Multiple sequence alignment - TraesCS7D01G494000

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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 TraesCS7D01G494000 chr7D 100.000 2708 0 0 1 2708 602041815 602044522 0.000000e+00 5001.0
1 TraesCS7D01G494000 chr7D 87.734 1231 87 29 691 1865 602410262 602409040 0.000000e+00 1378.0
2 TraesCS7D01G494000 chr7D 78.091 1100 130 72 736 1797 602072558 602073584 6.460000e-166 593.0
3 TraesCS7D01G494000 chr7D 86.278 532 51 10 991 1522 602295041 602294532 2.350000e-155 558.0
4 TraesCS7D01G494000 chr7D 89.697 330 34 0 1196 1525 602194635 602194306 3.220000e-114 422.0
5 TraesCS7D01G494000 chr7D 77.419 217 21 12 734 932 602632794 602632588 1.330000e-18 104.0
6 TraesCS7D01G494000 chr7D 85.897 78 3 3 854 931 602194874 602194805 2.890000e-10 76.8
7 TraesCS7D01G494000 chr7A 90.764 1570 78 27 345 1861 693814847 693816402 0.000000e+00 2034.0
8 TraesCS7D01G494000 chr7A 93.986 848 50 1 1860 2706 693816461 693817308 0.000000e+00 1282.0
9 TraesCS7D01G494000 chr7A 94.898 490 24 1 2218 2706 694078368 694077879 0.000000e+00 765.0
10 TraesCS7D01G494000 chr7A 80.933 965 103 53 686 1616 693838239 693839156 0.000000e+00 688.0
11 TraesCS7D01G494000 chr7A 84.458 489 59 12 1041 1525 694022593 694022118 1.470000e-127 466.0
12 TraesCS7D01G494000 chr7A 83.281 317 36 13 1559 1861 694075480 694075167 2.660000e-70 276.0
13 TraesCS7D01G494000 chr7B 91.789 1157 58 18 798 1930 681688511 681689654 0.000000e+00 1576.0
14 TraesCS7D01G494000 chr7B 82.749 1368 124 47 654 1952 682791823 682790499 0.000000e+00 1116.0
15 TraesCS7D01G494000 chr7B 95.011 461 16 4 1860 2313 681689646 681690106 0.000000e+00 717.0
16 TraesCS7D01G494000 chr7B 92.908 423 28 2 2288 2708 681692312 681692734 4.960000e-172 614.0
17 TraesCS7D01G494000 chr7B 77.817 1136 132 67 686 1791 681750187 681751232 2.320000e-165 592.0
18 TraesCS7D01G494000 chr7B 82.889 637 72 23 1035 1667 682886414 682885811 3.070000e-149 538.0
19 TraesCS7D01G494000 chr7B 82.625 518 48 20 1278 1791 681780146 681780625 1.160000e-113 420.0
20 TraesCS7D01G494000 chrUn 81.297 925 95 34 734 1645 87232647 87231788 0.000000e+00 678.0


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 TraesCS7D01G494000 chr7D 602041815 602044522 2707 False 5001.0 5001 100.0000 1 2708 1 chr7D.!!$F1 2707
1 TraesCS7D01G494000 chr7D 602409040 602410262 1222 True 1378.0 1378 87.7340 691 1865 1 chr7D.!!$R2 1174
2 TraesCS7D01G494000 chr7D 602072558 602073584 1026 False 593.0 593 78.0910 736 1797 1 chr7D.!!$F2 1061
3 TraesCS7D01G494000 chr7D 602294532 602295041 509 True 558.0 558 86.2780 991 1522 1 chr7D.!!$R1 531
4 TraesCS7D01G494000 chr7D 602194306 602194874 568 True 249.4 422 87.7970 854 1525 2 chr7D.!!$R4 671
5 TraesCS7D01G494000 chr7A 693814847 693817308 2461 False 1658.0 2034 92.3750 345 2706 2 chr7A.!!$F2 2361
6 TraesCS7D01G494000 chr7A 693838239 693839156 917 False 688.0 688 80.9330 686 1616 1 chr7A.!!$F1 930
7 TraesCS7D01G494000 chr7A 694075167 694078368 3201 True 520.5 765 89.0895 1559 2706 2 chr7A.!!$R2 1147
8 TraesCS7D01G494000 chr7B 682790499 682791823 1324 True 1116.0 1116 82.7490 654 1952 1 chr7B.!!$R1 1298
9 TraesCS7D01G494000 chr7B 681688511 681692734 4223 False 969.0 1576 93.2360 798 2708 3 chr7B.!!$F3 1910
10 TraesCS7D01G494000 chr7B 681750187 681751232 1045 False 592.0 592 77.8170 686 1791 1 chr7B.!!$F1 1105
11 TraesCS7D01G494000 chr7B 682885811 682886414 603 True 538.0 538 82.8890 1035 1667 1 chr7B.!!$R2 632
12 TraesCS7D01G494000 chrUn 87231788 87232647 859 True 678.0 678 81.2970 734 1645 1 chrUn.!!$R1 911

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
60 61 0.03563 ACTAAGCTGGCTTCTGGCTG 60.036 55.0 11.28 0.0 41.46 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 3403 0.947244 GTCCGCTTGCATGATTAGGG 59.053 55.0 3.33 0.0 0.0 3.53 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
19 20 2.528041 GATATTTCTCCCGCTTCCGT 57.472 50.000 0.00 0.00 0.00 4.69
20 21 2.135933 GATATTTCTCCCGCTTCCGTG 58.864 52.381 0.00 0.00 0.00 4.94
21 22 0.461339 TATTTCTCCCGCTTCCGTGC 60.461 55.000 0.00 0.00 0.00 5.34
49 50 5.508872 GCAGAAGCAATGATTACTAAGCTG 58.491 41.667 0.00 0.00 41.58 4.24
50 51 5.505324 GCAGAAGCAATGATTACTAAGCTGG 60.505 44.000 0.00 0.00 41.58 4.85
52 53 4.162040 AGCAATGATTACTAAGCTGGCT 57.838 40.909 0.00 0.00 0.00 4.75
53 54 4.530875 AGCAATGATTACTAAGCTGGCTT 58.469 39.130 12.54 12.54 39.83 4.35
55 56 4.578105 GCAATGATTACTAAGCTGGCTTCT 59.422 41.667 11.28 1.43 37.47 2.85
56 57 5.505324 GCAATGATTACTAAGCTGGCTTCTG 60.505 44.000 11.28 8.54 37.47 3.02
57 58 4.142609 TGATTACTAAGCTGGCTTCTGG 57.857 45.455 11.28 6.28 37.47 3.86
58 59 2.403252 TTACTAAGCTGGCTTCTGGC 57.597 50.000 11.28 0.00 37.47 4.85
