Multiple sequence alignment - TraesCS2B01G387000

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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 TraesCS2B01G387000 chr2B 100.000 3228 0 0 1 3228 550215458 550212231 0.000000e+00 5962.0
1 TraesCS2B01G387000 chr2D 93.084 2169 73 32 485 2619 471056758 471054633 0.000000e+00 3103.0
2 TraesCS2B01G387000 chr2D 89.355 620 54 8 2611 3228 471053177 471052568 0.000000e+00 769.0
3 TraesCS2B01G387000 chr2D 86.875 160 18 3 1 159 55923573 55923416 3.310000e-40 176.0
4 TraesCS2B01G387000 chr2D 85.256 156 20 3 10 163 4278080 4277926 1.200000e-34 158.0
5 TraesCS2B01G387000 chr2D 77.926 299 23 22 177 466 471057005 471056741 2.600000e-31 147.0
6 TraesCS2B01G387000 chr2D 86.614 127 17 0 1293 1419 165468246 165468120 1.210000e-29 141.0
7 TraesCS2B01G387000 chr2D 93.651 63 3 1 3166 3228 471052572 471052511 3.430000e-15 93.5
8 TraesCS2B01G387000 chr2A 90.237 2407 103 53 863 3228 612835420 612833105 0.000000e+00 3022.0
9 TraesCS2B01G387000 chr2A 79.730 518 46 35 299 764 612836415 612835905 1.440000e-83 320.0
10 TraesCS2B01G387000 chr2A 86.290 124 17 0 1293 1416 185285018 185285141 5.620000e-28 135.0
11 TraesCS2B01G387000 chr6D 79.301 372 31 30 1622 1976 309719548 309719890 5.420000e-53 219.0
12 TraesCS2B01G387000 chr6D 91.489 141 12 0 1276 1416 309719056 309719196 9.140000e-46 195.0
13 TraesCS2B01G387000 chr6D 84.516 155 24 0 1 155 454955317 454955163 1.550000e-33 154.0
14 TraesCS2B01G387000 chr6A 78.763 372 33 30 1622 1976 446521693 446522035 1.170000e-49 207.0
15 TraesCS2B01G387000 chr6A 92.908 141 10 0 1276 1416 446521226 446521366 4.220000e-49 206.0
16 TraesCS2B01G387000 chr6A 83.721 86 10 3 1601 1685 428426469 428426551 9.600000e-11 78.7
17 TraesCS2B01G387000 chr6B 92.908 141 10 0 1276 1416 477689721 477689861 4.220000e-49 206.0
18 TraesCS2B01G387000 chr6B 78.226 372 35 30 1622 1976 477691822 477692164 2.540000e-46 196.0
19 TraesCS2B01G387000 chr4A 86.452 155 21 0 1 155 685341213 685341059 1.540000e-38 171.0
20 TraesCS2B01G387000 chr5A 85.030 167 19 5 1 164 118755889 118756052 7.160000e-37 165.0
21 TraesCS2B01G387000 chr5A 79.528 127 22 4 1293 1417 663379381 663379505 1.600000e-13 87.9
22 TraesCS2B01G387000 chr7B 83.735 166 24 2 1 165 591726537 591726374 1.550000e-33 154.0
23 TraesCS2B01G387000 chr7B 80.952 126 22 2 1293 1417 77432169 77432293 7.370000e-17 99.0
24 TraesCS2B01G387000 chr7D 84.177 158 24 1 1 157 59113414 59113571 5.580000e-33 152.0
25 TraesCS2B01G387000 chr1B 84.049 163 20 4 1 157 610013914 610013752 5.580000e-33 152.0
26 TraesCS2B01G387000 chr5B 83.648 159 25 1 1 158 670301032 670301190 7.220000e-32 148.0
27 TraesCS2B01G387000 chr1D 89.474 95 8 2 1622 1715 449982995 449982902 5.660000e-23 119.0
28 TraesCS2B01G387000 chr1D 88.421 95 9 2 1622 1715 449660778 449660871 2.630000e-21 113.0
29 TraesCS2B01G387000 chr1A 88.421 95 9 2 1622 1715 544928194 544928287 2.630000e-21 113.0
30 TraesCS2B01G387000 chr1A 88.421 95 9 2 1622 1715 545009107 545009014 2.630000e-21 113.0


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 TraesCS2B01G387000 chr2B 550212231 550215458 3227 True 5962.000 5962 100.0000 1 3228 1 chr2B.!!$R1 3227
1 TraesCS2B01G387000 chr2D 471052511 471057005 4494 True 1028.125 3103 88.5040 177 3228 4 chr2D.!!$R4 3051
2 TraesCS2B01G387000 chr2A 612833105 612836415 3310 True 1671.000 3022 84.9835 299 3228 2 chr2A.!!$R1 2929
3 TraesCS2B01G387000 chr6D 309719056 309719890 834 False 207.000 219 85.3950 1276 1976 2 chr6D.!!$F1 700
4 TraesCS2B01G387000 chr6A 446521226 446522035 809 False 206.500 207 85.8355 1276 1976 2 chr6A.!!$F2 700
5 TraesCS2B01G387000 chr6B 477689721 477692164 2443 False 201.000 206 85.5670 1276 1976 2 chr6B.!!$F1 700

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
782 870 0.036732 AGCAGCAGGTGAAAATCCGA 59.963 50.0 3.02 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2632 6450 0.753867 TGTCGCAGTTGTACCCTTGA 59.246 50.0 0.0 0.0 0.0 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.512485 AAAACCCGTTTAAAAGGCCG 57.488 45.000 14.08 4.99 31.63 6.13
21 22 1.689984 AAACCCGTTTAAAAGGCCGA 58.310 45.000 14.08 0.00 0.00 5.54
22 23 1.689984 AACCCGTTTAAAAGGCCGAA 58.310 45.000 14.08 0.00 0.00 4.30
23 24 1.689984 ACCCGTTTAAAAGGCCGAAA 58.310 45.000 14.08 0.00 0.00 3.46
24 25 2.030371 ACCCGTTTAAAAGGCCGAAAA 58.970 42.857 14.08 0.00 0.00 2.29
25 26 2.223782 ACCCGTTTAAAAGGCCGAAAAC 60.224 45.455 14.08 6.18 0.00 2.43
27 28 1.449048 CGTTTAAAAGGCCGAAAACGC 59.551 47.619 24.15 5.56 44.94 4.84
