGTCTGAAGTATTATTTGCCCCG 59.752 47.826 0.00 0.00 0.00 5.73
343 344 1.337118 ATTTGCCCCGTGTCAAATGT 58.663 45.000 5.56 0.00 40.27 2.71
374 375 0.899253 CCATGGTTGGCATGTGACCA 60.899 55.000 10.96 10.96 46.57 4.02
420 424 2.732763 TGCCATGCATTGCCTTAACTA 58.267 42.857 19.17 0.00 31.71 2.24
427 431 3.756434 TGCATTGCCTTAACTAGTTGGAC 59.244 43.478 18.56 8.48 0.00 4.02
444 449 3.815809 TGGACAGGAACGAAAACAATCT 58.184 40.909 0.00 0.00 0.00 2.40
449 454 7.494625 TGGACAGGAACGAAAACAATCTATATC 59.505 37.037 0.00 0.00 0.00 1.63
450 455 7.306632 GGACAGGAACGAAAACAATCTATATCG 60.307 40.741 0.00 0.00 36.45 2.92
488 505 2.906354 GTACCAACGATGCCTTCTGAT 58.094 47.619 0.00 0.00 0.00 2.90
512 529 1.202758 TGCGTCCATTTGAGTGAACCT 60.203 47.619 0.00 0.00 0.00 3.50
603 633 0.039437 CACCTAACACGAGTCGCTGT 60.039 55.000 13.59 13.15 0.00 4.40
604 634 0.240411 ACCTAACACGAGTCGCTGTC 59.760 55.000 13.59 0.00 0.00 3.51
688 984 5.649395 TGTTACGTACTTGTGTAGGAGCTAT 59.351 40.000 0.00 0.00 37.79 2.97
707 1003 2.036958 TCCACCGCAGATTTGGTATG 57.963 50.000 0.00 0.00 36.50 2.39
715 1011 3.544048 CGCAGATTTGGTATGCTACGTTG 60.544 47.826 0.00 0.00 42.82 4.10
716 1012 3.242739 GCAGATTTGGTATGCTACGTTGG 60.243 47.826 0.00 0.00 41.77 3.77
717 1013 4.188462 CAGATTTGGTATGCTACGTTGGA 58.812 43.478 0.00 0.00 0.00 3.53
718 1014 4.271049 CAGATTTGGTATGCTACGTTGGAG 59.729 45.833 0.00 0.00 0.00 3.86
722 1018 1.068741 GGTATGCTACGTTGGAGGAGG 59.931 57.143 0.00 0.00 0.00 4.30
740 1036 1.520787 GTACCCACCGGCGAATCAG 60.521 63.158 9.30 0.00 0.00 2.90
887 1229 6.422100 CGTCTATAAATAGCATGCACAAGTCT 59.578 38.462 21.98 0.00 0.00 3.24
993 1350 3.753272 ACGCTCAGTAATCTGTTGCATTT 59.247 39.130 0.00 0.00 41.91 2.32
1016 1373 2.437359 GATGCAAGGCCTCGCAGT 60.437 61.111 25.04 12.22 42.37 4.40
1068 1425 1.973812 GGTGTTTCTGCTGGGCTCC 60.974 63.158 0.00 0.00 0.00 4.70
1071 1431 3.952508 TTTCTGCTGGGCTCCGCA 61.953 61.111 1.65 1.65 33.65 5.69
1180 1540 1.810441 AACGGCGTCAACAACACGA 60.810 52.632 15.17 0.00 39.75 4.35
1181 1541 1.360194 AACGGCGTCAACAACACGAA 61.360 50.000 15.17 0.00 39.75 3.85
1368 1728 1.905637 TCTACGACAAGCAGGAGTCA 58.094 50.000 0.00 0.00 34.48 3.41
1476 5808 2.035940 AAGACGCGGGACCTCTCT 59.964 61.111 12.47 0.00 0.00 3.10
1512 5844 2.802667 CGACTTCTTCATGGCGCGG 61.803 63.158 8.83 0.00 0.00 6.46
1599 5931 2.306341 AGCTCTACGAGTGCTACGTA 57.694 50.000 8.88 0.00 42.55 3.57
1700 6035 5.106712 TGCTTTCGATTTATCTTGGTGTGTC 60.107 40.000 0.00 0.00 0.00 3.67
2080 11161 5.163824 GGGATATGTCATATCGTGTGCATTG 60.164 44.000 21.35 0.00 41.99 2.82
2297 11411 6.202516 ACCAATATTGACCACGGTTTATTG 57.797 37.500 17.23 14.47 32.23 1.90
2356 11470 5.504665 CGAAATTTCAAACTGAGACTGTGCT 60.505 40.000 17.99 0.00 0.00 4.40
2510 11635 1.728068 GTGCCCGTTTTGGTTGTTTT 58.272 45.000 0.00 0.00 35.15 2.43
2511 11636 1.395262 GTGCCCGTTTTGGTTGTTTTG 59.605 47.619 0.00 0.00 35.15 2.44
