Multiple sequence alignment - TraesCS1D01G108100

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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 TraesCS1D01G108100 chr1D 100.000 2741 0 0 1 2741 100902416 100905156 0.000000e+00 5062.0
1 TraesCS1D01G108100 chr1D 83.444 151 18 6 255 402 367836858 367837004 1.710000e-27 134.0
2 TraesCS1D01G108100 chr1A 90.585 1179 67 18 848 2008 104433604 104432452 0.000000e+00 1522.0
3 TraesCS1D01G108100 chr1A 88.146 658 61 11 206 857 104434661 104434015 0.000000e+00 767.0
4 TraesCS1D01G108100 chr1A 81.765 170 23 8 247 412 463190763 463190598 4.760000e-28 135.0
5 TraesCS1D01G108100 chr1B 90.388 1134 77 13 409 1529 150778293 150777179 0.000000e+00 1461.0
6 TraesCS1D01G108100 chr1B 90.633 395 32 3 1521 1912 150776983 150776591 1.120000e-143 520.0
7 TraesCS1D01G108100 chr1B 93.709 302 15 4 116 417 150797655 150797358 1.500000e-122 449.0
8 TraesCS1D01G108100 chr1B 86.977 215 17 6 409 615 150780152 150779941 5.900000e-57 231.0
9 TraesCS1D01G108100 chr1B 94.737 95 5 0 1914 2008 150776050 150775956 6.120000e-32 148.0
10 TraesCS1D01G108100 chr1B 97.500 40 1 0 333 372 527380620 527380581 4.900000e-08 69.4
11 TraesCS1D01G108100 chr3D 96.458 734 24 2 2008 2741 10001633 10002364 0.000000e+00 1210.0
12 TraesCS1D01G108100 chr3D 84.034 119 14 3 280 396 553869293 553869408 2.890000e-20 110.0
13 TraesCS1D01G108100 chr6D 94.708 737 36 2 2006 2741 49849685 49850419 0.000000e+00 1142.0
14 TraesCS1D01G108100 chr6B 94.286 735 38 3 2007 2741 488872997 488873727 0.000000e+00 1122.0
15 TraesCS1D01G108100 chr6B 88.983 118 8 3 4 121 668893727 668893839 1.020000e-29 141.0
16 TraesCS1D01G108100 chr2A 93.733 734 43 2 2008 2741 718110936 718111666 0.000000e+00 1098.0
17 TraesCS1D01G108100 chr5D 91.995 737 51 7 2007 2741 219540140 219539410 0.000000e+00 1027.0
18 TraesCS1D01G108100 chr7D 91.896 728 51 7 2007 2733 236008450 236009170 0.000000e+00 1011.0
19 TraesCS1D01G108100 chr5A 90.654 749 59 8 2002 2741 708302464 708301718 0.000000e+00 985.0
20 TraesCS1D01G108100 chr3B 90.470 745 61 7 1998 2741 223509396 223510131 0.000000e+00 974.0
21 TraesCS1D01G108100 chr2D 90.761 736 57 9 2008 2741 385698223 385697497 0.000000e+00 972.0
22 TraesCS1D01G108100 chr2D 90.909 121 11 0 1 121 580260522 580260642 2.180000e-36 163.0
23 TraesCS1D01G108100 chr2D 93.103 58 1 1 113 170 580260677 580260731 6.290000e-12 82.4
24 TraesCS1D01G108100 chr4D 90.909 121 11 0 1 121 419336623 419336503 2.180000e-36 163.0
25 TraesCS1D01G108100 chr4D 88.525 122 13 1 1 121 450160087 450159966 2.200000e-31 147.0
26 TraesCS1D01G108100 chr4B 90.909 121 11 0 1 121 599823618 599823498 2.180000e-36 163.0
27 TraesCS1D01G108100 chr4B 87.302 126 11 4 1 121 68653892 68654017 3.680000e-29 139.0
28 TraesCS1D01G108100 chr3A 84.375 160 19 3 255 412 87927674 87927519 4.730000e-33 152.0
29 TraesCS1D01G108100 chr7B 88.525 122 13 1 1 121 222550398 222550519 2.200000e-31 147.0
30 TraesCS1D01G108100 chr4A 88.430 121 14 0 1 121 169690173 169690053 2.200000e-31 147.0
31 TraesCS1D01G108100 chr2B 88.430 121 14 0 1 121 76071511 76071631 2.200000e-31 147.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G108100 chr1D 100902416 100905156 2740 False 5062.0 5062 100.00000 1 2741 1 chr1D.!!$F1 2740
1 TraesCS1D01G108100 chr1A 104432452 104434661 2209 True 1144.5 1522 89.36550 206 2008 2 chr1A.!!$R2 1802
2 TraesCS1D01G108100 chr1B 150775956 150780152 4196 True 590.0 1461 90.68375 409 2008 4 chr1B.!!$R3 1599
3 TraesCS1D01G108100 chr3D 10001633 10002364 731 False 1210.0 1210 96.45800 2008 2741 1 chr3D.!!$F1 733
4 TraesCS1D01G108100 chr6D 49849685 49850419 734 False 1142.0 1142 94.70800 2006 2741 1 chr6D.!!$F1 735
5 TraesCS1D01G108100 chr6B 488872997 488873727 730 False 1122.0 1122 94.28600 2007 2741 1 chr6B.!!$F1 734
6 TraesCS1D01G108100 chr2A 718110936 718111666 730 False 1098.0 1098 93.73300 2008 2741 1 chr2A.!!$F1 733
7 TraesCS1D01G108100 chr5D 219539410 219540140 730 True 1027.0 1027 91.99500 2007 2741 1 chr5D.!!$R1 734
8 TraesCS1D01G108100 chr7D 236008450 236009170 720 False 1011.0 1011 91.89600 2007 2733 1 chr7D.!!$F1 726
