Multiple sequence alignment - TraesCS4D01G110000

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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 TraesCS4D01G110000 chr4D 100.000 3227 0 0 1 3227 89437034 89433808 0.000000e+00 5960
1 TraesCS4D01G110000 chr4B 91.608 2848 146 29 211 3000 126509467 126506655 0.000000e+00 3849
2 TraesCS4D01G110000 chr4B 90.594 202 8 4 3030 3227 126506591 126506397 1.150000e-64 257
3 TraesCS4D01G110000 chr4A 91.522 2760 140 31 211 2910 501977200 501974475 0.000000e+00 3714
4 TraesCS4D01G110000 chr4A 98.462 65 0 1 3063 3126 501974281 501974217 2.630000e-21 113
5 TraesCS4D01G110000 chr5B 81.967 1037 168 12 1189 2217 222127510 222126485 0.000000e+00 861
6 TraesCS4D01G110000 chr5D 81.660 1036 173 10 1189 2217 208536931 208535906 0.000000e+00 845
7 TraesCS4D01G110000 chr5A 81.660 1036 173 10 1189 2217 269320612 269319587 0.000000e+00 845


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 TraesCS4D01G110000 chr4D 89433808 89437034 3226 True 5960.0 5960 100.000 1 3227 1 chr4D.!!$R1 3226
1 TraesCS4D01G110000 chr4B 126506397 126509467 3070 True 2053.0 3849 91.101 211 3227 2 chr4B.!!$R1 3016
2 TraesCS4D01G110000 chr4A 501974217 501977200 2983 True 1913.5 3714 94.992 211 3126 2 chr4A.!!$R1 2915
3 TraesCS4D01G110000 chr5B 222126485 222127510 1025 True 861.0 861 81.967 1189 2217 1 chr5B.!!$R1 1028
4 TraesCS4D01G110000 chr5D 208535906 208536931 1025 True 845.0 845 81.660 1189 2217 1 chr5D.!!$R1 1028
5 TraesCS4D01G110000 chr5A 269319587 269320612 1025 True 845.0 845 81.660 1189 2217 1 chr5A.!!$R1 1028

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
51 52 0.036010 AGGGAAGGTGTGATCAAGCG 60.036 55.0 0.0 0.0 0.00 4.68 F
53 54 0.036388 GGAAGGTGTGATCAAGCGGA 60.036 55.0 0.0 0.0 0.00 5.54 F
57 58 0.099436 GGTGTGATCAAGCGGATTGC 59.901 55.0 0.0 0.0 46.98 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 1496 2.764128 GGCCCTCGTGGATCTCCA 60.764 66.667 4.76 0.0 45.3 3.86 R
2103 2157 2.594013 TTCATGGCGCTGCACACA 60.594 55.556 7.64 0.0 0.0 3.72 R
2268 2322 1.210672 GAGAGCTACCTATCGCCGC 59.789 63.158 0.00 0.0 0.0 6.53 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
18 19 2.681348 AGTGGCACATCAGCTCTCT 58.319 52.632 21.41 0.00 44.52 3.10
19 20 0.982704 AGTGGCACATCAGCTCTCTT 59.017 50.000 21.41 0.00 44.52 2.85
20 21 1.350351 AGTGGCACATCAGCTCTCTTT 59.650 47.619 21.41 0.00 44.52 2.52
21 22 1.736681 GTGGCACATCAGCTCTCTTTC 59.263 52.381 13.86 0.00 44.52 2.62
22 23 1.339438 TGGCACATCAGCTCTCTTTCC 60.339 52.381 0.00 0.00 34.17 3.13
23 24 1.377536 GCACATCAGCTCTCTTTCCC 58.622 55.000 0.00 0.00 0.00 3.97
24 25 1.649664 CACATCAGCTCTCTTTCCCG 58.350 55.000 0.00 0.00 0.00 5.14
25 26 1.205655 CACATCAGCTCTCTTTCCCGA 59.794 52.381 0.00 0.00 0.00 5.14
26 27 1.205893 ACATCAGCTCTCTTTCCCGAC 59.794 52.381 0.00 0.00 0.00 4.79
27 28 0.827368 ATCAGCTCTCTTTCCCGACC 59.173 55.000 0.00 0.00 0.00 4.79
28 29 0.541998 TCAGCTCTCTTTCCCGACCA 60.542 55.000 0.00 0.00 0.00 4.02
29 30 0.321671 CAGCTCTCTTTCCCGACCAA 59.678 55.000 0.00 0.00 0.00 3.67
30 31 0.610687 AGCTCTCTTTCCCGACCAAG 59.389 55.000 0.00 0.00 0.00 3.61
31 32 0.608640 GCTCTCTTTCCCGACCAAGA 59.391 55.000 0.00 0.00 0.00 3.02
32 33 1.002087 GCTCTCTTTCCCGACCAAGAA 59.998 52.381 0.00 0.00 0.00 2.52
33 34 2.933056 GCTCTCTTTCCCGACCAAGAAG 60.933 54.545 0.00 0.00 0.00 2.85
34 35 1.623811 TCTCTTTCCCGACCAAGAAGG 59.376 52.381 0.00 0.00 45.67 3.46
35 36 0.690762 TCTTTCCCGACCAAGAAGGG 59.309 55.000 0.00 0.00 46.40 3.95
40 41 2.067197 CCGACCAAGAAGGGAAGGT 58.933 57.895 0.00 0.00 43.89 3.50
41 42 0.321653 CCGACCAAGAAGGGAAGGTG 60.322 60.000 0.00 0.00 43.89 4.00
42 43 0.396811 CGACCAAGAAGGGAAGGTGT 59.603 55.000 0.00 0.00 43.89 4.16
43 44 1.878102 CGACCAAGAAGGGAAGGTGTG 60.878 57.143 0.00 0.00 43.89 3.82
44 45 1.420138 GACCAAGAAGGGAAGGTGTGA 59.580 52.381 0.00 0.00 43.89 3.58
45 46 2.040412 GACCAAGAAGGGAAGGTGTGAT 59.960 50.000 0.00 0.00 43.89 3.06
46 47 2.040412 ACCAAGAAGGGAAGGTGTGATC 59.960 50.000 0.00 0.00 43.89 2.92
47 48 2.040278 CCAAGAAGGGAAGGTGTGATCA 59.960 50.000 0.00 0.00 0.00 2.92
