Multiple sequence alignment - TraesCS2B01G098600

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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 TraesCS2B01G098600 chr2B 100.000 3146 0 0 1 3146 58343589 58346734 0.000000e+00 5810.0
1 TraesCS2B01G098600 chr2B 89.130 1702 104 36 677 2351 58312074 58310427 0.000000e+00 2043.0
2 TraesCS2B01G098600 chr2B 85.544 1757 131 51 419 2151 58092443 58090786 0.000000e+00 1724.0
3 TraesCS2B01G098600 chr2B 88.699 1460 85 30 698 2151 58536345 58537730 0.000000e+00 1709.0
4 TraesCS2B01G098600 chr2B 95.017 903 45 0 1250 2152 58237226 58236324 0.000000e+00 1419.0
5 TraesCS2B01G098600 chr2B 93.631 738 38 3 2417 3146 58540050 58540786 0.000000e+00 1094.0
6 TraesCS2B01G098600 chr2B 83.768 690 82 23 2454 3127 753100510 753101185 7.410000e-176 627.0
7 TraesCS2B01G098600 chr2B 81.172 563 52 33 698 1233 58238830 58238295 1.360000e-108 403.0
8 TraesCS2B01G098600 chr2B 92.105 190 6 2 2237 2426 58538093 58538273 3.110000e-65 259.0
9 TraesCS2B01G098600 chr2B 83.088 272 25 12 1203 1468 57787758 57788014 8.780000e-56 228.0
10 TraesCS2B01G098600 chr2B 87.755 196 21 3 2454 2648 23470851 23471044 3.160000e-55 226.0
11 TraesCS2B01G098600 chr2B 86.391 169 6 7 2287 2443 58236226 58236063 5.400000e-38 169.0
12 TraesCS2B01G098600 chr2B 97.500 80 1 1 2099 2177 58537899 58537978 5.470000e-28 135.0
13 TraesCS2B01G098600 chr2B 93.333 90 3 3 419 507 58239040 58238953 2.550000e-26 130.0
14 TraesCS2B01G098600 chr2B 92.424 66 2 1 2180 2245 58538021 58538083 1.200000e-14 91.6
15 TraesCS2B01G098600 chr2B 100.000 32 0 0 963 994 58238946 58238915 3.390000e-05 60.2
16 TraesCS2B01G098600 chr2A 88.940 1971 131 41 419 2347 38569406 38571331 0.000000e+00 2351.0
17 TraesCS2B01G098600 chr2A 88.342 1930 140 44 419 2315 38516973 38515096 0.000000e+00 2239.0
18 TraesCS2B01G098600 chr2A 83.179 541 46 25 1905 2425 38398170 38397655 1.330000e-123 453.0
19 TraesCS2B01G098600 chr2D 88.939 1781 110 44 419 2159 35242781 35241048 0.000000e+00 2117.0
20 TraesCS2B01G098600 chr2D 94.529 1316 62 6 846 2159 35314918 35316225 0.000000e+00 2023.0
21 TraesCS2B01G098600 chr2D 85.877 701 65 14 2454 3146 181285177 181285851 0.000000e+00 715.0
22 TraesCS2B01G098600 chr2D 86.826 167 17 3 1905 2071 35332339 35332500 6.930000e-42 182.0
23 TraesCS2B01G098600 chr2D 87.059 170 10 4 2257 2422 35501318 35501479 6.930000e-42 182.0
24 TraesCS2B01G098600 chr7D 87.607 702 73 8 2454 3144 161536479 161535781 0.000000e+00 802.0
25 TraesCS2B01G098600 chr7D 92.632 380 24 2 2771 3146 60233715 60234094 7.670000e-151 544.0
26 TraesCS2B01G098600 chr1D 86.139 707 71 19 2454 3146 261725137 261725830 0.000000e+00 737.0
27 TraesCS2B01G098600 chr1D 86.624 157 19 2 2454 2610 229878111 229878265 4.170000e-39 172.0
28 TraesCS2B01G098600 chr6B 84.758 702 75 14 2454 3146 90976500 90977178 0.000000e+00 675.0
29 TraesCS2B01G098600 chr6B 92.000 100 7 1 240 339 68712912 68713010 4.230000e-29 139.0
30 TraesCS2B01G098600 chr6B 94.444 54 3 0 365 418 42435070 42435123 2.010000e-12 84.2
31 TraesCS2B01G098600 chr3B 84.483 696 71 15 2454 3137 436837452 436836782 0.000000e+00 652.0
32 TraesCS2B01G098600 chr3B 88.350 206 21 3 2454 2658 181681886 181682089 8.720000e-61 244.0
33 TraesCS2B01G098600 chr5B 84.180 689 81 20 2454 3127 610368915 610368240 0.000000e+00 643.0
34 TraesCS2B01G098600 chr5B 89.637 386 33 5 2766 3146 685089468 685089085 4.720000e-133 484.0
35 TraesCS2B01G098600 chr7A 82.893 719 82 18 2456 3146 191170244 191169539 2.680000e-170 608.0
36 TraesCS2B01G098600 chr5A 81.933 714 96 15 2454 3146 678336240 678335539 9.790000e-160 573.0
37 TraesCS2B01G098600 chr5D 88.298 188 21 1 2454 2641 502648761 502648575 1.140000e-54 224.0
38 TraesCS2B01G098600 chr6D 86.624 157 19 2 2454 2610 412444302 412444456 4.170000e-39 172.0
39 TraesCS2B01G098600 chr6A 93.220 59 4 0 360 418 611823187 611823245 1.550000e-13 87.9
40 TraesCS2B01G098600 chr4D 91.489 47 4 0 1490 1536 300858221 300858175 7.280000e-07 65.8
41 TraesCS2B01G098600 chr1A 97.059 34 1 0 367 400 22762210 22762177 1.220000e-04 58.4
42 TraesCS2B01G098600 chr1A 100.000 28 0 0 373 400 13271899 13271926 6.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G098600 chr2B 58343589 58346734 3145 False 5810.00 5810 100.0000 1 3146 1 chr2B.!!$F3 3145
1 TraesCS2B01G098600 chr2B 58310427 58312074 1647 True 2043.00 2043 89.1300 677 2351 1 chr2B.!!$R2 1674
2 TraesCS2B01G098600 chr2B 58090786 58092443 1657 True 1724.00 1724 85.5440 419 2151 1 chr2B.!!$R1 1732
3 TraesCS2B01G098600 chr2B 58536345 58540786 4441 False 657.72 1709 92.8718 698 3146 5 chr2B.!!$F5 2448
4 TraesCS2B01G098600 chr2B 753100510 753101185 675 False 627.00 627 83.7680 2454 3127 1 chr2B.!!$F4 673
5 TraesCS2B01G098600 chr2B 58236063 58239040 2977 True 436.24 1419 91.1826 419 2443 5 chr2B.!!$R3 2024
6 TraesCS2B01G098600 chr2A 38569406 38571331 1925 False 2351.00 2351 88.9400 419 2347 1 chr2A.!!$F1 1928
7 TraesCS2B01G098600 chr2A 38515096 38516973 1877 True 2239.00 2239 88.3420 419 2315 1 chr2A.!!$R2 1896
8 TraesCS2B01G098600 chr2A 38397655 38398170 515 True 453.00 453 83.1790 1905 2425 1 chr2A.!!$R1 520
9 TraesCS2B01G098600 chr2D 35241048 35242781 1733 True 2117.00 2117 88.9390 419 2159 1 chr2D.!!$R1 1740
10 TraesCS2B01G098600 chr2D 35314918 35316225 1307 False 2023.00 2023 94.5290 846 2159 1 chr2D.!!$F1 1313