9 TraesCS1D01G108100 chr5A 708301718 708302464 746 True 985.0 985 90.65400 2002 2741 1 chr5A.!!$R1 739
10 TraesCS1D01G108100 chr3B 223509396 223510131 735 False 974.0 974 90.47000 1998 2741 1 chr3B.!!$F1 743
11 TraesCS1D01G108100 chr2D 385697497 385698223 726 True 972.0 972 90.76100 2008 2741 1 chr2D.!!$R1 733

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
580 2446 0.116342 TGAGTAGCTCCCCCTTGTGA 59.884 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 4310 0.03213 AGGCATACCAGTGCGTATCG 59.968 55.0 2.37 0.0 45.97 2.92 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
22 23 5.457650 GCGAGGACAGAAAATTCTCTAAC 57.542 43.478 0.00 0.00 34.74 2.34
23 24 4.330347 GCGAGGACAGAAAATTCTCTAACC 59.670 45.833 0.00 0.00 34.74 2.85
24 25 5.725362 CGAGGACAGAAAATTCTCTAACCT 58.275 41.667 5.86 5.86 34.74 3.50
25 26 5.808030 CGAGGACAGAAAATTCTCTAACCTC 59.192 44.000 16.89 16.89 40.16 3.85
26 27 6.572509 CGAGGACAGAAAATTCTCTAACCTCA 60.573 42.308 22.22 0.00 41.73 3.86
27 28 7.264294 AGGACAGAAAATTCTCTAACCTCAT 57.736 36.000 1.53 0.00 34.74 2.90
28 29 7.108847 AGGACAGAAAATTCTCTAACCTCATG 58.891 38.462 1.53 0.00 34.74 3.07
29 30 7.038017 AGGACAGAAAATTCTCTAACCTCATGA 60.038 37.037 0.00 0.00 34.74 3.07
30 31 7.065204 GGACAGAAAATTCTCTAACCTCATGAC 59.935 40.741 0.00 0.00 34.74 3.06
31 32 7.453393 ACAGAAAATTCTCTAACCTCATGACA 58.547 34.615 0.00 0.00 34.74 3.58
32 33 8.105829 ACAGAAAATTCTCTAACCTCATGACAT 58.894 33.333 0.00 0.00 34.74 3.06
33 34 8.610896 CAGAAAATTCTCTAACCTCATGACATC 58.389 37.037 0.00 0.00 34.74 3.06
34 35 7.493971 AGAAAATTCTCTAACCTCATGACATCG 59.506 37.037 0.00 0.00 29.94 3.84
35 36 3.717400 TCTCTAACCTCATGACATCGC 57.283 47.619 0.00 0.00 0.00 4.58
36 37 2.362397 TCTCTAACCTCATGACATCGCC 59.638 50.000 0.00 0.00 0.00 5.54
37 38 2.101415 CTCTAACCTCATGACATCGCCA 59.899 50.000 0.00 0.00 0.00 5.69
38 39 2.499693 TCTAACCTCATGACATCGCCAA 59.500 45.455 0.00 0.00 0.00 4.52
39 40 2.198827 AACCTCATGACATCGCCAAA 57.801 45.000 0.00 0.00 0.00 3.28
40 41 2.198827 ACCTCATGACATCGCCAAAA 57.801 45.000 0.00 0.00 0.00 2.44
41 42 2.086869 ACCTCATGACATCGCCAAAAG 58.913 47.619 0.00 0.00 0.00 2.27
42 43 2.290260 ACCTCATGACATCGCCAAAAGA 60.290 45.455 0.00 0.00 0.00 2.52
43 44 2.749076 CCTCATGACATCGCCAAAAGAA 59.251 45.455 0.00 0.00 0.00 2.52
44 45 3.426695 CCTCATGACATCGCCAAAAGAAC 60.427 47.826 0.00 0.00 0.00 3.01
45 46 2.159430 TCATGACATCGCCAAAAGAACG 59.841 45.455 0.00 0.00 0.00 3.95
46 47 1.872388 TGACATCGCCAAAAGAACGA 58.128 45.000 0.00 0.00 40.53 3.85
47 48 1.798223 TGACATCGCCAAAAGAACGAG 59.202 47.619 0.00 0.00 39.48 4.18
48 49 2.066262 GACATCGCCAAAAGAACGAGA 58.934 47.619 0.00 0.00 39.48 4.04
49 50 2.069273 ACATCGCCAAAAGAACGAGAG 58.931 47.619 0.00 0.00 39.48 3.20
81 82 9.599866 TTATTCTCACAAAATACGATGATCACT 57.400 29.630 0.00 0.00 0.00 3.41
83 84 8.634475 TTCTCACAAAATACGATGATCACTAG 57.366 34.615 0.00 0.00 0.00 2.57
84 85 7.996385 TCTCACAAAATACGATGATCACTAGA 58.004 34.615 0.00 0.00 0.00 2.43
85 86 7.915923 TCTCACAAAATACGATGATCACTAGAC 59.084 37.037 0.00 0.00 0.00 2.59
86 87 6.691388 TCACAAAATACGATGATCACTAGACG 59.309 38.462 0.00 2.16 0.00 4.18
87 88 6.691388 CACAAAATACGATGATCACTAGACGA 59.309 38.462 0.00 0.00 0.00 4.20
88 89 7.379797 CACAAAATACGATGATCACTAGACGAT 59.620 37.037 0.00 0.00 0.00 3.73
89 90 7.379797 ACAAAATACGATGATCACTAGACGATG 59.620 37.037 0.00 0.00 0.00 3.84
90 91 6.803154 AATACGATGATCACTAGACGATGA 57.197 37.500 0.00 0.00 0.00 2.92
91 92 4.475763 ACGATGATCACTAGACGATGAC 57.524 45.455 0.00 0.00 0.00 3.06
92 93 3.059529 ACGATGATCACTAGACGATGACG 60.060 47.826 0.00 6.20 45.75 4.35
93 94 3.184581 CGATGATCACTAGACGATGACGA 59.815 47.826 0.00 0.00 42.66 4.20
94 95 4.318831 CGATGATCACTAGACGATGACGAA 60.319 45.833 0.00 0.00 42.66 3.85
95 96 4.957759 TGATCACTAGACGATGACGAAA 57.042 40.909 0.00 0.00 42.66 3.46
96 97 5.305139 TGATCACTAGACGATGACGAAAA 57.695 39.130 0.00 0.00 42.66 2.29
97 98 5.891451 TGATCACTAGACGATGACGAAAAT 58.109 37.500 0.00 0.00 42.66 1.82
98 99 5.971792 TGATCACTAGACGATGACGAAAATC 59.028 40.000 0.00 0.00 42.66 2.17
115 116 6.912815 CGAAAATCGTAGTACTGTGAAGATG 58.087 40.000 5.39 0.00 34.72 2.90
116 117 6.506513 CGAAAATCGTAGTACTGTGAAGATGC 60.507 42.308 5.39 0.00 34.72 3.91
117 118 3.400505 TCGTAGTACTGTGAAGATGCG 57.599 47.619 5.39 0.00 0.00 4.73