28 29 1.449048 GTTTAAAAGGCCGAAAACGCG 59.551 47.619 3.53 3.53 0.00 6.01
29 30 0.662085 TTAAAAGGCCGAAAACGCGT 59.338 45.000 5.58 5.58 0.00 6.01
30 31 0.041135 TAAAAGGCCGAAAACGCGTG 60.041 50.000 14.98 0.00 0.00 5.34
31 32 3.817274 AAAGGCCGAAAACGCGTGC 62.817 57.895 14.98 11.86 0.00 5.34
35 36 4.003011 CCGAAAACGCGTGCGGAA 62.003 61.111 31.93 0.00 46.29 4.30
36 37 2.052941 CGAAAACGCGTGCGGAAA 60.053 55.556 14.98 0.00 44.69 3.13
37 38 1.651730 CGAAAACGCGTGCGGAAAA 60.652 52.632 14.98 0.00 44.69 2.29
38 39 1.194896 CGAAAACGCGTGCGGAAAAA 61.195 50.000 14.98 0.00 44.69 1.94
39 40 1.125270 GAAAACGCGTGCGGAAAAAT 58.875 45.000 14.98 0.00 44.69 1.82
40 41 2.308811 GAAAACGCGTGCGGAAAAATA 58.691 42.857 14.98 0.00 44.69 1.40
41 42 2.402640 AAACGCGTGCGGAAAAATAA 57.597 40.000 14.98 0.00 44.69 1.40
42 43 2.402640 AACGCGTGCGGAAAAATAAA 57.597 40.000 14.98 0.00 44.69 1.40
43 44 2.402640 ACGCGTGCGGAAAAATAAAA 57.597 40.000 12.93 0.00 44.69 1.52
44 45 2.728922 ACGCGTGCGGAAAAATAAAAA 58.271 38.095 12.93 0.00 44.69 1.94
66 67 6.693315 AAAAATTCAAAGAGAACGTCCAGA 57.307 33.333 0.00 0.00 39.49 3.86
67 68 5.674933 AAATTCAAAGAGAACGTCCAGAC 57.325 39.130 0.00 0.00 39.49 3.51
68 69 2.814280 TCAAAGAGAACGTCCAGACC 57.186 50.000 0.00 0.00 0.00 3.85
69 70 1.000607 TCAAAGAGAACGTCCAGACCG 60.001 52.381 0.00 0.00 0.00 4.79
70 71 0.319641 AAAGAGAACGTCCAGACCGC 60.320 55.000 0.00 0.00 0.00 5.68
71 72 2.473664 AAGAGAACGTCCAGACCGCG 62.474 60.000 0.00 0.00 0.00 6.46
72 73 2.974489 GAGAACGTCCAGACCGCGA 61.974 63.158 8.23 0.00 0.00 5.87
73 74 2.804090 GAACGTCCAGACCGCGAC 60.804 66.667 8.23 0.40 0.00 5.19
74 75 3.547249 GAACGTCCAGACCGCGACA 62.547 63.158 8.23 0.00 0.00 4.35
75 76 2.814183 GAACGTCCAGACCGCGACAT 62.814 60.000 8.23 0.00 0.00 3.06
76 77 2.880879 CGTCCAGACCGCGACATG 60.881 66.667 8.23 2.04 0.00 3.21
77 78 2.261671 GTCCAGACCGCGACATGT 59.738 61.111 8.23 0.00 0.00 3.21
78 79 2.094659 GTCCAGACCGCGACATGTG 61.095 63.158 8.23 0.87 0.00 3.21
84 85 3.490759 CCGCGACATGTGGCAGAC 61.491 66.667 28.81 3.65 42.37 3.51
85 86 3.842126 CGCGACATGTGGCAGACG 61.842 66.667 28.81 14.71 33.73 4.18
86 87 3.490759 GCGACATGTGGCAGACGG 61.491 66.667 25.73 0.00 34.31 4.79
87 88 3.490759 CGACATGTGGCAGACGGC 61.491 66.667 1.15 0.00 43.74 5.68
88 89 2.046892 GACATGTGGCAGACGGCT 60.047 61.111 1.15 0.00 44.01 5.52
89 90 2.359107 ACATGTGGCAGACGGCTG 60.359 61.111 15.93 15.93 45.13 4.85
90 91 3.129502 CATGTGGCAGACGGCTGG 61.130 66.667 22.33 1.26 42.53 4.85
91 92 4.415150 ATGTGGCAGACGGCTGGG 62.415 66.667 22.33 0.00 42.53 4.45
93 94 4.767255 GTGGCAGACGGCTGGGAG 62.767 72.222 22.33 0.00 42.53 4.30
103 104 3.741476 GCTGGGAGCGTGCCAAAG 61.741 66.667 0.56 0.00 37.44 2.77
104 105 2.032528 CTGGGAGCGTGCCAAAGA 59.967 61.111 0.56 0.00 37.44 2.52
105 106 1.600636 CTGGGAGCGTGCCAAAGAA 60.601 57.895 0.56 0.00 37.44 2.52
106 107 1.856265 CTGGGAGCGTGCCAAAGAAC 61.856 60.000 0.56 0.00 37.44 3.01
107 108 2.556287 GGAGCGTGCCAAAGAACG 59.444 61.111 0.00 0.00 42.61 3.95
111 112 3.329231 CGTGCCAAAGAACGCTGA 58.671 55.556 0.00 0.00 32.40 4.26
112 113 1.868997 CGTGCCAAAGAACGCTGAT 59.131 52.632 0.00 0.00 32.40 2.90
113 114 0.179215 CGTGCCAAAGAACGCTGATC 60.179 55.000 0.00 0.00 32.40 2.92
114 115 0.179215 GTGCCAAAGAACGCTGATCG 60.179 55.000 0.00 0.00 45.38 3.69
126 127 3.567576 CGCTGATCGTTATGAGGATCT 57.432 47.619 17.75 0.00 43.95 2.75
127 128 3.497118 CGCTGATCGTTATGAGGATCTC 58.503 50.000 17.75 10.52 43.95 2.75
128 129 3.497118 GCTGATCGTTATGAGGATCTCG 58.503 50.000 17.75 11.47 43.95 4.04
129 130 3.189495 GCTGATCGTTATGAGGATCTCGA 59.811 47.826 17.75 1.53 43.95 4.04
130 131 4.320567 GCTGATCGTTATGAGGATCTCGAA 60.321 45.833 17.75 1.24 43.95 3.71
131 132 5.363979 TGATCGTTATGAGGATCTCGAAG 57.636 43.478 17.75 0.00 43.95 3.79
132 133 4.216472 TGATCGTTATGAGGATCTCGAAGG 59.784 45.833 17.75 0.00 43.95 3.46
133 134 3.816994 TCGTTATGAGGATCTCGAAGGA 58.183 45.455 0.00 0.00 34.92 3.36
134 135 3.815962 TCGTTATGAGGATCTCGAAGGAG 59.184 47.826 0.00 0.00 41.89 3.69
135 136 3.610585 CGTTATGAGGATCTCGAAGGAGC 60.611 52.174 0.00 0.00 40.26 4.70
136 137 0.958091 ATGAGGATCTCGAAGGAGCG 59.042 55.000 0.00 0.00 40.26 5.03
137 138 1.007849 GAGGATCTCGAAGGAGCGC 60.008 63.158 0.00 0.00 40.26 5.92
138 139 1.452145 GAGGATCTCGAAGGAGCGCT 61.452 60.000 11.27 11.27 40.26 5.92
139 140 1.007849 GGATCTCGAAGGAGCGCTC 60.008 63.158 29.38 29.38 40.26 5.03
140 141 1.369930 GATCTCGAAGGAGCGCTCG 60.370 63.158 29.81 20.01 40.26 5.03
141 142 2.054140 GATCTCGAAGGAGCGCTCGT 62.054 60.000 29.81 27.91 40.26 4.18
142 143 1.658686 ATCTCGAAGGAGCGCTCGTT 61.659 55.000 37.37 37.37 40.26 3.85