59 60 1.573108 TACTAAGCTGGCTTCTGGCT 58.427 50.000 11.28 0.00 41.46 4.75
60 61 0.035630 ACTAAGCTGGCTTCTGGCTG 60.036 55.000 11.28 0.00 41.46 4.85
61 62 0.747283 CTAAGCTGGCTTCTGGCTGG 60.747 60.000 11.28 0.00 41.46 4.85
62 63 2.202236 TAAGCTGGCTTCTGGCTGGG 62.202 60.000 11.28 0.00 41.46 4.45
64 65 2.360852 CTGGCTTCTGGCTGGGTG 60.361 66.667 0.00 0.00 41.46 4.61
65 66 3.933048 CTGGCTTCTGGCTGGGTGG 62.933 68.421 0.00 0.00 41.46 4.61
68 69 2.437897 CTTCTGGCTGGGTGGCTT 59.562 61.111 0.00 0.00 42.34 4.35
69 70 1.228675 CTTCTGGCTGGGTGGCTTT 60.229 57.895 0.00 0.00 42.34 3.51
70 71 0.829182 CTTCTGGCTGGGTGGCTTTT 60.829 55.000 0.00 0.00 42.34 2.27
72 73 0.827507 TCTGGCTGGGTGGCTTTTTC 60.828 55.000 0.00 0.00 42.34 2.29
73 74 1.820010 CTGGCTGGGTGGCTTTTTCC 61.820 60.000 0.00 0.00 42.34 3.13
74 75 2.650778 GCTGGGTGGCTTTTTCCG 59.349 61.111 0.00 0.00 0.00 4.30
75 76 2.200337 GCTGGGTGGCTTTTTCCGT 61.200 57.895 0.00 0.00 0.00 4.69
76 77 1.956802 CTGGGTGGCTTTTTCCGTC 59.043 57.895 0.00 0.00 0.00 4.79
77 78 1.852067 CTGGGTGGCTTTTTCCGTCG 61.852 60.000 0.00 0.00 0.00 5.12
78 79 1.598685 GGGTGGCTTTTTCCGTCGA 60.599 57.895 0.00 0.00 0.00 4.20
79 80 0.958876 GGGTGGCTTTTTCCGTCGAT 60.959 55.000 0.00 0.00 0.00 3.59
80 81 0.168128 GGTGGCTTTTTCCGTCGATG 59.832 55.000 0.00 0.00 0.00 3.84
81 82 0.168128 GTGGCTTTTTCCGTCGATGG 59.832 55.000 18.13 18.13 0.00 3.51
82 83 1.136774 GGCTTTTTCCGTCGATGGC 59.863 57.895 19.40 5.78 0.00 4.40
83 84 1.305930 GGCTTTTTCCGTCGATGGCT 61.306 55.000 19.40 0.00 0.00 4.75
84 85 0.097150 GCTTTTTCCGTCGATGGCTC 59.903 55.000 19.40 0.43 0.00 4.70
87 88 2.107950 TTTTCCGTCGATGGCTCATT 57.892 45.000 19.40 0.00 0.00 2.57
88 89 1.651987 TTTCCGTCGATGGCTCATTC 58.348 50.000 19.40 0.00 0.00 2.67
89 90 0.534873 TTCCGTCGATGGCTCATTCA 59.465 50.000 19.40 0.00 0.00 2.57
90 91 0.752658 TCCGTCGATGGCTCATTCAT 59.247 50.000 19.40 0.00 0.00 2.57
91 92 1.138859 TCCGTCGATGGCTCATTCATT 59.861 47.619 19.40 0.00 0.00 2.57
95 96 3.302935 CGTCGATGGCTCATTCATTCAAG 60.303 47.826 0.00 0.00 0.00 3.02
96 97 3.873361 GTCGATGGCTCATTCATTCAAGA 59.127 43.478 0.00 0.00 0.00 3.02
97 98 3.873361 TCGATGGCTCATTCATTCAAGAC 59.127 43.478 0.00 0.00 0.00 3.01
99 100 4.495349 CGATGGCTCATTCATTCAAGACAC 60.495 45.833 0.00 0.00 27.36 3.67
100 101 4.025040 TGGCTCATTCATTCAAGACACT 57.975 40.909 0.00 0.00 0.00 3.55
101 102 3.754850 TGGCTCATTCATTCAAGACACTG 59.245 43.478 0.00 0.00 0.00 3.66
102 103 3.128242 GGCTCATTCATTCAAGACACTGG 59.872 47.826 0.00 0.00 0.00 4.00
103 104 3.755378 GCTCATTCATTCAAGACACTGGT 59.245 43.478 0.00 0.00 0.00 4.00
104 105 4.379186 GCTCATTCATTCAAGACACTGGTG 60.379 45.833 0.00 0.00 0.00 4.17
105 106 3.503363 TCATTCATTCAAGACACTGGTGC 59.497 43.478 0.17 0.00 0.00 5.01
107 108 2.497138 TCATTCAAGACACTGGTGCAG 58.503 47.619 0.17 0.00 37.52 4.41
115 116 3.483587 ACTGGTGCAGTGGGTAGG 58.516 61.111 0.00 0.00 43.63 3.18
116 117 2.224159 ACTGGTGCAGTGGGTAGGG 61.224 63.158 0.00 0.00 43.63 3.53
117 118 2.933287 TGGTGCAGTGGGTAGGGG 60.933 66.667 0.00 0.00 0.00 4.79
118 119 2.609610 GGTGCAGTGGGTAGGGGA 60.610 66.667 0.00 0.00 0.00 4.81
119 120 2.228480 GGTGCAGTGGGTAGGGGAA 61.228 63.158 0.00 0.00 0.00 3.97
121 122 0.394352 GTGCAGTGGGTAGGGGAATG 60.394 60.000 0.00 0.00 0.00 2.67
123 124 0.846693 GCAGTGGGTAGGGGAATGAT 59.153 55.000 0.00 0.00 0.00 2.45
124 125 1.215423 GCAGTGGGTAGGGGAATGATT 59.785 52.381 0.00 0.00 0.00 2.57
125 126 2.749800 GCAGTGGGTAGGGGAATGATTC 60.750 54.545 0.00 0.00 0.00 2.52
126 127 2.780010 CAGTGGGTAGGGGAATGATTCT 59.220 50.000 5.03 0.00 0.00 2.40
127 128 3.973973 CAGTGGGTAGGGGAATGATTCTA 59.026 47.826 5.03 0.00 0.00 2.10
128 129 4.412199 CAGTGGGTAGGGGAATGATTCTAA 59.588 45.833 5.03 0.00 0.00 2.10
129 130 4.660771 AGTGGGTAGGGGAATGATTCTAAG 59.339 45.833 5.03 0.00 0.00 2.18
130 131 3.980698 TGGGTAGGGGAATGATTCTAAGG 59.019 47.826 5.03 0.00 0.00 2.69
131 132 3.330998 GGGTAGGGGAATGATTCTAAGGG 59.669 52.174 5.03 0.00 0.00 3.95
134 135 6.030082 GGTAGGGGAATGATTCTAAGGGATA 58.970 44.000 5.03 0.00 0.00 2.59
135 136 6.504279 GGTAGGGGAATGATTCTAAGGGATAA 59.496 42.308 5.03 0.00 0.00 1.75
139 140 6.717084 GGGGAATGATTCTAAGGGATAACAAG 59.283 42.308 5.03 0.00 0.00 3.16
140 141 6.717084 GGGAATGATTCTAAGGGATAACAAGG 59.283 42.308 5.03 0.00 0.00 3.61
141 142 7.290813 GGAATGATTCTAAGGGATAACAAGGT 58.709 38.462 5.03 0.00 0.00 3.50
142 143 7.780271 GGAATGATTCTAAGGGATAACAAGGTT 59.220 37.037 5.03 0.00 0.00 3.50
143 144 8.525290 AATGATTCTAAGGGATAACAAGGTTG 57.475 34.615 0.00 0.00 0.00 3.77
144 145 5.885912 TGATTCTAAGGGATAACAAGGTTGC 59.114 40.000 0.00 0.00 0.00 4.17
145 146 3.869065 TCTAAGGGATAACAAGGTTGCG 58.131 45.455 0.00 0.00 0.00 4.85
146 147 1.834188 AAGGGATAACAAGGTTGCGG 58.166 50.000 0.00 0.00 0.00 5.69