118 119 3.004862 TCGTAGTACTGTGAAGATGCGA 58.995 45.455 5.39 0.00 0.00 5.10
119 120 3.063588 TCGTAGTACTGTGAAGATGCGAG 59.936 47.826 5.39 0.00 0.00 5.03
120 121 2.949451 AGTACTGTGAAGATGCGAGG 57.051 50.000 0.00 0.00 0.00 4.63
121 122 1.478510 AGTACTGTGAAGATGCGAGGG 59.521 52.381 0.00 0.00 0.00 4.30
122 123 0.824109 TACTGTGAAGATGCGAGGGG 59.176 55.000 0.00 0.00 0.00 4.79
123 124 0.904865 ACTGTGAAGATGCGAGGGGA 60.905 55.000 0.00 0.00 0.00 4.81
124 125 0.460987 CTGTGAAGATGCGAGGGGAC 60.461 60.000 0.00 0.00 0.00 4.46
144 145 2.969827 AAAAATTCCTGGCGGCGG 59.030 55.556 11.58 11.58 0.00 6.13
145 146 3.295304 AAAAATTCCTGGCGGCGGC 62.295 57.895 27.76 27.76 38.90 6.53
164 165 4.410743 GCGCTGCTGCAAACCCTC 62.411 66.667 16.29 0.00 39.64 4.30
165 166 4.093952 CGCTGCTGCAAACCCTCG 62.094 66.667 16.29 0.00 39.64 4.63
166 167 4.410743 GCTGCTGCAAACCCTCGC 62.411 66.667 11.11 0.00 39.41 5.03
167 168 2.670934 CTGCTGCAAACCCTCGCT 60.671 61.111 3.02 0.00 0.00 4.93
168 169 2.203337 TGCTGCAAACCCTCGCTT 60.203 55.556 0.00 0.00 0.00 4.68
169 170 2.256461 GCTGCAAACCCTCGCTTG 59.744 61.111 0.00 0.00 0.00 4.01
170 171 2.555547 GCTGCAAACCCTCGCTTGT 61.556 57.895 0.00 0.00 0.00 3.16
171 172 1.576421 CTGCAAACCCTCGCTTGTC 59.424 57.895 0.00 0.00 0.00 3.18
172 173 1.856265 CTGCAAACCCTCGCTTGTCC 61.856 60.000 0.00 0.00 0.00 4.02
173 174 2.966309 GCAAACCCTCGCTTGTCCG 61.966 63.158 0.00 0.00 0.00 4.79
174 175 1.597027 CAAACCCTCGCTTGTCCGT 60.597 57.895 0.00 0.00 0.00 4.69
175 176 1.147600 AAACCCTCGCTTGTCCGTT 59.852 52.632 0.00 0.00 0.00 4.44
176 177 0.464916 AAACCCTCGCTTGTCCGTTT 60.465 50.000 0.00 0.00 0.00 3.60
177 178 0.464916 AACCCTCGCTTGTCCGTTTT 60.465 50.000 0.00 0.00 0.00 2.43
178 179 1.164041 ACCCTCGCTTGTCCGTTTTG 61.164 55.000 0.00 0.00 0.00 2.44
179 180 0.882927 CCCTCGCTTGTCCGTTTTGA 60.883 55.000 0.00 0.00 0.00 2.69
180 181 1.156736 CCTCGCTTGTCCGTTTTGAT 58.843 50.000 0.00 0.00 0.00 2.57
181 182 1.135972 CCTCGCTTGTCCGTTTTGATG 60.136 52.381 0.00 0.00 0.00 3.07
182 183 1.798223 CTCGCTTGTCCGTTTTGATGA 59.202 47.619 0.00 0.00 0.00 2.92
183 184 2.416547 CTCGCTTGTCCGTTTTGATGAT 59.583 45.455 0.00 0.00 0.00 2.45
184 185 2.415168 TCGCTTGTCCGTTTTGATGATC 59.585 45.455 0.00 0.00 0.00 2.92
185 186 2.416547 CGCTTGTCCGTTTTGATGATCT 59.583 45.455 0.00 0.00 0.00 2.75
186 187 3.725895 CGCTTGTCCGTTTTGATGATCTG 60.726 47.826 0.00 0.00 0.00 2.90
187 188 3.426695 GCTTGTCCGTTTTGATGATCTGG 60.427 47.826 0.00 0.00 0.00 3.86
188 189 3.417069 TGTCCGTTTTGATGATCTGGT 57.583 42.857 0.00 0.00 0.00 4.00
189 190 3.073678 TGTCCGTTTTGATGATCTGGTG 58.926 45.455 0.00 0.00 0.00 4.17
190 191 2.420022 GTCCGTTTTGATGATCTGGTGG 59.580 50.000 0.00 0.00 0.00 4.61
191 192 2.039746 TCCGTTTTGATGATCTGGTGGT 59.960 45.455 0.00 0.00 0.00 4.16
192 193 2.819608 CCGTTTTGATGATCTGGTGGTT 59.180 45.455 0.00 0.00 0.00 3.67
193 194 3.119849 CCGTTTTGATGATCTGGTGGTTC 60.120 47.826 0.00 0.00 0.00 3.62
194 195 3.119849 CGTTTTGATGATCTGGTGGTTCC 60.120 47.826 0.00 0.00 0.00 3.62
195 196 4.082125 GTTTTGATGATCTGGTGGTTCCT 58.918 43.478 0.00 0.00 37.07 3.36
196 197 5.253330 GTTTTGATGATCTGGTGGTTCCTA 58.747 41.667 0.00 0.00 37.07 2.94
197 198 5.512942 TTTGATGATCTGGTGGTTCCTAA 57.487 39.130 0.00 0.00 37.07 2.69
198 199 4.487714 TGATGATCTGGTGGTTCCTAAC 57.512 45.455 0.00 0.00 37.07 2.34
199 200 3.843619 TGATGATCTGGTGGTTCCTAACA 59.156 43.478 0.00 0.00 37.07 2.41
200 201 4.474651 TGATGATCTGGTGGTTCCTAACAT 59.525 41.667 0.00 0.00 37.07 2.71
201 202 4.487714 TGATCTGGTGGTTCCTAACATC 57.512 45.455 0.00 0.00 37.07 3.06
202 203 3.843619 TGATCTGGTGGTTCCTAACATCA 59.156 43.478 0.00 0.00 37.07 3.07
203 204 3.981071 TCTGGTGGTTCCTAACATCAG 57.019 47.619 0.00 0.00 45.03 2.90
204 205 3.248024 TCTGGTGGTTCCTAACATCAGT 58.752 45.455 3.62 0.00 44.25 3.41
208 209 4.348461 TGGTGGTTCCTAACATCAGTGTAA 59.652 41.667 0.00 0.00 35.73 2.41
212 213 5.761234 TGGTTCCTAACATCAGTGTAACAAC 59.239 40.000 0.00 0.00 41.43 3.32
215 216 7.040686 GGTTCCTAACATCAGTGTAACAACATT 60.041 37.037 0.00 0.00 41.43 2.71
243 244 8.413309 AAACATTTCTTGAGATCCAGAATTGA 57.587 30.769 18.12 0.00 0.00 2.57
244 245 7.627298 ACATTTCTTGAGATCCAGAATTGAG 57.373 36.000 18.12 5.33 0.00 3.02