143 144 1.022982 TCTCGAAGGAGCGCTCGTTA 61.023 55.000 36.96 24.85 40.26 3.18
144 145 0.179171 CTCGAAGGAGCGCTCGTTAA 60.179 55.000 36.96 27.64 37.75 2.01
145 146 0.454600 TCGAAGGAGCGCTCGTTAAT 59.545 50.000 36.96 21.62 37.75 1.40
146 147 1.135199 TCGAAGGAGCGCTCGTTAATT 60.135 47.619 36.96 21.28 37.75 1.40
147 148 2.097954 TCGAAGGAGCGCTCGTTAATTA 59.902 45.455 36.96 22.60 37.75 1.40
148 149 2.468040 CGAAGGAGCGCTCGTTAATTAG 59.532 50.000 36.96 23.67 37.75 1.73
149 150 3.445857 GAAGGAGCGCTCGTTAATTAGT 58.554 45.455 36.96 19.55 37.75 2.24
150 151 3.521947 AGGAGCGCTCGTTAATTAGTT 57.478 42.857 29.81 3.47 0.00 2.24
151 152 3.187700 AGGAGCGCTCGTTAATTAGTTG 58.812 45.455 29.81 0.00 0.00 3.16
152 153 2.285660 GGAGCGCTCGTTAATTAGTTGC 60.286 50.000 29.81 8.45 0.00 4.17
153 154 2.603560 GAGCGCTCGTTAATTAGTTGCT 59.396 45.455 23.61 7.90 31.95 3.91
154 155 2.603560 AGCGCTCGTTAATTAGTTGCTC 59.396 45.455 2.64 0.00 0.00 4.26
155 156 2.603560 GCGCTCGTTAATTAGTTGCTCT 59.396 45.455 0.00 0.00 0.00 4.09
156 157 3.301899 GCGCTCGTTAATTAGTTGCTCTC 60.302 47.826 0.00 0.00 0.00 3.20
157 158 3.243177 CGCTCGTTAATTAGTTGCTCTCC 59.757 47.826 0.00 0.00 0.00 3.71
158 159 3.556365 GCTCGTTAATTAGTTGCTCTCCC 59.444 47.826 0.00 0.00 0.00 4.30
159 160 4.755411 CTCGTTAATTAGTTGCTCTCCCA 58.245 43.478 0.00 0.00 0.00 4.37
160 161 5.155278 TCGTTAATTAGTTGCTCTCCCAA 57.845 39.130 0.00 0.00 0.00 4.12
161 162 5.553123 TCGTTAATTAGTTGCTCTCCCAAA 58.447 37.500 0.00 0.00 0.00 3.28
162 163 5.998981 TCGTTAATTAGTTGCTCTCCCAAAA 59.001 36.000 0.00 0.00 0.00 2.44
163 164 6.072893 TCGTTAATTAGTTGCTCTCCCAAAAC 60.073 38.462 0.00 0.00 0.00 2.43
164 165 6.387465 GTTAATTAGTTGCTCTCCCAAAACC 58.613 40.000 0.00 0.00 0.00 3.27
165 166 3.586470 TTAGTTGCTCTCCCAAAACCA 57.414 42.857 0.00 0.00 0.00 3.67
166 167 2.452600 AGTTGCTCTCCCAAAACCAA 57.547 45.000 0.00 0.00 0.00 3.67
167 168 2.031870 AGTTGCTCTCCCAAAACCAAC 58.968 47.619 0.00 0.00 34.39 3.77
168 169 1.754226 GTTGCTCTCCCAAAACCAACA 59.246 47.619 0.00 0.00 34.36 3.33
169 170 2.365293 GTTGCTCTCCCAAAACCAACAT 59.635 45.455 0.00 0.00 34.36 2.71
170 171 2.238521 TGCTCTCCCAAAACCAACATC 58.761 47.619 0.00 0.00 0.00 3.06
171 172 2.238521 GCTCTCCCAAAACCAACATCA 58.761 47.619 0.00 0.00 0.00 3.07
172 173 2.627699 GCTCTCCCAAAACCAACATCAA 59.372 45.455 0.00 0.00 0.00 2.57
173 174 3.305608 GCTCTCCCAAAACCAACATCAAG 60.306 47.826 0.00 0.00 0.00 3.02
174 175 2.627699 TCTCCCAAAACCAACATCAAGC 59.372 45.455 0.00 0.00 0.00 4.01
175 176 2.629617 CTCCCAAAACCAACATCAAGCT 59.370 45.455 0.00 0.00 0.00 3.74
187 188 3.983741 ACATCAAGCTAGGAATAGACGC 58.016 45.455 0.00 0.00 0.00 5.19
190 191 4.465632 TCAAGCTAGGAATAGACGCAAA 57.534 40.909 0.00 0.00 0.00 3.68
191 192 4.827692 TCAAGCTAGGAATAGACGCAAAA 58.172 39.130 0.00 0.00 0.00 2.44
273 274 8.262601 TGATTCTATCCACCTAGCATCTTAAA 57.737 34.615 0.00 0.00 0.00 1.52
274 275 8.713971 TGATTCTATCCACCTAGCATCTTAAAA 58.286 33.333 0.00 0.00 0.00 1.52
275 276 9.561069 GATTCTATCCACCTAGCATCTTAAAAA 57.439 33.333 0.00 0.00 0.00 1.94
276 277 8.732746 TTCTATCCACCTAGCATCTTAAAAAC 57.267 34.615 0.00 0.00 0.00 2.43
277 278 7.280356 TCTATCCACCTAGCATCTTAAAAACC 58.720 38.462 0.00 0.00 0.00 3.27
278 279 5.514500 TCCACCTAGCATCTTAAAAACCT 57.486 39.130 0.00 0.00 0.00 3.50
279 280 5.253330 TCCACCTAGCATCTTAAAAACCTG 58.747 41.667 0.00 0.00 0.00 4.00
280 281 5.010282 CCACCTAGCATCTTAAAAACCTGT 58.990 41.667 0.00 0.00 0.00 4.00
281 282 6.013206 TCCACCTAGCATCTTAAAAACCTGTA 60.013 38.462 0.00 0.00 0.00 2.74
282 283 6.316390 CCACCTAGCATCTTAAAAACCTGTAG 59.684 42.308 0.00 0.00 0.00 2.74
283 284 6.316390 CACCTAGCATCTTAAAAACCTGTAGG 59.684 42.308 0.00 0.00 42.17 3.18
284 285 5.823045 CCTAGCATCTTAAAAACCTGTAGGG 59.177 44.000 2.53 0.00 40.27 3.53
285 286 4.017126 AGCATCTTAAAAACCTGTAGGGC 58.983 43.478 2.53 0.00 40.27 5.19
286 287 3.181500 GCATCTTAAAAACCTGTAGGGCG 60.181 47.826 2.53 0.00 40.27 6.13
287 288 4.258543 CATCTTAAAAACCTGTAGGGCGA 58.741 43.478 2.53 0.00 40.27 5.54
288 289 3.934068 TCTTAAAAACCTGTAGGGCGAG 58.066 45.455 2.53 0.00 40.27 5.03
289 290 3.579586 TCTTAAAAACCTGTAGGGCGAGA 59.420 43.478 2.53 0.00 40.27 4.04
290 291 2.943036 AAAAACCTGTAGGGCGAGAA 57.057 45.000 2.53 0.00 40.27 2.87
291 292 3.434940 AAAAACCTGTAGGGCGAGAAT 57.565 42.857 2.53 0.00 40.27 2.40
292 293 2.693267 AAACCTGTAGGGCGAGAATC 57.307 50.000 2.53 0.00 40.27 2.52
293 294 1.568504 AACCTGTAGGGCGAGAATCA 58.431 50.000 2.53 0.00 40.27 2.57
294 295 1.794714 ACCTGTAGGGCGAGAATCAT 58.205 50.000 2.53 0.00 40.27 2.45
295 296 1.414181 ACCTGTAGGGCGAGAATCATG 59.586 52.381 2.53 0.00 40.27 3.07