147 148 0.696501 AGGGATAACAAGGTTGCGGT 59.303 50.000 0.00 0.00 0.00 5.68
148 149 1.074889 AGGGATAACAAGGTTGCGGTT 59.925 47.619 0.00 0.00 0.00 4.44
150 151 3.053917 AGGGATAACAAGGTTGCGGTTAT 60.054 43.478 0.00 0.00 39.65 1.89
152 153 4.158949 GGGATAACAAGGTTGCGGTTATTT 59.841 41.667 0.00 0.00 37.72 1.40
154 155 5.803461 GGATAACAAGGTTGCGGTTATTTTC 59.197 40.000 0.00 0.00 37.72 2.29
157 158 4.616953 ACAAGGTTGCGGTTATTTTCTTG 58.383 39.130 0.00 0.00 37.12 3.02
159 160 4.499037 AGGTTGCGGTTATTTTCTTGAC 57.501 40.909 0.00 0.00 0.00 3.18
160 161 3.886505 AGGTTGCGGTTATTTTCTTGACA 59.113 39.130 0.00 0.00 0.00 3.58
162 163 5.708230 AGGTTGCGGTTATTTTCTTGACATA 59.292 36.000 0.00 0.00 0.00 2.29
163 164 6.377146 AGGTTGCGGTTATTTTCTTGACATAT 59.623 34.615 0.00 0.00 0.00 1.78
164 165 6.691388 GGTTGCGGTTATTTTCTTGACATATC 59.309 38.462 0.00 0.00 0.00 1.63
165 166 6.043327 TGCGGTTATTTTCTTGACATATCG 57.957 37.500 0.00 0.00 0.00 2.92
166 167 5.813157 TGCGGTTATTTTCTTGACATATCGA 59.187 36.000 0.00 0.00 0.00 3.59
167 168 6.481976 TGCGGTTATTTTCTTGACATATCGAT 59.518 34.615 2.16 2.16 0.00 3.59
168 169 7.011950 TGCGGTTATTTTCTTGACATATCGATT 59.988 33.333 1.71 0.00 0.00 3.34
180 181 8.926715 TTGACATATCGATTTATATTCCTCCG 57.073 34.615 1.71 0.00 0.00 4.63
181 182 6.978659 TGACATATCGATTTATATTCCTCCGC 59.021 38.462 1.71 0.00 0.00 5.54
183 184 7.327975 ACATATCGATTTATATTCCTCCGCAA 58.672 34.615 1.71 0.00 0.00 4.85
184 185 7.277981 ACATATCGATTTATATTCCTCCGCAAC 59.722 37.037 1.71 0.00 0.00 4.17
188 189 6.073276 TCGATTTATATTCCTCCGCAACAATG 60.073 38.462 0.00 0.00 0.00 2.82
199 200 3.406682 CAACAATGCCTTCGAAGCC 57.593 52.632 19.99 9.71 0.00 4.35
201 202 0.605319 AACAATGCCTTCGAAGCCGA 60.605 50.000 19.99 5.59 43.96 5.54
211 212 1.274596 TCGAAGCCGAAATTAGCGTC 58.725 50.000 0.00 1.62 42.51 5.19
212 213 3.781212 GAAGCCGAAATTAGCGTCG 57.219 52.632 0.00 0.00 37.01 5.12
213 214 0.997196 GAAGCCGAAATTAGCGTCGT 59.003 50.000 0.00 0.00 35.48 4.34
214 215 0.997196 AAGCCGAAATTAGCGTCGTC 59.003 50.000 0.00 0.00 35.48 4.20
216 217 0.997196 GCCGAAATTAGCGTCGTCTT 59.003 50.000 0.00 0.00 35.48 3.01
217 218 2.159338 AGCCGAAATTAGCGTCGTCTTA 60.159 45.455 0.00 0.00 35.48 2.10
218 219 2.215812 GCCGAAATTAGCGTCGTCTTAG 59.784 50.000 0.00 0.00 35.48 2.18
221 222 4.204573 CCGAAATTAGCGTCGTCTTAGAAG 59.795 45.833 0.00 0.00 35.48 2.85
222 223 4.204573 CGAAATTAGCGTCGTCTTAGAAGG 59.795 45.833 0.00 0.00 32.61 3.46
225 226 0.818296 AGCGTCGTCTTAGAAGGCAT 59.182 50.000 0.39 0.00 0.00 4.40
226 227 0.924090 GCGTCGTCTTAGAAGGCATG 59.076 55.000 0.39 0.00 0.00 4.06
228 229 2.186076 CGTCGTCTTAGAAGGCATGTC 58.814 52.381 0.39 0.00 0.00 3.06
229 230 2.415491 CGTCGTCTTAGAAGGCATGTCA 60.415 50.000 0.00 0.00 0.00 3.58
230 231 3.735208 CGTCGTCTTAGAAGGCATGTCAT 60.735 47.826 0.00 0.00 0.00 3.06
231 232 4.184629 GTCGTCTTAGAAGGCATGTCATT 58.815 43.478 0.00 0.00 0.00 2.57
232 233 4.033358 GTCGTCTTAGAAGGCATGTCATTG 59.967 45.833 0.00 0.00 0.00 2.82
233 234 4.081697 TCGTCTTAGAAGGCATGTCATTGA 60.082 41.667 0.00 0.00 0.00 2.57
234 235 4.631377 CGTCTTAGAAGGCATGTCATTGAA 59.369 41.667 0.00 0.00 0.00 2.69
235 236 5.446473 CGTCTTAGAAGGCATGTCATTGAAC 60.446 44.000 0.00 0.00 0.00 3.18
237 238 6.094603 GTCTTAGAAGGCATGTCATTGAACAT 59.905 38.462 0.00 0.00 40.49 2.71
246 247 4.177165 TGTCATTGAACATGCAATGGTC 57.823 40.909 19.63 15.01 44.29 4.02
251 252 1.900237 GAACATGCAATGGTCGAAGC 58.100 50.000 0.00 0.00 44.29 3.86
252 253 1.470098 GAACATGCAATGGTCGAAGCT 59.530 47.619 0.00 0.00 44.29 3.74
253 254 1.200716 AACATGCAATGGTCGAAGCTG 59.799 47.619 0.00 0.00 44.29 4.24
254 255 0.099968 CATGCAATGGTCGAAGCTGG 59.900 55.000 0.00 0.00 41.79 4.85
255 256 0.322816 ATGCAATGGTCGAAGCTGGT 60.323 50.000 0.00 0.00 0.00 4.00
256 257 0.323302 TGCAATGGTCGAAGCTGGTA 59.677 50.000 0.00 0.00 0.00 3.25
260 261 3.625764 GCAATGGTCGAAGCTGGTAATAA 59.374 43.478 0.00 0.00 0.00 1.40
262 263 5.221048 GCAATGGTCGAAGCTGGTAATAATT 60.221 40.000 0.00 0.00 0.00 1.40
263 264 6.017440 GCAATGGTCGAAGCTGGTAATAATTA 60.017 38.462 0.00 0.00 0.00 1.40
264 265 7.308589 GCAATGGTCGAAGCTGGTAATAATTAT 60.309 37.037 0.00 0.00 0.00 1.28
265 266 7.907214 ATGGTCGAAGCTGGTAATAATTATC 57.093 36.000 0.00 0.00 0.00 1.75
266 267 6.228258 TGGTCGAAGCTGGTAATAATTATCC 58.772 40.000 0.00 0.00 0.00 2.59
267 268 6.183361 TGGTCGAAGCTGGTAATAATTATCCA 60.183 38.462 0.00 2.29 0.00 3.41
268 269 6.708949 GGTCGAAGCTGGTAATAATTATCCAA 59.291 38.462 7.18 0.00 0.00 3.53
269 270 7.390718 GGTCGAAGCTGGTAATAATTATCCAAT 59.609 37.037 7.18 0.00 0.00 3.16
271 272 7.606456 TCGAAGCTGGTAATAATTATCCAATCC 59.394 37.037 7.18 3.57 0.00 3.01
272 273 7.413000 CGAAGCTGGTAATAATTATCCAATCCG 60.413 40.741 7.18 5.51 0.00 4.18
273 274 7.016153 AGCTGGTAATAATTATCCAATCCGA 57.984 36.000 7.18 0.00 0.00 4.55