245 246 6.602406 ACATTTCTTGAGATCCAGAATTGAGG 59.398 38.462 18.12 2.90 0.00 3.86
253 254 2.726821 TCCAGAATTGAGGTCAATGCC 58.273 47.619 5.98 2.38 45.06 4.40
268 269 5.177326 GTCAATGCCATAATGAGCCAAAAA 58.823 37.500 0.00 0.00 0.00 1.94
269 270 5.063817 GTCAATGCCATAATGAGCCAAAAAC 59.936 40.000 0.00 0.00 0.00 2.43
270 271 5.046448 TCAATGCCATAATGAGCCAAAAACT 60.046 36.000 0.00 0.00 0.00 2.66
274 275 6.397272 TGCCATAATGAGCCAAAAACTAAAG 58.603 36.000 0.00 0.00 0.00 1.85
275 276 6.014669 TGCCATAATGAGCCAAAAACTAAAGT 60.015 34.615 0.00 0.00 0.00 2.66
279 280 6.463995 AATGAGCCAAAAACTAAAGTCACA 57.536 33.333 0.00 0.00 0.00 3.58
339 340 8.868916 TGTCTTTTGTTTTTCAAGCTATGTTTC 58.131 29.630 0.00 0.00 37.35 2.78
375 376 8.984891 TTCAAATTTTATGACAGCCTACATTG 57.015 30.769 0.00 0.00 0.00 2.82
378 379 9.027129 CAAATTTTATGACAGCCTACATTGATG 57.973 33.333 0.00 0.00 0.00 3.07
390 391 5.106197 GCCTACATTGATGTTGTGTGAATGA 60.106 40.000 1.46 0.00 41.97 2.57
479 2340 5.353400 GGGAACTACGAACCCTCAAAAATAG 59.647 44.000 0.00 0.00 40.39 1.73
513 2374 1.276421 ACGAACTTGCTGTGAGGCTAT 59.724 47.619 0.00 0.00 0.00 2.97
517 2378 3.146104 ACTTGCTGTGAGGCTATTTGT 57.854 42.857 0.00 0.00 0.00 2.83
556 2417 8.571461 ACAAATACAACTTCATGTCATGATCT 57.429 30.769 16.19 1.97 39.39 2.75
561 2422 6.413052 ACAACTTCATGTCATGATCTAGCTT 58.587 36.000 16.19 5.90 39.39 3.74
565 2426 5.866159 TCATGTCATGATCTAGCTTGAGT 57.134 39.130 11.62 0.00 33.59 3.41
566 2427 6.966534 TCATGTCATGATCTAGCTTGAGTA 57.033 37.500 11.62 0.00 33.59 2.59
567 2428 6.979465 TCATGTCATGATCTAGCTTGAGTAG 58.021 40.000 11.62 0.00 33.59 2.57
568 2429 6.516360 TCATGTCATGATCTAGCTTGAGTAGC 60.516 42.308 11.62 0.00 41.49 3.58
580 2446 0.116342 TGAGTAGCTCCCCCTTGTGA 59.884 55.000 0.00 0.00 0.00 3.58
585 2451 1.920835 GCTCCCCCTTGTGAGAGGT 60.921 63.158 0.00 0.00 34.88 3.85
598 2464 2.955660 GTGAGAGGTCAGATCGAGGAAT 59.044 50.000 0.00 0.00 31.53 3.01
601 2467 1.410517 GAGGTCAGATCGAGGAATGCA 59.589 52.381 0.00 0.00 0.00 3.96
612 2478 2.743664 CGAGGAATGCACTCACATTTCA 59.256 45.455 0.00 0.00 40.31 2.69
619 2485 1.394917 GCACTCACATTTCAGCGGTAG 59.605 52.381 0.00 0.00 0.00 3.18
748 2614 4.079253 GGATGTGGTTTCTTTTCAGGCTA 58.921 43.478 0.00 0.00 0.00 3.93
749 2615 4.082733 GGATGTGGTTTCTTTTCAGGCTAC 60.083 45.833 0.00 0.00 0.00 3.58
750 2616 4.164843 TGTGGTTTCTTTTCAGGCTACT 57.835 40.909 0.00 0.00 0.00 2.57
842 2708 2.513157 CGATCGCCGATCAAACGCA 61.513 57.895 25.17 0.00 38.84 5.24
909 3194 2.112297 TTGAGCGTTGGACCCACC 59.888 61.111 0.00 0.00 39.54 4.61
934 3219 1.379443 AGTCACTGATCCGCCCGTA 60.379 57.895 0.00 0.00 0.00 4.02
962 3247 2.022129 CAGGAAGTCGTCGGCACAC 61.022 63.158 0.00 0.00 0.00 3.82
963 3248 2.028484 GGAAGTCGTCGGCACACA 59.972 61.111 0.00 0.00 0.00 3.72
975 3260 1.606668 CGGCACACACAACCAACTATT 59.393 47.619 0.00 0.00 0.00 1.73
981 3266 3.737266 ACACACAACCAACTATTCGTACG 59.263 43.478 9.53 9.53 0.00 3.67
1016 3305 5.422650 GTCCCTCTCTACATAAACAGACCTT 59.577 44.000 0.00 0.00 0.00 3.50
1123 3420 1.676678 CCTACTAGCTGCAGCCGGAA 61.677 60.000 34.39 17.13 43.38 4.30
1131 3428 0.962356 CTGCAGCCGGAAACCAAGAT 60.962 55.000 5.05 0.00 0.00 2.40
1143 3443 1.228831 CCAAGATGGCCACCACCAA 60.229 57.895 8.16 0.00 44.65 3.67
1156 3456 1.786441 ACCACCAAGGGGAAATCAAGA 59.214 47.619 0.00 0.00 43.89 3.02
1174 3474 1.934220 GACAGCCGAGATGGACACGA 61.934 60.000 0.00 0.00 42.00 4.35
1195 3495 3.334054 GCCTGCTGGACCCTTCCT 61.334 66.667 14.77 0.00 43.31 3.36
1291 3591 0.110328 CTACGACGACGACAGTTGCT 60.110 55.000 15.32 0.00 42.66 3.91
1300 3600 0.318441 CGACAGTTGCTTCCAGGAGA 59.682 55.000 0.00 0.00 0.00 3.71
1562 4063 0.744771 GGTTTCCTCATCTCCCGTGC 60.745 60.000 0.00 0.00 0.00 5.34
1691 4192 1.692519 ACCCACTGCTTAGTTTCGTCT 59.307 47.619 0.00 0.00 0.00 4.18
1693 4194 1.986378 CCACTGCTTAGTTTCGTCTCG 59.014 52.381 0.00 0.00 0.00 4.04
1790 4291 0.387622 TAAGCGTCCGTGTGTAGTGC 60.388 55.000 0.00 0.00 0.00 4.40
1791 4292 3.467119 GCGTCCGTGTGTAGTGCG 61.467 66.667 0.00 0.00 0.00 5.34
1803 4304 5.171516 CGTGTGTAGTGCGTATATCTTTCAG 59.828 44.000 0.00 0.00 0.00 3.02
1805 4306 7.191551 GTGTGTAGTGCGTATATCTTTCAGTA 58.808 38.462 0.00 0.00 0.00 2.74
1809 4310 8.504815 TGTAGTGCGTATATCTTTCAGTAGATC 58.495 37.037 0.00 0.00 36.34 2.75