2594 11719 3.862877 ACATGCAAGACCCATATAGCA 57.137 42.857 0.00 0.00 36.34 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.581099 TTACTTCTGTTTTCTTTTCAAATGTCC 57.419 29.630 0.00 0.00 0.00 4.02
3 4 8.531530 CCGTTACTTCTGTTTTCTTTTCAAATG 58.468 33.333 0.00 0.00 0.00 2.32
5 6 7.595604 ACCGTTACTTCTGTTTTCTTTTCAAA 58.404 30.769 0.00 0.00 0.00 2.69
7 8 6.746745 ACCGTTACTTCTGTTTTCTTTTCA 57.253 33.333 0.00 0.00 0.00 2.69
9 10 6.534793 TCGTACCGTTACTTCTGTTTTCTTTT 59.465 34.615 0.00 0.00 0.00 2.27
10 11 6.042143 TCGTACCGTTACTTCTGTTTTCTTT 58.958 36.000 0.00 0.00 0.00 2.52
11 12 5.591099 TCGTACCGTTACTTCTGTTTTCTT 58.409 37.500 0.00 0.00 0.00 2.52
12 13 5.186996 TCGTACCGTTACTTCTGTTTTCT 57.813 39.130 0.00 0.00 0.00 2.52
13 14 4.143452 GCTCGTACCGTTACTTCTGTTTTC 60.143 45.833 0.00 0.00 0.00 2.29
14 15 3.737774 GCTCGTACCGTTACTTCTGTTTT 59.262 43.478 0.00 0.00 0.00 2.43
15 16 3.311966 GCTCGTACCGTTACTTCTGTTT 58.688 45.455 0.00 0.00 0.00 2.83
16 17 2.352127 GGCTCGTACCGTTACTTCTGTT 60.352 50.000 0.00 0.00 0.00 3.16
17 18 1.200948 GGCTCGTACCGTTACTTCTGT 59.799 52.381 0.00 0.00 0.00 3.41
18 19 1.471684 AGGCTCGTACCGTTACTTCTG 59.528 52.381 0.00 0.00 33.69 3.02
19 20 1.831580 AGGCTCGTACCGTTACTTCT 58.168 50.000 0.00 0.00 33.69 2.85
20 21 2.643933 AAGGCTCGTACCGTTACTTC 57.356 50.000 0.00 0.00 33.69 3.01
22 23 1.067354 CCAAAGGCTCGTACCGTTACT 60.067 52.381 0.00 0.00 29.70 2.24
25 26 1.670083 GCCAAAGGCTCGTACCGTT 60.670 57.895 0.00 0.00 46.69 4.44
26 27 2.047560 GCCAAAGGCTCGTACCGT 60.048 61.111 0.00 0.00 46.69 4.83
36 37 6.397272 TGCACAAAAATCTTATAGCCAAAGG 58.603 36.000 0.00 0.00 0.00 3.11
37 38 7.546667 ACATGCACAAAAATCTTATAGCCAAAG 59.453 33.333 0.00 0.00 0.00 2.77
38 39 7.331440 CACATGCACAAAAATCTTATAGCCAAA 59.669 33.333 0.00 0.00 0.00 3.28
39 40 6.812656 CACATGCACAAAAATCTTATAGCCAA 59.187 34.615 0.00 0.00 0.00 4.52
40 41 6.071447 ACACATGCACAAAAATCTTATAGCCA 60.071 34.615 0.00 0.00 0.00 4.75
41 42 6.254157 CACACATGCACAAAAATCTTATAGCC 59.746 38.462 0.00 0.00 0.00 3.93
42 43 6.808212 ACACACATGCACAAAAATCTTATAGC 59.192 34.615 0.00 0.00 0.00 2.97
44 45 9.786105 CATACACACATGCACAAAAATCTTATA 57.214 29.630 0.00 0.00 0.00 0.98
45 46 8.306038 ACATACACACATGCACAAAAATCTTAT 58.694 29.630 0.00 0.00 0.00 1.73
46 47 7.656412 ACATACACACATGCACAAAAATCTTA 58.344 30.769 0.00 0.00 0.00 2.10
47 48 6.514947 ACATACACACATGCACAAAAATCTT 58.485 32.000 0.00 0.00 0.00 2.40
48 49 6.088016 ACATACACACATGCACAAAAATCT 57.912 33.333 0.00 0.00 0.00 2.40
49 50 6.200665 ACAACATACACACATGCACAAAAATC 59.799 34.615 0.00 0.00 0.00 2.17
50 51 6.047870 ACAACATACACACATGCACAAAAAT 58.952 32.000 0.00 0.00 0.00 1.82
51 52 5.414360 ACAACATACACACATGCACAAAAA 58.586 33.333 0.00 0.00 0.00 1.94
52 53 5.003692 ACAACATACACACATGCACAAAA 57.996 34.783 0.00 0.00 0.00 2.44
53 54 4.645762 ACAACATACACACATGCACAAA 57.354 36.364 0.00 0.00 0.00 2.83
54 55 4.645762 AACAACATACACACATGCACAA 57.354 36.364 0.00 0.00 0.00 3.33
55 56 4.645762 AAACAACATACACACATGCACA 57.354 36.364 0.00 0.00 0.00 4.57