275 276 8.768397 AGCTGGTAATAATTATCCAATCCGATA 58.232 33.333 7.18 0.00 0.00 2.92
276 277 9.046296 GCTGGTAATAATTATCCAATCCGATAG 57.954 37.037 7.18 0.00 0.00 2.08
290 291 2.737467 CGATAGTTCGGTGGCAATTG 57.263 50.000 0.00 0.00 41.74 2.32
291 292 1.268032 CGATAGTTCGGTGGCAATTGC 60.268 52.381 22.47 22.47 41.74 3.56
293 294 1.164411 TAGTTCGGTGGCAATTGCTG 58.836 50.000 28.42 16.23 41.70 4.41
295 296 0.387239 GTTCGGTGGCAATTGCTGTC 60.387 55.000 28.42 18.01 41.70 3.51
296 297 0.537143 TTCGGTGGCAATTGCTGTCT 60.537 50.000 28.42 0.00 41.70 3.41
297 298 0.537143 TCGGTGGCAATTGCTGTCTT 60.537 50.000 28.42 0.00 41.70 3.01
298 299 0.387622 CGGTGGCAATTGCTGTCTTG 60.388 55.000 28.42 11.16 41.70 3.02
299 300 0.961019 GGTGGCAATTGCTGTCTTGA 59.039 50.000 28.42 3.11 41.70 3.02
301 302 2.754552 GGTGGCAATTGCTGTCTTGATA 59.245 45.455 28.42 3.19 41.70 2.15
302 303 3.181493 GGTGGCAATTGCTGTCTTGATAG 60.181 47.826 28.42 0.00 41.70 2.08
303 304 3.691118 GTGGCAATTGCTGTCTTGATAGA 59.309 43.478 28.42 0.00 41.70 1.98
304 305 4.337555 GTGGCAATTGCTGTCTTGATAGAT 59.662 41.667 28.42 0.00 41.70 1.98
305 306 4.577693 TGGCAATTGCTGTCTTGATAGATC 59.422 41.667 28.42 8.32 41.70 2.75
306 307 4.577693 GGCAATTGCTGTCTTGATAGATCA 59.422 41.667 28.42 0.00 41.70 2.92
312 313 4.041049 GCTGTCTTGATAGATCAGTCACG 58.959 47.826 0.00 0.00 38.19 4.35
314 315 5.491635 TGTCTTGATAGATCAGTCACGAG 57.508 43.478 6.75 1.54 38.19 4.18
315 316 4.336713 TGTCTTGATAGATCAGTCACGAGG 59.663 45.833 6.75 0.00 38.19 4.63
316 317 3.885901 TCTTGATAGATCAGTCACGAGGG 59.114 47.826 0.00 0.00 38.19 4.30
317 318 2.587522 TGATAGATCAGTCACGAGGGG 58.412 52.381 0.00 0.00 32.11 4.79
318 319 2.174854 TGATAGATCAGTCACGAGGGGA 59.825 50.000 0.00 0.00 32.11 4.81
319 320 3.181428 TGATAGATCAGTCACGAGGGGAT 60.181 47.826 0.00 0.00 32.11 3.85
321 322 3.534357 AGATCAGTCACGAGGGGATAT 57.466 47.619 0.00 0.00 0.00 1.63
322 323 3.426615 AGATCAGTCACGAGGGGATATC 58.573 50.000 0.00 0.00 0.00 1.63
323 324 2.748209 TCAGTCACGAGGGGATATCA 57.252 50.000 4.83 0.00 0.00 2.15
325 326 2.959030 TCAGTCACGAGGGGATATCAAG 59.041 50.000 4.83 0.00 0.00 3.02
326 327 2.959030 CAGTCACGAGGGGATATCAAGA 59.041 50.000 4.83 0.00 0.00 3.02
327 328 3.384789 CAGTCACGAGGGGATATCAAGAA 59.615 47.826 4.83 0.00 0.00 2.52
328 329 3.639094 AGTCACGAGGGGATATCAAGAAG 59.361 47.826 4.83 0.00 0.00 2.85
329 330 2.365617 TCACGAGGGGATATCAAGAAGC 59.634 50.000 4.83 0.00 0.00 3.86
331 332 2.630580 ACGAGGGGATATCAAGAAGCTC 59.369 50.000 4.83 0.00 0.00 4.09
334 335 2.896685 AGGGGATATCAAGAAGCTCTCG 59.103 50.000 4.83 0.00 0.00 4.04
336 337 2.611722 GGGATATCAAGAAGCTCTCGGC 60.612 54.545 4.83 0.00 42.19 5.54
345 346 2.202676 GCTCTCGGCTCTTCGTGG 60.203 66.667 0.00 0.00 38.06 4.94
346 347 2.995872 GCTCTCGGCTCTTCGTGGT 61.996 63.158 0.00 0.00 38.06 4.16
347 348 1.587054 CTCTCGGCTCTTCGTGGTT 59.413 57.895 0.00 0.00 0.00 3.67
348 349 0.038159 CTCTCGGCTCTTCGTGGTTT 60.038 55.000 0.00 0.00 0.00 3.27
351 352 2.232941 TCTCGGCTCTTCGTGGTTTATT 59.767 45.455 0.00 0.00 0.00 1.40
353 354 3.514645 TCGGCTCTTCGTGGTTTATTAC 58.485 45.455 0.00 0.00 0.00 1.89
354 355 3.056678 TCGGCTCTTCGTGGTTTATTACA 60.057 43.478 0.00 0.00 0.00 2.41
361 362 9.615295 GCTCTTCGTGGTTTATTACATTAAAAA 57.385 29.630 0.00 0.00 0.00 1.94
368 369 9.685828 GTGGTTTATTACATTAAAAAGTGAGCA 57.314 29.630 0.00 0.00 0.00 4.26
385 386 9.757227 AAAGTGAGCATAGTCATAGTAGAATTC 57.243 33.333 0.00 0.00 0.00 2.17
397 398 9.868277 GTCATAGTAGAATTCCTCATAATCCAG 57.132 37.037 0.65 0.00 0.00 3.86
399 400 8.538701 CATAGTAGAATTCCTCATAATCCAGCT 58.461 37.037 0.65 0.00 0.00 4.24
400 401 9.775539 ATAGTAGAATTCCTCATAATCCAGCTA 57.224 33.333 0.65 0.00 0.00 3.32
427 428 7.573968 AATATTGAACATTCTGAAGGTAGCC 57.426 36.000 8.23 2.29 0.00 3.93
428 429 4.365514 TTGAACATTCTGAAGGTAGCCA 57.634 40.909 8.23 4.73 0.00 4.75
442 443 2.674563 TAGCCACGCTTGCTGGTTGT 62.675 55.000 4.37 2.67 40.44 3.32
444 445 2.480610 CCACGCTTGCTGGTTGTGT 61.481 57.895 0.00 0.00 0.00 3.72
445 446 1.433064 CACGCTTGCTGGTTGTGTT 59.567 52.632 0.00 0.00 0.00 3.32
446 447 0.592247 CACGCTTGCTGGTTGTGTTC 60.592 55.000 0.00 0.00 0.00 3.18
453 454 4.215399 GCTTGCTGGTTGTGTTCTGTTATA 59.785 41.667 0.00 0.00 0.00 0.98
456 457 4.994852 TGCTGGTTGTGTTCTGTTATAGAC 59.005 41.667 0.00 0.00 34.43 2.59
458 459 5.107065 GCTGGTTGTGTTCTGTTATAGACAC 60.107 44.000 0.00 0.00 37.66 3.67
465 466 5.061064 GTGTTCTGTTATAGACACTGCTTCG 59.939 44.000 0.00 0.00 35.94 3.79
488 489 5.123186 CGGAATTTGTATTGGCAGACTGTAA 59.877 40.000 3.99 0.67 0.00 2.41
489 490 6.183360 CGGAATTTGTATTGGCAGACTGTAAT 60.183 38.462 3.99 8.08 0.00 1.89
498 499 5.546621 TGGCAGACTGTAATACTATTCCC 57.453 43.478 3.99 0.00 0.00 3.97
523 524 9.476202 CCGAGGAATAAAATCAACTTTTTCTTT 57.524 29.630 0.00 0.00 38.09 2.52