1815 4316 7.579808 GCGTATATCTTTCAGTAGATCGATACG 59.420 40.741 16.79 16.79 43.77 3.06
1817 4318 5.690997 ATCTTTCAGTAGATCGATACGCA 57.309 39.130 0.00 0.00 28.74 5.24
1825 4326 3.560902 AGATCGATACGCACTGGTATG 57.439 47.619 0.00 0.00 33.39 2.39
1826 4327 1.986378 GATCGATACGCACTGGTATGC 59.014 52.381 0.00 0.00 42.48 3.14
1845 4349 5.592587 ATGCCTAGTACTCCATCTCTACT 57.407 43.478 0.00 0.00 0.00 2.57
1919 4962 8.729805 TCTTTGGTTTAAATTGTTCAAGCAAT 57.270 26.923 0.00 0.00 37.85 3.56
2159 5208 8.481974 TCAATCATACAATCTTTGCAAAATGG 57.518 30.769 13.84 9.67 0.00 3.16
2187 5236 1.463056 TCAGTTTGCGGCTTCGTAATG 59.537 47.619 0.00 0.00 38.21 1.90
2222 5271 4.527427 TCCATGCCACAATCAAATGAGAAA 59.473 37.500 0.00 0.00 0.00 2.52
2226 5275 5.668471 TGCCACAATCAAATGAGAAAAACA 58.332 33.333 0.00 0.00 0.00 2.83
2504 5560 1.067060 GGGCAACAAAGTGACAGGAAC 59.933 52.381 0.00 0.00 39.74 3.62
2515 5571 3.576982 AGTGACAGGAACTTTACATCGGA 59.423 43.478 0.00 0.00 34.60 4.55
2623 5679 4.569966 TGCAGCCAACAACAACAATTAAAG 59.430 37.500 0.00 0.00 0.00 1.85
2712 5769 7.468922 TTCTTACAGAGCACGATGATTATTG 57.531 36.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.330347 GGTTAGAGAATTTTCTGTCCTCGC 59.670 45.833 8.71 0.00 37.73 5.03
1 2 5.725362 AGGTTAGAGAATTTTCTGTCCTCG 58.275 41.667 8.71 0.00 37.73 4.63
2 3 6.702329 TGAGGTTAGAGAATTTTCTGTCCTC 58.298 40.000 26.25 26.25 42.27 3.71
4 5 7.065204 GTCATGAGGTTAGAGAATTTTCTGTCC 59.935 40.741 8.71 10.05 37.73 4.02
5 6 7.604164 TGTCATGAGGTTAGAGAATTTTCTGTC 59.396 37.037 8.71 2.06 37.73 3.51
7 8 7.912056 TGTCATGAGGTTAGAGAATTTTCTG 57.088 36.000 8.71 0.00 37.73 3.02
8 9 7.493971 CGATGTCATGAGGTTAGAGAATTTTCT 59.506 37.037 3.71 3.71 41.00 2.52
10 11 6.037610 GCGATGTCATGAGGTTAGAGAATTTT 59.962 38.462 0.00 0.00 0.00 1.82
11 12 5.525378 GCGATGTCATGAGGTTAGAGAATTT 59.475 40.000 0.00 0.00 0.00 1.82
12 13 5.053145 GCGATGTCATGAGGTTAGAGAATT 58.947 41.667 0.00 0.00 0.00 2.17
13 14 4.502259 GGCGATGTCATGAGGTTAGAGAAT 60.502 45.833 0.00 0.00 0.00 2.40
14 15 3.181475 GGCGATGTCATGAGGTTAGAGAA 60.181 47.826 0.00 0.00 0.00 2.87
15 16 2.362397 GGCGATGTCATGAGGTTAGAGA 59.638 50.000 0.00 0.00 0.00 3.10
16 17 2.101415 TGGCGATGTCATGAGGTTAGAG 59.899 50.000 0.00 0.00 0.00 2.43
17 18 2.107366 TGGCGATGTCATGAGGTTAGA 58.893 47.619 0.00 0.00 0.00 2.10
18 19 2.602257 TGGCGATGTCATGAGGTTAG 57.398 50.000 0.00 0.00 0.00 2.34
19 20 3.342377 TTTGGCGATGTCATGAGGTTA 57.658 42.857 0.00 0.00 0.00 2.85
20 21 2.198827 TTTGGCGATGTCATGAGGTT 57.801 45.000 0.00 0.00 0.00 3.50
21 22 2.086869 CTTTTGGCGATGTCATGAGGT 58.913 47.619 0.00 0.00 0.00 3.85
22 23 2.358957 TCTTTTGGCGATGTCATGAGG 58.641 47.619 0.00 0.00 0.00 3.86
23 24 3.725895 CGTTCTTTTGGCGATGTCATGAG 60.726 47.826 0.00 0.00 0.00 2.90
24 25 2.159430 CGTTCTTTTGGCGATGTCATGA 59.841 45.455 0.00 0.00 0.00 3.07
25 26 2.159430 TCGTTCTTTTGGCGATGTCATG 59.841 45.455 0.00 0.00 0.00 3.07
26 27 2.416547 CTCGTTCTTTTGGCGATGTCAT 59.583 45.455 0.00 0.00 34.04 3.06
27 28 1.798223 CTCGTTCTTTTGGCGATGTCA 59.202 47.619 0.00 0.00 34.04 3.58
28 29 2.066262 TCTCGTTCTTTTGGCGATGTC 58.934 47.619 0.00 0.00 34.04 3.06
29 30 2.069273 CTCTCGTTCTTTTGGCGATGT 58.931 47.619 0.00 0.00 34.04 3.06
30 31 2.069273 ACTCTCGTTCTTTTGGCGATG 58.931 47.619 0.00 0.00 34.04 3.84
31 32 2.457366 ACTCTCGTTCTTTTGGCGAT 57.543 45.000 0.00 0.00 34.04 4.58
32 33 3.374220 TTACTCTCGTTCTTTTGGCGA 57.626 42.857 0.00 0.00 0.00 5.54
33 34 4.663636 ATTTACTCTCGTTCTTTTGGCG 57.336 40.909 0.00 0.00 0.00 5.69
34 35 8.965986 AATAAATTTACTCTCGTTCTTTTGGC 57.034 30.769 0.00 0.00 0.00 4.52
39 40 9.706691 TGTGAGAATAAATTTACTCTCGTTCTT 57.293 29.630 24.14 3.99 38.49 2.52
40 41 9.706691 TTGTGAGAATAAATTTACTCTCGTTCT 57.293 29.630 24.14 16.63 38.49 3.01
55 56 9.599866 AGTGATCATCGTATTTTGTGAGAATAA 57.400 29.630 0.00 0.00 0.00 1.40
57 58 9.254133 CTAGTGATCATCGTATTTTGTGAGAAT 57.746 33.333 0.00 0.00 0.00 2.40
58 59 8.466798 TCTAGTGATCATCGTATTTTGTGAGAA 58.533 33.333 0.00 0.00 0.00 2.87
59 60 7.915923 GTCTAGTGATCATCGTATTTTGTGAGA 59.084 37.037 0.00 0.00 0.00 3.27
60 61 7.096844 CGTCTAGTGATCATCGTATTTTGTGAG 60.097 40.741 0.00 0.00 0.00 3.51
61 62 6.691388 CGTCTAGTGATCATCGTATTTTGTGA 59.309 38.462 0.00 0.00 0.00 3.58