11 TraesCS2B01G098600 chr2D 181285177 181285851 674 False 715.00 715 85.8770 2454 3146 1 chr2D.!!$F4 692
12 TraesCS2B01G098600 chr7D 161535781 161536479 698 True 802.00 802 87.6070 2454 3144 1 chr7D.!!$R1 690
13 TraesCS2B01G098600 chr1D 261725137 261725830 693 False 737.00 737 86.1390 2454 3146 1 chr1D.!!$F2 692
14 TraesCS2B01G098600 chr6B 90976500 90977178 678 False 675.00 675 84.7580 2454 3146 1 chr6B.!!$F3 692
15 TraesCS2B01G098600 chr3B 436836782 436837452 670 True 652.00 652 84.4830 2454 3137 1 chr3B.!!$R1 683
16 TraesCS2B01G098600 chr5B 610368240 610368915 675 True 643.00 643 84.1800 2454 3127 1 chr5B.!!$R1 673
17 TraesCS2B01G098600 chr7A 191169539 191170244 705 True 608.00 608 82.8930 2456 3146 1 chr7A.!!$R1 690
18 TraesCS2B01G098600 chr5A 678335539 678336240 701 True 573.00 573 81.9330 2454 3146 1 chr5A.!!$R1 692

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
894 953 0.036875 CTCACTCAACCCCACTTCCC 59.963 60.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 3662 0.455464 CCAAGCACGCACACATGATG 60.455 55.0 0.0 0.0 0.0 3.07 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.582728 TTGCCTGTTCTTGCAAAGTG 57.417 45.000 0.00 0.00 46.34 3.16
27 28 1.761449 TGCCTGTTCTTGCAAAGTGA 58.239 45.000 0.00 0.00 46.34 3.41
28 29 2.098614 TGCCTGTTCTTGCAAAGTGAA 58.901 42.857 0.00 0.00 46.34 3.18
29 30 2.495270 TGCCTGTTCTTGCAAAGTGAAA 59.505 40.909 0.00 0.00 46.34 2.69
30 31 2.860136 GCCTGTTCTTGCAAAGTGAAAC 59.140 45.455 0.00 1.42 46.34 2.78
31 32 5.886096 TGCCTGTTCTTGCAAAGTGAAACT 61.886 41.667 0.00 0.00 46.34 2.66
32 33 6.609666 TGCCTGTTCTTGCAAAGTGAAACTA 61.610 40.000 0.00 0.00 46.34 2.24
33 34 7.857561 TGCCTGTTCTTGCAAAGTGAAACTAT 61.858 38.462 0.00 0.00 46.34 2.12
34 35 9.244283 TGCCTGTTCTTGCAAAGTGAAACTATT 62.244 37.037 0.00 0.00 46.34 1.73
51 52 9.581099 TGAAACTATTTTCAGTTTGAGGAAAAC 57.419 29.630 4.26 0.00 46.23 2.43
52 53 8.743099 GAAACTATTTTCAGTTTGAGGAAAACG 58.257 33.333 6.00 0.00 46.23 3.60
85 86 6.321848 ACAGAAAACCTAACCCAAAATACG 57.678 37.500 0.00 0.00 0.00 3.06
86 87 5.158494 CAGAAAACCTAACCCAAAATACGC 58.842 41.667 0.00 0.00 0.00 4.42
87 88 5.048294 CAGAAAACCTAACCCAAAATACGCT 60.048 40.000 0.00 0.00 0.00 5.07
88 89 6.149807 CAGAAAACCTAACCCAAAATACGCTA 59.850 38.462 0.00 0.00 0.00 4.26
89 90 6.888088 AGAAAACCTAACCCAAAATACGCTAT 59.112 34.615 0.00 0.00 0.00 2.97
90 91 8.048514 AGAAAACCTAACCCAAAATACGCTATA 58.951 33.333 0.00 0.00 0.00 1.31
91 92 8.756486 AAAACCTAACCCAAAATACGCTATAT 57.244 30.769 0.00 0.00 0.00 0.86
92 93 9.850198 AAAACCTAACCCAAAATACGCTATATA 57.150 29.630 0.00 0.00 0.00 0.86
119 120 7.645058 ATTAAATCTTAGGATGTTGGTGTGG 57.355 36.000 0.00 0.00 31.75 4.17
120 121 4.657814 AATCTTAGGATGTTGGTGTGGT 57.342 40.909 0.00 0.00 31.75 4.16
121 122 3.695830 TCTTAGGATGTTGGTGTGGTC 57.304 47.619 0.00 0.00 0.00 4.02
122 123 2.976185 TCTTAGGATGTTGGTGTGGTCA 59.024 45.455 0.00 0.00 0.00 4.02
123 124 3.392947 TCTTAGGATGTTGGTGTGGTCAA 59.607 43.478 0.00 0.00 0.00 3.18
124 125 2.978156 AGGATGTTGGTGTGGTCAAT 57.022 45.000 0.00 0.00 0.00 2.57
125 126 3.243359 AGGATGTTGGTGTGGTCAATT 57.757 42.857 0.00 0.00 0.00 2.32
126 127 3.575805 AGGATGTTGGTGTGGTCAATTT 58.424 40.909 0.00 0.00 0.00 1.82
127 128 3.966665 AGGATGTTGGTGTGGTCAATTTT 59.033 39.130 0.00 0.00 0.00 1.82
128 129 4.057432 GGATGTTGGTGTGGTCAATTTTG 58.943 43.478 0.00 0.00 0.00 2.44
129 130 4.202202 GGATGTTGGTGTGGTCAATTTTGA 60.202 41.667 0.00 0.00 34.20 2.69
130 131 5.511202 GGATGTTGGTGTGGTCAATTTTGAT 60.511 40.000 0.00 0.00 39.73 2.57
131 132 4.691175 TGTTGGTGTGGTCAATTTTGATG 58.309 39.130 0.00 0.00 39.73 3.07
132 133 4.057432 GTTGGTGTGGTCAATTTTGATGG 58.943 43.478 0.00 0.00 39.73 3.51
133 134 3.570540 TGGTGTGGTCAATTTTGATGGA 58.429 40.909 0.00 0.00 39.73 3.41
134 135 4.158786 TGGTGTGGTCAATTTTGATGGAT 58.841 39.130 0.00 0.00 39.73 3.41
135 136 4.592351 TGGTGTGGTCAATTTTGATGGATT 59.408 37.500 0.00 0.00 39.73 3.01
136 137 4.931002 GGTGTGGTCAATTTTGATGGATTG 59.069 41.667 0.00 0.00 39.73 2.67
137 138 5.511202 GGTGTGGTCAATTTTGATGGATTGT 60.511 40.000 0.00 0.00 39.73 2.71
138 139 5.990996 GTGTGGTCAATTTTGATGGATTGTT 59.009 36.000 0.00 0.00 39.73 2.83
139 140 7.151308 GTGTGGTCAATTTTGATGGATTGTTA 58.849 34.615 0.00 0.00 39.73 2.41
140 141 7.655328 GTGTGGTCAATTTTGATGGATTGTTAA 59.345 33.333 0.00 0.00 39.73 2.01
141 142 8.373981 TGTGGTCAATTTTGATGGATTGTTAAT 58.626 29.630 0.00 0.00 39.73 1.40
142 143 9.218440 GTGGTCAATTTTGATGGATTGTTAATT 57.782 29.630 0.00 0.00 39.73 1.40
150 151 9.921637 TTTTGATGGATTGTTAATTAGAACCAC 57.078 29.630 0.00 0.00 0.00 4.16
151 152 8.642935 TTGATGGATTGTTAATTAGAACCACA 57.357 30.769 0.00 0.00 0.00 4.17
152 153 8.642935 TGATGGATTGTTAATTAGAACCACAA 57.357 30.769 2.93 2.93 0.00 3.33
153 154 8.519526 TGATGGATTGTTAATTAGAACCACAAC 58.480 33.333 2.57 0.00 30.40 3.32
154 155 7.825331 TGGATTGTTAATTAGAACCACAACA 57.175 32.000 2.57 0.00 30.40 3.33
155 156 8.239038 TGGATTGTTAATTAGAACCACAACAA 57.761 30.769 2.57 2.47 39.41 2.83
156 157 8.696374 TGGATTGTTAATTAGAACCACAACAAA 58.304 29.630 2.57 0.00 38.80 2.83
157 158 9.191995 GGATTGTTAATTAGAACCACAACAAAG 57.808 33.333 2.57 0.00 38.80 2.77
158 159 9.744468 GATTGTTAATTAGAACCACAACAAAGT 57.256 29.630 2.57 0.00 38.80 2.66
159 160 8.918961 TTGTTAATTAGAACCACAACAAAGTG 57.081 30.769 0.00 0.00 34.09 3.16
160 161 8.282455 TGTTAATTAGAACCACAACAAAGTGA 57.718 30.769 0.00 0.00 42.05 3.41