560 561 6.162079 TGAGTGCTGAAAAATGAAAAACACA 58.838 32.000 0.00 0.00 0.00 3.72
619 620 2.355010 ACAGCAAAAACAGCTCCTCT 57.645 45.000 0.00 0.00 41.14 3.69
647 648 1.627864 AAATCCAGTCAAAACGGGGG 58.372 50.000 0.00 0.00 40.76 5.40
725 734 3.827898 GTGTCCCTCTCCCTCGCG 61.828 72.222 0.00 0.00 0.00 5.87
730 739 4.521062 CCTCTCCCTCGCGCCAAG 62.521 72.222 0.00 0.00 0.00 3.61
731 740 3.452786 CTCTCCCTCGCGCCAAGA 61.453 66.667 0.00 0.37 0.00 3.02
802 885 3.243053 TCCTTCCGCCGGAACCAA 61.243 61.111 15.93 0.00 36.71 3.67
945 1046 1.006832 GAACAACACATCCGGATCCG 58.993 55.000 27.65 27.65 39.44 4.18
1399 1592 1.080637 GGTGATGCGCAACATGCAA 60.081 52.632 23.64 0.00 46.87 4.08
1601 2935 0.381801 GCTCTCTGCTTCTCTCCTCG 59.618 60.000 0.00 0.00 38.95 4.63
1797 3170 2.263077 GTTCTCAGTGATAGTGCCACG 58.737 52.381 0.00 0.00 39.38 4.94
1883 3318 5.402270 CCTGCATTTTCCAGTTAAAAAGACG 59.598 40.000 0.00 0.00 32.42 4.18
1968 3403 7.015779 ACTGTTATCTCCTATTCTTCTTAGCCC 59.984 40.741 0.00 0.00 0.00 5.19
2058 3493 2.846193 TCTATGGGCGATAAACAAGGC 58.154 47.619 0.00 0.00 0.00 4.35
2135 3577 4.848357 ACATGGGTACAAGATTTCAGGAG 58.152 43.478 0.00 0.00 0.00 3.69
2164 3606 6.588373 GGCTTGATTTAGATCCGAGAAGATAC 59.412 42.308 0.00 0.00 0.00 2.24
2185 3627 9.012161 AGATACGTTCTTCAAGTACTATATCCC 57.988 37.037 0.00 0.00 0.00 3.85
2238 3680 7.436673 GGTATAGTTGTCACTCACTGATTCATC 59.563 40.741 0.00 0.00 34.06 2.92
2366 6039 8.110612 CGTATGTCAATTTCAATACACTCTCAC 58.889 37.037 0.00 0.00 0.00 3.51
2427 6101 5.779529 ATTTCAATGCCAGGTCACATATC 57.220 39.130 0.00 0.00 0.00 1.63
2466 6141 4.061357 TCGATTTACACAACCTGTCACA 57.939 40.909 0.00 0.00 33.91 3.58
2472 6147 6.795098 TTTACACAACCTGTCACATATCAC 57.205 37.500 0.00 0.00 33.91 3.06
2519 6194 6.441088 ACATCTCACCTCTTTTAGTTTCCT 57.559 37.500 0.00 0.00 0.00 3.36
2566 6241 8.633075 TTCAGTTTCAATTTCAACAATCAGAC 57.367 30.769 0.49 0.00 0.00 3.51
2623 6298 2.443632 TGTCAGTTTCAATACACCCCCA 59.556 45.455 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.810412 GCACGGAAGCGGGAGAAATAT 60.810 52.381 0.00 0.00 0.00 1.28
3 4 1.745489 GCACGGAAGCGGGAGAAAT 60.745 57.895 0.00 0.00 0.00 2.17
26 27 5.505324 CCAGCTTAGTAATCATTGCTTCTGC 60.505 44.000 0.00 0.00 40.20 4.26
27 28 5.505324 GCCAGCTTAGTAATCATTGCTTCTG 60.505 44.000 0.00 0.07 0.00 3.02
29 30 4.578105 AGCCAGCTTAGTAATCATTGCTTC 59.422 41.667 0.00 0.00 0.00 3.86
30 31 4.530875 AGCCAGCTTAGTAATCATTGCTT 58.469 39.130 0.00 0.00 0.00 3.91
32 33 4.578105 AGAAGCCAGCTTAGTAATCATTGC 59.422 41.667 4.57 0.00 36.26 3.56
33 34 5.008415 CCAGAAGCCAGCTTAGTAATCATTG 59.992 44.000 4.57 0.00 36.26 2.82
34 35 5.128919 CCAGAAGCCAGCTTAGTAATCATT 58.871 41.667 4.57 0.00 36.26 2.57
37 38 2.875317 GCCAGAAGCCAGCTTAGTAATC 59.125 50.000 4.57 0.00 36.26 1.75
38 39 2.507471 AGCCAGAAGCCAGCTTAGTAAT 59.493 45.455 4.57 0.00 45.47 1.89
39 40 1.909302 AGCCAGAAGCCAGCTTAGTAA 59.091 47.619 4.57 0.00 45.47 2.24
41 42 0.035630 CAGCCAGAAGCCAGCTTAGT 60.036 55.000 4.57 0.00 45.47 2.24
43 44 1.300963 CCAGCCAGAAGCCAGCTTA 59.699 57.895 4.57 0.00 45.47 3.09
46 47 4.357279 ACCCAGCCAGAAGCCAGC 62.357 66.667 0.00 0.00 45.47 4.85
47 48 2.360852 CACCCAGCCAGAAGCCAG 60.361 66.667 0.00 0.00 45.47 4.85
50 51 3.875510 AAGCCACCCAGCCAGAAGC 62.876 63.158 0.00 0.00 44.25 3.86
52 53 0.398381 AAAAAGCCACCCAGCCAGAA 60.398 50.000 0.00 0.00 0.00 3.02
53 54 0.827507 GAAAAAGCCACCCAGCCAGA 60.828 55.000 0.00 0.00 0.00 3.86
55 56 1.836604 GGAAAAAGCCACCCAGCCA 60.837 57.895 0.00 0.00 0.00 4.75
56 57 2.931068 CGGAAAAAGCCACCCAGCC 61.931 63.158 0.00 0.00 0.00 4.85
57 58 2.142357 GACGGAAAAAGCCACCCAGC 62.142 60.000 0.00 0.00 0.00 4.85
58 59 1.852067 CGACGGAAAAAGCCACCCAG 61.852 60.000 0.00 0.00 0.00 4.45
59 60 1.894756 CGACGGAAAAAGCCACCCA 60.895 57.895 0.00 0.00 0.00 4.51
60 61 0.958876 ATCGACGGAAAAAGCCACCC 60.959 55.000 0.00 0.00 0.00 4.61
61 62 0.168128 CATCGACGGAAAAAGCCACC 59.832 55.000 0.00 0.00 0.00 4.61
62 63 0.168128 CCATCGACGGAAAAAGCCAC 59.832 55.000 0.00 0.00 0.00 5.01
64 65 1.136774 GCCATCGACGGAAAAAGCC 59.863 57.895 0.00 0.00 0.00 4.35
65 66 0.097150 GAGCCATCGACGGAAAAAGC 59.903 55.000 0.00 0.00 0.00 3.51
66 67 1.438651 TGAGCCATCGACGGAAAAAG 58.561 50.000 0.00 0.00 0.00 2.27
68 69 2.006888 GAATGAGCCATCGACGGAAAA 58.993 47.619 0.00 0.00 0.00 2.29
69 70 1.066502 TGAATGAGCCATCGACGGAAA 60.067 47.619 0.00 0.00 0.00 3.13
70 71 0.534873 TGAATGAGCCATCGACGGAA 59.465 50.000 0.00 0.00 0.00 4.30
72 73 1.528586 GAATGAATGAGCCATCGACGG 59.471 52.381 0.00 0.00 0.00 4.79
73 74 2.204237 TGAATGAATGAGCCATCGACG 58.796 47.619 0.00 0.00 0.00 5.12
74 75 3.873361 TCTTGAATGAATGAGCCATCGAC 59.127 43.478 0.00 0.00 0.00 4.20
75 76 3.873361 GTCTTGAATGAATGAGCCATCGA 59.127 43.478 0.00 0.00 0.00 3.59
76 77 3.624410 TGTCTTGAATGAATGAGCCATCG 59.376 43.478 0.00 0.00 0.00 3.84
