Multiple sequence alignment - TraesCS6A01G221800

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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 TraesCS6A01G221800 chr6A 100.000 1802 0 0 922 2723 412849571 412847770 0.000000e+00 3328.0
1 TraesCS6A01G221800 chr6A 84.369 499 71 5 2213 2706 6721262 6720766 1.470000e-132 483.0
2 TraesCS6A01G221800 chr6A 100.000 202 0 0 1 202 412850492 412850291 9.210000e-100 374.0
3 TraesCS6A01G221800 chr6A 97.500 80 2 0 1477 1556 428779 428700 1.310000e-28 137.0
4 TraesCS6A01G221800 chr6B 93.739 559 17 5 922 1480 469707819 469707279 0.000000e+00 822.0
5 TraesCS6A01G221800 chr6B 93.273 550 28 8 1575 2122 469707257 469706715 0.000000e+00 802.0
6 TraesCS6A01G221800 chr6B 91.765 510 38 3 2218 2723 469706379 469705870 0.000000e+00 706.0
7 TraesCS6A01G221800 chr7D 83.066 685 90 11 2044 2706 442765920 442765240 1.400000e-167 599.0
8 TraesCS6A01G221800 chr6D 92.765 387 17 8 1564 1945 303981773 303981393 1.430000e-152 549.0
9 TraesCS6A01G221800 chr6D 87.500 376 30 9 1106 1480 303982136 303981777 4.190000e-113 418.0
10 TraesCS6A01G221800 chr6D 92.694 219 15 1 1951 2169 303981305 303981088 5.660000e-82 315.0
11 TraesCS6A01G221800 chr6D 91.026 234 17 3 2493 2722 303978886 303978653 2.040000e-81 313.0
12 TraesCS6A01G221800 chr6D 86.195 297 24 8 2165 2444 303979186 303978890 3.410000e-79 305.0
13 TraesCS6A01G221800 chr6D 95.000 120 5 1 992 1110 303982317 303982198 1.290000e-43 187.0
14 TraesCS6A01G221800 chr1B 81.129 620 97 13 2048 2652 424417191 424416577 1.900000e-131 479.0
15 TraesCS6A01G221800 chr2A 82.872 397 62 4 2322 2713 755025093 755025488 4.310000e-93 351.0
16 TraesCS6A01G221800 chr2A 92.473 93 5 1 1472 1562 722077294 722077202 6.120000e-27 132.0
17 TraesCS6A01G221800 chr2A 91.579 95 5 2 1471 1562 632953001 632952907 7.910000e-26 128.0
18 TraesCS6A01G221800 chr2A 88.462 78 9 0 1393 1470 620212897 620212820 8.030000e-16 95.3
19 TraesCS6A01G221800 chrUn 100.000 155 0 0 922 1076 453558224 453558378 1.230000e-73 287.0
20 TraesCS6A01G221800 chr2D 95.402 87 2 1 1478 1562 643235908 643235822 1.310000e-28 137.0
21 TraesCS6A01G221800 chr2B 94.382 89 3 1 1476 1562 354879123 354879211 4.730000e-28 135.0
22 TraesCS6A01G221800 chr2B 92.391 92 6 1 1466 1556 337084144 337084235 2.200000e-26 130.0
23 TraesCS6A01G221800 chr2B 87.179 78 10 0 1393 1470 559553993 559553916 3.730000e-14 89.8
24 TraesCS6A01G221800 chr3D 92.391 92 5 1 1475 1564 22679057 22679148 2.200000e-26 130.0