56 57 5.964887 AAAAACAACATACACACATGCAC 57.035 34.783 0.00 0.00 0.00 4.57
75 76 6.369340 TGCTCTCGGTTTCGATAACATAAAAA 59.631 34.615 10.99 0.00 45.04 1.94
76 77 5.870433 TGCTCTCGGTTTCGATAACATAAAA 59.130 36.000 10.99 0.00 45.04 1.52
77 78 5.412640 TGCTCTCGGTTTCGATAACATAAA 58.587 37.500 10.99 0.00 45.04 1.40
78 79 5.001237 TGCTCTCGGTTTCGATAACATAA 57.999 39.130 10.99 0.00 45.04 1.90
79 80 4.642445 TGCTCTCGGTTTCGATAACATA 57.358 40.909 10.99 0.86 45.04 2.29
80 81 3.520290 TGCTCTCGGTTTCGATAACAT 57.480 42.857 10.99 0.00 45.04 2.71
81 82 3.306917 TTGCTCTCGGTTTCGATAACA 57.693 42.857 10.99 0.00 45.04 2.41
82 83 4.657075 TTTTGCTCTCGGTTTCGATAAC 57.343 40.909 0.00 0.00 45.04 1.89
83 84 4.331717 GGATTTTGCTCTCGGTTTCGATAA 59.668 41.667 0.00 0.00 45.04 1.75
84 85 3.869246 GGATTTTGCTCTCGGTTTCGATA 59.131 43.478 0.00 0.00 45.04 2.92
85 86 2.678336 GGATTTTGCTCTCGGTTTCGAT 59.322 45.455 0.00 0.00 45.04 3.59
86 87 2.073816 GGATTTTGCTCTCGGTTTCGA 58.926 47.619 0.00 0.00 43.86 3.71
87 88 1.130561 GGGATTTTGCTCTCGGTTTCG 59.869 52.381 0.00 0.00 37.82 3.46
88 89 2.159382 TGGGATTTTGCTCTCGGTTTC 58.841 47.619 0.00 0.00 0.00 2.78
89 90 2.286365 TGGGATTTTGCTCTCGGTTT 57.714 45.000 0.00 0.00 0.00 3.27
90 91 1.886542 GTTGGGATTTTGCTCTCGGTT 59.113 47.619 0.00 0.00 0.00 4.44
91 92 1.202879 TGTTGGGATTTTGCTCTCGGT 60.203 47.619 0.00 0.00 0.00 4.69
92 93 1.470098 CTGTTGGGATTTTGCTCTCGG 59.530 52.381 0.00 0.00 0.00 4.63
93 94 2.154462 ACTGTTGGGATTTTGCTCTCG 58.846 47.619 0.00 0.00 0.00 4.04
94 95 4.579869 TCTACTGTTGGGATTTTGCTCTC 58.420 43.478 0.00 0.00 0.00 3.20
95 96 4.640771 TCTACTGTTGGGATTTTGCTCT 57.359 40.909 0.00 0.00 0.00 4.09
96 97 5.904362 ATTCTACTGTTGGGATTTTGCTC 57.096 39.130 0.00 0.00 0.00 4.26
97 98 6.721318 TCTATTCTACTGTTGGGATTTTGCT 58.279 36.000 0.00 0.00 0.00 3.91
98 99 7.391148 TTCTATTCTACTGTTGGGATTTTGC 57.609 36.000 0.00 0.00 0.00 3.68
99 100 8.408601 CCATTCTATTCTACTGTTGGGATTTTG 58.591 37.037 0.00 0.00 0.00 2.44
100 101 8.336235 TCCATTCTATTCTACTGTTGGGATTTT 58.664 33.333 0.00 0.00 0.00 1.82
101 102 7.872138 TCCATTCTATTCTACTGTTGGGATTT 58.128 34.615 0.00 0.00 0.00 2.17
102 103 7.451731 TCCATTCTATTCTACTGTTGGGATT 57.548 36.000 0.00 0.00 0.00 3.01
103 104 7.451731 TTCCATTCTATTCTACTGTTGGGAT 57.548 36.000 0.00 0.00 0.00 3.85
104 105 6.884472 TTCCATTCTATTCTACTGTTGGGA 57.116 37.500 0.00 0.00 0.00 4.37
105 106 6.037172 CGTTTCCATTCTATTCTACTGTTGGG 59.963 42.308 0.00 0.00 0.00 4.12
106 107 6.037172 CCGTTTCCATTCTATTCTACTGTTGG 59.963 42.308 0.00 0.00 0.00 3.77
107 108 6.594159 ACCGTTTCCATTCTATTCTACTGTTG 59.406 38.462 0.00 0.00 0.00 3.33
108 109 6.708285 ACCGTTTCCATTCTATTCTACTGTT 58.292 36.000 0.00 0.00 0.00 3.16
109 110 6.154706 AGACCGTTTCCATTCTATTCTACTGT 59.845 38.462 0.00 0.00 0.00 3.55
110 111 6.574350 AGACCGTTTCCATTCTATTCTACTG 58.426 40.000 0.00 0.00 0.00 2.74
111 112 6.793505 AGACCGTTTCCATTCTATTCTACT 57.206 37.500 0.00 0.00 0.00 2.57