48 49 3.498481 CCAAGAAGGGAAGGTGTGATCAA 60.498 47.826 0.00 0.00 0.00 2.57
49 50 3.710209 AGAAGGGAAGGTGTGATCAAG 57.290 47.619 0.00 0.00 0.00 3.02
50 51 2.087646 GAAGGGAAGGTGTGATCAAGC 58.912 52.381 0.00 0.00 0.00 4.01
51 52 0.036010 AGGGAAGGTGTGATCAAGCG 60.036 55.000 0.00 0.00 0.00 4.68
52 53 1.026718 GGGAAGGTGTGATCAAGCGG 61.027 60.000 0.00 0.00 0.00 5.52
53 54 0.036388 GGAAGGTGTGATCAAGCGGA 60.036 55.000 0.00 0.00 0.00 5.54
54 55 1.407437 GGAAGGTGTGATCAAGCGGAT 60.407 52.381 0.00 0.00 39.53 4.18
55 56 2.359900 GAAGGTGTGATCAAGCGGATT 58.640 47.619 0.00 0.00 36.00 3.01
56 57 1.742761 AGGTGTGATCAAGCGGATTG 58.257 50.000 0.00 0.00 40.52 2.67
57 58 0.099436 GGTGTGATCAAGCGGATTGC 59.901 55.000 0.00 0.00 46.98 3.56
79 80 6.309712 GCAATTGCATATGATGTACAGACT 57.690 37.500 25.36 0.00 41.59 3.24
80 81 6.732154 GCAATTGCATATGATGTACAGACTT 58.268 36.000 25.36 0.00 41.59 3.01
81 82 6.854892 GCAATTGCATATGATGTACAGACTTC 59.145 38.462 25.36 0.00 41.59 3.01
82 83 6.775939 ATTGCATATGATGTACAGACTTCG 57.224 37.500 6.97 0.00 33.44 3.79
83 84 5.262588 TGCATATGATGTACAGACTTCGT 57.737 39.130 6.97 0.00 33.44 3.85
84 85 5.281727 TGCATATGATGTACAGACTTCGTC 58.718 41.667 6.97 0.00 33.44 4.20
85 86 4.380087 GCATATGATGTACAGACTTCGTCG 59.620 45.833 6.97 0.00 37.67 5.12
86 87 5.748592 CATATGATGTACAGACTTCGTCGA 58.251 41.667 0.33 0.00 37.67 4.20
87 88 4.696899 ATGATGTACAGACTTCGTCGAA 57.303 40.909 7.57 7.57 37.67 3.71
88 89 4.696899 TGATGTACAGACTTCGTCGAAT 57.303 40.909 8.36 0.00 37.67 3.34
89 90 4.659088 TGATGTACAGACTTCGTCGAATC 58.341 43.478 8.36 8.43 37.67 2.52
90 91 3.113325 TGTACAGACTTCGTCGAATCG 57.887 47.619 8.36 0.00 37.67 3.34
91 92 2.738314 TGTACAGACTTCGTCGAATCGA 59.262 45.455 8.36 0.00 37.67 3.59
92 93 2.983402 ACAGACTTCGTCGAATCGAA 57.017 45.000 7.01 10.04 45.46 3.71
93 94 2.582687 ACAGACTTCGTCGAATCGAAC 58.417 47.619 7.01 0.94 43.36 3.95
94 95 1.912110 CAGACTTCGTCGAATCGAACC 59.088 52.381 7.01 0.00 43.36 3.62
95 96 1.811359 AGACTTCGTCGAATCGAACCT 59.189 47.619 7.01 5.07 43.36 3.50
96 97 1.912110 GACTTCGTCGAATCGAACCTG 59.088 52.381 7.01 1.23 43.36 4.00
97 98 1.269166 CTTCGTCGAATCGAACCTGG 58.731 55.000 7.01 0.00 43.36 4.45
98 99 0.883153 TTCGTCGAATCGAACCTGGA 59.117 50.000 7.01 0.00 43.36 3.86
99 100 1.100510 TCGTCGAATCGAACCTGGAT 58.899 50.000 7.01 0.00 37.72 3.41
100 101 1.200483 CGTCGAATCGAACCTGGATG 58.800 55.000 7.01 0.00 37.72 3.51
101 102 1.469251 CGTCGAATCGAACCTGGATGT 60.469 52.381 7.01 0.00 37.72 3.06
102 103 1.927174 GTCGAATCGAACCTGGATGTG 59.073 52.381 7.01 0.00 37.72 3.21
103 104 1.134818 TCGAATCGAACCTGGATGTGG 60.135 52.381 1.57 0.00 31.06 4.17
104 105 1.017387 GAATCGAACCTGGATGTGGC 58.983 55.000 0.00 0.00 0.00 5.01
105 106 0.744414 AATCGAACCTGGATGTGGCG 60.744 55.000 0.00 0.00 0.00 5.69
106 107 1.613317 ATCGAACCTGGATGTGGCGA 61.613 55.000 0.00 0.00 32.76 5.54
107 108 1.811266 CGAACCTGGATGTGGCGAG 60.811 63.158 0.00 0.00 0.00 5.03
108 109 1.450312 GAACCTGGATGTGGCGAGG 60.450 63.158 0.00 0.00 39.41 4.63
109 110 2.607750 ACCTGGATGTGGCGAGGT 60.608 61.111 0.00 0.00 41.45 3.85
110 111 2.224159 ACCTGGATGTGGCGAGGTT 61.224 57.895 0.00 0.00 43.38 3.50
111 112 1.450312 CCTGGATGTGGCGAGGTTC 60.450 63.158 0.00 0.00 0.00 3.62
112 113 1.450312 CTGGATGTGGCGAGGTTCC 60.450 63.158 0.00 0.00 0.00 3.62
113 114 2.184020 CTGGATGTGGCGAGGTTCCA 62.184 60.000 0.00 0.00 35.29 3.53
114 115 1.002624 GGATGTGGCGAGGTTCCAA 60.003 57.895 0.00 0.00 35.01 3.53
115 116 1.305930 GGATGTGGCGAGGTTCCAAC 61.306 60.000 0.00 0.00 35.01 3.77
116 117 0.321653 GATGTGGCGAGGTTCCAACT 60.322 55.000 0.00 0.00 35.01 3.16
117 118 0.606401 ATGTGGCGAGGTTCCAACTG 60.606 55.000 0.00 0.00 35.01 3.16
118 119 1.070786 GTGGCGAGGTTCCAACTGA 59.929 57.895 0.00 0.00 35.01 3.41
119 120 0.321653 GTGGCGAGGTTCCAACTGAT 60.322 55.000 0.00 0.00 35.01 2.90
120 121 0.321564 TGGCGAGGTTCCAACTGATG 60.322 55.000 0.00 0.00 0.00 3.07
128 129 2.360350 CCAACTGATGGTGCCGCT 60.360 61.111 0.00 0.00 44.85 5.52
129 130 1.078497 CCAACTGATGGTGCCGCTA 60.078 57.895 0.00 0.00 44.85 4.26