25 TraesCS6A01G221800 chr3D 93.258 89 4 1 1478 1564 22767898 22767810 2.200000e-26 130.0
26 TraesCS6A01G221800 chr3D 91.579 95 5 3 1477 1568 6467314 6467408 7.910000e-26 128.0


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 TraesCS6A01G221800 chr6A 412847770 412850492 2722 True 1851.000000 3328 100.000000 1 2723 2 chr6A.!!$R3 2722
1 TraesCS6A01G221800 chr6B 469705870 469707819 1949 True 776.666667 822 92.925667 922 2723 3 chr6B.!!$R1 1801
2 TraesCS6A01G221800 chr7D 442765240 442765920 680 True 599.000000 599 83.066000 2044 2706 1 chr7D.!!$R1 662
3 TraesCS6A01G221800 chr6D 303978653 303982317 3664 True 347.833333 549 90.863333 992 2722 6 chr6D.!!$R1 1730
4 TraesCS6A01G221800 chr1B 424416577 424417191 614 True 479.000000 479 81.129000 2048 2652 1 chr1B.!!$R1 604

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
132 133 0.038744 AGAGGCTGGGGTTTGACATG 59.961 55.0 0.0 0.0 0.0 3.21 F
1298 1367 0.250166 AAGGTCAAGGTGCGTGGTAC 60.250 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 1681 0.104120 AAACAAGAAAAGGCACCGGC 59.896 50.0 0.0 0.0 40.13 6.13 R
2671 5025 0.038744 ACATCTCCACCAAGCCAAGG 59.961 55.0 0.0 0.0 0.00 3.61 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
30 31 6.049955 TCCAGTAGGACAATAACCTTCAAG 57.950 41.667 0.00 0.00 39.61 3.02
31 32 5.783360 TCCAGTAGGACAATAACCTTCAAGA 59.217 40.000 0.00 0.00 39.61 3.02
32 33 6.443849 TCCAGTAGGACAATAACCTTCAAGAT 59.556 38.462 0.00 0.00 39.61 2.40
33 34 6.540189 CCAGTAGGACAATAACCTTCAAGATG 59.460 42.308 0.00 0.00 38.76 2.90
34 35 6.540189 CAGTAGGACAATAACCTTCAAGATGG 59.460 42.308 0.00 0.82 38.76 3.51
35 36 4.860022 AGGACAATAACCTTCAAGATGGG 58.140 43.478 6.90 0.00 33.55 4.00
36 37 3.381590 GGACAATAACCTTCAAGATGGGC 59.618 47.826 6.90 0.00 0.00 5.36
37 38 4.273318 GACAATAACCTTCAAGATGGGCT 58.727 43.478 6.90 0.00 0.00 5.19
38 39 4.019174 ACAATAACCTTCAAGATGGGCTG 58.981 43.478 6.90 1.81 0.00 4.85
39 40 2.128771 TAACCTTCAAGATGGGCTGC 57.871 50.000 6.90 0.00 0.00 5.25
40 41 0.962356 AACCTTCAAGATGGGCTGCG 60.962 55.000 6.90 0.00 0.00 5.18
41 42 1.078214 CCTTCAAGATGGGCTGCGA 60.078 57.895 0.00 0.00 0.00 5.10
42 43 0.465097 CCTTCAAGATGGGCTGCGAT 60.465 55.000 0.00 0.00 0.00 4.58
43 44 0.661552 CTTCAAGATGGGCTGCGATG 59.338 55.000 0.00 0.00 0.00 3.84
44 45 0.252761 TTCAAGATGGGCTGCGATGA 59.747 50.000 0.00 0.00 0.00 2.92
45 46 0.179065 TCAAGATGGGCTGCGATGAG 60.179 55.000 0.00 0.00 0.00 2.90
46 47 0.463295 CAAGATGGGCTGCGATGAGT 60.463 55.000 0.00 0.00 0.00 3.41
47 48 0.179062 AAGATGGGCTGCGATGAGTC 60.179 55.000 0.00 0.00 0.00 3.36