296 297 1.506493 CTGTAGGGCGAGAATCATGC 58.494 55.000 0.00 0.00 33.17 4.06
297 298 1.069823 CTGTAGGGCGAGAATCATGCT 59.930 52.381 0.00 0.00 33.17 3.79
307 308 4.084641 GCGAGAATCATGCTGACTATGAAC 60.085 45.833 0.00 0.00 38.01 3.18
318 319 1.852895 GACTATGAACGATGCCACGTC 59.147 52.381 5.80 1.87 45.83 4.34
323 324 2.227968 GAACGATGCCACGTCAGCAC 62.228 60.000 11.74 5.94 45.83 4.40
348 349 0.322456 GCAAGCCTGACATACCCACA 60.322 55.000 0.00 0.00 0.00 4.17
349 350 1.683011 GCAAGCCTGACATACCCACAT 60.683 52.381 0.00 0.00 0.00 3.21
384 396 3.151958 AAGACGTGTCAGCGTGGCT 62.152 57.895 0.00 0.00 45.79 4.75
401 413 6.151144 AGCGTGGCTCATTTCTTAAATTACTT 59.849 34.615 0.00 0.00 30.62 2.24
403 415 6.747280 CGTGGCTCATTTCTTAAATTACTTGG 59.253 38.462 0.00 0.00 0.00 3.61
444 461 1.806542 GAAGTTGGAGCGATCAAAGCA 59.193 47.619 1.84 0.00 37.01 3.91
453 470 2.168106 AGCGATCAAAGCAGAGTGATCT 59.832 45.455 10.87 0.00 45.28 2.75
454 471 2.539274 GCGATCAAAGCAGAGTGATCTC 59.461 50.000 10.87 0.98 45.28 2.75
493 510 4.640805 TTGTTTTTGACTAGATCGCGAC 57.359 40.909 12.93 5.67 0.00 5.19
544 616 1.557443 CGTCCAGTTGAGAACGCACC 61.557 60.000 0.00 0.00 36.23 5.01
549 621 2.281484 TTGAGAACGCACCCTGCC 60.281 61.111 0.00 0.00 41.12 4.85
567 644 2.262603 CTGCCGTCTGCTGCAGTA 59.737 61.111 27.24 10.46 44.47 2.74
637 717 3.011032 ACCCAAGGCATTGAATTCTCTCT 59.989 43.478 13.66 0.00 38.83 3.10
693 780 0.673333 TCATGCGTCTTCAATGCGGT 60.673 50.000 0.00 0.00 43.27 5.68
699 786 1.074775 TCTTCAATGCGGTGCCCTT 59.925 52.632 0.00 0.00 0.00 3.95
719 806 2.755876 TCTGCCCGTCAGCTCGAT 60.756 61.111 0.00 0.00 42.56 3.59
733 820 4.519350 TCAGCTCGATCACTTATTATCGGT 59.481 41.667 5.04 0.00 43.94 4.69
782 870 0.036732 AGCAGCAGGTGAAAATCCGA 59.963 50.000 3.02 0.00 0.00 4.55
882 1356 0.396435 TCCTTGTCTGTGTCGCCAAT 59.604 50.000 0.00 0.00 0.00 3.16
890 1364 4.015406 TGTCGCCAATCGCCCAGT 62.015 61.111 0.00 0.00 38.27 4.00
922 1396 2.866351 CTGCCTACTACTCCTCCTACC 58.134 57.143 0.00 0.00 0.00 3.18
941 1415 2.103538 CGGTGGTGGATACGTCGG 59.896 66.667 0.00 0.00 42.51 4.79
942 1416 2.703798 CGGTGGTGGATACGTCGGT 61.704 63.158 0.00 0.00 42.51 4.69
943 1417 1.140375 GGTGGTGGATACGTCGGTC 59.860 63.158 0.00 0.00 42.51 4.79
949 1423 2.138320 GTGGATACGTCGGTCGATCTA 58.862 52.381 0.92 0.00 42.86 1.98
978 1452 3.475774 GCGCGTCCATTTCGTCGT 61.476 61.111 8.43 0.00 33.37 4.34
979 1453 2.687436 CGCGTCCATTTCGTCGTC 59.313 61.111 0.00 0.00 0.00 4.20
983 1457 1.005294 CGTCCATTTCGTCGTCGGTT 61.005 55.000 1.55 0.00 37.69 4.44
1180 1655 0.666913 ATTCCATGCATGCGCTCTTC 59.333 50.000 21.69 0.00 39.64 2.87
1187 1662 0.933796 GCATGCGCTCTTCCTACTTC 59.066 55.000 9.73 0.00 34.30 3.01
1224 1699 1.660560 CCCTTTCTTCAGCCATGCCG 61.661 60.000 0.00 0.00 0.00 5.69
1226 1701 1.588824 CTTTCTTCAGCCATGCCGCA 61.589 55.000 0.00 0.00 0.00 5.69
1227 1702 1.865788 TTTCTTCAGCCATGCCGCAC 61.866 55.000 0.00 0.00 0.00 5.34
1232 1707 3.860605 AGCCATGCCGCACGGATA 61.861 61.111 10.29 0.62 37.50 2.59
1265 1752 1.463674 GGCGATTTGGTTGAGGTGAT 58.536 50.000 0.00 0.00 0.00 3.06
1274 1765 2.592032 TTGAGGTGATGAGGGCGCA 61.592 57.895 10.83 0.00 0.00 6.09
1402 1893 2.270205 CTCCAGCTCCACGCCATT 59.730 61.111 0.00 0.00 40.39 3.16
1464 3581 7.980742 CACATTTCGTGCTACTACAGTATAA 57.019 36.000 0.00 0.00 39.19 0.98
1543 3851 6.092944 TCAACGAACGATGCCATTTATTAAGT 59.907 34.615 0.14 0.00 0.00 2.24
1606 3915 0.108804 ACGCTGTTCTATCGTGGTGG 60.109 55.000 0.00 0.00 34.92 4.61
1879 4203 4.664677 GCGACCACCAGCGTGACT 62.665 66.667 0.00 0.00 43.14 3.41
2719 6547 2.569853 TCCAAGTACACACCCTACCATG 59.430 50.000 0.00 0.00 0.00 3.66
2747 6575 4.039488 GGGTGTACATAATCCATACACGGA 59.961 45.833 0.00 0.00 46.31 4.69
2794 6622 6.437928 CGATCTTCATCCAACAGTTGAAAAA 58.562 36.000 15.36 3.07 34.53 1.94
2825 6653 2.999355 GCTGTTCATCTTCAGTCTCCAC 59.001 50.000 0.00 0.00 34.57 4.02
2838 6666 3.007290 CAGTCTCCACCTTCTTCATCACA 59.993 47.826 0.00 0.00 0.00 3.58
2913 6741 0.030369 CACGGCCGTACTAGTCATCC 59.970 60.000 33.70 0.00 0.00 3.51
2916 6744 1.814634 CGGCCGTACTAGTCATCCTCT 60.815 57.143 19.50 0.00 0.00 3.69
2936 6764 1.772156 GGCCATCCCTCTAAGCCCT 60.772 63.158 0.00 0.00 37.66 5.19
2955 6784 0.867746 TGCACAGCGATGAACAACTC 59.132 50.000 8.12 0.00 0.00 3.01
2958 6787 0.317160 ACAGCGATGAACAACTCCGA 59.683 50.000 8.12 0.00 0.00 4.55
2959 6788 0.716108 CAGCGATGAACAACTCCGAC 59.284 55.000 0.00 0.00 0.00 4.79
2963 6792 2.259618 CGATGAACAACTCCGACGATT 58.740 47.619 0.00 0.00 0.00 3.34
2968 6797 0.246635 ACAACTCCGACGATTCCCTG 59.753 55.000 0.00 0.00 0.00 4.45
2971 6800 1.330655 ACTCCGACGATTCCCTGCAT 61.331 55.000 0.00 0.00 0.00 3.96