161 162 8.740906 TGTTAATTAGAACCACAACAAAGTGAA 58.259 29.630 0.00 0.00 42.05 3.18
162 163 9.575783 GTTAATTAGAACCACAACAAAGTGAAA 57.424 29.630 0.00 0.00 42.05 2.69
165 166 7.876896 TTAGAACCACAACAAAGTGAAAAAC 57.123 32.000 0.00 0.00 42.05 2.43
166 167 5.848406 AGAACCACAACAAAGTGAAAAACA 58.152 33.333 0.00 0.00 42.05 2.83
167 168 6.284459 AGAACCACAACAAAGTGAAAAACAA 58.716 32.000 0.00 0.00 42.05 2.83
168 169 6.934083 AGAACCACAACAAAGTGAAAAACAAT 59.066 30.769 0.00 0.00 42.05 2.71
169 170 6.479095 ACCACAACAAAGTGAAAAACAATG 57.521 33.333 0.00 0.00 42.05 2.82
170 171 5.106752 ACCACAACAAAGTGAAAAACAATGC 60.107 36.000 0.00 0.00 42.05 3.56
171 172 5.122082 CCACAACAAAGTGAAAAACAATGCT 59.878 36.000 0.00 0.00 42.05 3.79
172 173 6.312426 CCACAACAAAGTGAAAAACAATGCTA 59.688 34.615 0.00 0.00 42.05 3.49
173 174 7.148507 CCACAACAAAGTGAAAAACAATGCTAA 60.149 33.333 0.00 0.00 42.05 3.09
174 175 8.389603 CACAACAAAGTGAAAAACAATGCTAAT 58.610 29.630 0.00 0.00 42.05 1.73
175 176 8.389603 ACAACAAAGTGAAAAACAATGCTAATG 58.610 29.630 0.00 0.00 0.00 1.90
176 177 8.389603 CAACAAAGTGAAAAACAATGCTAATGT 58.610 29.630 0.00 0.00 0.00 2.71
177 178 7.908230 ACAAAGTGAAAAACAATGCTAATGTG 58.092 30.769 0.00 0.00 0.00 3.21
178 179 6.529463 AAGTGAAAAACAATGCTAATGTGC 57.471 33.333 0.00 0.00 0.00 4.57
179 180 5.846203 AGTGAAAAACAATGCTAATGTGCT 58.154 33.333 0.00 0.00 0.00 4.40
180 181 5.922544 AGTGAAAAACAATGCTAATGTGCTC 59.077 36.000 0.00 0.00 0.00 4.26
181 182 5.691305 GTGAAAAACAATGCTAATGTGCTCA 59.309 36.000 0.00 0.00 0.00 4.26
182 183 6.366877 GTGAAAAACAATGCTAATGTGCTCAT 59.633 34.615 0.00 0.00 35.59 2.90
183 184 7.541783 GTGAAAAACAATGCTAATGTGCTCATA 59.458 33.333 0.93 0.00 33.49 2.15
184 185 7.541783 TGAAAAACAATGCTAATGTGCTCATAC 59.458 33.333 0.93 0.00 33.49 2.39
185 186 5.505173 AACAATGCTAATGTGCTCATACC 57.495 39.130 0.93 0.00 33.49 2.73
186 187 4.525996 ACAATGCTAATGTGCTCATACCA 58.474 39.130 0.93 0.65 33.49 3.25
187 188 5.135383 ACAATGCTAATGTGCTCATACCAT 58.865 37.500 0.93 2.89 33.49 3.55
188 189 6.298361 ACAATGCTAATGTGCTCATACCATA 58.702 36.000 0.93 0.00 33.49 2.74
189 190 6.944290 ACAATGCTAATGTGCTCATACCATAT 59.056 34.615 0.93 0.00 33.49 1.78
190 191 7.449395 ACAATGCTAATGTGCTCATACCATATT 59.551 33.333 0.93 0.00 33.49 1.28
191 192 8.301720 CAATGCTAATGTGCTCATACCATATTT 58.698 33.333 0.93 0.00 33.49 1.40
192 193 7.822161 TGCTAATGTGCTCATACCATATTTT 57.178 32.000 0.93 0.00 33.49 1.82
193 194 8.236585 TGCTAATGTGCTCATACCATATTTTT 57.763 30.769 0.93 0.00 33.49 1.94
194 195 9.348476 TGCTAATGTGCTCATACCATATTTTTA 57.652 29.630 0.93 0.00 33.49 1.52
220 221 7.066307 AGAAAACAGCAATTTTCCCTATTGT 57.934 32.000 17.22 0.66 45.72 2.71
221 222 8.189119 AGAAAACAGCAATTTTCCCTATTGTA 57.811 30.769 17.22 0.00 45.72 2.41
222 223 8.815912 AGAAAACAGCAATTTTCCCTATTGTAT 58.184 29.630 17.22 0.00 45.72 2.29
251 252 9.508642 TTTGTTTGTAGTATGATGTACAATGGA 57.491 29.630 0.00 0.00 38.58 3.41
252 253 9.508642 TTGTTTGTAGTATGATGTACAATGGAA 57.491 29.630 0.00 0.00 38.58 3.53
253 254 9.508642 TGTTTGTAGTATGATGTACAATGGAAA 57.491 29.630 0.00 0.00 38.58 3.13
257 258 8.952278 TGTAGTATGATGTACAATGGAAAAACC 58.048 33.333 0.00 0.00 39.54 3.27
258 259 9.174166 GTAGTATGATGTACAATGGAAAAACCT 57.826 33.333 0.00 0.00 39.86 3.50
259 260 8.650143 AGTATGATGTACAATGGAAAAACCTT 57.350 30.769 0.00 0.00 39.86 3.50
260 261 8.522830 AGTATGATGTACAATGGAAAAACCTTG 58.477 33.333 0.00 0.00 39.86 3.61
261 262 6.968263 TGATGTACAATGGAAAAACCTTGA 57.032 33.333 0.00 0.00 39.86 3.02
262 263 7.353414 TGATGTACAATGGAAAAACCTTGAA 57.647 32.000 0.00 0.00 39.86 2.69
263 264 7.786030 TGATGTACAATGGAAAAACCTTGAAA 58.214 30.769 0.00 0.00 39.86 2.69
264 265 7.708752 TGATGTACAATGGAAAAACCTTGAAAC 59.291 33.333 0.00 0.00 39.86 2.78
265 266 7.176589 TGTACAATGGAAAAACCTTGAAACT 57.823 32.000 0.00 0.00 39.86 2.66
266 267 7.616313 TGTACAATGGAAAAACCTTGAAACTT 58.384 30.769 0.00 0.00 39.86 2.66
267 268 6.983474 ACAATGGAAAAACCTTGAAACTTG 57.017 33.333 0.00 0.00 39.86 3.16
268 269 5.353956 ACAATGGAAAAACCTTGAAACTTGC 59.646 36.000 0.00 0.00 39.86 4.01
269 270 4.543590 TGGAAAAACCTTGAAACTTGCA 57.456 36.364 0.00 0.00 39.86 4.08
270 271 4.249661 TGGAAAAACCTTGAAACTTGCAC 58.750 39.130 0.00 0.00 39.86 4.57
271 272 3.621268 GGAAAAACCTTGAAACTTGCACC 59.379 43.478 0.00 0.00 35.41 5.01
272 273 3.971245 AAAACCTTGAAACTTGCACCA 57.029 38.095 0.00 0.00 0.00 4.17
273 274 3.971245 AAACCTTGAAACTTGCACCAA 57.029 38.095 0.00 0.00 0.00 3.67
274 275 3.971245 AACCTTGAAACTTGCACCAAA 57.029 38.095 0.00 0.00 0.00 3.28
275 276 3.525268 ACCTTGAAACTTGCACCAAAG 57.475 42.857 0.00 0.00 0.00 2.77
276 277 2.831526 ACCTTGAAACTTGCACCAAAGT 59.168 40.909 0.00 0.00 42.21 2.66
277 278 3.119137 ACCTTGAAACTTGCACCAAAGTC 60.119 43.478 0.00 0.00 39.48 3.01
278 279 3.131046 CCTTGAAACTTGCACCAAAGTCT 59.869 43.478 0.00 0.00 39.48 3.24
279 280 4.338118 CCTTGAAACTTGCACCAAAGTCTA 59.662 41.667 0.00 0.00 39.48 2.59
280 281 5.010012 CCTTGAAACTTGCACCAAAGTCTAT 59.990 40.000 0.00 0.00 39.48 1.98
281 282 5.437289 TGAAACTTGCACCAAAGTCTATG 57.563 39.130 0.00 0.00 39.48 2.23
282 283 4.887071 TGAAACTTGCACCAAAGTCTATGT 59.113 37.500 0.00 0.00 39.48 2.29
283 284 6.058833 TGAAACTTGCACCAAAGTCTATGTA 58.941 36.000 0.00 0.00 39.48 2.29
284 285 6.204688 TGAAACTTGCACCAAAGTCTATGTAG 59.795 38.462 0.00 0.00 39.48 2.74
285 286 5.483685 ACTTGCACCAAAGTCTATGTAGA 57.516 39.130 0.00 0.00 35.44 2.59
286 287 5.482908 ACTTGCACCAAAGTCTATGTAGAG 58.517 41.667 0.00 0.00 35.44 2.43