48 49 1.596477 GATGGGCTGCGATGAGTCC 60.596 63.158 0.00 0.00 38.32 3.85
49 50 3.002583 TGGGCTGCGATGAGTCCA 61.003 61.111 0.00 0.00 45.80 4.02
50 51 2.369633 TGGGCTGCGATGAGTCCAT 61.370 57.895 0.00 0.00 43.04 3.41
51 52 1.596477 GGGCTGCGATGAGTCCATC 60.596 63.158 0.00 0.00 44.38 3.51
57 58 4.018609 GATGAGTCCATCGCGGTG 57.981 61.111 13.72 13.72 39.70 4.94
58 59 1.592669 GATGAGTCCATCGCGGTGG 60.593 63.158 32.79 32.79 39.70 4.61
59 60 3.740128 ATGAGTCCATCGCGGTGGC 62.740 63.158 33.69 26.36 39.19 5.01
78 79 4.400961 GCAGACAGCGGAAGGCCT 62.401 66.667 0.00 0.00 45.17 5.19
79 80 2.125350 CAGACAGCGGAAGGCCTC 60.125 66.667 5.23 0.00 45.17 4.70
80 81 3.764466 AGACAGCGGAAGGCCTCG 61.764 66.667 5.23 7.81 45.17 4.63
81 82 3.760035 GACAGCGGAAGGCCTCGA 61.760 66.667 17.43 0.00 45.17 4.04
82 83 3.296709 GACAGCGGAAGGCCTCGAA 62.297 63.158 17.43 0.00 45.17 3.71
83 84 2.047274 CAGCGGAAGGCCTCGAAA 60.047 61.111 17.43 0.00 45.17 3.46
84 85 1.671054 CAGCGGAAGGCCTCGAAAA 60.671 57.895 17.43 0.00 45.17 2.29
85 86 1.026718 CAGCGGAAGGCCTCGAAAAT 61.027 55.000 17.43 0.00 45.17 1.82
86 87 1.026718 AGCGGAAGGCCTCGAAAATG 61.027 55.000 17.43 0.00 45.17 2.32
87 88 1.993369 GCGGAAGGCCTCGAAAATGG 61.993 60.000 17.43 0.00 34.80 3.16
88 89 0.392461 CGGAAGGCCTCGAAAATGGA 60.392 55.000 5.23 0.00 0.00 3.41
89 90 1.747206 CGGAAGGCCTCGAAAATGGAT 60.747 52.381 5.23 0.00 0.00 3.41
90 91 1.678101 GGAAGGCCTCGAAAATGGATG 59.322 52.381 5.23 0.00 0.00 3.51
91 92 1.678101 GAAGGCCTCGAAAATGGATGG 59.322 52.381 5.23 0.00 0.00 3.51
92 93 0.106519 AGGCCTCGAAAATGGATGGG 60.107 55.000 0.00 0.00 0.00 4.00
93 94 1.109323 GGCCTCGAAAATGGATGGGG 61.109 60.000 0.00 0.00 0.00 4.96
94 95 1.109323 GCCTCGAAAATGGATGGGGG 61.109 60.000 0.00 0.00 0.00 5.40
95 96 1.109323 CCTCGAAAATGGATGGGGGC 61.109 60.000 0.00 0.00 0.00 5.80
96 97 1.447317 CTCGAAAATGGATGGGGGCG 61.447 60.000 0.00 0.00 0.00 6.13
97 98 2.489275 CGAAAATGGATGGGGGCGG 61.489 63.158 0.00 0.00 0.00 6.13
98 99 2.763710 AAAATGGATGGGGGCGGC 60.764 61.111 0.00 0.00 0.00 6.53
117 118 1.160137 CGAAGCTTGGTGGAAAGAGG 58.840 55.000 2.10 0.00 0.00 3.69
118 119 0.884514 GAAGCTTGGTGGAAAGAGGC 59.115 55.000 2.10 0.00 0.00 4.70
119 120 0.480252 AAGCTTGGTGGAAAGAGGCT 59.520 50.000 0.00 0.00 0.00 4.58
120 121 0.251077 AGCTTGGTGGAAAGAGGCTG 60.251 55.000 0.00 0.00 0.00 4.85
121 122 1.246737 GCTTGGTGGAAAGAGGCTGG 61.247 60.000 0.00 0.00 0.00 4.85
122 123 0.610232 CTTGGTGGAAAGAGGCTGGG 60.610 60.000 0.00 0.00 0.00 4.45
123 124 2.080336 TTGGTGGAAAGAGGCTGGGG 62.080 60.000 0.00 0.00 0.00 4.96