2978 6807 1.152673 GATTCCCTGCATCCCACCC 60.153 63.158 0.00 0.00 0.00 4.61
2982 6811 3.016971 CCTGCATCCCACCCTCCA 61.017 66.667 0.00 0.00 0.00 3.86
2991 6820 4.227134 CACCCTCCAGCGATCCCG 62.227 72.222 0.00 0.00 39.16 5.14
3008 6837 2.751688 GTGCACCCTCCCCGTAAA 59.248 61.111 5.22 0.00 0.00 2.01
3030 6859 4.706842 ATAGATAATGGGTCCGTTGCTT 57.293 40.909 4.81 0.00 0.00 3.91
3033 6862 0.988832 TAATGGGTCCGTTGCTTCCT 59.011 50.000 4.81 0.00 0.00 3.36
3036 6865 1.671379 GGGTCCGTTGCTTCCTCAC 60.671 63.158 0.00 0.00 0.00 3.51
3160 6989 4.098960 CAGCCACATGAGGAATAGCAAAAT 59.901 41.667 13.99 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.429971 TCGGCCTTTTAAACGGGTTTTT 59.570 40.909 12.29 0.00 34.23 1.94
1 2 2.030371 TCGGCCTTTTAAACGGGTTTT 58.970 42.857 12.29 0.00 34.23 2.43
2 3 1.689984 TCGGCCTTTTAAACGGGTTT 58.310 45.000 12.29 2.05 36.63 3.27
3 4 1.689984 TTCGGCCTTTTAAACGGGTT 58.310 45.000 12.29 0.00 0.00 4.11
4 5 1.689984 TTTCGGCCTTTTAAACGGGT 58.310 45.000 12.29 0.00 0.00 5.28
5 6 2.396601 GTTTTCGGCCTTTTAAACGGG 58.603 47.619 12.29 7.33 0.00 5.28
6 7 2.045586 CGTTTTCGGCCTTTTAAACGG 58.954 47.619 22.55 6.37 45.26 4.44
8 9 1.449048 CGCGTTTTCGGCCTTTTAAAC 59.551 47.619 0.00 5.09 44.29 2.01
9 10 1.065251 ACGCGTTTTCGGCCTTTTAAA 59.935 42.857 5.58 0.00 44.29 1.52
10 11 0.662085 ACGCGTTTTCGGCCTTTTAA 59.338 45.000 5.58 0.00 44.29 1.52
11 12 0.041135 CACGCGTTTTCGGCCTTTTA 60.041 50.000 10.22 0.00 44.29 1.52
12 13 1.298788 CACGCGTTTTCGGCCTTTT 60.299 52.632 10.22 0.00 44.29 2.27
13 14 2.330041 CACGCGTTTTCGGCCTTT 59.670 55.556 10.22 0.00 44.29 3.11
14 15 4.322385 GCACGCGTTTTCGGCCTT 62.322 61.111 10.22 0.00 44.29 4.35
18 19 2.968330 TTTTCCGCACGCGTTTTCGG 62.968 55.000 28.08 28.08 44.29 4.30
20 21 1.125270 ATTTTTCCGCACGCGTTTTC 58.875 45.000 10.22 0.04 37.81 2.29
21 22 2.402640 TATTTTTCCGCACGCGTTTT 57.597 40.000 10.22 0.00 37.81 2.43
22 23 2.402640 TTATTTTTCCGCACGCGTTT 57.597 40.000 10.22 0.00 37.81 3.60
23 24 2.402640 TTTATTTTTCCGCACGCGTT 57.597 40.000 10.22 0.00 37.81 4.84
24 25 2.402640 TTTTATTTTTCCGCACGCGT 57.597 40.000 5.58 5.58 37.81 6.01
43 44 6.459710 GGTCTGGACGTTCTCTTTGAATTTTT 60.460 38.462 0.00 0.00 36.99 1.94
44 45 5.008712 GGTCTGGACGTTCTCTTTGAATTTT 59.991 40.000 0.00 0.00 36.99 1.82
45 46 4.515567 GGTCTGGACGTTCTCTTTGAATTT 59.484 41.667 0.00 0.00 36.99 1.82
46 47 4.065789 GGTCTGGACGTTCTCTTTGAATT 58.934 43.478 0.00 0.00 36.99 2.17
47 48 3.665190 GGTCTGGACGTTCTCTTTGAAT 58.335 45.455 0.00 0.00 36.99 2.57
48 49 2.545113 CGGTCTGGACGTTCTCTTTGAA 60.545 50.000 0.00 0.00 0.00 2.69
49 50 1.000607 CGGTCTGGACGTTCTCTTTGA 60.001 52.381 0.00 0.00 0.00 2.69
50 51 1.419374 CGGTCTGGACGTTCTCTTTG 58.581 55.000 0.00 0.00 0.00 2.77
51 52 0.319641 GCGGTCTGGACGTTCTCTTT 60.320 55.000 0.00 0.00 0.00 2.52
52 53 1.289380 GCGGTCTGGACGTTCTCTT 59.711 57.895 0.00 0.00 0.00 2.85
53 54 2.963371 GCGGTCTGGACGTTCTCT 59.037 61.111 0.00 0.00 0.00 3.10
54 55 2.504244 CGCGGTCTGGACGTTCTC 60.504 66.667 0.00 0.00 0.00 2.87
55 56 2.981909 TCGCGGTCTGGACGTTCT 60.982 61.111 6.13 0.00 0.00 3.01
56 57 2.804090 GTCGCGGTCTGGACGTTC 60.804 66.667 6.13 0.00 0.00 3.95
57 58 2.927580 ATGTCGCGGTCTGGACGTT 61.928 57.895 6.13 0.00 35.95 3.99
58 59 3.371063 ATGTCGCGGTCTGGACGT 61.371 61.111 6.13 0.00 35.95 4.34
59 60 2.880879 CATGTCGCGGTCTGGACG 60.881 66.667 6.13 0.00 35.95 4.79
60 61 2.094659 CACATGTCGCGGTCTGGAC 61.095 63.158 6.13 0.00 0.00 4.02
61 62 2.261361 CACATGTCGCGGTCTGGA 59.739 61.111 6.13 0.00 0.00 3.86
62 63 2.815211 CCACATGTCGCGGTCTGG 60.815 66.667 6.13 0.20 0.00 3.86
63 64 3.490759 GCCACATGTCGCGGTCTG 61.491 66.667 6.13 3.54 0.00 3.51
64 65 3.939837 CTGCCACATGTCGCGGTCT 62.940 63.158 15.37 0.00 0.00 3.85
65 66 3.490759 CTGCCACATGTCGCGGTC 61.491 66.667 15.37 0.00 0.00 4.79
66 67 4.002506 TCTGCCACATGTCGCGGT 62.003 61.111 21.54 0.00 32.96 5.68
67 68 3.490759 GTCTGCCACATGTCGCGG 61.491 66.667 17.24 17.24 0.00 6.46
68 69 3.842126 CGTCTGCCACATGTCGCG 61.842 66.667 10.93 0.00 0.00 5.87
69 70 3.490759 CCGTCTGCCACATGTCGC 61.491 66.667 8.67 8.67 0.00 5.19
70 71 3.490759 GCCGTCTGCCACATGTCG 61.491 66.667 0.00 0.00 0.00 4.35
71 72 2.046892 AGCCGTCTGCCACATGTC 60.047 61.111 0.00 0.00 42.71 3.06
72 73 2.359107 CAGCCGTCTGCCACATGT 60.359 61.111 0.00 0.00 42.71 3.21
73 74 3.129502 CCAGCCGTCTGCCACATG 61.130 66.667 0.00 0.00 42.71 3.21
74 75 4.415150 CCCAGCCGTCTGCCACAT 62.415 66.667 0.00 0.00 42.71 3.21
76 77 4.767255 CTCCCAGCCGTCTGCCAC 62.767 72.222 0.00 0.00 42.71 5.01
86 87 3.741476 CTTTGGCACGCTCCCAGC 61.741 66.667 0.00 0.00 38.02 4.85