112 113 6.641723 GCTAGACCGTTTCCATTCTATTCTAC 59.358 42.308 0.00 0.00 0.00 2.59
113 114 6.514541 CGCTAGACCGTTTCCATTCTATTCTA 60.515 42.308 0.00 0.00 0.00 2.10
114 115 5.602628 GCTAGACCGTTTCCATTCTATTCT 58.397 41.667 0.00 0.00 0.00 2.40
115 116 4.444720 CGCTAGACCGTTTCCATTCTATTC 59.555 45.833 0.00 0.00 0.00 1.75
116 117 4.142004 ACGCTAGACCGTTTCCATTCTATT 60.142 41.667 0.00 0.00 38.47 1.73
117 118 3.383825 ACGCTAGACCGTTTCCATTCTAT 59.616 43.478 0.00 0.00 38.47 1.98
118 119 2.756760 ACGCTAGACCGTTTCCATTCTA 59.243 45.455 0.00 0.00 38.47 2.10
119 120 1.549170 ACGCTAGACCGTTTCCATTCT 59.451 47.619 0.00 0.00 38.47 2.40
120 121 1.925185 GACGCTAGACCGTTTCCATTC 59.075 52.381 0.00 0.00 42.24 2.67
121 122 1.549170 AGACGCTAGACCGTTTCCATT 59.451 47.619 0.00 0.00 42.24 3.16
122 123 1.135083 CAGACGCTAGACCGTTTCCAT 60.135 52.381 0.00 0.00 42.24 3.41
123 124 0.242825 CAGACGCTAGACCGTTTCCA 59.757 55.000 0.00 0.00 42.24 3.53
124 125 0.243095 ACAGACGCTAGACCGTTTCC 59.757 55.000 0.00 0.00 42.24 3.13
125 126 1.068748 TGACAGACGCTAGACCGTTTC 60.069 52.381 0.00 0.00 42.24 2.78
126 127 0.956633 TGACAGACGCTAGACCGTTT 59.043 50.000 0.00 0.00 42.24 3.60
127 128 1.135373 CATGACAGACGCTAGACCGTT 60.135 52.381 0.00 0.00 42.24 4.44
128 129 0.452184 CATGACAGACGCTAGACCGT 59.548 55.000 0.00 0.00 45.30 4.83
129 130 0.867753 GCATGACAGACGCTAGACCG 60.868 60.000 0.00 0.00 0.00 4.79
130 131 0.173481 TGCATGACAGACGCTAGACC 59.827 55.000 0.00 0.00 0.00 3.85
131 132 1.857217 CATGCATGACAGACGCTAGAC 59.143 52.381 22.59 0.00 0.00 2.59
132 133 1.750778 TCATGCATGACAGACGCTAGA 59.249 47.619 25.42 0.00 0.00 2.43
133 134 2.214387 TCATGCATGACAGACGCTAG 57.786 50.000 25.42 0.00 0.00 3.42
134 135 2.896745 ATCATGCATGACAGACGCTA 57.103 45.000 30.92 6.46 40.03 4.26
135 136 2.034104 AATCATGCATGACAGACGCT 57.966 45.000 30.92 11.19 40.03 5.07
136 137 5.121298 ACATATAATCATGCATGACAGACGC 59.879 40.000 30.92 0.00 40.03 5.19
137 138 6.716898 ACATATAATCATGCATGACAGACG 57.283 37.500 30.92 19.07 40.03 4.18
139 140 9.223099 CCTTAACATATAATCATGCATGACAGA 57.777 33.333 30.92 18.96 40.03 3.41
140 141 9.006839 ACCTTAACATATAATCATGCATGACAG 57.993 33.333 30.92 18.00 40.03 3.51
141 142 8.785946 CACCTTAACATATAATCATGCATGACA 58.214 33.333 30.92 21.43 40.03 3.58
142 143 9.002600 TCACCTTAACATATAATCATGCATGAC 57.997 33.333 30.92 0.00 40.03 3.06
143 144 9.002600 GTCACCTTAACATATAATCATGCATGA 57.997 33.333 30.47 30.47 41.70 3.07
144 145 8.785946 TGTCACCTTAACATATAATCATGCATG 58.214 33.333 21.07 21.07 0.00 4.06
145 146 8.922931 TGTCACCTTAACATATAATCATGCAT 57.077 30.769 0.00 0.00 0.00 3.96
146 147 8.785946 CATGTCACCTTAACATATAATCATGCA 58.214 33.333 0.00 0.00 35.62 3.96
147 148 8.786898 ACATGTCACCTTAACATATAATCATGC 58.213 33.333 0.00 0.00 35.62 4.06
149 150 9.208022 CGACATGTCACCTTAACATATAATCAT 57.792 33.333 24.93 0.00 35.62 2.45
150 151 8.417884 TCGACATGTCACCTTAACATATAATCA 58.582 33.333 24.93 0.00 35.62 2.57