287 288 5.246203 ACTTGCACCAAAGTCTATGTAGAGA 59.754 40.000 0.00 0.00 35.44 3.10
288 289 5.738619 TGCACCAAAGTCTATGTAGAGAA 57.261 39.130 0.00 0.00 32.01 2.87
289 290 6.109156 TGCACCAAAGTCTATGTAGAGAAA 57.891 37.500 0.00 0.00 32.01 2.52
290 291 6.530120 TGCACCAAAGTCTATGTAGAGAAAA 58.470 36.000 0.00 0.00 32.01 2.29
291 292 7.168219 TGCACCAAAGTCTATGTAGAGAAAAT 58.832 34.615 0.00 0.00 32.01 1.82
292 293 8.318412 TGCACCAAAGTCTATGTAGAGAAAATA 58.682 33.333 0.00 0.00 32.01 1.40
293 294 9.331282 GCACCAAAGTCTATGTAGAGAAAATAT 57.669 33.333 0.00 0.00 32.01 1.28
324 325 9.816354 AAAGTTGAAATTGTATTAGTTTGCTGT 57.184 25.926 0.00 0.00 0.00 4.40
325 326 9.816354 AAGTTGAAATTGTATTAGTTTGCTGTT 57.184 25.926 0.00 0.00 0.00 3.16
326 327 9.816354 AGTTGAAATTGTATTAGTTTGCTGTTT 57.184 25.926 0.00 0.00 0.00 2.83
338 339 8.528044 TTAGTTTGCTGTTTATATTTAGGGGG 57.472 34.615 0.00 0.00 0.00 5.40
379 380 3.249961 GGGGGCCCCGGATTCTAG 61.250 72.222 35.11 0.00 36.85 2.43
380 381 2.447959 GGGGCCCCGGATTCTAGT 60.448 66.667 29.50 0.00 0.00 2.57
381 382 2.076803 GGGGCCCCGGATTCTAGTT 61.077 63.158 29.50 0.00 0.00 2.24
382 383 1.642513 GGGGCCCCGGATTCTAGTTT 61.643 60.000 29.50 0.00 0.00 2.66
383 384 0.257905 GGGCCCCGGATTCTAGTTTT 59.742 55.000 12.23 0.00 0.00 2.43
384 385 1.389555 GGCCCCGGATTCTAGTTTTG 58.610 55.000 0.73 0.00 0.00 2.44
385 386 0.738975 GCCCCGGATTCTAGTTTTGC 59.261 55.000 0.73 0.00 0.00 3.68
386 387 1.389555 CCCCGGATTCTAGTTTTGCC 58.610 55.000 0.73 0.00 0.00 4.52
387 388 1.389555 CCCGGATTCTAGTTTTGCCC 58.610 55.000 0.73 0.00 0.00 5.36
388 389 1.389555 CCGGATTCTAGTTTTGCCCC 58.610 55.000 0.00 0.00 0.00 5.80
389 390 1.014352 CGGATTCTAGTTTTGCCCCG 58.986 55.000 0.00 0.00 0.00 5.73
390 391 1.389555 GGATTCTAGTTTTGCCCCGG 58.610 55.000 0.00 0.00 0.00 5.73
391 392 1.389555 GATTCTAGTTTTGCCCCGGG 58.610 55.000 15.80 15.80 0.00 5.73
406 407 2.361230 GGGCCCCCGAAAACTGAG 60.361 66.667 12.23 0.00 0.00 3.35
407 408 2.361230 GGCCCCCGAAAACTGAGG 60.361 66.667 0.00 0.00 0.00 3.86
408 409 2.754375 GCCCCCGAAAACTGAGGA 59.246 61.111 0.00 0.00 0.00 3.71
409 410 1.674651 GCCCCCGAAAACTGAGGAC 60.675 63.158 0.00 0.00 0.00 3.85
410 411 1.002502 CCCCCGAAAACTGAGGACC 60.003 63.158 0.00 0.00 0.00 4.46
411 412 1.375523 CCCCGAAAACTGAGGACCG 60.376 63.158 0.00 0.00 0.00 4.79
412 413 1.375523 CCCGAAAACTGAGGACCGG 60.376 63.158 0.00 0.00 36.98 5.28
413 414 2.033194 CCGAAAACTGAGGACCGGC 61.033 63.158 0.00 0.00 0.00 6.13
414 415 2.033194 CGAAAACTGAGGACCGGCC 61.033 63.158 0.00 3.58 0.00 6.13
415 416 1.674651 GAAAACTGAGGACCGGCCC 60.675 63.158 0.00 0.00 37.37 5.80
416 417 2.125766 GAAAACTGAGGACCGGCCCT 62.126 60.000 10.05 10.05 39.77 5.19
417 418 2.411765 AAAACTGAGGACCGGCCCTG 62.412 60.000 16.78 2.61 36.49 4.45
480 481 0.886563 AGCTTGCAGGCTGTGAATTC 59.113 50.000 24.00 0.00 41.43 2.17
586 589 7.559897 TCTTTTTGACTGAAATGGAGTAAGGTT 59.440 33.333 0.00 0.00 0.00 3.50
607 610 3.011818 TGTGGTGCATGTCAGATTCATC 58.988 45.455 0.00 0.00 0.00 2.92
611 614 5.530171 GTGGTGCATGTCAGATTCATCTAAT 59.470 40.000 0.00 0.00 34.85 1.73
612 615 5.529800 TGGTGCATGTCAGATTCATCTAATG 59.470 40.000 0.00 0.00 34.85 1.90
613 616 5.450171 GTGCATGTCAGATTCATCTAATGC 58.550 41.667 16.91 16.91 42.12 3.56
614 617 4.212636 TGCATGTCAGATTCATCTAATGCG 59.787 41.667 17.77 0.00 43.29 4.73
615 618 4.212847 GCATGTCAGATTCATCTAATGCGT 59.787 41.667 12.17 0.00 37.51 5.24
616 619 5.676953 CATGTCAGATTCATCTAATGCGTG 58.323 41.667 0.00 0.00 34.85 5.34
617 620 3.557185 TGTCAGATTCATCTAATGCGTGC 59.443 43.478 0.00 0.00 34.85 5.34
618 621 3.557185 GTCAGATTCATCTAATGCGTGCA 59.443 43.478 0.00 0.00 34.85 4.57
619 622 4.212847 GTCAGATTCATCTAATGCGTGCAT 59.787 41.667 0.51 0.51 34.79 3.96
641 644 3.387947 GCTCGTCCCCCTTTCCGA 61.388 66.667 0.00 0.00 0.00 4.55
644 647 3.001406 CGTCCCCCTTTCCGACCT 61.001 66.667 0.00 0.00 0.00 3.85
645 648 1.683365 CGTCCCCCTTTCCGACCTA 60.683 63.158 0.00 0.00 0.00 3.08
652 655 0.815615 CCTTTCCGACCTATGGCAGC 60.816 60.000 0.00 0.00 0.00 5.25
662 665 1.151668 CTATGGCAGCGAAGGTATGC 58.848 55.000 0.00 0.00 39.25 3.14
663 666 0.599991 TATGGCAGCGAAGGTATGCG 60.600 55.000 0.00 0.00 40.90 4.73
664 667 2.511600 GGCAGCGAAGGTATGCGT 60.512 61.111 0.00 0.00 40.90 5.24
665 668 2.703409 GCAGCGAAGGTATGCGTG 59.297 61.111 0.00 0.00 35.08 5.34
666 669 2.703409 CAGCGAAGGTATGCGTGC 59.297 61.111 0.00 0.00 35.08 5.34
667 670 1.811266 CAGCGAAGGTATGCGTGCT 60.811 57.895 0.00 0.00 35.08 4.40
668 671 1.519455 AGCGAAGGTATGCGTGCTC 60.519 57.895 0.00 0.00 35.08 4.26
671 679 1.472276 CGAAGGTATGCGTGCTCGTC 61.472 60.000 10.18 3.07 39.49 4.20
694 702 4.260948 CCTTCTTTCAGCAACTGACAAGTC 60.261 45.833 0.00 0.00 40.46 3.01
695 703 2.866156 TCTTTCAGCAACTGACAAGTCG 59.134 45.455 0.00 0.00 40.46 4.18
696 704 2.309528 TTCAGCAACTGACAAGTCGT 57.690 45.000 0.00 0.00 40.46 4.34
744 765 6.761731 TTTAATCGCATTCAACCAAGTTTG 57.238 33.333 0.00 0.00 0.00 2.93
843 874 3.834813 GGATATAGAGCACTGGACCATCA 59.165 47.826 0.00 0.00 0.00 3.07
844 875 4.081752 GGATATAGAGCACTGGACCATCAG 60.082 50.000 0.00 0.00 40.40 2.90
878 937 4.873827 GTGTCACTTTCAGTTAACCACTCA 59.126 41.667 0.88 0.00 30.92 3.41
882 941 5.105106 TCACTTTCAGTTAACCACTCACTCA 60.105 40.000 0.88 0.00 30.92 3.41
883 942 5.584649 CACTTTCAGTTAACCACTCACTCAA 59.415 40.000 0.88 0.00 30.92 3.02
884 943 5.585047 ACTTTCAGTTAACCACTCACTCAAC 59.415 40.000 0.88 0.00 30.92 3.18
885 944 4.067972 TCAGTTAACCACTCACTCAACC 57.932 45.455 0.88 0.00 30.92 3.77