130 131 1.091771 CCAACTGATGGTGCCGCTAG 61.092 60.000 0.00 0.00 44.85 3.42
131 132 0.391661 CAACTGATGGTGCCGCTAGT 60.392 55.000 0.00 0.00 0.00 2.57
132 133 0.391661 AACTGATGGTGCCGCTAGTG 60.392 55.000 0.00 0.00 0.00 2.74
133 134 1.219124 CTGATGGTGCCGCTAGTGT 59.781 57.895 1.99 0.00 0.00 3.55
134 135 1.079197 TGATGGTGCCGCTAGTGTG 60.079 57.895 1.99 0.00 0.00 3.82
135 136 2.436646 ATGGTGCCGCTAGTGTGC 60.437 61.111 1.99 6.21 0.00 4.57
136 137 2.859273 GATGGTGCCGCTAGTGTGCT 62.859 60.000 14.95 0.00 0.00 4.40
137 138 2.815647 GGTGCCGCTAGTGTGCTC 60.816 66.667 14.95 11.97 0.00 4.26
138 139 2.048222 GTGCCGCTAGTGTGCTCA 60.048 61.111 14.95 0.00 0.00 4.26
139 140 1.448540 GTGCCGCTAGTGTGCTCAT 60.449 57.895 14.95 0.00 0.00 2.90
140 141 1.021390 GTGCCGCTAGTGTGCTCATT 61.021 55.000 14.95 0.00 0.00 2.57
141 142 0.534873 TGCCGCTAGTGTGCTCATTA 59.465 50.000 14.95 0.00 0.00 1.90
142 143 1.066502 TGCCGCTAGTGTGCTCATTAA 60.067 47.619 14.95 0.00 0.00 1.40
143 144 1.594862 GCCGCTAGTGTGCTCATTAAG 59.405 52.381 1.99 0.00 0.00 1.85
144 145 2.738643 GCCGCTAGTGTGCTCATTAAGA 60.739 50.000 1.99 0.00 0.00 2.10
145 146 3.521560 CCGCTAGTGTGCTCATTAAGAA 58.478 45.455 1.99 0.00 0.00 2.52
146 147 4.122776 CCGCTAGTGTGCTCATTAAGAAT 58.877 43.478 1.99 0.00 0.00 2.40
147 148 4.572389 CCGCTAGTGTGCTCATTAAGAATT 59.428 41.667 1.99 0.00 0.00 2.17
148 149 5.753438 CCGCTAGTGTGCTCATTAAGAATTA 59.247 40.000 1.99 0.00 0.00 1.40
149 150 6.257849 CCGCTAGTGTGCTCATTAAGAATTAA 59.742 38.462 1.99 0.00 45.80 1.40
150 151 7.340699 CGCTAGTGTGCTCATTAAGAATTAAG 58.659 38.462 0.00 0.00 44.82 1.85
151 152 7.010552 CGCTAGTGTGCTCATTAAGAATTAAGT 59.989 37.037 0.00 0.00 44.82 2.24
152 153 9.314321 GCTAGTGTGCTCATTAAGAATTAAGTA 57.686 33.333 0.00 0.00 44.82 2.24
154 155 8.202745 AGTGTGCTCATTAAGAATTAAGTAGC 57.797 34.615 9.82 9.82 44.82 3.58
155 156 7.010552 AGTGTGCTCATTAAGAATTAAGTAGCG 59.989 37.037 11.12 0.00 46.67 4.26
156 157 6.130058 GTGCTCATTAAGAATTAAGTAGCGC 58.870 40.000 0.00 0.00 46.67 5.92
157 158 5.815222 TGCTCATTAAGAATTAAGTAGCGCA 59.185 36.000 11.47 0.00 46.67 6.09
158 159 6.315144 TGCTCATTAAGAATTAAGTAGCGCAA 59.685 34.615 11.47 0.00 46.67 4.85
159 160 7.148323 TGCTCATTAAGAATTAAGTAGCGCAAA 60.148 33.333 11.47 0.00 46.67 3.68
160 161 7.696453 GCTCATTAAGAATTAAGTAGCGCAAAA 59.304 33.333 11.47 0.00 44.82 2.44
161 162 9.554724 CTCATTAAGAATTAAGTAGCGCAAAAA 57.445 29.630 11.47 0.00 44.82 1.94
188 189 3.436700 AAAAATAAGTAGCGCATGGCC 57.563 42.857 11.47 0.00 45.17 5.36
189 190 2.348411 AAATAAGTAGCGCATGGCCT 57.652 45.000 11.47 0.00 45.17 5.19
190 191 1.597742 AATAAGTAGCGCATGGCCTG 58.402 50.000 11.47 0.34 45.17 4.85
205 206 3.927555 CCTGCCAAAGGTCTACGAA 57.072 52.632 0.00 0.00 41.74 3.85
206 207 2.178912 CCTGCCAAAGGTCTACGAAA 57.821 50.000 0.00 0.00 41.74 3.46
207 208 2.711542 CCTGCCAAAGGTCTACGAAAT 58.288 47.619 0.00 0.00 41.74 2.17
208 209 2.678336 CCTGCCAAAGGTCTACGAAATC 59.322 50.000 0.00 0.00 41.74 2.17
209 210 3.334691 CTGCCAAAGGTCTACGAAATCA 58.665 45.455 0.00 0.00 0.00 2.57
223 224 1.606668 GAAATCAGTTGTTCGGTGCCA 59.393 47.619 0.00 0.00 0.00 4.92
242 243 3.241067 CAACATTTTGGAGGGCATGAG 57.759 47.619 0.00 0.00 0.00 2.90
245 246 1.753073 CATTTTGGAGGGCATGAGTCC 59.247 52.381 0.00 0.00 40.92 3.85
246 247 0.322456 TTTTGGAGGGCATGAGTCCG 60.322 55.000 0.00 0.00 46.92 4.79
248 249 0.982852 TTGGAGGGCATGAGTCCGAT 60.983 55.000 0.00 0.00 46.92 4.18
251 252 1.625818 GGAGGGCATGAGTCCGATTAT 59.374 52.381 0.00 0.00 46.92 1.28
253 254 3.118956 GGAGGGCATGAGTCCGATTATAG 60.119 52.174 0.00 0.00 46.92 1.31
256 257 2.263077 GCATGAGTCCGATTATAGGCG 58.737 52.381 0.00 0.00 0.00 5.52
261 262 3.382227 TGAGTCCGATTATAGGCGTGAAA 59.618 43.478 0.00 0.00 0.00 2.69
265 266 3.382227 TCCGATTATAGGCGTGAAACTCA 59.618 43.478 0.00 0.00 31.75 3.41
269 270 6.355638 CGATTATAGGCGTGAAACTCATTTC 58.644 40.000 0.00 0.00 43.96 2.17
276 277 2.157668 CGTGAAACTCATTTCCGACCAG 59.842 50.000 0.00 0.00 43.18 4.00
278 279 3.186613 GTGAAACTCATTTCCGACCAGAC 59.813 47.826 0.00 0.00 43.18 3.51