151 152 8.700644 GTCGACATGTCACCTTAACATATAATC 58.299 37.037 24.93 0.00 35.62 1.75
152 153 8.421784 AGTCGACATGTCACCTTAACATATAAT 58.578 33.333 24.93 0.76 35.62 1.28
153 154 7.778083 AGTCGACATGTCACCTTAACATATAA 58.222 34.615 24.93 0.00 35.62 0.98
154 155 7.342769 AGTCGACATGTCACCTTAACATATA 57.657 36.000 24.93 0.00 35.62 0.86
155 156 6.222038 AGTCGACATGTCACCTTAACATAT 57.778 37.500 24.93 1.98 35.62 1.78
156 157 5.654603 AGTCGACATGTCACCTTAACATA 57.345 39.130 24.93 0.00 35.62 2.29
157 158 4.537135 AGTCGACATGTCACCTTAACAT 57.463 40.909 24.93 3.21 37.85 2.71
158 159 5.456548 TTAGTCGACATGTCACCTTAACA 57.543 39.130 24.93 2.77 0.00 2.41
159 160 6.774354 TTTTAGTCGACATGTCACCTTAAC 57.226 37.500 24.93 12.11 0.00 2.01
160 161 8.928733 GTTATTTTAGTCGACATGTCACCTTAA 58.071 33.333 24.93 15.56 0.00 1.85
161 162 8.089597 TGTTATTTTAGTCGACATGTCACCTTA 58.910 33.333 24.93 10.83 0.00 2.69
162 163 6.932400 TGTTATTTTAGTCGACATGTCACCTT 59.068 34.615 24.93 9.97 0.00 3.50
163 164 6.367969 GTGTTATTTTAGTCGACATGTCACCT 59.632 38.462 24.93 19.98 0.00 4.00
164 165 6.146510 TGTGTTATTTTAGTCGACATGTCACC 59.853 38.462 24.93 14.19 0.00 4.02
165 166 7.007697 GTGTGTTATTTTAGTCGACATGTCAC 58.992 38.462 24.93 19.92 0.00 3.67
166 167 6.926826 AGTGTGTTATTTTAGTCGACATGTCA 59.073 34.615 24.93 9.94 0.00 3.58
167 168 7.347508 AGTGTGTTATTTTAGTCGACATGTC 57.652 36.000 19.50 16.21 0.00 3.06
168 169 7.095355 GGAAGTGTGTTATTTTAGTCGACATGT 60.095 37.037 19.50 0.00 0.00 3.21
169 170 7.234384 GGAAGTGTGTTATTTTAGTCGACATG 58.766 38.462 19.50 0.00 0.00 3.21
170 171 6.370718 GGGAAGTGTGTTATTTTAGTCGACAT 59.629 38.462 19.50 4.76 0.00 3.06
171 172 5.697633 GGGAAGTGTGTTATTTTAGTCGACA 59.302 40.000 19.50 0.48 0.00 4.35
172 173 5.930569 AGGGAAGTGTGTTATTTTAGTCGAC 59.069 40.000 7.70 7.70 0.00 4.20
173 174 6.105397 AGGGAAGTGTGTTATTTTAGTCGA 57.895 37.500 0.00 0.00 0.00 4.20
174 175 6.796705 AAGGGAAGTGTGTTATTTTAGTCG 57.203 37.500 0.00 0.00 0.00 4.18
176 177 9.239551 GGAATAAGGGAAGTGTGTTATTTTAGT 57.760 33.333 0.00 0.00 0.00 2.24
177 178 9.238368 TGGAATAAGGGAAGTGTGTTATTTTAG 57.762 33.333 0.00 0.00 0.00 1.85
178 179 9.762381 ATGGAATAAGGGAAGTGTGTTATTTTA 57.238 29.630 0.00 0.00 0.00 1.52
179 180 8.664669 ATGGAATAAGGGAAGTGTGTTATTTT 57.335 30.769 0.00 0.00 0.00 1.82
180 181 9.762381 TTATGGAATAAGGGAAGTGTGTTATTT 57.238 29.630 0.00 0.00 32.95 1.40
181 182 9.936329 ATTATGGAATAAGGGAAGTGTGTTATT 57.064 29.630 0.00 0.00 42.97 1.40
191 192 9.802039 ACGCTTTTATATTATGGAATAAGGGAA 57.198 29.630 0.00 0.00 42.97 3.97
192 193 9.802039 AACGCTTTTATATTATGGAATAAGGGA 57.198 29.630 0.00 0.00 42.97 4.20
228 229 8.857098 TCCGTCTCATAATATAAAAGCTACACT 58.143 33.333 0.00 0.00 0.00 3.55
229 230 9.130312 CTCCGTCTCATAATATAAAAGCTACAC 57.870 37.037 0.00 0.00 0.00 2.90
230 231 8.304596 CCTCCGTCTCATAATATAAAAGCTACA 58.695 37.037 0.00 0.00 0.00 2.74
231 232 7.760340 CCCTCCGTCTCATAATATAAAAGCTAC 59.240 40.741 0.00 0.00 0.00 3.58