886 945 3.139077 CAGTTAACCACTCACTCAACCC 58.861 50.000 0.88 0.00 30.92 4.11
887 946 2.105993 AGTTAACCACTCACTCAACCCC 59.894 50.000 0.88 0.00 0.00 4.95
888 947 1.809133 TAACCACTCACTCAACCCCA 58.191 50.000 0.00 0.00 0.00 4.96
889 948 0.182775 AACCACTCACTCAACCCCAC 59.817 55.000 0.00 0.00 0.00 4.61
890 949 0.694444 ACCACTCACTCAACCCCACT 60.694 55.000 0.00 0.00 0.00 4.00
891 950 0.474184 CCACTCACTCAACCCCACTT 59.526 55.000 0.00 0.00 0.00 3.16
892 951 1.543429 CCACTCACTCAACCCCACTTC 60.543 57.143 0.00 0.00 0.00 3.01
893 952 0.765510 ACTCACTCAACCCCACTTCC 59.234 55.000 0.00 0.00 0.00 3.46
894 953 0.036875 CTCACTCAACCCCACTTCCC 59.963 60.000 0.00 0.00 0.00 3.97
895 954 0.401395 TCACTCAACCCCACTTCCCT 60.401 55.000 0.00 0.00 0.00 4.20
896 955 0.036875 CACTCAACCCCACTTCCCTC 59.963 60.000 0.00 0.00 0.00 4.30
897 956 1.134438 ACTCAACCCCACTTCCCTCC 61.134 60.000 0.00 0.00 0.00 4.30
898 957 2.185310 CTCAACCCCACTTCCCTCCG 62.185 65.000 0.00 0.00 0.00 4.63
899 958 3.647771 AACCCCACTTCCCTCCGC 61.648 66.667 0.00 0.00 0.00 5.54
900 959 4.658786 ACCCCACTTCCCTCCGCT 62.659 66.667 0.00 0.00 0.00 5.52
958 1039 2.047179 GTGGGTCGAGCACCTTCC 60.047 66.667 17.59 0.00 45.95 3.46
1122 1207 1.398451 CCGTCTGAAATGCACGAACAC 60.398 52.381 0.00 0.00 35.49 3.32
1128 1213 2.030363 TGAAATGCACGAACACCAATCC 60.030 45.455 0.00 0.00 0.00 3.01
1161 1253 5.019785 AGTAGAACTTCAAGACGGTTTGT 57.980 39.130 0.00 0.00 0.00 2.83
2040 3206 1.012486 CGGCTGACAACGGGTACTTC 61.012 60.000 0.00 0.00 0.00 3.01
2170 3361 2.881352 GCTAGTCAGCGACGTGGC 60.881 66.667 15.38 15.38 38.22 5.01
2171 3362 2.202623 CTAGTCAGCGACGTGGCC 60.203 66.667 19.50 3.98 37.67 5.36
2173 3364 1.374343 CTAGTCAGCGACGTGGCCTA 61.374 60.000 19.50 12.13 37.67 3.93
2230 3662 2.019984 GAAGTGATGAAGGGACCATGC 58.980 52.381 0.00 0.00 0.00 4.06
2323 3777 3.795101 CGTTATCCGAATTCGCTGTAGTT 59.205 43.478 22.36 6.15 39.56 2.24
2336 3790 4.209703 TCGCTGTAGTTTAGTTTTCAACGG 59.790 41.667 0.00 0.00 36.23 4.44
2481 5734 3.067601 AGGGTTAGGTTTGCGAAAAACAG 59.932 43.478 6.70 0.00 32.04 3.16
2489 5742 5.766174 AGGTTTGCGAAAAACAGTAGGATAA 59.234 36.000 6.70 0.00 32.04 1.75
2555 5808 2.684001 AAAACACTGATCGGCGGATA 57.316 45.000 7.21 0.00 31.51 2.59
2724 6030 3.591835 CTCGCTCGCCCCTCTCTC 61.592 72.222 0.00 0.00 0.00 3.20
3002 6370 6.710295 TGCTAGCACTGAAAACTTAGATTTCA 59.290 34.615 14.93 15.10 42.73 2.69
3123 6493 1.740025 GTTGTGCAGAGAAGGTATGGC 59.260 52.381 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.761449 TCACTTTGCAAGAACAGGCA 58.239 45.000 0.00 0.00 38.46 4.75
9 10 2.860136 GTTTCACTTTGCAAGAACAGGC 59.140 45.455 0.00 0.00 0.00 4.85
10 11 4.376340 AGTTTCACTTTGCAAGAACAGG 57.624 40.909 0.00 0.00 0.00 4.00
11 12 7.992180 AAATAGTTTCACTTTGCAAGAACAG 57.008 32.000 0.00 0.00 0.00 3.16
12 13 8.031864 TGAAAATAGTTTCACTTTGCAAGAACA 58.968 29.630 13.98 0.00 46.48 3.18
13 14 8.406172 TGAAAATAGTTTCACTTTGCAAGAAC 57.594 30.769 13.98 1.89 46.48 3.01
14 15 8.250332 ACTGAAAATAGTTTCACTTTGCAAGAA 58.750 29.630 13.98 0.00 46.48 2.52
15 16 7.771183 ACTGAAAATAGTTTCACTTTGCAAGA 58.229 30.769 13.98 0.00 46.48 3.02
16 17 7.992180 ACTGAAAATAGTTTCACTTTGCAAG 57.008 32.000 13.98 5.21 46.48 4.01
17 18 8.655092 CAAACTGAAAATAGTTTCACTTTGCAA 58.345 29.630 24.34 0.00 46.48 4.08
18 19 8.031864 TCAAACTGAAAATAGTTTCACTTTGCA 58.968 29.630 27.57 19.88 46.48 4.08
19 20 8.406172 TCAAACTGAAAATAGTTTCACTTTGC 57.594 30.769 27.57 4.41 46.48 3.68
20 21 9.023967 CCTCAAACTGAAAATAGTTTCACTTTG 57.976 33.333 27.03 27.03 46.48 2.77
21 22 8.966868 TCCTCAAACTGAAAATAGTTTCACTTT 58.033 29.630 13.98 13.89 46.48 2.66
22 23 8.519799 TCCTCAAACTGAAAATAGTTTCACTT 57.480 30.769 13.98 9.06 46.48 3.16
23 24 8.519799 TTCCTCAAACTGAAAATAGTTTCACT 57.480 30.769 13.98 3.36 46.48 3.41
24 25 9.581099 TTTTCCTCAAACTGAAAATAGTTTCAC 57.419 29.630 13.98 0.00 46.48 3.18
25 26 9.581099 GTTTTCCTCAAACTGAAAATAGTTTCA 57.419 29.630 16.70 16.70 45.15 2.69
26 27 8.743099 CGTTTTCCTCAAACTGAAAATAGTTTC 58.257 33.333 8.68 8.68 45.15 2.78
28 29 7.992008 TCGTTTTCCTCAAACTGAAAATAGTT 58.008 30.769 0.00 0.00 42.51 2.24
29 30 7.562454 TCGTTTTCCTCAAACTGAAAATAGT 57.438 32.000 0.00 0.00 42.51 2.12
32 33 9.810545 TTTTATCGTTTTCCTCAAACTGAAAAT 57.189 25.926 0.00 0.00 42.51 1.82
33 34 9.640963 TTTTTATCGTTTTCCTCAAACTGAAAA 57.359 25.926 0.00 0.00 42.51 2.29
59 60 8.517056 CGTATTTTGGGTTAGGTTTTCTGTATT 58.483 33.333 0.00 0.00 0.00 1.89
60 61 7.362315 GCGTATTTTGGGTTAGGTTTTCTGTAT 60.362 37.037 0.00 0.00 0.00 2.29
61 62 6.072563 GCGTATTTTGGGTTAGGTTTTCTGTA 60.073 38.462 0.00 0.00 0.00 2.74
62 63 5.278610 GCGTATTTTGGGTTAGGTTTTCTGT 60.279 40.000 0.00 0.00 0.00 3.41
63 64 5.048294 AGCGTATTTTGGGTTAGGTTTTCTG 60.048 40.000 0.00 0.00 0.00 3.02
64 65 5.074804 AGCGTATTTTGGGTTAGGTTTTCT 58.925 37.500 0.00 0.00 0.00 2.52
65 66 5.381174 AGCGTATTTTGGGTTAGGTTTTC 57.619 39.130 0.00 0.00 0.00 2.29
66 67 8.756486 ATATAGCGTATTTTGGGTTAGGTTTT 57.244 30.769 0.00 0.00 0.00 2.43
93 94 9.184523 CCACACCAACATCCTAAGATTTAATTA 57.815 33.333 0.00 0.00 0.00 1.40
94 95 7.673926 ACCACACCAACATCCTAAGATTTAATT 59.326 33.333 0.00 0.00 0.00 1.40
95 96 7.182060 ACCACACCAACATCCTAAGATTTAAT 58.818 34.615 0.00 0.00 0.00 1.40
96 97 6.548321 ACCACACCAACATCCTAAGATTTAA 58.452 36.000 0.00 0.00 0.00 1.52
97 98 6.134535 ACCACACCAACATCCTAAGATTTA 57.865 37.500 0.00 0.00 0.00 1.40
98 99 4.998051 ACCACACCAACATCCTAAGATTT 58.002 39.130 0.00 0.00 0.00 2.17