87 88 1.600636 TTCTTTGGCACGCTCCCAG 60.601 57.895 0.00 0.00 33.13 4.45
88 89 1.896660 GTTCTTTGGCACGCTCCCA 60.897 57.895 0.00 0.00 0.00 4.37
89 90 2.954611 GTTCTTTGGCACGCTCCC 59.045 61.111 0.00 0.00 0.00 4.30
90 91 2.556287 CGTTCTTTGGCACGCTCC 59.444 61.111 0.00 0.00 0.00 4.70
94 95 0.179215 GATCAGCGTTCTTTGGCACG 60.179 55.000 0.00 0.00 39.49 5.34
95 96 0.179215 CGATCAGCGTTCTTTGGCAC 60.179 55.000 0.00 0.00 34.64 5.01
96 97 2.161831 CGATCAGCGTTCTTTGGCA 58.838 52.632 0.00 0.00 34.64 4.92
107 108 3.189495 TCGAGATCCTCATAACGATCAGC 59.811 47.826 0.00 0.00 37.87 4.26
108 109 5.363979 TTCGAGATCCTCATAACGATCAG 57.636 43.478 0.00 0.00 37.87 2.90
109 110 4.216472 CCTTCGAGATCCTCATAACGATCA 59.784 45.833 0.00 0.00 37.87 2.92
110 111 4.456222 TCCTTCGAGATCCTCATAACGATC 59.544 45.833 0.00 0.00 36.03 3.69
111 112 4.399219 TCCTTCGAGATCCTCATAACGAT 58.601 43.478 0.00 0.00 0.00 3.73
112 113 3.815962 CTCCTTCGAGATCCTCATAACGA 59.184 47.826 0.00 0.00 38.52 3.85
113 114 3.610585 GCTCCTTCGAGATCCTCATAACG 60.611 52.174 0.00 0.00 38.52 3.18
114 115 3.610585 CGCTCCTTCGAGATCCTCATAAC 60.611 52.174 0.00 0.00 38.52 1.89
115 116 2.554462 CGCTCCTTCGAGATCCTCATAA 59.446 50.000 0.00 0.00 38.52 1.90
116 117 2.155279 CGCTCCTTCGAGATCCTCATA 58.845 52.381 0.00 0.00 38.52 2.15
117 118 0.958091 CGCTCCTTCGAGATCCTCAT 59.042 55.000 0.00 0.00 38.52 2.90
118 119 1.729470 GCGCTCCTTCGAGATCCTCA 61.729 60.000 0.00 0.00 38.52 3.86
119 120 1.007849 GCGCTCCTTCGAGATCCTC 60.008 63.158 0.00 0.00 38.52 3.71
120 121 1.452145 GAGCGCTCCTTCGAGATCCT 61.452 60.000 27.22 0.00 38.52 3.24
121 122 1.007849 GAGCGCTCCTTCGAGATCC 60.008 63.158 27.22 0.00 38.52 3.36
122 123 1.369930 CGAGCGCTCCTTCGAGATC 60.370 63.158 30.66 3.74 38.52 2.75
123 124 1.658686 AACGAGCGCTCCTTCGAGAT 61.659 55.000 30.66 8.22 38.52 2.75
124 125 1.022982 TAACGAGCGCTCCTTCGAGA 61.023 55.000 30.66 8.40 38.52 4.04
125 126 0.179171 TTAACGAGCGCTCCTTCGAG 60.179 55.000 30.66 17.99 39.33 4.04
126 127 0.454600 ATTAACGAGCGCTCCTTCGA 59.545 50.000 30.66 17.20 0.00 3.71
127 128 1.278238 AATTAACGAGCGCTCCTTCG 58.722 50.000 30.66 22.24 0.00 3.79
128 129 3.445857 ACTAATTAACGAGCGCTCCTTC 58.554 45.455 30.66 8.16 0.00 3.46
129 130 3.521947 ACTAATTAACGAGCGCTCCTT 57.478 42.857 30.66 26.03 0.00 3.36
130 131 3.187700 CAACTAATTAACGAGCGCTCCT 58.812 45.455 30.66 20.33 0.00 3.69
131 132 2.285660 GCAACTAATTAACGAGCGCTCC 60.286 50.000 30.66 13.79 0.00 4.70
132 133 2.603560 AGCAACTAATTAACGAGCGCTC 59.396 45.455 27.64 27.64 0.00 5.03
133 134 2.603560 GAGCAACTAATTAACGAGCGCT 59.396 45.455 11.27 11.27 0.00 5.92
134 135 2.603560 AGAGCAACTAATTAACGAGCGC 59.396 45.455 0.00 0.00 0.00 5.92
135 136 3.243177 GGAGAGCAACTAATTAACGAGCG 59.757 47.826 0.00 0.00 0.00 5.03
136 137 3.556365 GGGAGAGCAACTAATTAACGAGC 59.444 47.826 0.00 0.00 0.00 5.03
137 138 4.755411 TGGGAGAGCAACTAATTAACGAG 58.245 43.478 0.00 0.00 0.00 4.18
138 139 4.811969 TGGGAGAGCAACTAATTAACGA 57.188 40.909 0.00 0.00 0.00 3.85
139 140 5.873179 TTTGGGAGAGCAACTAATTAACG 57.127 39.130 0.00 0.00 0.00 3.18
140 141 6.015772 TGGTTTTGGGAGAGCAACTAATTAAC 60.016 38.462 0.00 0.00 0.00 2.01
141 142 6.071984 TGGTTTTGGGAGAGCAACTAATTAA 58.928 36.000 0.00 0.00 0.00 1.40
142 143 5.636123 TGGTTTTGGGAGAGCAACTAATTA 58.364 37.500 0.00 0.00 0.00 1.40
143 144 4.479158 TGGTTTTGGGAGAGCAACTAATT 58.521 39.130 0.00 0.00 0.00 1.40
144 145 4.112634 TGGTTTTGGGAGAGCAACTAAT 57.887 40.909 0.00 0.00 0.00 1.73
145 146 3.586470 TGGTTTTGGGAGAGCAACTAA 57.414 42.857 0.00 0.00 0.00 2.24
146 147 3.219281 GTTGGTTTTGGGAGAGCAACTA 58.781 45.455 10.19 0.00 45.69 2.24
147 148 2.031870 GTTGGTTTTGGGAGAGCAACT 58.968 47.619 10.19 0.00 45.69 3.16
148 149 2.509052 GTTGGTTTTGGGAGAGCAAC 57.491 50.000 3.17 3.17 43.96 4.17
149 150 2.151502 TGTTGGTTTTGGGAGAGCAA 57.848 45.000 0.00 0.00 0.00 3.91
150 151 2.238521 GATGTTGGTTTTGGGAGAGCA 58.761 47.619 0.00 0.00 0.00 4.26
151 152 2.238521 TGATGTTGGTTTTGGGAGAGC 58.761 47.619 0.00 0.00 0.00 4.09
152 153 3.305608 GCTTGATGTTGGTTTTGGGAGAG 60.306 47.826 0.00 0.00 0.00 3.20
153 154 2.627699 GCTTGATGTTGGTTTTGGGAGA 59.372 45.455 0.00 0.00 0.00 3.71
154 155 2.629617 AGCTTGATGTTGGTTTTGGGAG 59.370 45.455 0.00 0.00 0.00 4.30
155 156 2.676748 AGCTTGATGTTGGTTTTGGGA 58.323 42.857 0.00 0.00 0.00 4.37
156 157 3.056607 CCTAGCTTGATGTTGGTTTTGGG 60.057 47.826 0.00 0.00 0.00 4.12
157 158 3.826157 TCCTAGCTTGATGTTGGTTTTGG 59.174 43.478 0.00 0.00 0.00 3.28
158 159 5.452078 TTCCTAGCTTGATGTTGGTTTTG 57.548 39.130 0.00 0.00 0.00 2.44
159 160 7.121315 GTCTATTCCTAGCTTGATGTTGGTTTT 59.879 37.037 0.00 0.00 0.00 2.43