232 233 7.672660 TCCCTCCGTCTCATAATATAAAAGCTA 59.327 37.037 0.00 0.00 0.00 3.32
233 234 6.497259 TCCCTCCGTCTCATAATATAAAAGCT 59.503 38.462 0.00 0.00 0.00 3.74
234 235 6.590677 GTCCCTCCGTCTCATAATATAAAAGC 59.409 42.308 0.00 0.00 0.00 3.51
235 236 7.897864 AGTCCCTCCGTCTCATAATATAAAAG 58.102 38.462 0.00 0.00 0.00 2.27
236 237 7.850935 AGTCCCTCCGTCTCATAATATAAAA 57.149 36.000 0.00 0.00 0.00 1.52
237 238 9.543231 AATAGTCCCTCCGTCTCATAATATAAA 57.457 33.333 0.00 0.00 0.00 1.40
238 239 9.543231 AAATAGTCCCTCCGTCTCATAATATAA 57.457 33.333 0.00 0.00 0.00 0.98
240 241 9.716556 ATAAATAGTCCCTCCGTCTCATAATAT 57.283 33.333 0.00 0.00 0.00 1.28
241 242 9.186837 GATAAATAGTCCCTCCGTCTCATAATA 57.813 37.037 0.00 0.00 0.00 0.98
242 243 7.674348 TGATAAATAGTCCCTCCGTCTCATAAT 59.326 37.037 0.00 0.00 0.00 1.28
243 244 7.008332 TGATAAATAGTCCCTCCGTCTCATAA 58.992 38.462 0.00 0.00 0.00 1.90
244 245 6.549242 TGATAAATAGTCCCTCCGTCTCATA 58.451 40.000 0.00 0.00 0.00 2.15
245 246 5.394738 TGATAAATAGTCCCTCCGTCTCAT 58.605 41.667 0.00 0.00 0.00 2.90
246 247 4.800023 TGATAAATAGTCCCTCCGTCTCA 58.200 43.478 0.00 0.00 0.00 3.27
247 248 5.244178 ACATGATAAATAGTCCCTCCGTCTC 59.756 44.000 0.00 0.00 0.00 3.36
248 249 5.148502 ACATGATAAATAGTCCCTCCGTCT 58.851 41.667 0.00 0.00 0.00 4.18
249 250 5.470047 ACATGATAAATAGTCCCTCCGTC 57.530 43.478 0.00 0.00 0.00 4.79
250 251 4.022242 CGACATGATAAATAGTCCCTCCGT 60.022 45.833 0.00 0.00 0.00 4.69
251 252 4.217767 TCGACATGATAAATAGTCCCTCCG 59.782 45.833 0.00 0.00 0.00 4.63
252 253 5.715070 CTCGACATGATAAATAGTCCCTCC 58.285 45.833 0.00 0.00 0.00 4.30
253 254 5.164954 GCTCGACATGATAAATAGTCCCTC 58.835 45.833 0.00 0.00 0.00 4.30
254 255 4.321304 CGCTCGACATGATAAATAGTCCCT 60.321 45.833 0.00 0.00 0.00 4.20
255 256 3.921021 CGCTCGACATGATAAATAGTCCC 59.079 47.826 0.00 0.00 0.00 4.46
256 257 4.795268 TCGCTCGACATGATAAATAGTCC 58.205 43.478 0.00 0.00 0.00 3.85
257 258 6.749216 TTTCGCTCGACATGATAAATAGTC 57.251 37.500 0.00 0.00 0.00 2.59
258 259 8.082852 ACTATTTCGCTCGACATGATAAATAGT 58.917 33.333 0.00 13.21 39.30 2.12
259 260 8.454293 ACTATTTCGCTCGACATGATAAATAG 57.546 34.615 0.00 12.35 38.32 1.73
260 261 8.812147 AACTATTTCGCTCGACATGATAAATA 57.188 30.769 0.00 0.00 0.00 1.40
261 262 7.715265 AACTATTTCGCTCGACATGATAAAT 57.285 32.000 0.00 0.00 0.00 1.40
262 263 7.534085 AAACTATTTCGCTCGACATGATAAA 57.466 32.000 0.00 0.00 0.00 1.40
263 264 8.699749 CATAAACTATTTCGCTCGACATGATAA 58.300 33.333 0.00 0.00 0.00 1.75
264 265 7.328493 CCATAAACTATTTCGCTCGACATGATA 59.672 37.037 0.00 0.00 0.00 2.15
265 266 6.146184 CCATAAACTATTTCGCTCGACATGAT 59.854 38.462 0.00 0.00 0.00 2.45
266 267 5.462068 CCATAAACTATTTCGCTCGACATGA 59.538 40.000 0.00 0.00 0.00 3.07
267 268 5.670097 CCATAAACTATTTCGCTCGACATG 58.330 41.667 1.64 0.00 0.00 3.21
268 269 4.211374 GCCATAAACTATTTCGCTCGACAT 59.789 41.667 0.00 0.00 0.00 3.06
269 270 3.554324 GCCATAAACTATTTCGCTCGACA 59.446 43.478 0.00 0.00 0.00 4.35