99 100 4.042809 TGACCACACCAACATCCTAAGATT 59.957 41.667 0.00 0.00 0.00 2.40
100 101 3.587061 TGACCACACCAACATCCTAAGAT 59.413 43.478 0.00 0.00 0.00 2.40
101 102 2.976185 TGACCACACCAACATCCTAAGA 59.024 45.455 0.00 0.00 0.00 2.10
102 103 3.417069 TGACCACACCAACATCCTAAG 57.583 47.619 0.00 0.00 0.00 2.18
103 104 3.866703 TTGACCACACCAACATCCTAA 57.133 42.857 0.00 0.00 0.00 2.69
104 105 4.380843 AATTGACCACACCAACATCCTA 57.619 40.909 0.00 0.00 0.00 2.94
105 106 2.978156 ATTGACCACACCAACATCCT 57.022 45.000 0.00 0.00 0.00 3.24
106 107 4.057432 CAAAATTGACCACACCAACATCC 58.943 43.478 0.00 0.00 0.00 3.51
107 108 4.942852 TCAAAATTGACCACACCAACATC 58.057 39.130 0.00 0.00 31.01 3.06
108 109 5.299148 CATCAAAATTGACCACACCAACAT 58.701 37.500 0.00 0.00 40.49 2.71
109 110 4.442612 CCATCAAAATTGACCACACCAACA 60.443 41.667 0.00 0.00 40.49 3.33
110 111 4.057432 CCATCAAAATTGACCACACCAAC 58.943 43.478 0.00 0.00 40.49 3.77
111 112 3.963374 TCCATCAAAATTGACCACACCAA 59.037 39.130 0.00 0.00 40.49 3.67
112 113 3.570540 TCCATCAAAATTGACCACACCA 58.429 40.909 0.00 0.00 40.49 4.17
113 114 4.806640 ATCCATCAAAATTGACCACACC 57.193 40.909 0.00 0.00 40.49 4.16
114 115 5.540911 ACAATCCATCAAAATTGACCACAC 58.459 37.500 0.00 0.00 40.49 3.82
115 116 5.804944 ACAATCCATCAAAATTGACCACA 57.195 34.783 0.00 0.00 40.49 4.17
116 117 8.776376 ATTAACAATCCATCAAAATTGACCAC 57.224 30.769 0.00 0.00 40.49 4.16
124 125 9.921637 GTGGTTCTAATTAACAATCCATCAAAA 57.078 29.630 0.00 0.00 0.00 2.44
125 126 9.083422 TGTGGTTCTAATTAACAATCCATCAAA 57.917 29.630 0.00 0.00 0.00 2.69
126 127 8.642935 TGTGGTTCTAATTAACAATCCATCAA 57.357 30.769 0.00 0.00 0.00 2.57
127 128 8.519526 GTTGTGGTTCTAATTAACAATCCATCA 58.480 33.333 3.64 0.00 33.67 3.07
128 129 8.519526 TGTTGTGGTTCTAATTAACAATCCATC 58.480 33.333 3.64 0.00 33.67 3.51
129 130 8.415950 TGTTGTGGTTCTAATTAACAATCCAT 57.584 30.769 3.64 0.00 33.67 3.41
130 131 7.825331 TGTTGTGGTTCTAATTAACAATCCA 57.175 32.000 3.64 0.00 33.67 3.41
131 132 9.191995 CTTTGTTGTGGTTCTAATTAACAATCC 57.808 33.333 0.00 0.00 37.71 3.01
132 133 9.744468 ACTTTGTTGTGGTTCTAATTAACAATC 57.256 29.630 0.00 0.00 37.71 2.67
133 134 9.528018 CACTTTGTTGTGGTTCTAATTAACAAT 57.472 29.630 0.00 0.00 37.71 2.71
134 135 8.740906 TCACTTTGTTGTGGTTCTAATTAACAA 58.259 29.630 0.00 0.00 38.40 2.83
135 136 8.282455 TCACTTTGTTGTGGTTCTAATTAACA 57.718 30.769 0.00 0.00 38.40 2.41
136 137 9.575783 TTTCACTTTGTTGTGGTTCTAATTAAC 57.424 29.630 0.00 0.00 38.40 2.01
139 140 8.931775 GTTTTTCACTTTGTTGTGGTTCTAATT 58.068 29.630 0.00 0.00 38.40 1.40
140 141 8.091449 TGTTTTTCACTTTGTTGTGGTTCTAAT 58.909 29.630 0.00 0.00 38.40 1.73
141 142 7.434492 TGTTTTTCACTTTGTTGTGGTTCTAA 58.566 30.769 0.00 0.00 38.40 2.10
142 143 6.982852 TGTTTTTCACTTTGTTGTGGTTCTA 58.017 32.000 0.00 0.00 38.40 2.10
143 144 5.848406 TGTTTTTCACTTTGTTGTGGTTCT 58.152 33.333 0.00 0.00 38.40 3.01
144 145 6.532365 TTGTTTTTCACTTTGTTGTGGTTC 57.468 33.333 0.00 0.00 38.40 3.62
145 146 6.567511 GCATTGTTTTTCACTTTGTTGTGGTT 60.568 34.615 0.00 0.00 38.40 3.67
146 147 5.106752 GCATTGTTTTTCACTTTGTTGTGGT 60.107 36.000 0.00 0.00 38.40 4.16
147 148 5.122082 AGCATTGTTTTTCACTTTGTTGTGG 59.878 36.000 0.00 0.00 38.40 4.17
148 149 6.168164 AGCATTGTTTTTCACTTTGTTGTG 57.832 33.333 0.00 0.00 39.15 3.33
149 150 7.897575 TTAGCATTGTTTTTCACTTTGTTGT 57.102 28.000 0.00 0.00 0.00 3.32
150 151 8.389603 ACATTAGCATTGTTTTTCACTTTGTTG 58.610 29.630 0.00 0.00 0.00 3.33
151 152 8.389603 CACATTAGCATTGTTTTTCACTTTGTT 58.610 29.630 0.00 0.00 0.00 2.83
152 153 7.465781 GCACATTAGCATTGTTTTTCACTTTGT 60.466 33.333 0.00 0.00 0.00 2.83
153 154 6.847289 GCACATTAGCATTGTTTTTCACTTTG 59.153 34.615 0.00 0.00 0.00 2.77
154 155 6.762661 AGCACATTAGCATTGTTTTTCACTTT 59.237 30.769 0.00 0.00 36.85 2.66
155 156 6.282930 AGCACATTAGCATTGTTTTTCACTT 58.717 32.000 0.00 0.00 36.85 3.16
156 157 5.846203 AGCACATTAGCATTGTTTTTCACT 58.154 33.333 0.00 0.00 36.85 3.41
157 158 5.691305 TGAGCACATTAGCATTGTTTTTCAC 59.309 36.000 0.00 0.00 36.85 3.18
158 159 5.840715 TGAGCACATTAGCATTGTTTTTCA 58.159 33.333 0.00 0.00 36.85 2.69
159 160 6.956299 ATGAGCACATTAGCATTGTTTTTC 57.044 33.333 0.00 0.00 36.85 2.29
160 161 6.813152 GGTATGAGCACATTAGCATTGTTTTT 59.187 34.615 0.83 0.00 37.87 1.94
161 162 6.071447 TGGTATGAGCACATTAGCATTGTTTT 60.071 34.615 0.83 0.00 37.87 2.43
162 163 5.418524 TGGTATGAGCACATTAGCATTGTTT 59.581 36.000 0.83 0.00 37.87 2.83
163 164 4.949238 TGGTATGAGCACATTAGCATTGTT 59.051 37.500 0.83 0.00 37.87 2.83
164 165 4.525996 TGGTATGAGCACATTAGCATTGT 58.474 39.130 0.83 0.00 37.87 2.71
165 166 5.700722 ATGGTATGAGCACATTAGCATTG 57.299 39.130 0.83 0.00 37.87 2.82
166 167 8.413309 AAATATGGTATGAGCACATTAGCATT 57.587 30.769 16.61 5.05 37.87 3.56
167 168 8.413309 AAAATATGGTATGAGCACATTAGCAT 57.587 30.769 0.83 11.33 37.87 3.79
168 169 7.822161 AAAATATGGTATGAGCACATTAGCA 57.178 32.000 0.83 5.17 37.87 3.49
194 195 8.815912 ACAATAGGGAAAATTGCTGTTTTCTAT 58.184 29.630 19.36 13.56 43.94 1.98
195 196 8.189119 ACAATAGGGAAAATTGCTGTTTTCTA 57.811 30.769 19.36 10.48 43.94 2.10
196 197 7.066307 ACAATAGGGAAAATTGCTGTTTTCT 57.934 32.000 19.36 9.16 43.94 2.52
225 226 9.508642 TCCATTGTACATCATACTACAAACAAA 57.491 29.630 0.00 0.00 36.64 2.83
226 227 9.508642 TTCCATTGTACATCATACTACAAACAA 57.491 29.630 0.00 0.00 36.64 2.83
227 228 9.508642 TTTCCATTGTACATCATACTACAAACA 57.491 29.630 0.00 0.00 36.64 2.83
231 232 8.952278 GGTTTTTCCATTGTACATCATACTACA 58.048 33.333 0.00 0.00 35.97 2.74