279 280 3.181459 TGAAACTCATTTCCGACCAGACA 60.181 43.478 0.00 0.00 43.18 3.41
287 288 2.536761 TCCGACCAGACAATCGTTTT 57.463 45.000 0.00 0.00 36.60 2.43
294 295 5.277154 CGACCAGACAATCGTTTTTAGTTGT 60.277 40.000 0.00 0.00 37.49 3.32
296 297 5.587043 ACCAGACAATCGTTTTTAGTTGTGA 59.413 36.000 0.00 0.00 35.15 3.58
297 298 6.262273 ACCAGACAATCGTTTTTAGTTGTGAT 59.738 34.615 0.00 0.00 35.15 3.06
299 300 7.132213 CAGACAATCGTTTTTAGTTGTGATGT 58.868 34.615 0.00 0.00 35.15 3.06
309 310 9.736023 GTTTTTAGTTGTGATGTTCTTCAAGAT 57.264 29.630 0.00 0.00 0.00 2.40
311 312 5.368256 AGTTGTGATGTTCTTCAAGATGC 57.632 39.130 0.00 0.00 0.00 3.91
318 319 7.040548 TGTGATGTTCTTCAAGATGCATAACAA 60.041 33.333 15.30 5.06 32.90 2.83
410 424 3.444029 CCCCATCAAGGTTCCTCAAAAT 58.556 45.455 0.00 0.00 34.66 1.82
440 454 1.673920 TCGCTGTGAGCATCGTATGTA 59.326 47.619 0.00 0.00 42.58 2.29
516 530 7.945134 ACAAATTTCTGTCTAAAGTCAAGCAT 58.055 30.769 0.00 0.00 0.00 3.79
522 536 7.137490 TCTGTCTAAAGTCAAGCATCATTTG 57.863 36.000 0.00 0.00 0.00 2.32
538 553 5.247507 TCATTTGCTCGTAAAATCATGGG 57.752 39.130 0.00 0.00 0.00 4.00
545 560 3.728845 TCGTAAAATCATGGGAGCTAGC 58.271 45.455 6.62 6.62 0.00 3.42
747 786 1.909700 TTCAACAGGTGCAAGGGATC 58.090 50.000 0.00 0.00 0.00 3.36
877 925 0.529337 ACCTCATCGCAGCTTCATCG 60.529 55.000 0.00 0.00 0.00 3.84
922 970 2.836360 ACGACCCGCACCCGATAT 60.836 61.111 0.00 0.00 36.29 1.63
923 971 2.049433 CGACCCGCACCCGATATC 60.049 66.667 0.00 0.00 36.29 1.63
924 972 2.049433 GACCCGCACCCGATATCG 60.049 66.667 18.31 18.31 36.29 2.92
2252 2306 5.345702 CATCATCAAGAATCCGCATTTTGT 58.654 37.500 0.00 0.00 0.00 2.83
2285 2339 2.269529 GGCGGCGATAGGTAGCTCT 61.270 63.158 12.98 0.00 0.00 4.09
2506 2569 4.335272 GCTAATTCTTGAGTTACTTGCGC 58.665 43.478 0.00 0.00 0.00 6.09
2622 2701 9.167311 GTTCTTGACTCTATAATGTCCACATTT 57.833 33.333 10.15 2.27 43.48 2.32
2627 2706 9.330063 TGACTCTATAATGTCCACATTTTCATC 57.670 33.333 10.15 3.23 43.48 2.92
2633 2712 4.255833 TGTCCACATTTTCATCTTTGGC 57.744 40.909 0.00 0.00 0.00 4.52
2708 2789 3.552294 GTCTAGAGAAATGCCGCAGTTAC 59.448 47.826 5.96 4.29 0.00 2.50
2720 2801 1.613255 CGCAGTTACAAATGTCCCCCT 60.613 52.381 0.00 0.00 0.00 4.79
2767 2850 7.100409 GGACTATTTCCCAGTTCTCTATATGC 58.900 42.308 0.00 0.00 38.70 3.14
2933 3023 5.402270 GCAGAACACAAACGCTTCAAATAAT 59.598 36.000 0.00 0.00 0.00 1.28
2947 3037 8.184192 CGCTTCAAATAATTCTGAATACCAAGT 58.816 33.333 2.85 0.00 31.40 3.16
3000 3119 7.659390 GGCTTATGATCAAGAGCTACAAAGTAT 59.341 37.037 24.31 0.00 35.53 2.12
3001 3120 9.698309 GCTTATGATCAAGAGCTACAAAGTATA 57.302 33.333 20.43 0.00 32.54 1.47
3014 3133 9.350951 AGCTACAAAGTATAATAAAATCCCCAC 57.649 33.333 0.00 0.00 0.00 4.61
3015 3134 8.573885 GCTACAAAGTATAATAAAATCCCCACC 58.426 37.037 0.00 0.00 0.00 4.61
3018 3137 8.923270 ACAAAGTATAATAAAATCCCCACCATG 58.077 33.333 0.00 0.00 0.00 3.66
3019 3138 8.923270 CAAAGTATAATAAAATCCCCACCATGT 58.077 33.333 0.00 0.00 0.00 3.21
3024 3143 8.823220 ATAATAAAATCCCCACCATGTATAGC 57.177 34.615 0.00 0.00 0.00 2.97
3025 3144 4.814224 AAAATCCCCACCATGTATAGCT 57.186 40.909 0.00 0.00 0.00 3.32
3026 3145 4.814224 AAATCCCCACCATGTATAGCTT 57.186 40.909 0.00 0.00 0.00 3.74
3027 3146 4.814224 AATCCCCACCATGTATAGCTTT 57.186 40.909 0.00 0.00 0.00 3.51
3028 3147 4.814224 ATCCCCACCATGTATAGCTTTT 57.186 40.909 0.00 0.00 0.00 2.27
3034 3218 5.527582 CCCACCATGTATAGCTTTTACAGAC 59.472 44.000 12.88 0.00 33.36 3.51
3049 3233 8.024865 GCTTTTACAGACCACGGTTAATAAAAT 58.975 33.333 10.43 0.00 0.00 1.82
3141 3328 6.053650 TGGCTTATGATCTCTTGACTGAATG 58.946 40.000 0.00 0.00 0.00 2.67
3194 3383 0.758734 CTGTCAGGTCTCCACCAACA 59.241 55.000 0.00 0.00 46.68 3.33
3195 3384 0.468226 TGTCAGGTCTCCACCAACAC 59.532 55.000 0.00 0.00 46.68 3.32
3196 3385 0.250338 GTCAGGTCTCCACCAACACC 60.250 60.000 0.00 0.00 46.68 4.16
3197 3386 0.692756 TCAGGTCTCCACCAACACCA 60.693 55.000 0.00 0.00 46.68 4.17
3198 3387 0.182537 CAGGTCTCCACCAACACCAA 59.817 55.000 0.00 0.00 46.68 3.67
3199 3388 0.182775 AGGTCTCCACCAACACCAAC 59.817 55.000 0.00 0.00 46.68 3.77