270 271 3.554324 TGCCATAAACTATTTCGCTCGAC 59.446 43.478 0.00 0.00 0.00 4.20
271 272 3.787785 TGCCATAAACTATTTCGCTCGA 58.212 40.909 0.00 0.00 0.00 4.04
272 273 3.059597 CCTGCCATAAACTATTTCGCTCG 60.060 47.826 0.00 0.00 0.00 5.03
273 274 3.877508 ACCTGCCATAAACTATTTCGCTC 59.122 43.478 0.00 0.00 0.00 5.03
274 275 3.886123 ACCTGCCATAAACTATTTCGCT 58.114 40.909 0.00 0.00 0.00 4.93
275 276 5.941948 ATACCTGCCATAAACTATTTCGC 57.058 39.130 0.00 0.00 0.00 4.70
276 277 7.870954 TCTGTATACCTGCCATAAACTATTTCG 59.129 37.037 0.00 0.00 0.00 3.46
277 278 9.726438 ATCTGTATACCTGCCATAAACTATTTC 57.274 33.333 0.00 0.00 0.00 2.17
278 279 9.507329 CATCTGTATACCTGCCATAAACTATTT 57.493 33.333 0.00 0.00 0.00 1.40
279 280 7.607991 GCATCTGTATACCTGCCATAAACTATT 59.392 37.037 0.00 0.00 0.00 1.73
280 281 7.038017 AGCATCTGTATACCTGCCATAAACTAT 60.038 37.037 14.86 0.00 35.21 2.12
281 282 6.270000 AGCATCTGTATACCTGCCATAAACTA 59.730 38.462 14.86 0.00 35.21 2.24
282 283 5.072329 AGCATCTGTATACCTGCCATAAACT 59.928 40.000 14.86 0.00 35.21 2.66
283 284 5.308825 AGCATCTGTATACCTGCCATAAAC 58.691 41.667 14.86 0.00 35.21 2.01
284 285 5.551233 GAGCATCTGTATACCTGCCATAAA 58.449 41.667 14.86 0.00 35.21 1.40
285 286 5.152623 GAGCATCTGTATACCTGCCATAA 57.847 43.478 14.86 0.00 35.21 1.90
286 287 4.808414 GAGCATCTGTATACCTGCCATA 57.192 45.455 14.86 0.00 35.21 2.74
287 288 3.692257 GAGCATCTGTATACCTGCCAT 57.308 47.619 14.86 2.57 35.21 4.40
301 302 2.645730 ACTTCAGACGACAGAGCATC 57.354 50.000 0.00 0.00 0.00 3.91
302 303 4.727507 AATACTTCAGACGACAGAGCAT 57.272 40.909 0.00 0.00 0.00 3.79
303 304 5.836821 ATAATACTTCAGACGACAGAGCA 57.163 39.130 0.00 0.00 0.00 4.26
304 305 6.508721 GCAAATAATACTTCAGACGACAGAGC 60.509 42.308 0.00 0.00 0.00 4.09
305 306 6.019479 GGCAAATAATACTTCAGACGACAGAG 60.019 42.308 0.00 0.00 0.00 3.35
306 307 5.810587 GGCAAATAATACTTCAGACGACAGA 59.189 40.000 0.00 0.00 0.00 3.41
307 308 5.006746 GGGCAAATAATACTTCAGACGACAG 59.993 44.000 0.00 0.00 0.00 3.51
308 309 4.873827 GGGCAAATAATACTTCAGACGACA 59.126 41.667 0.00 0.00 0.00 4.35
309 310 4.272748 GGGGCAAATAATACTTCAGACGAC 59.727 45.833 0.00 0.00 0.00 4.34
310 311 4.448210 GGGGCAAATAATACTTCAGACGA 58.552 43.478 0.00 0.00 0.00 4.20
311 312 3.247648 CGGGGCAAATAATACTTCAGACG 59.752 47.826 0.00 0.00 0.00 4.18
312 313 4.035208 CACGGGGCAAATAATACTTCAGAC 59.965 45.833 0.00 0.00 0.00 3.51
313 314 4.196193 CACGGGGCAAATAATACTTCAGA 58.804 43.478 0.00 0.00 0.00 3.27
314 315 3.945285 ACACGGGGCAAATAATACTTCAG 59.055 43.478 0.00 0.00 0.00 3.02
315 316 3.942748 GACACGGGGCAAATAATACTTCA 59.057 43.478 0.00 0.00 0.00 3.02
316 317 3.942748 TGACACGGGGCAAATAATACTTC 59.057 43.478 0.00 0.00 0.00 3.01
317 318 3.958018 TGACACGGGGCAAATAATACTT 58.042 40.909 0.00 0.00 0.00 2.24
318 319 3.637911 TGACACGGGGCAAATAATACT 57.362 42.857 0.00 0.00 0.00 2.12
319 320 4.705337 TTTGACACGGGGCAAATAATAC 57.295 40.909 16.49 0.00 0.00 1.89
320 321 4.707448 ACATTTGACACGGGGCAAATAATA 59.293 37.500 30.31 3.64 41.37 0.98