77 78 4.639310 AGTGTCTTGAATGAATGAGCCATC 59.361 41.667 0.00 0.00 0.00 3.51
78 79 4.398358 CAGTGTCTTGAATGAATGAGCCAT 59.602 41.667 0.00 0.00 0.00 4.40
79 80 3.754850 CAGTGTCTTGAATGAATGAGCCA 59.245 43.478 0.00 0.00 0.00 4.75
80 81 3.128242 CCAGTGTCTTGAATGAATGAGCC 59.872 47.826 0.00 0.00 0.00 4.70
81 82 3.755378 ACCAGTGTCTTGAATGAATGAGC 59.245 43.478 0.00 0.00 0.00 4.26
82 83 4.379186 GCACCAGTGTCTTGAATGAATGAG 60.379 45.833 0.00 0.00 0.00 2.90
83 84 3.503363 GCACCAGTGTCTTGAATGAATGA 59.497 43.478 0.00 0.00 0.00 2.57
84 85 3.253921 TGCACCAGTGTCTTGAATGAATG 59.746 43.478 0.00 0.00 0.00 2.67
87 88 2.158769 ACTGCACCAGTGTCTTGAATGA 60.159 45.455 0.00 0.00 43.63 2.57
88 89 2.224606 ACTGCACCAGTGTCTTGAATG 58.775 47.619 0.00 0.00 43.63 2.67
89 90 2.645838 ACTGCACCAGTGTCTTGAAT 57.354 45.000 0.00 0.00 43.63 2.57
99 100 2.671070 CCCTACCCACTGCACCAG 59.329 66.667 0.00 0.00 37.52 4.00
100 101 2.933287 CCCCTACCCACTGCACCA 60.933 66.667 0.00 0.00 0.00 4.17
101 102 1.571773 ATTCCCCTACCCACTGCACC 61.572 60.000 0.00 0.00 0.00 5.01
102 103 0.394352 CATTCCCCTACCCACTGCAC 60.394 60.000 0.00 0.00 0.00 4.57
103 104 0.548926 TCATTCCCCTACCCACTGCA 60.549 55.000 0.00 0.00 0.00 4.41
104 105 0.846693 ATCATTCCCCTACCCACTGC 59.153 55.000 0.00 0.00 0.00 4.40
105 106 2.780010 AGAATCATTCCCCTACCCACTG 59.220 50.000 0.00 0.00 0.00 3.66
107 108 4.202472 CCTTAGAATCATTCCCCTACCCAC 60.202 50.000 0.00 0.00 0.00 4.61
109 110 3.330998 CCCTTAGAATCATTCCCCTACCC 59.669 52.174 0.00 0.00 0.00 3.69
110 111 4.240323 TCCCTTAGAATCATTCCCCTACC 58.760 47.826 0.00 0.00 0.00 3.18
111 112 7.017254 TGTTATCCCTTAGAATCATTCCCCTAC 59.983 40.741 0.00 0.00 0.00 3.18
112 113 7.086260 TGTTATCCCTTAGAATCATTCCCCTA 58.914 38.462 0.00 0.00 0.00 3.53
113 114 5.917087 TGTTATCCCTTAGAATCATTCCCCT 59.083 40.000 0.00 0.00 0.00 4.79
114 115 6.200878 TGTTATCCCTTAGAATCATTCCCC 57.799 41.667 0.00 0.00 0.00 4.81
115 116 6.717084 CCTTGTTATCCCTTAGAATCATTCCC 59.283 42.308 0.00 0.00 0.00 3.97
116 117 7.290813 ACCTTGTTATCCCTTAGAATCATTCC 58.709 38.462 0.00 0.00 0.00 3.01
117 118 8.624776 CAACCTTGTTATCCCTTAGAATCATTC 58.375 37.037 0.00 0.00 0.00 2.67
118 119 7.068716 GCAACCTTGTTATCCCTTAGAATCATT 59.931 37.037 0.00 0.00 0.00 2.57
119 120 6.547510 GCAACCTTGTTATCCCTTAGAATCAT 59.452 38.462 0.00 0.00 0.00 2.45
121 122 5.007724 CGCAACCTTGTTATCCCTTAGAATC 59.992 44.000 0.00 0.00 0.00 2.52
123 124 4.258543 CGCAACCTTGTTATCCCTTAGAA 58.741 43.478 0.00 0.00 0.00 2.10
124 125 3.370103 CCGCAACCTTGTTATCCCTTAGA 60.370 47.826 0.00 0.00 0.00 2.10
125 126 2.943033 CCGCAACCTTGTTATCCCTTAG 59.057 50.000 0.00 0.00 0.00 2.18
126 127 2.306512 ACCGCAACCTTGTTATCCCTTA 59.693 45.455 0.00 0.00 0.00 2.69
127 128 1.074889 ACCGCAACCTTGTTATCCCTT 59.925 47.619 0.00 0.00 0.00 3.95
128 129 0.696501 ACCGCAACCTTGTTATCCCT 59.303 50.000 0.00 0.00 0.00 4.20
129 130 1.541379 AACCGCAACCTTGTTATCCC 58.459 50.000 0.00 0.00 0.00 3.85
130 131 4.976224 AATAACCGCAACCTTGTTATCC 57.024 40.909 0.00 0.00 34.88 2.59
131 132 6.617879 AGAAAATAACCGCAACCTTGTTATC 58.382 36.000 0.00 0.00 34.88 1.75
134 135 4.929819 AGAAAATAACCGCAACCTTGTT 57.070 36.364 0.00 0.00 0.00 2.83
135 136 4.339814 TCAAGAAAATAACCGCAACCTTGT 59.660 37.500 0.00 0.00 33.54 3.16
139 140 4.231718 TGTCAAGAAAATAACCGCAACC 57.768 40.909 0.00 0.00 0.00 3.77
140 141 6.410914 CGATATGTCAAGAAAATAACCGCAAC 59.589 38.462 0.00 0.00 0.00 4.17
141 142 6.314152 TCGATATGTCAAGAAAATAACCGCAA 59.686 34.615 0.00 0.00 0.00 4.85
142 143 5.813157 TCGATATGTCAAGAAAATAACCGCA 59.187 36.000 0.00 0.00 0.00 5.69
143 144 6.281848 TCGATATGTCAAGAAAATAACCGC 57.718 37.500 0.00 0.00 0.00 5.68
154 155 9.025020 CGGAGGAATATAAATCGATATGTCAAG 57.975 37.037 0.00 0.00 0.00 3.02
157 158 6.978659 TGCGGAGGAATATAAATCGATATGTC 59.021 38.462 0.00 0.00 0.00 3.06
159 160 7.277760 TGTTGCGGAGGAATATAAATCGATATG 59.722 37.037 0.00 0.00 41.93 1.78
160 161 7.327975 TGTTGCGGAGGAATATAAATCGATAT 58.672 34.615 0.00 0.00 41.93 1.63
162 163 5.547465 TGTTGCGGAGGAATATAAATCGAT 58.453 37.500 0.00 0.00 41.93 3.59
163 164 4.951254 TGTTGCGGAGGAATATAAATCGA 58.049 39.130 0.00 0.00 41.93 3.59
164 165 5.666969 TTGTTGCGGAGGAATATAAATCG 57.333 39.130 0.00 0.00 41.93 3.34
165 166 5.858581 GCATTGTTGCGGAGGAATATAAATC 59.141 40.000 0.00 0.00 41.93 2.17
166 167 5.772521 GCATTGTTGCGGAGGAATATAAAT 58.227 37.500 0.00 0.00 41.93 1.40
167 168 5.181690 GCATTGTTGCGGAGGAATATAAA 57.818 39.130 0.00 0.00 41.93 1.40
168 169 4.829064 GCATTGTTGCGGAGGAATATAA 57.171 40.909 0.00 0.00 41.93 0.98
192 193 1.274596 GACGCTAATTTCGGCTTCGA 58.725 50.000 5.09 0.00 41.62 3.71
193 194 0.044161 CGACGCTAATTTCGGCTTCG 60.044 55.000 10.34 10.34 41.93 3.79
194 195 0.997196 ACGACGCTAATTTCGGCTTC 59.003 50.000 0.00 0.00 39.63 3.86