3207 3396 1.266718 CACCAACACCAACCTTGATCG 59.733 52.381 0.00 0.00 0.00 3.69
3224 3413 2.660670 TCGGGCCAAAAAGGTAAAGA 57.339 45.000 4.39 0.00 40.61 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.982704 AAGAGAGCTGATGTGCCACT 59.017 50.000 0.00 0.00 0.00 4.00
1 2 1.736681 GAAAGAGAGCTGATGTGCCAC 59.263 52.381 0.00 0.00 0.00 5.01
2 3 1.339438 GGAAAGAGAGCTGATGTGCCA 60.339 52.381 0.00 0.00 0.00 4.92
3 4 1.377536 GGAAAGAGAGCTGATGTGCC 58.622 55.000 0.00 0.00 0.00 5.01
4 5 1.377536 GGGAAAGAGAGCTGATGTGC 58.622 55.000 0.00 0.00 0.00 4.57
5 6 1.205655 TCGGGAAAGAGAGCTGATGTG 59.794 52.381 0.00 0.00 0.00 3.21
6 7 1.205893 GTCGGGAAAGAGAGCTGATGT 59.794 52.381 0.00 0.00 0.00 3.06
7 8 1.472376 GGTCGGGAAAGAGAGCTGATG 60.472 57.143 0.00 0.00 32.67 3.07
8 9 0.827368 GGTCGGGAAAGAGAGCTGAT 59.173 55.000 0.00 0.00 32.67 2.90
9 10 0.541998 TGGTCGGGAAAGAGAGCTGA 60.542 55.000 0.00 0.00 36.03 4.26
10 11 0.321671 TTGGTCGGGAAAGAGAGCTG 59.678 55.000 0.00 0.00 36.03 4.24
11 12 0.610687 CTTGGTCGGGAAAGAGAGCT 59.389 55.000 0.00 0.00 36.03 4.09
12 13 0.608640 TCTTGGTCGGGAAAGAGAGC 59.391 55.000 0.00 0.00 35.64 4.09
13 14 2.354203 CCTTCTTGGTCGGGAAAGAGAG 60.354 54.545 0.00 0.00 34.09 3.20
14 15 1.623811 CCTTCTTGGTCGGGAAAGAGA 59.376 52.381 0.00 0.00 34.09 3.10
15 16 1.339151 CCCTTCTTGGTCGGGAAAGAG 60.339 57.143 0.00 0.00 40.55 2.85
16 17 0.690762 CCCTTCTTGGTCGGGAAAGA 59.309 55.000 0.00 0.00 40.55 2.52
17 18 0.690762 TCCCTTCTTGGTCGGGAAAG 59.309 55.000 0.00 0.00 43.79 2.62
18 19 2.857087 TCCCTTCTTGGTCGGGAAA 58.143 52.632 0.00 0.00 43.79 3.13
19 20 4.652166 TCCCTTCTTGGTCGGGAA 57.348 55.556 0.00 0.00 43.79 3.97
20 21 1.198759 CCTTCCCTTCTTGGTCGGGA 61.199 60.000 0.00 0.00 45.02 5.14
21 22 1.299976 CCTTCCCTTCTTGGTCGGG 59.700 63.158 0.00 0.00 39.41 5.14
22 23 0.321653 CACCTTCCCTTCTTGGTCGG 60.322 60.000 0.00 0.00 0.00 4.79
23 24 0.396811 ACACCTTCCCTTCTTGGTCG 59.603 55.000 0.00 0.00 0.00 4.79
24 25 1.420138 TCACACCTTCCCTTCTTGGTC 59.580 52.381 0.00 0.00 0.00 4.02
25 26 1.518367 TCACACCTTCCCTTCTTGGT 58.482 50.000 0.00 0.00 0.00 3.67
26 27 2.040278 TGATCACACCTTCCCTTCTTGG 59.960 50.000 0.00 0.00 0.00 3.61
27 28 3.423539 TGATCACACCTTCCCTTCTTG 57.576 47.619 0.00 0.00 0.00 3.02
28 29 3.812167 GCTTGATCACACCTTCCCTTCTT 60.812 47.826 0.00 0.00 0.00 2.52
29 30 2.290577 GCTTGATCACACCTTCCCTTCT 60.291 50.000 0.00 0.00 0.00 2.85
30 31 2.087646 GCTTGATCACACCTTCCCTTC 58.912 52.381 0.00 0.00 0.00 3.46
31 32 1.611673 CGCTTGATCACACCTTCCCTT 60.612 52.381 0.00 0.00 0.00 3.95
32 33 0.036010 CGCTTGATCACACCTTCCCT 60.036 55.000 0.00 0.00 0.00 4.20
33 34 1.026718 CCGCTTGATCACACCTTCCC 61.027 60.000 0.00 0.00 0.00 3.97
34 35 0.036388 TCCGCTTGATCACACCTTCC 60.036 55.000 0.00 0.00 0.00 3.46
35 36 2.029838 ATCCGCTTGATCACACCTTC 57.970 50.000 0.00 0.00 0.00 3.46
36 37 2.086869 CAATCCGCTTGATCACACCTT 58.913 47.619 0.00 0.00 36.97 3.50
37 38 1.742761 CAATCCGCTTGATCACACCT 58.257 50.000 0.00 0.00 36.97 4.00
38 39 0.099436 GCAATCCGCTTGATCACACC 59.901 55.000 0.00 0.00 36.97 4.16
39 40 0.804364 TGCAATCCGCTTGATCACAC 59.196 50.000 0.00 0.00 43.06 3.82
40 41 1.532523 TTGCAATCCGCTTGATCACA 58.467 45.000 0.00 0.00 43.06 3.58
41 42 2.855963 CAATTGCAATCCGCTTGATCAC 59.144 45.455 13.38 0.00 43.06 3.06
42 43 2.736081 GCAATTGCAATCCGCTTGATCA 60.736 45.455 25.36 0.00 43.06 2.92
43 44 1.856597 GCAATTGCAATCCGCTTGATC 59.143 47.619 25.36 0.66 43.06 2.92
44 45 1.930567 GCAATTGCAATCCGCTTGAT 58.069 45.000 25.36 0.00 43.06 2.57
45 46 3.422122 GCAATTGCAATCCGCTTGA 57.578 47.368 25.36 0.00 43.06 3.02
56 57 6.309712 AGTCTGTACATCATATGCAATTGC 57.690 37.500 23.69 23.69 42.50 3.56
57 58 7.067728 CGAAGTCTGTACATCATATGCAATTG 58.932 38.462 0.00 0.00 0.00 2.32
58 59 6.763135 ACGAAGTCTGTACATCATATGCAATT 59.237 34.615 0.00 0.00 29.74 2.32
59 60 6.283694 ACGAAGTCTGTACATCATATGCAAT 58.716 36.000 0.00 0.00 29.74 3.56
60 61 5.660460 ACGAAGTCTGTACATCATATGCAA 58.340 37.500 0.00 0.00 29.74 4.08
61 62 5.262588 ACGAAGTCTGTACATCATATGCA 57.737 39.130 0.00 0.00 29.74 3.96
80 81 1.100510 ATCCAGGTTCGATTCGACGA 58.899 50.000 8.55 0.00 40.55 4.20