62 63 6.691388 TCGTCTAGTGATCATCGTATTTTGTG 59.309 38.462 0.00 0.00 0.00 3.33
63 64 6.792326 TCGTCTAGTGATCATCGTATTTTGT 58.208 36.000 0.00 0.00 0.00 2.83
64 65 7.591426 TCATCGTCTAGTGATCATCGTATTTTG 59.409 37.037 0.00 0.00 0.00 2.44
65 66 7.591795 GTCATCGTCTAGTGATCATCGTATTTT 59.408 37.037 0.00 0.00 0.00 1.82
66 67 7.078851 GTCATCGTCTAGTGATCATCGTATTT 58.921 38.462 0.00 0.00 0.00 1.40
67 68 6.604012 GTCATCGTCTAGTGATCATCGTATT 58.396 40.000 0.00 0.00 0.00 1.89
68 69 5.163943 CGTCATCGTCTAGTGATCATCGTAT 60.164 44.000 0.00 0.00 0.00 3.06
69 70 4.150098 CGTCATCGTCTAGTGATCATCGTA 59.850 45.833 0.00 0.00 0.00 3.43
70 71 3.059529 CGTCATCGTCTAGTGATCATCGT 60.060 47.826 0.00 0.00 0.00 3.73
71 72 3.184581 TCGTCATCGTCTAGTGATCATCG 59.815 47.826 0.00 0.05 38.33 3.84
72 73 4.733972 TCGTCATCGTCTAGTGATCATC 57.266 45.455 0.00 0.00 38.33 2.92
73 74 5.500645 TTTCGTCATCGTCTAGTGATCAT 57.499 39.130 0.00 0.00 38.33 2.45
74 75 4.957759 TTTCGTCATCGTCTAGTGATCA 57.042 40.909 0.00 0.00 38.33 2.92
75 76 5.114273 CGATTTTCGTCATCGTCTAGTGATC 59.886 44.000 5.76 0.00 38.98 2.92
76 77 4.970611 CGATTTTCGTCATCGTCTAGTGAT 59.029 41.667 5.76 0.00 38.98 3.06
77 78 4.340263 CGATTTTCGTCATCGTCTAGTGA 58.660 43.478 5.76 0.00 38.98 3.41
78 79 4.661539 CGATTTTCGTCATCGTCTAGTG 57.338 45.455 5.76 0.00 38.98 2.74
91 92 6.506513 GCATCTTCACAGTACTACGATTTTCG 60.507 42.308 0.00 0.00 46.93 3.46
92 93 6.506513 CGCATCTTCACAGTACTACGATTTTC 60.507 42.308 0.00 0.00 0.00 2.29
93 94 5.288712 CGCATCTTCACAGTACTACGATTTT 59.711 40.000 0.00 0.00 0.00 1.82
94 95 4.798907 CGCATCTTCACAGTACTACGATTT 59.201 41.667 0.00 0.00 0.00 2.17
95 96 4.095932 TCGCATCTTCACAGTACTACGATT 59.904 41.667 0.00 0.00 0.00 3.34
96 97 3.626217 TCGCATCTTCACAGTACTACGAT 59.374 43.478 0.00 0.00 0.00 3.73
97 98 3.004862 TCGCATCTTCACAGTACTACGA 58.995 45.455 0.00 0.00 0.00 3.43
98 99 3.355270 CTCGCATCTTCACAGTACTACG 58.645 50.000 0.00 0.00 0.00 3.51
99 100 3.489398 CCCTCGCATCTTCACAGTACTAC 60.489 52.174 0.00 0.00 0.00 2.73
100 101 2.688446 CCCTCGCATCTTCACAGTACTA 59.312 50.000 0.00 0.00 0.00 1.82
101 102 1.478510 CCCTCGCATCTTCACAGTACT 59.521 52.381 0.00 0.00 0.00 2.73
102 103 1.471676 CCCCTCGCATCTTCACAGTAC 60.472 57.143 0.00 0.00 0.00 2.73
103 104 0.824109 CCCCTCGCATCTTCACAGTA 59.176 55.000 0.00 0.00 0.00 2.74
104 105 0.904865 TCCCCTCGCATCTTCACAGT 60.905 55.000 0.00 0.00 0.00 3.55
105 106 0.460987 GTCCCCTCGCATCTTCACAG 60.461 60.000 0.00 0.00 0.00 3.66
106 107 1.596934 GTCCCCTCGCATCTTCACA 59.403 57.895 0.00 0.00 0.00 3.58
107 108 1.153349 GGTCCCCTCGCATCTTCAC 60.153 63.158 0.00 0.00 0.00 3.18
108 109 1.198094 TTGGTCCCCTCGCATCTTCA 61.198 55.000 0.00 0.00 0.00 3.02
109 110 0.035439 TTTGGTCCCCTCGCATCTTC 60.035 55.000 0.00 0.00 0.00 2.87
110 111 0.404040 TTTTGGTCCCCTCGCATCTT 59.596 50.000 0.00 0.00 0.00 2.40
111 112 0.404040 TTTTTGGTCCCCTCGCATCT 59.596 50.000 0.00 0.00 0.00 2.90
112 113 2.955609 TTTTTGGTCCCCTCGCATC 58.044 52.632 0.00 0.00 0.00 3.91
127 128 2.969827 CCGCCGCCAGGAATTTTT 59.030 55.556 0.00 0.00 41.02 1.94
128 129 3.758931 GCCGCCGCCAGGAATTTT 61.759 61.111 0.00 0.00 41.02 1.82
147 148 4.410743 GAGGGTTTGCAGCAGCGC 62.411 66.667 0.00 0.00 46.23 5.92
148 149 4.093952 CGAGGGTTTGCAGCAGCG 62.094 66.667 0.00 0.00 46.23 5.18
149 150 4.410743 GCGAGGGTTTGCAGCAGC 62.411 66.667 0.00 0.00 42.57 5.25
150 151 2.263741 AAGCGAGGGTTTGCAGCAG 61.264 57.895 0.00 0.00 36.07 4.24
151 152 2.203337 AAGCGAGGGTTTGCAGCA 60.203 55.556 0.00 0.00 36.07 4.41
152 153 2.256461 CAAGCGAGGGTTTGCAGC 59.744 61.111 0.00 0.00 36.07 5.25
153 154 1.576421 GACAAGCGAGGGTTTGCAG 59.424 57.895 0.00 0.00 37.84 4.41
154 155 1.896660 GGACAAGCGAGGGTTTGCA 60.897 57.895 0.00 0.00 37.84 4.08
155 156 2.954611 GGACAAGCGAGGGTTTGC 59.045 61.111 0.00 0.00 37.84 3.68
156 157 1.164041 AACGGACAAGCGAGGGTTTG 61.164 55.000 0.00 0.00 39.90 2.93
157 158 0.464916 AAACGGACAAGCGAGGGTTT 60.465 50.000 0.00 0.00 0.00 3.27
158 159 0.464916 AAAACGGACAAGCGAGGGTT 60.465 50.000 0.00 0.00 0.00 4.11
159 160 1.147600 AAAACGGACAAGCGAGGGT 59.852 52.632 0.00 0.00 0.00 4.34
160 161 0.882927 TCAAAACGGACAAGCGAGGG 60.883 55.000 0.00 0.00 0.00 4.30
161 162 1.135972 CATCAAAACGGACAAGCGAGG 60.136 52.381 0.00 0.00 0.00 4.63