195 196 0.997196 GACGACGCTAATTTCGGCTT 59.003 50.000 0.00 0.00 40.30 4.35
196 197 2.662150 GACGACGCTAATTTCGGCT 58.338 52.632 0.00 0.00 40.30 5.52
197 198 0.997196 AAGACGACGCTAATTTCGGC 59.003 50.000 0.00 0.00 44.03 5.54
199 200 4.204573 CCTTCTAAGACGACGCTAATTTCG 59.795 45.833 0.00 0.00 41.14 3.46
201 202 3.864003 GCCTTCTAAGACGACGCTAATTT 59.136 43.478 0.00 0.00 0.00 1.82
202 203 3.119245 TGCCTTCTAAGACGACGCTAATT 60.119 43.478 0.00 0.00 0.00 1.40
203 204 2.426024 TGCCTTCTAAGACGACGCTAAT 59.574 45.455 0.00 0.00 0.00 1.73
204 205 1.814394 TGCCTTCTAAGACGACGCTAA 59.186 47.619 0.00 0.00 0.00 3.09
205 206 1.456296 TGCCTTCTAAGACGACGCTA 58.544 50.000 0.00 0.00 0.00 4.26
207 208 0.924090 CATGCCTTCTAAGACGACGC 59.076 55.000 0.00 0.00 0.00 5.19
208 209 2.186076 GACATGCCTTCTAAGACGACG 58.814 52.381 0.00 0.00 0.00 5.12
209 210 3.232213 TGACATGCCTTCTAAGACGAC 57.768 47.619 0.00 0.00 0.00 4.34
211 212 4.183865 TCAATGACATGCCTTCTAAGACG 58.816 43.478 0.00 0.00 0.00 4.18
212 213 5.412594 TGTTCAATGACATGCCTTCTAAGAC 59.587 40.000 0.00 0.00 0.00 3.01
213 214 5.559770 TGTTCAATGACATGCCTTCTAAGA 58.440 37.500 0.00 0.00 0.00 2.10
214 215 5.885230 TGTTCAATGACATGCCTTCTAAG 57.115 39.130 0.00 0.00 0.00 2.18
229 230 3.674138 GCTTCGACCATTGCATGTTCAAT 60.674 43.478 0.00 0.00 37.16 2.57
230 231 2.351641 GCTTCGACCATTGCATGTTCAA 60.352 45.455 0.00 0.00 0.00 2.69
231 232 1.199789 GCTTCGACCATTGCATGTTCA 59.800 47.619 0.00 0.00 0.00 3.18
232 233 1.470098 AGCTTCGACCATTGCATGTTC 59.530 47.619 0.00 0.00 0.00 3.18
233 234 1.200716 CAGCTTCGACCATTGCATGTT 59.799 47.619 0.00 0.00 0.00 2.71
234 235 0.806868 CAGCTTCGACCATTGCATGT 59.193 50.000 0.00 0.00 0.00 3.21
235 236 0.099968 CCAGCTTCGACCATTGCATG 59.900 55.000 0.00 0.00 0.00 4.06
237 238 0.323302 TACCAGCTTCGACCATTGCA 59.677 50.000 0.00 0.00 0.00 4.08
238 239 1.448985 TTACCAGCTTCGACCATTGC 58.551 50.000 0.00 0.00 0.00 3.56
242 243 6.183361 TGGATAATTATTACCAGCTTCGACCA 60.183 38.462 0.00 0.00 0.00 4.02
243 244 6.228258 TGGATAATTATTACCAGCTTCGACC 58.772 40.000 0.00 0.00 0.00 4.79
244 245 7.724305 TTGGATAATTATTACCAGCTTCGAC 57.276 36.000 0.00 0.00 33.85 4.20
245 246 7.606456 GGATTGGATAATTATTACCAGCTTCGA 59.394 37.037 0.00 0.00 33.85 3.71
246 247 7.413000 CGGATTGGATAATTATTACCAGCTTCG 60.413 40.741 0.00 2.74 33.85 3.79
247 248 7.606456 TCGGATTGGATAATTATTACCAGCTTC 59.394 37.037 0.00 2.97 33.85 3.86
249 250 7.016153 TCGGATTGGATAATTATTACCAGCT 57.984 36.000 0.00 0.00 33.85 4.24
271 272 1.268032 GCAATTGCCACCGAACTATCG 60.268 52.381 20.06 0.00 41.07 2.92
272 273 2.017049 AGCAATTGCCACCGAACTATC 58.983 47.619 26.45 0.00 43.38 2.08
273 274 1.745087 CAGCAATTGCCACCGAACTAT 59.255 47.619 26.45 0.94 43.38 2.12
275 276 0.823356 ACAGCAATTGCCACCGAACT 60.823 50.000 26.45 2.53 43.38 3.01
276 277 0.387239 GACAGCAATTGCCACCGAAC 60.387 55.000 26.45 7.99 43.38 3.95
277 278 0.537143 AGACAGCAATTGCCACCGAA 60.537 50.000 26.45 0.00 43.38 4.30
278 279 0.537143 AAGACAGCAATTGCCACCGA 60.537 50.000 26.45 0.00 43.38 4.69
279 280 0.387622 CAAGACAGCAATTGCCACCG 60.388 55.000 26.45 14.88 43.38 4.94
280 281 0.961019 TCAAGACAGCAATTGCCACC 59.039 50.000 26.45 15.00 43.38 4.61
281 282 3.691118 TCTATCAAGACAGCAATTGCCAC 59.309 43.478 26.45 17.13 43.38 5.01
282 283 3.954200 TCTATCAAGACAGCAATTGCCA 58.046 40.909 26.45 2.89 43.38 4.92
283 284 4.577693 TGATCTATCAAGACAGCAATTGCC 59.422 41.667 26.45 11.77 36.70 4.52
284 285 5.296283 ACTGATCTATCAAGACAGCAATTGC 59.704 40.000 23.05 23.05 35.77 3.56
285 286 6.537660 TGACTGATCTATCAAGACAGCAATTG 59.462 38.462 0.00 0.00 35.77 2.32
286 287 6.538021 GTGACTGATCTATCAAGACAGCAATT 59.462 38.462 0.00 0.00 35.77 2.32
288 289 5.414360 GTGACTGATCTATCAAGACAGCAA 58.586 41.667 0.00 0.00 35.77 3.91
289 290 4.439289 CGTGACTGATCTATCAAGACAGCA 60.439 45.833 6.81 0.00 35.77 4.41
290 291 4.041049 CGTGACTGATCTATCAAGACAGC 58.959 47.826 6.81 0.00 35.77 4.40
291 292 5.491635 TCGTGACTGATCTATCAAGACAG 57.508 43.478 9.96 0.00 37.13 3.51
293 294 4.261405 CCCTCGTGACTGATCTATCAAGAC 60.261 50.000 9.96 0.00 36.18 3.01
295 296 3.005261 CCCCTCGTGACTGATCTATCAAG 59.995 52.174 0.00 0.52 36.18 3.02
296 297 2.959030 CCCCTCGTGACTGATCTATCAA 59.041 50.000 0.00 0.00 36.18 2.57
297 298 2.174854 TCCCCTCGTGACTGATCTATCA 59.825 50.000 0.00 0.00 35.16 2.15
298 299 2.865079 TCCCCTCGTGACTGATCTATC 58.135 52.381 0.00 0.00 0.00 2.08
299 300 3.534357 ATCCCCTCGTGACTGATCTAT 57.466 47.619 0.00 0.00 0.00 1.98
301 302 3.181428 TGATATCCCCTCGTGACTGATCT 60.181 47.826 0.00 0.00 0.00 2.75
302 303 3.157881 TGATATCCCCTCGTGACTGATC 58.842 50.000 0.00 0.00 0.00 2.92
303 304 3.244887 TGATATCCCCTCGTGACTGAT 57.755 47.619 0.00 0.00 0.00 2.90
304 305 2.748209 TGATATCCCCTCGTGACTGA 57.252 50.000 0.00 0.00 0.00 3.41
305 306 2.959030 TCTTGATATCCCCTCGTGACTG 59.041 50.000 0.00 0.00 0.00 3.51