81 82 1.200483 CATCCAGGTTCGATTCGACG 58.800 55.000 8.55 0.00 34.89 5.12
82 83 1.927174 CACATCCAGGTTCGATTCGAC 59.073 52.381 8.55 4.35 34.89 4.20
83 84 1.134818 CCACATCCAGGTTCGATTCGA 60.135 52.381 4.29 4.29 0.00 3.71
84 85 1.290203 CCACATCCAGGTTCGATTCG 58.710 55.000 0.00 0.00 0.00 3.34
85 86 1.017387 GCCACATCCAGGTTCGATTC 58.983 55.000 0.00 0.00 0.00 2.52
86 87 0.744414 CGCCACATCCAGGTTCGATT 60.744 55.000 0.00 0.00 0.00 3.34
87 88 1.153369 CGCCACATCCAGGTTCGAT 60.153 57.895 0.00 0.00 0.00 3.59
88 89 2.225791 CTCGCCACATCCAGGTTCGA 62.226 60.000 0.00 0.00 0.00 3.71
89 90 1.811266 CTCGCCACATCCAGGTTCG 60.811 63.158 0.00 0.00 0.00 3.95
90 91 1.450312 CCTCGCCACATCCAGGTTC 60.450 63.158 0.00 0.00 0.00 3.62
91 92 1.779061 AACCTCGCCACATCCAGGTT 61.779 55.000 0.00 0.00 43.20 3.50
92 93 2.185310 GAACCTCGCCACATCCAGGT 62.185 60.000 0.00 0.00 41.27 4.00
93 94 1.450312 GAACCTCGCCACATCCAGG 60.450 63.158 0.00 0.00 0.00 4.45
94 95 1.450312 GGAACCTCGCCACATCCAG 60.450 63.158 0.00 0.00 0.00 3.86
95 96 1.773856 TTGGAACCTCGCCACATCCA 61.774 55.000 0.00 0.00 38.36 3.41
96 97 1.002624 TTGGAACCTCGCCACATCC 60.003 57.895 0.00 0.00 34.56 3.51
97 98 0.321653 AGTTGGAACCTCGCCACATC 60.322 55.000 0.00 0.00 34.56 3.06
98 99 0.606401 CAGTTGGAACCTCGCCACAT 60.606 55.000 0.00 0.00 34.56 3.21
99 100 1.227823 CAGTTGGAACCTCGCCACA 60.228 57.895 0.00 0.00 34.56 4.17
100 101 0.321653 ATCAGTTGGAACCTCGCCAC 60.322 55.000 0.00 0.00 34.56 5.01
101 102 0.321564 CATCAGTTGGAACCTCGCCA 60.322 55.000 0.00 0.00 0.00 5.69
102 103 2.471255 CATCAGTTGGAACCTCGCC 58.529 57.895 0.00 0.00 0.00 5.54
112 113 0.391661 ACTAGCGGCACCATCAGTTG 60.392 55.000 1.45 0.00 0.00 3.16
113 114 0.391661 CACTAGCGGCACCATCAGTT 60.392 55.000 1.45 0.00 0.00 3.16
114 115 1.219124 CACTAGCGGCACCATCAGT 59.781 57.895 1.45 0.00 0.00 3.41
115 116 1.086067 CACACTAGCGGCACCATCAG 61.086 60.000 1.45 0.00 0.00 2.90
116 117 1.079197 CACACTAGCGGCACCATCA 60.079 57.895 1.45 0.00 0.00 3.07
117 118 2.464459 GCACACTAGCGGCACCATC 61.464 63.158 1.45 0.00 0.00 3.51
118 119 2.436646 GCACACTAGCGGCACCAT 60.437 61.111 1.45 0.00 0.00 3.55
119 120 3.589654 GAGCACACTAGCGGCACCA 62.590 63.158 1.45 0.00 40.15 4.17
120 121 2.815647 GAGCACACTAGCGGCACC 60.816 66.667 1.45 0.00 40.15 5.01
121 122 1.021390 AATGAGCACACTAGCGGCAC 61.021 55.000 1.45 0.00 40.15 5.01
122 123 0.534873 TAATGAGCACACTAGCGGCA 59.465 50.000 1.45 0.00 40.15 5.69
123 124 1.594862 CTTAATGAGCACACTAGCGGC 59.405 52.381 0.00 0.00 40.15 6.53
124 125 3.165058 TCTTAATGAGCACACTAGCGG 57.835 47.619 0.00 0.00 40.15 5.52
125 126 5.725110 AATTCTTAATGAGCACACTAGCG 57.275 39.130 0.00 0.00 40.15 4.26
126 127 8.202745 ACTTAATTCTTAATGAGCACACTAGC 57.797 34.615 0.00 0.00 0.00 3.42
128 129 9.314321 GCTACTTAATTCTTAATGAGCACACTA 57.686 33.333 0.00 0.00 34.95 2.74
129 130 7.010552 CGCTACTTAATTCTTAATGAGCACACT 59.989 37.037 10.79 0.00 34.72 3.55
130 131 7.119997 CGCTACTTAATTCTTAATGAGCACAC 58.880 38.462 10.79 0.00 34.72 3.82
131 132 6.238103 GCGCTACTTAATTCTTAATGAGCACA 60.238 38.462 0.00 0.00 34.72 4.57
132 133 6.130058 GCGCTACTTAATTCTTAATGAGCAC 58.870 40.000 0.00 0.00 34.72 4.40
133 134 5.815222 TGCGCTACTTAATTCTTAATGAGCA 59.185 36.000 9.73 0.00 34.72 4.26
134 135 6.287107 TGCGCTACTTAATTCTTAATGAGC 57.713 37.500 9.73 0.00 33.10 4.26
135 136 9.554724 TTTTTGCGCTACTTAATTCTTAATGAG 57.445 29.630 9.73 0.00 0.00 2.90
168 169 3.023832 AGGCCATGCGCTACTTATTTTT 58.976 40.909 9.73 0.00 37.74 1.94
169 170 2.358898 CAGGCCATGCGCTACTTATTTT 59.641 45.455 9.73 0.00 37.74 1.82
170 171 1.949525 CAGGCCATGCGCTACTTATTT 59.050 47.619 9.73 0.00 37.74 1.40
171 172 1.597742 CAGGCCATGCGCTACTTATT 58.402 50.000 9.73 0.00 37.74 1.40
172 173 0.886490 GCAGGCCATGCGCTACTTAT 60.886 55.000 9.73 0.00 46.99 1.73
173 174 1.523711 GCAGGCCATGCGCTACTTA 60.524 57.895 9.73 0.00 46.99 2.24
174 175 2.825836 GCAGGCCATGCGCTACTT 60.826 61.111 9.73 0.00 46.99 2.24
188 189 3.334691 TGATTTCGTAGACCTTTGGCAG 58.665 45.455 0.00 0.00 34.32 4.85
189 190 3.244422 ACTGATTTCGTAGACCTTTGGCA 60.244 43.478 0.00 0.00 34.32 4.92