232 233 9.174166 AGGTTTTTCCATTGTACATCATACTAC 57.826 33.333 0.00 0.00 39.02 2.73
233 234 9.747898 AAGGTTTTTCCATTGTACATCATACTA 57.252 29.630 0.00 0.00 39.02 1.82
234 235 8.522830 CAAGGTTTTTCCATTGTACATCATACT 58.477 33.333 0.00 0.00 39.02 2.12
235 236 8.519526 TCAAGGTTTTTCCATTGTACATCATAC 58.480 33.333 0.00 0.00 39.02 2.39
236 237 8.642935 TCAAGGTTTTTCCATTGTACATCATA 57.357 30.769 0.00 0.00 39.02 2.15
237 238 7.537596 TCAAGGTTTTTCCATTGTACATCAT 57.462 32.000 0.00 0.00 39.02 2.45
238 239 6.968263 TCAAGGTTTTTCCATTGTACATCA 57.032 33.333 0.00 0.00 39.02 3.07
239 240 7.926018 AGTTTCAAGGTTTTTCCATTGTACATC 59.074 33.333 0.00 0.00 39.02 3.06
240 241 7.791029 AGTTTCAAGGTTTTTCCATTGTACAT 58.209 30.769 0.00 0.00 39.02 2.29
241 242 7.176589 AGTTTCAAGGTTTTTCCATTGTACA 57.823 32.000 0.00 0.00 39.02 2.90
242 243 7.465379 GCAAGTTTCAAGGTTTTTCCATTGTAC 60.465 37.037 0.00 0.00 39.02 2.90
243 244 6.536941 GCAAGTTTCAAGGTTTTTCCATTGTA 59.463 34.615 0.00 0.00 39.02 2.41
244 245 5.353956 GCAAGTTTCAAGGTTTTTCCATTGT 59.646 36.000 0.00 0.00 39.02 2.71
245 246 5.353678 TGCAAGTTTCAAGGTTTTTCCATTG 59.646 36.000 0.00 0.00 39.02 2.82
246 247 5.353956 GTGCAAGTTTCAAGGTTTTTCCATT 59.646 36.000 0.00 0.00 39.02 3.16
247 248 4.875536 GTGCAAGTTTCAAGGTTTTTCCAT 59.124 37.500 0.00 0.00 39.02 3.41
248 249 4.249661 GTGCAAGTTTCAAGGTTTTTCCA 58.750 39.130 0.00 0.00 39.02 3.53
249 250 3.621268 GGTGCAAGTTTCAAGGTTTTTCC 59.379 43.478 0.00 0.00 0.00 3.13
250 251 4.249661 TGGTGCAAGTTTCAAGGTTTTTC 58.750 39.130 0.00 0.00 0.00 2.29
251 252 4.278975 TGGTGCAAGTTTCAAGGTTTTT 57.721 36.364 0.00 0.00 0.00 1.94
252 253 3.971245 TGGTGCAAGTTTCAAGGTTTT 57.029 38.095 0.00 0.00 0.00 2.43
253 254 3.971245 TTGGTGCAAGTTTCAAGGTTT 57.029 38.095 0.00 0.00 0.00 3.27
254 255 3.260632 ACTTTGGTGCAAGTTTCAAGGTT 59.739 39.130 0.00 0.00 0.00 3.50
255 256 2.831526 ACTTTGGTGCAAGTTTCAAGGT 59.168 40.909 0.00 0.00 0.00 3.50
256 257 3.131046 AGACTTTGGTGCAAGTTTCAAGG 59.869 43.478 0.00 0.00 0.00 3.61
257 258 4.376340 AGACTTTGGTGCAAGTTTCAAG 57.624 40.909 0.00 0.00 0.00 3.02
258 259 5.359576 ACATAGACTTTGGTGCAAGTTTCAA 59.640 36.000 0.00 0.00 0.00 2.69
259 260 4.887071 ACATAGACTTTGGTGCAAGTTTCA 59.113 37.500 0.00 0.00 0.00 2.69
260 261 5.438761 ACATAGACTTTGGTGCAAGTTTC 57.561 39.130 0.00 0.00 0.00 2.78
261 262 6.296026 TCTACATAGACTTTGGTGCAAGTTT 58.704 36.000 0.00 0.00 0.00 2.66
262 263 5.865085 TCTACATAGACTTTGGTGCAAGTT 58.135 37.500 0.00 0.00 0.00 2.66
263 264 5.246203 TCTCTACATAGACTTTGGTGCAAGT 59.754 40.000 0.00 0.00 0.00 3.16
264 265 5.724328 TCTCTACATAGACTTTGGTGCAAG 58.276 41.667 0.00 0.00 0.00 4.01
265 266 5.738619 TCTCTACATAGACTTTGGTGCAA 57.261 39.130 0.00 0.00 0.00 4.08
266 267 5.738619 TTCTCTACATAGACTTTGGTGCA 57.261 39.130 0.00 0.00 0.00 4.57
267 268 7.617041 ATTTTCTCTACATAGACTTTGGTGC 57.383 36.000 0.00 0.00 0.00 5.01
298 299 9.816354 ACAGCAAACTAATACAATTTCAACTTT 57.184 25.926 0.00 0.00 0.00 2.66
299 300 9.816354 AACAGCAAACTAATACAATTTCAACTT 57.184 25.926 0.00 0.00 0.00 2.66
300 301 9.816354 AAACAGCAAACTAATACAATTTCAACT 57.184 25.926 0.00 0.00 0.00 3.16
312 313 9.143155 CCCCCTAAATATAAACAGCAAACTAAT 57.857 33.333 0.00 0.00 0.00 1.73
313 314 8.528044 CCCCCTAAATATAAACAGCAAACTAA 57.472 34.615 0.00 0.00 0.00 2.24
354 355 1.002403 CCGGGGCCCCCTAATTTTT 59.998 57.895 36.13 0.00 42.67 1.94
355 356 1.301160 ATCCGGGGCCCCCTAATTTT 61.301 55.000 36.13 10.26 42.67 1.82
356 357 1.301160 AATCCGGGGCCCCCTAATTT 61.301 55.000 36.13 18.32 42.67 1.82
357 358 1.703597 AATCCGGGGCCCCCTAATT 60.704 57.895 36.13 26.55 42.67 1.40
358 359 2.037677 AATCCGGGGCCCCCTAAT 60.038 61.111 36.13 22.36 42.67 1.73
359 360 1.975758 TAGAATCCGGGGCCCCCTAA 61.976 60.000 36.13 21.01 42.67 2.69
360 361 2.396651 CTAGAATCCGGGGCCCCCTA 62.397 65.000 36.13 26.49 42.67 3.53
361 362 3.786257 TAGAATCCGGGGCCCCCT 61.786 66.667 36.13 26.82 42.67 4.79
362 363 3.249961 CTAGAATCCGGGGCCCCC 61.250 72.222 36.13 20.88 41.09 5.40
363 364 1.642513 AAACTAGAATCCGGGGCCCC 61.643 60.000 33.22 33.22 0.00 5.80
364 365 0.257905 AAAACTAGAATCCGGGGCCC 59.742 55.000 15.76 15.76 0.00 5.80
365 366 1.389555 CAAAACTAGAATCCGGGGCC 58.610 55.000 0.00 0.00 0.00 5.80
366 367 0.738975 GCAAAACTAGAATCCGGGGC 59.261 55.000 0.00 0.00 0.00 5.80
367 368 1.389555 GGCAAAACTAGAATCCGGGG 58.610 55.000 0.00 0.00 0.00 5.73
368 369 1.389555 GGGCAAAACTAGAATCCGGG 58.610 55.000 0.00 0.00 0.00 5.73
369 370 1.389555 GGGGCAAAACTAGAATCCGG 58.610 55.000 0.00 0.00 0.00 5.14
370 371 1.014352 CGGGGCAAAACTAGAATCCG 58.986 55.000 0.00 0.00 0.00 4.18
371 372 1.389555 CCGGGGCAAAACTAGAATCC 58.610 55.000 0.00 0.00 0.00 3.01
372 373 1.389555 CCCGGGGCAAAACTAGAATC 58.610 55.000 14.71 0.00 0.00 2.52
373 374 3.588742 CCCGGGGCAAAACTAGAAT 57.411 52.632 14.71 0.00 0.00 2.40
389 390 2.361230 CTCAGTTTTCGGGGGCCC 60.361 66.667 15.76 15.76 0.00 5.80
390 391 2.361230 CCTCAGTTTTCGGGGGCC 60.361 66.667 0.00 0.00 0.00 5.80
391 392 1.674651 GTCCTCAGTTTTCGGGGGC 60.675 63.158 0.00 0.00 35.58 5.80
392 393 1.002502 GGTCCTCAGTTTTCGGGGG 60.003 63.158 0.00 0.00 36.97 5.40
393 394 1.375523 CGGTCCTCAGTTTTCGGGG 60.376 63.158 0.00 0.00 0.00 5.73
394 395 1.375523 CCGGTCCTCAGTTTTCGGG 60.376 63.158 0.00 0.00 34.54 5.14
395 396 2.033194 GCCGGTCCTCAGTTTTCGG 61.033 63.158 1.90 0.00 40.33 4.30
396 397 2.033194 GGCCGGTCCTCAGTTTTCG 61.033 63.158 1.90 0.00 0.00 3.46