162 163 1.798223 TCATCAAAACGGACAAGCGAG 59.202 47.619 0.00 0.00 0.00 5.03
163 164 1.872388 TCATCAAAACGGACAAGCGA 58.128 45.000 0.00 0.00 0.00 4.93
164 165 2.416547 AGATCATCAAAACGGACAAGCG 59.583 45.455 0.00 0.00 0.00 4.68
165 166 3.426695 CCAGATCATCAAAACGGACAAGC 60.427 47.826 0.00 0.00 0.00 4.01
166 167 3.753272 ACCAGATCATCAAAACGGACAAG 59.247 43.478 0.00 0.00 0.00 3.16
167 168 3.501828 CACCAGATCATCAAAACGGACAA 59.498 43.478 0.00 0.00 0.00 3.18
168 169 3.073678 CACCAGATCATCAAAACGGACA 58.926 45.455 0.00 0.00 0.00 4.02
169 170 2.420022 CCACCAGATCATCAAAACGGAC 59.580 50.000 0.00 0.00 0.00 4.79
170 171 2.039746 ACCACCAGATCATCAAAACGGA 59.960 45.455 0.00 0.00 0.00 4.69
171 172 2.436417 ACCACCAGATCATCAAAACGG 58.564 47.619 0.00 0.00 0.00 4.44
172 173 3.119849 GGAACCACCAGATCATCAAAACG 60.120 47.826 0.00 0.00 38.79 3.60
173 174 4.082125 AGGAACCACCAGATCATCAAAAC 58.918 43.478 0.00 0.00 42.04 2.43
174 175 4.387026 AGGAACCACCAGATCATCAAAA 57.613 40.909 0.00 0.00 42.04 2.44
175 176 5.222027 TGTTAGGAACCACCAGATCATCAAA 60.222 40.000 0.00 0.00 42.04 2.69
176 177 4.288366 TGTTAGGAACCACCAGATCATCAA 59.712 41.667 0.00 0.00 42.04 2.57
177 178 3.843619 TGTTAGGAACCACCAGATCATCA 59.156 43.478 0.00 0.00 42.04 3.07
178 179 4.487714 TGTTAGGAACCACCAGATCATC 57.512 45.455 0.00 0.00 42.04 2.92
179 180 4.474651 TGATGTTAGGAACCACCAGATCAT 59.525 41.667 0.00 0.00 42.04 2.45
180 181 3.843619 TGATGTTAGGAACCACCAGATCA 59.156 43.478 0.00 0.00 42.04 2.92
181 182 4.080863 ACTGATGTTAGGAACCACCAGATC 60.081 45.833 0.00 0.00 42.04 2.75
182 183 3.846588 ACTGATGTTAGGAACCACCAGAT 59.153 43.478 0.00 0.00 42.04 2.90
183 184 3.007940 CACTGATGTTAGGAACCACCAGA 59.992 47.826 0.00 0.00 42.04 3.86
184 185 3.244561 ACACTGATGTTAGGAACCACCAG 60.245 47.826 0.00 0.00 37.05 4.00
185 186 2.708861 ACACTGATGTTAGGAACCACCA 59.291 45.455 0.00 0.00 37.05 4.17
186 187 3.418684 ACACTGATGTTAGGAACCACC 57.581 47.619 0.00 0.00 34.46 4.61
187 188 5.302360 TGTTACACTGATGTTAGGAACCAC 58.698 41.667 0.00 0.00 40.48 4.16
188 189 5.554437 TGTTACACTGATGTTAGGAACCA 57.446 39.130 0.00 0.00 40.48 3.67
189 190 5.761234 TGTTGTTACACTGATGTTAGGAACC 59.239 40.000 0.00 0.00 40.48 3.62
190 191 6.854496 TGTTGTTACACTGATGTTAGGAAC 57.146 37.500 0.00 0.00 40.48 3.62
191 192 8.458573 AAATGTTGTTACACTGATGTTAGGAA 57.541 30.769 0.00 0.00 40.48 3.36
192 193 9.562408 TTAAATGTTGTTACACTGATGTTAGGA 57.438 29.630 0.00 0.00 40.48 2.94
196 197 9.862371 TGTTTTAAATGTTGTTACACTGATGTT 57.138 25.926 0.00 0.00 40.48 2.71
235 236 5.840243 TTATGGCATTGACCTCAATTCTG 57.160 39.130 4.78 0.00 43.48 3.02
236 237 6.131264 TCATTATGGCATTGACCTCAATTCT 58.869 36.000 4.78 0.00 43.48 2.40
243 244 2.091720 TGGCTCATTATGGCATTGACCT 60.092 45.455 4.78 0.00 35.04 3.85
244 245 2.309613 TGGCTCATTATGGCATTGACC 58.690 47.619 4.78 9.12 35.04 4.02
245 246 4.389890 TTTGGCTCATTATGGCATTGAC 57.610 40.909 4.78 0.00 39.67 3.18
253 254 8.081633 TGTGACTTTAGTTTTTGGCTCATTATG 58.918 33.333 0.00 0.00 0.00 1.90
317 318 8.467402 TTCGAAACATAGCTTGAAAAACAAAA 57.533 26.923 0.00 0.00 38.08 2.44
321 322 9.356929 CAAAATTCGAAACATAGCTTGAAAAAC 57.643 29.630 0.00 0.00 0.00 2.43
323 324 8.751335 GTCAAAATTCGAAACATAGCTTGAAAA 58.249 29.630 0.00 0.00 0.00 2.29
324 325 8.134895 AGTCAAAATTCGAAACATAGCTTGAAA 58.865 29.630 0.00 0.00 0.00 2.69
325 326 7.648142 AGTCAAAATTCGAAACATAGCTTGAA 58.352 30.769 0.00 0.00 0.00 2.69
326 327 7.202016 AGTCAAAATTCGAAACATAGCTTGA 57.798 32.000 0.00 1.36 0.00 3.02
327 328 7.591057 TGAAGTCAAAATTCGAAACATAGCTTG 59.409 33.333 0.00 0.00 0.00 4.01
328 329 7.648142 TGAAGTCAAAATTCGAAACATAGCTT 58.352 30.769 0.00 3.59 0.00 3.74
359 360 5.585844 CACAACATCAATGTAGGCTGTCATA 59.414 40.000 0.00 0.00 40.80 2.15
366 367 4.764679 TTCACACAACATCAATGTAGGC 57.235 40.909 0.00 0.00 40.80 3.93
375 376 8.524870 AAAAATTAGCTCATTCACACAACATC 57.475 30.769 0.00 0.00 0.00 3.06
401 402 8.635877 ACGTTGCACATTTTTAAAATGTCTAA 57.364 26.923 27.00 21.61 38.69 2.10
402 403 9.731819 TTACGTTGCACATTTTTAAAATGTCTA 57.268 25.926 27.00 18.09 38.69 2.59
404 405 8.536407 ACTTACGTTGCACATTTTTAAAATGTC 58.464 29.630 27.00 21.59 38.69 3.06
451 453 0.834687 AGGGTTCGTAGTTCCCTGCA 60.835 55.000 0.86 0.00 45.72 4.41