190 191 3.335579 ACTGATTTCGTAGACCTTTGGC 58.664 45.455 0.00 0.00 34.32 4.52
191 192 4.755123 ACAACTGATTTCGTAGACCTTTGG 59.245 41.667 0.00 0.00 34.32 3.28
192 193 5.924475 ACAACTGATTTCGTAGACCTTTG 57.076 39.130 0.00 0.00 34.32 2.77
193 194 5.176958 CGAACAACTGATTTCGTAGACCTTT 59.823 40.000 0.00 0.00 39.79 3.11
194 195 4.684703 CGAACAACTGATTTCGTAGACCTT 59.315 41.667 0.00 0.00 39.79 3.50
195 196 4.235360 CGAACAACTGATTTCGTAGACCT 58.765 43.478 0.00 0.00 39.79 3.85
196 197 3.367025 CCGAACAACTGATTTCGTAGACC 59.633 47.826 3.35 0.00 42.45 3.85
197 198 3.985925 ACCGAACAACTGATTTCGTAGAC 59.014 43.478 3.35 0.00 42.45 2.59
198 199 3.985279 CACCGAACAACTGATTTCGTAGA 59.015 43.478 3.35 0.00 42.45 2.59
199 200 3.423123 GCACCGAACAACTGATTTCGTAG 60.423 47.826 3.35 0.00 42.45 3.51
200 201 2.477375 GCACCGAACAACTGATTTCGTA 59.523 45.455 3.35 0.00 42.45 3.43
201 202 1.263217 GCACCGAACAACTGATTTCGT 59.737 47.619 3.35 0.00 42.45 3.85
202 203 1.399727 GGCACCGAACAACTGATTTCG 60.400 52.381 0.00 0.00 43.40 3.46
203 204 1.606668 TGGCACCGAACAACTGATTTC 59.393 47.619 0.00 0.00 0.00 2.17
204 205 1.686355 TGGCACCGAACAACTGATTT 58.314 45.000 0.00 0.00 0.00 2.17
205 206 1.336755 GTTGGCACCGAACAACTGATT 59.663 47.619 0.00 0.00 42.67 2.57
206 207 0.951558 GTTGGCACCGAACAACTGAT 59.048 50.000 0.00 0.00 42.67 2.90
207 208 0.393132 TGTTGGCACCGAACAACTGA 60.393 50.000 8.71 0.00 45.36 3.41
208 209 0.667993 ATGTTGGCACCGAACAACTG 59.332 50.000 8.71 0.00 45.36 3.16
209 210 1.398692 AATGTTGGCACCGAACAACT 58.601 45.000 8.71 0.00 45.36 3.16
223 224 2.827921 GACTCATGCCCTCCAAAATGTT 59.172 45.455 0.00 0.00 0.00 2.71
237 238 3.057526 TCACGCCTATAATCGGACTCATG 60.058 47.826 0.00 0.00 0.00 3.07
238 239 3.154710 TCACGCCTATAATCGGACTCAT 58.845 45.455 0.00 0.00 0.00 2.90
239 240 2.578786 TCACGCCTATAATCGGACTCA 58.421 47.619 0.00 0.00 0.00 3.41
242 243 3.714391 AGTTTCACGCCTATAATCGGAC 58.286 45.455 0.00 0.00 0.00 4.79
245 246 5.907197 AATGAGTTTCACGCCTATAATCG 57.093 39.130 0.00 0.00 0.00 3.34
246 247 6.564125 CGGAAATGAGTTTCACGCCTATAATC 60.564 42.308 3.64 0.00 44.42 1.75
248 249 4.569162 CGGAAATGAGTTTCACGCCTATAA 59.431 41.667 3.64 0.00 44.42 0.98
251 252 2.028839 TCGGAAATGAGTTTCACGCCTA 60.029 45.455 3.64 0.00 44.42 3.93
253 254 1.136057 GTCGGAAATGAGTTTCACGCC 60.136 52.381 3.64 0.00 44.42 5.68
256 257 3.186613 GTCTGGTCGGAAATGAGTTTCAC 59.813 47.826 3.64 0.00 44.42 3.18
261 262 3.600388 GATTGTCTGGTCGGAAATGAGT 58.400 45.455 0.00 0.00 0.00 3.41
265 266 2.762535 ACGATTGTCTGGTCGGAAAT 57.237 45.000 0.00 0.00 41.87 2.17
269 270 3.744426 ACTAAAAACGATTGTCTGGTCGG 59.256 43.478 0.00 0.00 41.87 4.79
276 277 7.855904 AGAACATCACAACTAAAAACGATTGTC 59.144 33.333 0.00 0.00 33.05 3.18
278 279 8.560576 AAGAACATCACAACTAAAAACGATTG 57.439 30.769 0.00 0.00 0.00 2.67
279 280 8.402472 TGAAGAACATCACAACTAAAAACGATT 58.598 29.630 0.00 0.00 0.00 3.34
287 288 6.486320 TGCATCTTGAAGAACATCACAACTAA 59.514 34.615 0.00 0.00 0.00 2.24
294 295 7.451501 TTGTTATGCATCTTGAAGAACATCA 57.548 32.000 14.81 7.68 30.71 3.07
296 297 8.308931 ACATTTGTTATGCATCTTGAAGAACAT 58.691 29.630 0.19 15.46 32.23 2.71
297 298 7.660112 ACATTTGTTATGCATCTTGAAGAACA 58.340 30.769 0.19 3.37 0.00 3.18
354 362 7.936584 TCATCGGTCAACTAAGAAAACAAAAT 58.063 30.769 0.00 0.00 0.00 1.82
371 384 2.167861 GGCACGAAGCTCATCGGTC 61.168 63.158 12.18 3.48 46.82 4.79
372 385 2.125512 GGCACGAAGCTCATCGGT 60.126 61.111 12.18 0.00 46.82 4.69
425 439 2.509052 TGGCTACATACGATGCTCAC 57.491 50.000 0.00 0.00 0.00 3.51
458 472 6.434965 TCAAGAAATGATGCAATCTTGGAAGA 59.565 34.615 19.98 0.00 45.81 2.87
516 530 4.946772 TCCCATGATTTTACGAGCAAATGA 59.053 37.500 0.00 0.00 0.00 2.57
522 536 2.565841 AGCTCCCATGATTTTACGAGC 58.434 47.619 0.00 0.00 42.37 5.03
525 539 3.466836 TGCTAGCTCCCATGATTTTACG 58.533 45.455 17.23 0.00 0.00 3.18
527 541 4.828939 CCAATGCTAGCTCCCATGATTTTA 59.171 41.667 17.23 0.00 0.00 1.52
585 605 2.872245 TGACAAGTTCCTTTCAAGCGAG 59.128 45.455 0.00 0.00 0.00 5.03
588 608 2.358898 TGCTGACAAGTTCCTTTCAAGC 59.641 45.455 0.00 0.00 0.00 4.01
606 628 8.579850 TTTGTAGATGGAGATTTGTAATTGCT 57.420 30.769 0.00 0.00 0.00 3.91