321 322 3.513515 ACATTTGACACGGGGCAAATAAT 59.486 39.130 30.31 18.87 41.37 1.28
322 323 2.894126 ACATTTGACACGGGGCAAATAA 59.106 40.909 30.31 4.54 41.37 1.40
323 324 2.520069 ACATTTGACACGGGGCAAATA 58.480 42.857 30.31 5.44 41.37 1.40
324 325 1.337118 ACATTTGACACGGGGCAAAT 58.663 45.000 25.93 25.93 43.38 2.32
325 326 1.115467 AACATTTGACACGGGGCAAA 58.885 45.000 23.28 23.28 38.25 3.68
326 327 0.387202 CAACATTTGACACGGGGCAA 59.613 50.000 0.00 0.00 0.00 4.52
327 328 1.459455 CCAACATTTGACACGGGGCA 61.459 55.000 0.00 0.00 0.00 5.36
328 329 1.175983 TCCAACATTTGACACGGGGC 61.176 55.000 0.00 0.00 0.00 5.80
333 334 1.541588 GGGAGCTCCAACATTTGACAC 59.458 52.381 33.29 8.26 37.91 3.67
420 424 2.993937 TGTTTTCGTTCCTGTCCAACT 58.006 42.857 0.00 0.00 0.00 3.16
427 431 6.479001 ACCGATATAGATTGTTTTCGTTCCTG 59.521 38.462 0.00 0.00 0.00 3.86
479 493 0.729690 GGACGCAAAGATCAGAAGGC 59.270 55.000 0.00 0.00 0.00 4.35
488 505 2.844946 TCACTCAAATGGACGCAAAGA 58.155 42.857 0.00 0.00 0.00 2.52
512 529 8.717821 GCAGAATATTCGTGGCATAAATTAGTA 58.282 33.333 18.65 0.00 0.00 1.82
603 633 6.366061 GCAGTCATGAATATGTAAGCATACGA 59.634 38.462 0.00 0.00 40.05 3.43
604 634 6.401474 GGCAGTCATGAATATGTAAGCATACG 60.401 42.308 0.00 0.00 40.05 3.06
606 636 5.939883 GGGCAGTCATGAATATGTAAGCATA 59.060 40.000 0.00 0.00 41.31 3.14
688 984 2.016604 GCATACCAAATCTGCGGTGGA 61.017 52.381 7.63 0.00 36.69 4.02
707 1003 0.459078 GGTACCTCCTCCAACGTAGC 59.541 60.000 4.06 0.00 0.00 3.58
722 1018 1.520787 CTGATTCGCCGGTGGGTAC 60.521 63.158 16.49 5.39 34.97 3.34
740 1036 7.227910 TCCAAGTGACCAGTCTTGTTTATAAAC 59.772 37.037 19.44 19.44 39.25 2.01
809 1139 2.227865 GCATGCCGGTAGAAAGTTTGAA 59.772 45.455 6.36 0.00 0.00 2.69
863 1205 7.721286 AGACTTGTGCATGCTATTTATAGAC 57.279 36.000 20.33 5.64 32.05 2.59
887 1229 6.110033 TCTTGTTGTTGTGTGTTAAGAGCTA 58.890 36.000 0.00 0.00 0.00 3.32
993 1350 2.555123 GAGGCCTTGCATCGTTGAA 58.445 52.632 6.77 0.00 27.73 2.69
1016 1373 2.810400 GCCAGTGACAGCTTGGAAGTTA 60.810 50.000 5.53 0.00 0.00 2.24
1340 1700 4.989168 CCTGCTTGTCGTAGAAGTAAAACT 59.011 41.667 0.00 0.00 39.69 2.66
1344 1704 3.825014 ACTCCTGCTTGTCGTAGAAGTAA 59.175 43.478 0.00 0.00 39.69 2.24
1440 5772 1.264045 TGTCATCCATGAGGTCCGCA 61.264 55.000 0.00 0.00 37.51 5.69
1599 5931 6.045459 TGTGCCACCCTAATATAAATCCTCAT 59.955 38.462 0.00 0.00 0.00 2.90
1700 6035 0.751277 TGACACACAAACCTGCCCTG 60.751 55.000 0.00 0.00 0.00 4.45
1949 10834 8.775527 TGCAGTAGTTTCGTTTATTGTATTTCA 58.224 29.630 0.00 0.00 0.00 2.69
2080 11161 1.878522 CACGGCACTATCCAGACGC 60.879 63.158 0.00 0.00 0.00 5.19
2356 11470 3.742882 CAGTTCTTTTGTCTCGAGCATCA 59.257 43.478 7.81 4.14 33.17 3.07
2483 11607 0.030101 CAAAACGGGCACGACACATT 59.970 50.000 19.19 0.00 44.60 2.71
2511 11636 5.520376 ACCATTACCTAATTGCATCTTGC 57.480 39.130 0.00 0.00 45.29 4.01


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

AutoCloner maintained by Alex Coulton.