160 161 6.599638 GTCTATTCCTAGCTTGATGTTGGTTT 59.400 38.462 0.00 0.00 0.00 3.27
161 162 6.116126 GTCTATTCCTAGCTTGATGTTGGTT 58.884 40.000 0.00 0.00 0.00 3.67
162 163 5.675538 GTCTATTCCTAGCTTGATGTTGGT 58.324 41.667 0.00 0.00 0.00 3.67
163 164 4.747108 CGTCTATTCCTAGCTTGATGTTGG 59.253 45.833 0.00 0.00 0.00 3.77
164 165 4.210120 GCGTCTATTCCTAGCTTGATGTTG 59.790 45.833 0.00 0.00 0.00 3.33
165 166 4.141937 TGCGTCTATTCCTAGCTTGATGTT 60.142 41.667 0.00 0.00 0.00 2.71
166 167 3.384789 TGCGTCTATTCCTAGCTTGATGT 59.615 43.478 0.00 0.00 0.00 3.06
167 168 3.982475 TGCGTCTATTCCTAGCTTGATG 58.018 45.455 0.00 0.00 0.00 3.07
168 169 4.672587 TTGCGTCTATTCCTAGCTTGAT 57.327 40.909 0.00 0.00 0.00 2.57
169 170 4.465632 TTTGCGTCTATTCCTAGCTTGA 57.534 40.909 0.00 0.00 0.00 3.02
170 171 5.545658 TTTTTGCGTCTATTCCTAGCTTG 57.454 39.130 0.00 0.00 0.00 4.01
204 205 1.405105 TCGCCTGAAAATTGGCTATGC 59.595 47.619 3.32 0.00 46.42 3.14
207 208 2.487762 CAAGTCGCCTGAAAATTGGCTA 59.512 45.455 3.32 0.00 46.42 3.93
210 211 1.000385 TGCAAGTCGCCTGAAAATTGG 60.000 47.619 0.00 0.00 41.33 3.16
235 236 9.998106 GGTGGATAGAATCAATTTAGCTAAGTA 57.002 33.333 6.24 0.00 0.00 2.24
236 237 8.718656 AGGTGGATAGAATCAATTTAGCTAAGT 58.281 33.333 6.24 0.21 0.00 2.24
273 274 1.906574 TGATTCTCGCCCTACAGGTTT 59.093 47.619 0.00 0.00 38.26 3.27
274 275 1.568504 TGATTCTCGCCCTACAGGTT 58.431 50.000 0.00 0.00 38.26 3.50
275 276 1.414181 CATGATTCTCGCCCTACAGGT 59.586 52.381 0.00 0.00 38.26 4.00
276 277 1.875576 GCATGATTCTCGCCCTACAGG 60.876 57.143 0.00 0.00 39.47 4.00
277 278 1.069823 AGCATGATTCTCGCCCTACAG 59.930 52.381 0.00 0.00 0.00 2.74
278 279 1.123077 AGCATGATTCTCGCCCTACA 58.877 50.000 0.00 0.00 0.00 2.74
279 280 1.069204 TCAGCATGATTCTCGCCCTAC 59.931 52.381 0.00 0.00 42.56 3.18
280 281 1.413118 TCAGCATGATTCTCGCCCTA 58.587 50.000 0.00 0.00 42.56 3.53
281 282 2.215191 TCAGCATGATTCTCGCCCT 58.785 52.632 0.00 0.00 42.56 5.19
282 283 4.863707 TCAGCATGATTCTCGCCC 57.136 55.556 0.00 0.00 42.56 6.13
292 293 2.222678 GGCATCGTTCATAGTCAGCATG 59.777 50.000 0.00 0.00 37.54 4.06
293 294 2.158914 TGGCATCGTTCATAGTCAGCAT 60.159 45.455 0.00 0.00 0.00 3.79
294 295 1.206849 TGGCATCGTTCATAGTCAGCA 59.793 47.619 0.00 0.00 0.00 4.41
295 296 1.594862 GTGGCATCGTTCATAGTCAGC 59.405 52.381 0.00 0.00 0.00 4.26
296 297 1.854743 CGTGGCATCGTTCATAGTCAG 59.145 52.381 0.00 0.00 0.00 3.51
297 298 1.203758 ACGTGGCATCGTTCATAGTCA 59.796 47.619 8.87 0.00 41.37 3.41
307 308 3.842126 CGTGCTGACGTGGCATCG 61.842 66.667 14.47 14.65 41.86 3.84
323 324 2.223340 GGTATGTCAGGCTTGCATTTCG 60.223 50.000 10.12 0.00 0.00 3.46
348 349 1.006813 TTGCCCATGTGTCCCCTAAT 58.993 50.000 0.00 0.00 0.00 1.73
349 350 0.331278 CTTGCCCATGTGTCCCCTAA 59.669 55.000 0.00 0.00 0.00 2.69
354 355 1.302511 ACGTCTTGCCCATGTGTCC 60.303 57.895 0.00 0.00 0.00 4.02
401 413 5.422012 TCTGAAGTGCTCATGTAGTAATCCA 59.578 40.000 0.00 0.00 32.14 3.41
403 415 7.038659 ACTTCTGAAGTGCTCATGTAGTAATC 58.961 38.462 21.47 0.00 41.01 1.75
408 425 4.391216 CCAACTTCTGAAGTGCTCATGTAG 59.609 45.833 22.67 3.15 41.91 2.74
464 481 9.607285 GCGATCTAGTCAAAAACAATAAAAGAA 57.393 29.630 0.00 0.00 0.00 2.52
465 482 7.955324 CGCGATCTAGTCAAAAACAATAAAAGA 59.045 33.333 0.00 0.00 0.00 2.52
466 483 7.955324 TCGCGATCTAGTCAAAAACAATAAAAG 59.045 33.333 3.71 0.00 0.00 2.27
467 484 7.742963 GTCGCGATCTAGTCAAAAACAATAAAA 59.257 33.333 14.06 0.00 0.00 1.52
468 485 7.117236 AGTCGCGATCTAGTCAAAAACAATAAA 59.883 33.333 14.06 0.00 0.00 1.40
469 486 6.588756 AGTCGCGATCTAGTCAAAAACAATAA 59.411 34.615 14.06 0.00 0.00 1.40
470 487 6.097356 AGTCGCGATCTAGTCAAAAACAATA 58.903 36.000 14.06 0.00 0.00 1.90
471 488 4.929808 AGTCGCGATCTAGTCAAAAACAAT 59.070 37.500 14.06 0.00 0.00 2.71
472 489 4.304110 AGTCGCGATCTAGTCAAAAACAA 58.696 39.130 14.06 0.00 0.00 2.83
473 490 3.909430 AGTCGCGATCTAGTCAAAAACA 58.091 40.909 14.06 0.00 0.00 2.83
474 491 4.384846 TCAAGTCGCGATCTAGTCAAAAAC 59.615 41.667 14.06 0.00 0.00 2.43
475 492 4.552355 TCAAGTCGCGATCTAGTCAAAAA 58.448 39.130 14.06 0.00 0.00 1.94
476 493 4.168922 TCAAGTCGCGATCTAGTCAAAA 57.831 40.909 14.06 0.00 0.00 2.44
477 494 3.842732 TCAAGTCGCGATCTAGTCAAA 57.157 42.857 14.06 0.00 0.00 2.69
478 495 4.371855 AATCAAGTCGCGATCTAGTCAA 57.628 40.909 14.06 0.00 0.00 3.18
479 496 4.371855 AAATCAAGTCGCGATCTAGTCA 57.628 40.909 14.06 0.00 0.00 3.41
480 497 5.704217 AAAAATCAAGTCGCGATCTAGTC 57.296 39.130 14.06 0.00 0.00 2.59
481 498 6.331061 AGTAAAAATCAAGTCGCGATCTAGT 58.669 36.000 14.06 0.00 0.00 2.57
482 499 6.814076 AGTAAAAATCAAGTCGCGATCTAG 57.186 37.500 14.06 3.01 0.00 2.43