615 637 6.552008 TGACCCTTTTTGTAGATGGAGATTT 58.448 36.000 0.00 0.00 0.00 2.17
747 786 1.221021 GAAGGGTTCCCGGCTACTG 59.779 63.158 0.00 0.00 0.00 2.74
768 807 5.665916 ACTGATTGATGATTTTGGGGTTC 57.334 39.130 0.00 0.00 0.00 3.62
870 918 5.903764 TTTGTTTTGGATTTGCGATGAAG 57.096 34.783 0.00 0.00 0.00 3.02
877 925 4.026062 GGAGACGTTTTGTTTTGGATTTGC 60.026 41.667 0.00 0.00 0.00 3.68
924 972 2.849646 AGAAGGGGGCGGCTATCC 60.850 66.667 9.56 8.66 0.00 2.59
925 973 2.744377 GAGAAGGGGGCGGCTATC 59.256 66.667 9.56 2.34 0.00 2.08
926 974 2.849646 GGAGAAGGGGGCGGCTAT 60.850 66.667 9.56 0.00 0.00 2.97
1227 1278 2.970974 GCACAGCAGAAACGCCTCC 61.971 63.158 0.00 0.00 0.00 4.30
1380 1431 4.308458 CGCCGGACCTGGTCAACA 62.308 66.667 26.94 0.00 33.68 3.33
1445 1496 2.764128 GGCCCTCGTGGATCTCCA 60.764 66.667 4.76 0.00 45.30 3.86
2103 2157 2.594013 TTCATGGCGCTGCACACA 60.594 55.556 7.64 0.00 0.00 3.72
2268 2322 1.210672 GAGAGCTACCTATCGCCGC 59.789 63.158 0.00 0.00 0.00 6.53
2478 2541 0.391130 ACTCAAGAATTAGCCGCGCA 60.391 50.000 8.75 0.00 0.00 6.09
2622 2701 2.027285 TCCAGATGACGCCAAAGATGAA 60.027 45.455 0.00 0.00 0.00 2.57
2627 2706 1.522668 TGTTCCAGATGACGCCAAAG 58.477 50.000 0.00 0.00 0.00 2.77
2633 2712 5.362556 AACTGAAAATGTTCCAGATGACG 57.637 39.130 0.00 0.00 32.28 4.35
2672 2751 9.429359 CATTTCTCTAGACAAAGAGTACAATGT 57.571 33.333 0.00 0.00 43.02 2.71
2689 2770 3.603158 TGTAACTGCGGCATTTCTCTA 57.397 42.857 8.95 0.00 0.00 2.43
2828 2911 4.168675 TGGGAATTTTATCCTGAGATGCCT 59.831 41.667 0.00 0.00 39.57 4.75
2933 3023 4.326826 CTCTTGCCACTTGGTATTCAGAA 58.673 43.478 0.00 0.00 37.57 3.02
2947 3037 4.392047 CATATGCTATTGTCCTCTTGCCA 58.608 43.478 0.00 0.00 0.00 4.92
3000 3119 7.995663 AGCTATACATGGTGGGGATTTTATTA 58.004 34.615 0.00 0.00 0.00 0.98
3001 3120 6.863322 AGCTATACATGGTGGGGATTTTATT 58.137 36.000 0.00 0.00 0.00 1.40
3002 3121 6.468972 AGCTATACATGGTGGGGATTTTAT 57.531 37.500 0.00 0.00 0.00 1.40
3003 3122 5.922960 AGCTATACATGGTGGGGATTTTA 57.077 39.130 0.00 0.00 0.00 1.52
3004 3123 4.814224 AGCTATACATGGTGGGGATTTT 57.186 40.909 0.00 0.00 0.00 1.82
3005 3124 4.814224 AAGCTATACATGGTGGGGATTT 57.186 40.909 0.00 0.00 0.00 2.17
3006 3125 4.814224 AAAGCTATACATGGTGGGGATT 57.186 40.909 0.00 0.00 0.00 3.01
3007 3126 4.814224 AAAAGCTATACATGGTGGGGAT 57.186 40.909 0.00 0.00 0.00 3.85
3008 3127 4.475381 TGTAAAAGCTATACATGGTGGGGA 59.525 41.667 7.92 0.00 0.00 4.81
3009 3128 4.787551 TGTAAAAGCTATACATGGTGGGG 58.212 43.478 7.92 0.00 0.00 4.96
3014 3133 5.234329 CGTGGTCTGTAAAAGCTATACATGG 59.766 44.000 11.47 3.60 33.12 3.66
3015 3134 5.234329 CCGTGGTCTGTAAAAGCTATACATG 59.766 44.000 11.47 0.00 33.12 3.21
3017 3136 4.221262 ACCGTGGTCTGTAAAAGCTATACA 59.779 41.667 10.78 10.78 0.00 2.29
3018 3137 4.752146 ACCGTGGTCTGTAAAAGCTATAC 58.248 43.478 0.00 0.00 0.00 1.47
3019 3138 5.410355 AACCGTGGTCTGTAAAAGCTATA 57.590 39.130 0.00 0.00 0.00 1.31
3023 3142 6.484818 TTATTAACCGTGGTCTGTAAAAGC 57.515 37.500 0.00 0.00 0.00 3.51
3026 3145 9.723601 ACTATTTTATTAACCGTGGTCTGTAAA 57.276 29.630 0.00 0.00 0.00 2.01
3027 3146 9.369904 GACTATTTTATTAACCGTGGTCTGTAA 57.630 33.333 0.00 0.00 0.00 2.41
3028 3147 8.752187 AGACTATTTTATTAACCGTGGTCTGTA 58.248 33.333 0.00 0.00 0.00 2.74
3034 3218 6.537301 TCTGCAGACTATTTTATTAACCGTGG 59.463 38.462 13.74 0.00 0.00 4.94
3049 3233 5.793817 TGCAATTTCTTACTCTGCAGACTA 58.206 37.500 13.74 5.58 38.06 2.59
3141 3328 3.319122 ACAAGGAAAGAAGAACACATGCC 59.681 43.478 0.00 0.00 0.00 4.40
3194 3383 2.075355 TTGGCCCGATCAAGGTTGGT 62.075 55.000 0.00 0.00 0.00 3.67
3195 3384 0.897863 TTTGGCCCGATCAAGGTTGG 60.898 55.000 0.00 0.00 0.00 3.77
3196 3385 0.965439 TTTTGGCCCGATCAAGGTTG 59.035 50.000 0.00 0.00 0.00 3.77
3197 3386 1.618343 CTTTTTGGCCCGATCAAGGTT 59.382 47.619 0.00 0.00 0.00 3.50
3198 3387 1.256812 CTTTTTGGCCCGATCAAGGT 58.743 50.000 0.00 0.00 0.00 3.50
3199 3388 0.532115 CCTTTTTGGCCCGATCAAGG 59.468 55.000 0.00 0.73 0.00 3.61


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

AutoCloner maintained by Alex Coulton.