479 2340 4.376514 GCAAGTTCGTAGTTCTCTGCTTTC 60.377 45.833 0.00 0.00 0.00 2.62
517 2378 7.268586 AGTTGTATTTGTTGTGTTTATTGGCA 58.731 30.769 0.00 0.00 0.00 4.92
561 2422 0.116342 TCACAAGGGGGAGCTACTCA 59.884 55.000 0.00 0.00 31.08 3.41
565 2426 0.325671 CCTCTCACAAGGGGGAGCTA 60.326 60.000 0.00 0.00 39.81 3.32
566 2427 1.614824 CCTCTCACAAGGGGGAGCT 60.615 63.158 0.00 0.00 39.81 4.09
567 2428 2.993853 CCTCTCACAAGGGGGAGC 59.006 66.667 0.00 0.00 39.81 4.70
580 2446 1.686052 GCATTCCTCGATCTGACCTCT 59.314 52.381 0.00 0.00 0.00 3.69
585 2451 2.102578 TGAGTGCATTCCTCGATCTGA 58.897 47.619 6.77 0.00 0.00 3.27
598 2464 0.534877 ACCGCTGAAATGTGAGTGCA 60.535 50.000 0.00 0.00 0.00 4.57
601 2467 2.688507 CACTACCGCTGAAATGTGAGT 58.311 47.619 0.00 0.00 0.00 3.41
619 2485 0.690762 TAGAGGGGTGAAAGTGGCAC 59.309 55.000 10.29 10.29 35.56 5.01
741 2607 5.521906 CTAATGAAGCACTAGTAGCCTGA 57.478 43.478 11.98 0.00 0.00 3.86
812 2678 4.873129 CGATCGTGGTGGAGCCCG 62.873 72.222 7.03 0.00 36.04 6.13
909 3194 2.480416 GGCGGATCAGTGACTCTAGTTG 60.480 54.545 0.00 0.00 0.00 3.16
910 3195 1.751924 GGCGGATCAGTGACTCTAGTT 59.248 52.381 0.00 0.00 0.00 2.24
916 3201 1.379443 TACGGGCGGATCAGTGACT 60.379 57.895 0.00 0.00 0.00 3.41
934 3219 1.202952 ACGACTTCCTGTGGAGTCTCT 60.203 52.381 0.00 0.00 32.07 3.10
962 3247 3.365820 GTCCGTACGAATAGTTGGTTGTG 59.634 47.826 18.76 0.00 0.00 3.33
963 3248 3.256631 AGTCCGTACGAATAGTTGGTTGT 59.743 43.478 18.76 0.00 0.00 3.32
975 3260 3.129502 CGGCAGGAGTCCGTACGA 61.130 66.667 18.76 0.00 41.85 3.43
1032 3325 2.588877 GGCAGTGTGCGTGTGAGT 60.589 61.111 0.00 0.00 46.21 3.41
1055 3348 5.643379 AGAAGAAAGACTAGCTCACTCAG 57.357 43.478 0.00 0.00 0.00 3.35
1060 3357 6.656632 TTCAGAAGAAGAAAGACTAGCTCA 57.343 37.500 0.00 0.00 0.00 4.26
1123 3420 1.228862 GGTGGTGGCCATCTTGGTT 60.229 57.895 18.94 0.00 40.46 3.67
1143 3443 0.035056 CGGCTGTCTTGATTTCCCCT 60.035 55.000 0.00 0.00 0.00 4.79
1148 3448 2.237143 TCCATCTCGGCTGTCTTGATTT 59.763 45.455 0.00 0.00 33.14 2.17
1151 3451 0.532573 GTCCATCTCGGCTGTCTTGA 59.467 55.000 0.00 0.00 33.14 3.02
1156 3456 1.938657 CTCGTGTCCATCTCGGCTGT 61.939 60.000 0.00 0.00 34.40 4.40
1174 3474 4.990910 AGGGTCCAGCAGGCCACT 62.991 66.667 5.01 0.00 34.08 4.00
1300 3600 3.692406 GTCGTCGCCCTCCTGGTT 61.692 66.667 0.00 0.00 36.04 3.67
1581 4082 3.320826 GGAGGATCTGGAAGTAGAGCTTC 59.679 52.174 0.00 0.00 43.44 3.86
1594 4095 2.202987 GGCAGTGCGGAGGATCTG 60.203 66.667 9.45 0.00 46.81 2.90
1642 4143 2.185350 CCTCCCGTGCAGCTACAG 59.815 66.667 0.00 0.00 0.00 2.74
1670 4171 1.798813 GACGAAACTAAGCAGTGGGTG 59.201 52.381 0.00 0.00 34.36 4.61
1674 4175 1.387084 GCGAGACGAAACTAAGCAGTG 59.613 52.381 0.00 0.00 34.36 3.66
1711 4212 1.725557 TAAGCAACGCAAACGGCCAA 61.726 50.000 2.24 0.00 46.04 4.52
1790 4291 7.579808 GCGTATCGATCTACTGAAAGATATACG 59.420 40.741 20.49 20.49 44.43 3.06
1791 4292 8.388853 TGCGTATCGATCTACTGAAAGATATAC 58.611 37.037 0.00 0.00 36.33 1.47
1803 4304 4.404324 CATACCAGTGCGTATCGATCTAC 58.596 47.826 0.00 0.00 0.00 2.59
1805 4306 2.351835 GCATACCAGTGCGTATCGATCT 60.352 50.000 0.00 0.00 35.10 2.75
1809 4310 0.032130 AGGCATACCAGTGCGTATCG 59.968 55.000 2.37 0.00 45.97 2.92
1815 4316 2.036089 GGAGTACTAGGCATACCAGTGC 59.964 54.545 0.00 0.00 44.31 4.40
1817 4318 3.682592 TGGAGTACTAGGCATACCAGT 57.317 47.619 0.00 0.00 39.06 4.00
1825 4326 6.718522 AAAAGTAGAGATGGAGTACTAGGC 57.281 41.667 0.00 0.00 0.00 3.93
1826 4327 8.294954 TGAAAAAGTAGAGATGGAGTACTAGG 57.705 38.462 0.00 0.00 0.00 3.02
1845 4349 5.010933 TCCAACCTTACACACACTGAAAAA 58.989 37.500 0.00 0.00 0.00 1.94
1919 4962 9.944376 AACATCATCTTGTAAGAAGCTTTAGTA 57.056 29.630 0.00 0.00 38.77 1.82
2159 5208 2.076863 AGCCGCAAACTGAACTATGAC 58.923 47.619 0.00 0.00 0.00 3.06
2187 5236 1.065199 TGGCATGGAGGTGAGAATGAC 60.065 52.381 0.00 0.00 0.00 3.06
2295 5345 4.071423 TCTTCGATTCAATTGTGGAGCAA 58.929 39.130 5.13 0.00 41.89 3.91
2504 5560 5.627172 TCGAAATTTTGCTCCGATGTAAAG 58.373 37.500 0.01 0.00 0.00 1.85
2515 5571 5.240713 GATGAGGTCATCGAAATTTTGCT 57.759 39.130 4.24 0.00 42.66 3.91
2623 5679 7.196331 GTCAACCTCCTATATTTTGTTGATGC 58.804 38.462 6.21 0.00 42.55 3.91


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

AutoCloner maintained by Alex Coulton.