483 500 7.478322 AGTAGTAAAAATCAAGTCGCGATCTA 58.522 34.615 14.06 0.00 0.00 1.98
484 501 6.331061 AGTAGTAAAAATCAAGTCGCGATCT 58.669 36.000 14.06 8.87 0.00 2.75
485 502 6.291690 GGAGTAGTAAAAATCAAGTCGCGATC 60.292 42.308 14.06 6.31 0.00 3.69
486 503 5.519206 GGAGTAGTAAAAATCAAGTCGCGAT 59.481 40.000 14.06 0.00 0.00 4.58
487 504 4.860907 GGAGTAGTAAAAATCAAGTCGCGA 59.139 41.667 3.71 3.71 0.00 5.87
488 505 4.863131 AGGAGTAGTAAAAATCAAGTCGCG 59.137 41.667 0.00 0.00 0.00 5.87
567 644 1.148310 GCACGATGTACAACTGCACT 58.852 50.000 16.78 0.00 0.00 4.40
589 669 2.281070 ACCCGTTGTCTGCTGCTG 60.281 61.111 0.00 0.00 0.00 4.41
590 670 2.031163 GACCCGTTGTCTGCTGCT 59.969 61.111 0.00 0.00 41.03 4.24
591 671 3.414700 CGACCCGTTGTCTGCTGC 61.415 66.667 0.00 0.00 42.13 5.25
733 820 1.155155 GAGTGGGGGAAAAAGGGCA 59.845 57.895 0.00 0.00 0.00 5.36
882 1356 1.679305 GAGAGTGGAGACTGGGCGA 60.679 63.158 0.00 0.00 30.16 5.54
890 1364 1.032657 GTAGGCAGCGAGAGTGGAGA 61.033 60.000 0.00 0.00 0.00 3.71
922 1396 2.497770 GACGTATCCACCACCGGG 59.502 66.667 6.32 0.00 41.29 5.73
960 1434 4.204891 CGACGAAATGGACGCGCC 62.205 66.667 5.73 9.63 37.10 6.53
964 1438 1.005294 AACCGACGACGAAATGGACG 61.005 55.000 9.28 0.00 42.66 4.79
1038 1512 2.325082 CGTCCACGGCCCTTTCTTG 61.325 63.158 0.00 0.00 35.37 3.02
1163 1637 1.820906 GGAAGAGCGCATGCATGGA 60.821 57.895 27.34 0.00 46.23 3.41
1224 1699 3.677596 CCAACCAAACAAATTATCCGTGC 59.322 43.478 0.00 0.00 0.00 5.34
1226 1701 3.306433 GCCCAACCAAACAAATTATCCGT 60.306 43.478 0.00 0.00 0.00 4.69
1227 1702 3.258228 GCCCAACCAAACAAATTATCCG 58.742 45.455 0.00 0.00 0.00 4.18
1229 1704 4.181309 TCGCCCAACCAAACAAATTATC 57.819 40.909 0.00 0.00 0.00 1.75
1230 1705 4.817318 ATCGCCCAACCAAACAAATTAT 57.183 36.364 0.00 0.00 0.00 1.28
1231 1706 4.608948 AATCGCCCAACCAAACAAATTA 57.391 36.364 0.00 0.00 0.00 1.40
1232 1707 3.483808 AATCGCCCAACCAAACAAATT 57.516 38.095 0.00 0.00 0.00 1.82
1274 1765 2.268076 GGTTCAACCCTGCACGCAT 61.268 57.895 0.00 0.00 30.04 4.73
1402 1893 1.436195 GCACTCACTTGTTGCCGACA 61.436 55.000 0.00 0.00 36.19 4.35
1416 1907 3.007473 ACAGTAGTAGGAGGAGCACTC 57.993 52.381 0.16 0.16 45.84 3.51
1464 3581 2.357327 TGCAAAGATACGCACGTACT 57.643 45.000 4.84 2.69 33.01 2.73
1606 3915 2.611518 CACCTGGTTGAGAAGATCGAC 58.388 52.381 0.00 0.00 41.11 4.20
1879 4203 2.043852 GAGGAGGACGAGGAGGCA 60.044 66.667 0.00 0.00 0.00 4.75
2632 6450 0.753867 TGTCGCAGTTGTACCCTTGA 59.246 50.000 0.00 0.00 0.00 3.02
2719 6547 1.134340 TGGATTATGTACACCCACGGC 60.134 52.381 0.00 0.00 0.00 5.68
2794 6622 1.002868 ATGAACAGCGCCAGAGCTT 60.003 52.632 2.29 0.00 46.80 3.74
2797 6625 1.005340 GAAGATGAACAGCGCCAGAG 58.995 55.000 2.29 0.00 0.00 3.35
2825 6653 3.185246 ACGGCTATGTGATGAAGAAGG 57.815 47.619 0.00 0.00 0.00 3.46
2887 6715 4.747529 GTACGGCCGTGGTGGGAC 62.748 72.222 40.02 25.03 38.63 4.46
2913 6741 1.202746 GCTTAGAGGGATGGCCAAGAG 60.203 57.143 10.96 0.00 35.15 2.85
2916 6744 1.645402 GGGCTTAGAGGGATGGCCAA 61.645 60.000 10.96 0.00 44.04 4.52
2936 6764 0.867746 GAGTTGTTCATCGCTGTGCA 59.132 50.000 0.00 0.00 0.00 4.57
2955 6784 1.595382 GGATGCAGGGAATCGTCGG 60.595 63.158 0.00 0.00 0.00 4.79
2958 6787 1.224592 GTGGGATGCAGGGAATCGT 59.775 57.895 0.00 0.00 0.00 3.73
2959 6788 1.526917 GGTGGGATGCAGGGAATCG 60.527 63.158 0.00 0.00 0.00 3.34
2963 6792 2.692368 GAGGGTGGGATGCAGGGA 60.692 66.667 0.00 0.00 0.00 4.20
2968 6797 4.864334 CGCTGGAGGGTGGGATGC 62.864 72.222 0.00 0.00 0.00 3.91
2971 6800 2.764128 GATCGCTGGAGGGTGGGA 60.764 66.667 0.00 0.00 0.00 4.37
2978 6807 4.147449 TGCACGGGATCGCTGGAG 62.147 66.667 8.28 0.00 40.63 3.86
2991 6820 0.323087 ATTTTACGGGGAGGGTGCAC 60.323 55.000 8.80 8.80 0.00 4.57
2999 6828 5.013391 GGACCCATTATCTATTTTACGGGGA 59.987 44.000 0.00 0.00 36.71 4.81
3000 6829 5.250982 GGACCCATTATCTATTTTACGGGG 58.749 45.833 0.00 0.00 36.71 5.73
3008 6837 4.706842 AGCAACGGACCCATTATCTATT 57.293 40.909 0.00 0.00 0.00 1.73
3030 6859 4.202398 GCCCAATGATCTATCTTGTGAGGA 60.202 45.833 0.00 0.00 0.00 3.71
3033 6862 4.711399 CAGCCCAATGATCTATCTTGTGA 58.289 43.478 0.00 0.00 0.00 3.58
3036 6865 3.502595 CAGCAGCCCAATGATCTATCTTG 59.497 47.826 0.00 0.00 0.00 3.02
3114 6943 1.973760 TTTTTCATGCGCCAGCCAT 59.026 47.368 4.18 0.00 44.33 4.40
3172 7001 4.001652 GGGCATCACATATGACTGATCTG 58.998 47.826 10.38 1.58 37.79 2.90
3173 7002 3.306571 CGGGCATCACATATGACTGATCT 60.307 47.826 10.38 0.00 37.79 2.75
3178 7007 1.486310 ACACGGGCATCACATATGACT 59.514 47.619 10.38 0.00 37.79 3.41


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

AutoCloner maintained by Alex Coulton.