306 307 3.314307 TCTTGATATCCCCTCGTGACT 57.686 47.619 0.00 0.00 0.00 3.41
312 313 3.056891 CGAGAGCTTCTTGATATCCCCTC 60.057 52.174 0.00 0.00 29.08 4.30
314 315 2.028567 CCGAGAGCTTCTTGATATCCCC 60.029 54.545 0.00 0.00 29.08 4.81
315 316 2.611722 GCCGAGAGCTTCTTGATATCCC 60.612 54.545 0.00 0.00 38.99 3.85
316 317 2.682836 GCCGAGAGCTTCTTGATATCC 58.317 52.381 0.00 0.00 38.99 2.59
328 329 2.202676 CCACGAAGAGCCGAGAGC 60.203 66.667 0.00 0.00 44.25 4.09
329 330 0.038159 AAACCACGAAGAGCCGAGAG 60.038 55.000 0.00 0.00 0.00 3.20
331 332 2.295253 ATAAACCACGAAGAGCCGAG 57.705 50.000 0.00 0.00 0.00 4.63
334 335 5.813080 AATGTAATAAACCACGAAGAGCC 57.187 39.130 0.00 0.00 0.00 4.70
341 342 8.846607 GCTCACTTTTTAATGTAATAAACCACG 58.153 33.333 0.00 0.00 0.00 4.94
342 343 9.685828 TGCTCACTTTTTAATGTAATAAACCAC 57.314 29.630 0.00 0.00 0.00 4.16
361 362 7.728083 AGGAATTCTACTATGACTATGCTCACT 59.272 37.037 5.23 0.00 0.00 3.41
362 363 7.891561 AGGAATTCTACTATGACTATGCTCAC 58.108 38.462 5.23 0.00 0.00 3.51
373 374 8.538701 AGCTGGATTATGAGGAATTCTACTATG 58.461 37.037 5.23 0.00 0.00 2.23
375 376 9.601810 TTAGCTGGATTATGAGGAATTCTACTA 57.398 33.333 5.23 0.00 0.00 1.82
413 414 0.905357 AGCGTGGCTACCTTCAGAAT 59.095 50.000 0.00 0.00 36.99 2.40
417 418 1.671054 GCAAGCGTGGCTACCTTCA 60.671 57.895 0.79 0.00 38.25 3.02
418 419 1.376037 AGCAAGCGTGGCTACCTTC 60.376 57.895 0.79 0.00 40.47 3.46
419 420 1.672356 CAGCAAGCGTGGCTACCTT 60.672 57.895 0.79 0.00 40.23 3.50
427 428 0.592247 GAACACAACCAGCAAGCGTG 60.592 55.000 0.00 0.00 0.00 5.34
428 429 0.748005 AGAACACAACCAGCAAGCGT 60.748 50.000 0.00 0.00 0.00 5.07
442 443 5.161358 CGAAGCAGTGTCTATAACAGAACA 58.839 41.667 0.00 0.00 38.97 3.18
444 445 4.461431 TCCGAAGCAGTGTCTATAACAGAA 59.539 41.667 0.00 0.00 38.97 3.02
445 446 4.014406 TCCGAAGCAGTGTCTATAACAGA 58.986 43.478 0.00 0.00 38.97 3.41
446 447 4.371855 TCCGAAGCAGTGTCTATAACAG 57.628 45.455 0.00 0.00 38.97 3.16
453 454 2.851195 ACAAATTCCGAAGCAGTGTCT 58.149 42.857 0.00 0.00 0.00 3.41
456 457 4.414852 CCAATACAAATTCCGAAGCAGTG 58.585 43.478 0.00 0.00 0.00 3.66
458 459 3.119531 TGCCAATACAAATTCCGAAGCAG 60.120 43.478 0.00 0.00 0.00 4.24
465 466 6.509418 TTACAGTCTGCCAATACAAATTCC 57.491 37.500 0.00 0.00 0.00 3.01
534 535 7.333921 TGTGTTTTTCATTTTTCAGCACTCAAT 59.666 29.630 0.00 0.00 0.00 2.57
547 548 6.822676 TGGAGCAAAAGATGTGTTTTTCATTT 59.177 30.769 0.00 0.00 0.00 2.32
560 561 6.515272 AATATTTCACGTGGAGCAAAAGAT 57.485 33.333 17.00 8.23 0.00 2.40
619 620 6.148948 CGTTTTGACTGGATTTTCATAGCAA 58.851 36.000 0.00 0.00 0.00 3.91
647 648 1.538950 CTACTATTCCTACCGCCCGTC 59.461 57.143 0.00 0.00 0.00 4.79
656 657 0.956633 CCGCGTGCCTACTATTCCTA 59.043 55.000 4.92 0.00 0.00 2.94
725 734 1.225745 CGCACGTTTCGATCTTGGC 60.226 57.895 1.05 0.00 0.00 4.52
726 735 0.366871 CTCGCACGTTTCGATCTTGG 59.633 55.000 9.69 0.00 35.25 3.61
727 736 0.246912 GCTCGCACGTTTCGATCTTG 60.247 55.000 9.69 1.08 35.25 3.02
728 737 0.666274 TGCTCGCACGTTTCGATCTT 60.666 50.000 9.69 0.00 35.25 2.40
729 738 0.666274 TTGCTCGCACGTTTCGATCT 60.666 50.000 9.69 0.00 35.25 2.75
730 739 0.370273 ATTGCTCGCACGTTTCGATC 59.630 50.000 9.69 6.93 35.25 3.69
731 740 0.095245 CATTGCTCGCACGTTTCGAT 59.905 50.000 9.69 0.00 35.25 3.59
945 1046 0.106967 GTGGGAGGCTGGGAGATTTC 60.107 60.000 0.00 0.00 0.00 2.17
1027 1151 4.450122 GATGTGCTGTGCGGTGCG 62.450 66.667 0.00 0.00 0.00 5.34
1029 1153 2.042259 ATGGATGTGCTGTGCGGTG 61.042 57.895 0.00 0.00 0.00 4.94
1030 1154 2.042259 CATGGATGTGCTGTGCGGT 61.042 57.895 0.00 0.00 0.00 5.68
1031 1155 2.767445 CCATGGATGTGCTGTGCGG 61.767 63.158 5.56 0.00 0.00 5.69
1322 1473 4.754667 GTCTTGGCGTCCGTCCCC 62.755 72.222 0.00 0.00 0.00 4.81
1330 1481 4.373116 ATGGCGTCGTCTTGGCGT 62.373 61.111 0.00 0.00 0.00 5.68
1331 1482 3.554692 GATGGCGTCGTCTTGGCG 61.555 66.667 0.92 0.00 0.00 5.69
1601 2935 1.132453 GCTCGCCTCCACAATAAAACC 59.868 52.381 0.00 0.00 0.00 3.27
1797 3170 2.165845 ACCTACACGCATTCAGTAGTCC 59.834 50.000 0.00 0.00 34.78 3.85
1968 3403 0.947244 GTCCGCTTGCATGATTAGGG 59.053 55.000 3.33 0.00 0.00 3.53
2135 3577 0.235926 GGATCTAAATCAAGCCGCGC 59.764 55.000 0.00 0.00 33.21 6.86
2164 3606 9.627395 CAATAGGGATATAGTACTTGAAGAACG 57.373 37.037 0.00 0.00 0.00 3.95
2185 3627 6.920817 ACATTGCATCATGGCTAATCAATAG 58.079 36.000 3.53 0.00 34.52 1.73
2238 3680 2.486191 GCATGAATGAGTGGTAGGAGGG 60.486 54.545 0.00 0.00 0.00 4.30
2427 6101 9.110617 GTAAATCGATATGTGATTTGCATTGAG 57.889 33.333 17.04 0.00 43.77 3.02
2494 6169 7.974504 AGGAAACTAAAAGAGGTGAGATGTAA 58.025 34.615 0.00 0.00 40.61 2.41
2513 6188 8.641499 TTTGAATTGTTGTGACATTAGGAAAC 57.359 30.769 0.00 0.00 35.29 2.78


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

AutoCloner maintained by Alex Coulton.