397 398 1.674651 GGGCCGGTCCTCAGTTTTC 60.675 63.158 20.78 0.00 34.39 2.29
398 399 2.154074 AGGGCCGGTCCTCAGTTTT 61.154 57.895 25.80 0.00 29.56 2.43
399 400 2.529389 AGGGCCGGTCCTCAGTTT 60.529 61.111 25.80 0.00 29.56 2.66
400 401 3.322466 CAGGGCCGGTCCTCAGTT 61.322 66.667 29.09 0.00 34.31 3.16
401 402 4.640690 ACAGGGCCGGTCCTCAGT 62.641 66.667 29.09 19.66 34.31 3.41
402 403 3.775654 GACAGGGCCGGTCCTCAG 61.776 72.222 29.09 18.85 34.31 3.35
403 404 4.316823 AGACAGGGCCGGTCCTCA 62.317 66.667 29.09 0.00 35.89 3.86
404 405 3.775654 CAGACAGGGCCGGTCCTC 61.776 72.222 29.09 16.57 35.89 3.71
405 406 4.640690 ACAGACAGGGCCGGTCCT 62.641 66.667 29.49 25.80 35.89 3.85
406 407 3.637273 AACAGACAGGGCCGGTCC 61.637 66.667 29.49 20.43 35.89 4.46
407 408 2.358737 CAACAGACAGGGCCGGTC 60.359 66.667 26.71 26.71 35.50 4.79
408 409 3.953775 CCAACAGACAGGGCCGGT 61.954 66.667 9.72 9.72 0.00 5.28
409 410 4.722700 CCCAACAGACAGGGCCGG 62.723 72.222 0.79 0.79 38.44 6.13
410 411 3.190738 TTCCCAACAGACAGGGCCG 62.191 63.158 0.00 0.00 45.07 6.13
411 412 1.303643 CTTCCCAACAGACAGGGCC 60.304 63.158 0.00 0.00 45.07 5.80
412 413 0.178990 AACTTCCCAACAGACAGGGC 60.179 55.000 0.00 0.00 45.07 5.19
413 414 2.364972 AAACTTCCCAACAGACAGGG 57.635 50.000 0.00 0.00 46.90 4.45
414 415 4.398319 ACATAAACTTCCCAACAGACAGG 58.602 43.478 0.00 0.00 0.00 4.00
415 416 8.041323 AGTATACATAAACTTCCCAACAGACAG 58.959 37.037 5.50 0.00 0.00 3.51
416 417 7.822334 CAGTATACATAAACTTCCCAACAGACA 59.178 37.037 5.50 0.00 0.00 3.41
417 418 7.201617 GCAGTATACATAAACTTCCCAACAGAC 60.202 40.741 5.50 0.00 0.00 3.51
459 460 1.335145 ATTCACAGCCTGCAAGCTTT 58.665 45.000 7.19 0.00 42.61 3.51
480 481 4.202367 ACCTGACTTGGTTTCTTAGACCTG 60.202 45.833 0.00 0.00 36.89 4.00
512 513 3.241067 AGCGCTTGAAATGAATGCATT 57.759 38.095 12.83 12.83 46.35 3.56
586 589 2.565046 TGAATCTGACATGCACCACA 57.435 45.000 0.00 0.00 0.00 4.17
607 610 4.273622 CACGCATGCACGCATTAG 57.726 55.556 19.57 0.50 33.90 1.73
641 644 1.070758 CATACCTTCGCTGCCATAGGT 59.929 52.381 16.11 16.11 43.23 3.08
644 647 0.599991 CGCATACCTTCGCTGCCATA 60.600 55.000 0.00 0.00 32.24 2.74
645 648 1.889105 CGCATACCTTCGCTGCCAT 60.889 57.895 0.00 0.00 32.24 4.40
652 655 1.472276 GACGAGCACGCATACCTTCG 61.472 60.000 2.62 0.00 43.96 3.79
662 665 1.063806 CTGAAAGAAGGACGAGCACG 58.936 55.000 0.76 0.76 40.58 5.34
663 666 0.793250 GCTGAAAGAAGGACGAGCAC 59.207 55.000 0.00 0.00 34.07 4.40
664 667 0.392706 TGCTGAAAGAAGGACGAGCA 59.607 50.000 0.00 0.00 34.07 4.26
665 668 1.195674 GTTGCTGAAAGAAGGACGAGC 59.804 52.381 0.00 0.00 34.07 5.03
666 669 2.478134 CAGTTGCTGAAAGAAGGACGAG 59.522 50.000 0.00 0.00 34.07 4.18
667 670 2.102420 TCAGTTGCTGAAAGAAGGACGA 59.898 45.455 0.00 0.00 37.57 4.20
668 671 2.221981 GTCAGTTGCTGAAAGAAGGACG 59.778 50.000 0.00 0.00 42.46 4.79
671 679 3.629398 ACTTGTCAGTTGCTGAAAGAAGG 59.371 43.478 18.46 4.99 42.46 3.46
694 702 0.532573 TCTGCAAGAGGAGCCTTACG 59.467 55.000 0.00 0.00 38.67 3.18
744 765 4.565564 AGTCGTAACAGAAACACAAGTCAC 59.434 41.667 0.00 0.00 0.00 3.67
843 874 4.042062 TGAAAGTGACACCATTGGAGATCT 59.958 41.667 10.37 0.00 0.00 2.75
844 875 4.326826 TGAAAGTGACACCATTGGAGATC 58.673 43.478 10.37 4.32 0.00 2.75
878 937 1.134438 GGAGGGAAGTGGGGTTGAGT 61.134 60.000 0.00 0.00 0.00 3.41
882 941 3.647771 GCGGAGGGAAGTGGGGTT 61.648 66.667 0.00 0.00 0.00 4.11
883 942 4.658786 AGCGGAGGGAAGTGGGGT 62.659 66.667 0.00 0.00 0.00 4.95
884 943 3.787001 GAGCGGAGGGAAGTGGGG 61.787 72.222 0.00 0.00 0.00 4.96
885 944 3.787001 GGAGCGGAGGGAAGTGGG 61.787 72.222 0.00 0.00 0.00 4.61
886 945 3.003173 TGGAGCGGAGGGAAGTGG 61.003 66.667 0.00 0.00 0.00 4.00
887 946 1.831652 AAGTGGAGCGGAGGGAAGTG 61.832 60.000 0.00 0.00 0.00 3.16
888 947 1.536662 AAGTGGAGCGGAGGGAAGT 60.537 57.895 0.00 0.00 0.00 3.01
889 948 1.078848 CAAGTGGAGCGGAGGGAAG 60.079 63.158 0.00 0.00 0.00 3.46
890 949 2.592993 CCAAGTGGAGCGGAGGGAA 61.593 63.158 0.00 0.00 37.39 3.97
891 950 3.003173 CCAAGTGGAGCGGAGGGA 61.003 66.667 0.00 0.00 37.39 4.20
892 951 4.785453 GCCAAGTGGAGCGGAGGG 62.785 72.222 0.18 0.00 37.39 4.30
899 958 2.187946 CCTAGGCGCCAAGTGGAG 59.812 66.667 31.54 14.63 37.39 3.86
900 959 4.096003 GCCTAGGCGCCAAGTGGA 62.096 66.667 31.54 5.06 37.39 4.02
1122 1207 1.390565 ACTACTCGAGTCGGGATTGG 58.609 55.000 23.89 1.60 29.95 3.16
1128 1213 3.931468 TGAAGTTCTACTACTCGAGTCGG 59.069 47.826 23.89 18.10 39.81 4.79
1161 1253 0.547553 TGGCATGGCAGCAGATTAGA 59.452 50.000 19.43 0.00 35.83 2.10
1230 1343 2.691011 GGAGTAGTAGTTCAGCCTCAGG 59.309 54.545 0.00 0.00 0.00 3.86
2178 3378 3.636929 TTAGTGCCCCATGCCACGG 62.637 63.158 0.00 0.00 40.16 4.94
2185 3385 6.324770 CCTCTGAATTATTTTTAGTGCCCCAT 59.675 38.462 0.00 0.00 0.00 4.00
2230 3662 0.455464 CCAAGCACGCACACATGATG 60.455 55.000 0.00 0.00 0.00 3.07
2323 3777 2.423892 TGTTGCAGCCGTTGAAAACTAA 59.576 40.909 0.00 0.00 46.99 2.24
2336 3790 3.631145 TTGAGATTTCAGTGTTGCAGC 57.369 42.857 0.00 0.00 34.15 5.25
2481 5734 7.907214 TTTCTGCAGAGAAACTTTATCCTAC 57.093 36.000 17.43 0.00 42.23 3.18
2489 5742 4.016444 TGGTGTTTTCTGCAGAGAAACTT 58.984 39.130 31.48 0.00 45.90 2.66
2555 5808 3.975168 AATAGCACTTAACACGGTCCT 57.025 42.857 0.00 0.00 0.00 3.85
2724 6030 1.752753 CGAGAGAGAGCAACATAGCG 58.247 55.000 0.00 0.00 40.15 4.26
2876 6236 2.498885 ACGCTAACCCTAACCCTAACTG 59.501 50.000 0.00 0.00 0.00 3.16
3002 6370 1.072965 CAACTCAGTCTCAGGGCCTTT 59.927 52.381 1.32 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.