124 125 2.539081 GGTGGAAAGAGGCTGGGGT 61.539 63.158 0.00 0.00 0.00 4.95
125 126 1.460699 GTGGAAAGAGGCTGGGGTT 59.539 57.895 0.00 0.00 0.00 4.11
126 127 0.178961 GTGGAAAGAGGCTGGGGTTT 60.179 55.000 0.00 0.00 0.00 3.27
127 128 0.178964 TGGAAAGAGGCTGGGGTTTG 60.179 55.000 0.00 0.00 0.00 2.93
128 129 0.112412 GGAAAGAGGCTGGGGTTTGA 59.888 55.000 0.00 0.00 0.00 2.69
129 130 1.248486 GAAAGAGGCTGGGGTTTGAC 58.752 55.000 0.00 0.00 0.00 3.18
130 131 0.555769 AAAGAGGCTGGGGTTTGACA 59.444 50.000 0.00 0.00 0.00 3.58
131 132 0.779997 AAGAGGCTGGGGTTTGACAT 59.220 50.000 0.00 0.00 0.00 3.06
132 133 0.038744 AGAGGCTGGGGTTTGACATG 59.961 55.000 0.00 0.00 0.00 3.21
133 134 0.967380 GAGGCTGGGGTTTGACATGG 60.967 60.000 0.00 0.00 0.00 3.66
134 135 1.984026 GGCTGGGGTTTGACATGGG 60.984 63.158 0.00 0.00 0.00 4.00
135 136 1.076549 GCTGGGGTTTGACATGGGA 59.923 57.895 0.00 0.00 0.00 4.37
136 137 0.541764 GCTGGGGTTTGACATGGGAA 60.542 55.000 0.00 0.00 0.00 3.97
137 138 1.256812 CTGGGGTTTGACATGGGAAC 58.743 55.000 0.00 0.00 0.00 3.62
146 147 3.135348 TTTGACATGGGAACAATGGCAAA 59.865 39.130 12.44 12.44 45.77 3.68
147 148 4.384537 TTTGACATGGGAACAATGGCAAAA 60.385 37.500 13.75 0.58 45.39 2.44
148 149 5.862846 TTTGACATGGGAACAATGGCAAAAA 60.863 36.000 13.75 0.00 45.39 1.94
149 150 7.139115 TTTGACATGGGAACAATGGCAAAAAT 61.139 34.615 13.75 0.00 45.39 1.82
150 151 8.555279 TTTGACATGGGAACAATGGCAAAAATT 61.555 33.333 13.75 0.00 45.39 1.82
155 156 6.537355 TGGGAACAATGGCAAAAATTTATCA 58.463 32.000 0.00 0.00 37.44 2.15
156 157 7.000472 TGGGAACAATGGCAAAAATTTATCAA 59.000 30.769 0.00 0.00 37.44 2.57
157 158 7.503566 TGGGAACAATGGCAAAAATTTATCAAA 59.496 29.630 0.00 0.00 37.44 2.69
158 159 8.522003 GGGAACAATGGCAAAAATTTATCAAAT 58.478 29.630 0.00 0.00 0.00 2.32
159 160 9.911138 GGAACAATGGCAAAAATTTATCAAATT 57.089 25.926 0.00 0.00 42.62 1.82
161 162 8.745464 ACAATGGCAAAAATTTATCAAATTGC 57.255 26.923 12.50 12.50 40.05 3.56
162 163 8.358148 ACAATGGCAAAAATTTATCAAATTGCA 58.642 25.926 19.32 9.82 40.05 4.08
163 164 9.360093 CAATGGCAAAAATTTATCAAATTGCAT 57.640 25.926 19.32 11.14 40.05 3.96
164 165 8.918961 ATGGCAAAAATTTATCAAATTGCATG 57.081 26.923 19.32 0.00 40.05 4.06
165 166 7.313646 TGGCAAAAATTTATCAAATTGCATGG 58.686 30.769 19.32 0.00 40.05 3.66
166 167 6.752815 GGCAAAAATTTATCAAATTGCATGGG 59.247 34.615 19.32 0.00 40.05 4.00
167 168 6.253942 GCAAAAATTTATCAAATTGCATGGGC 59.746 34.615 14.95 0.00 40.05 5.36
168 169 6.453926 AAAATTTATCAAATTGCATGGGCC 57.546 33.333 0.00 0.00 40.05 5.80
169 170 2.886862 TTATCAAATTGCATGGGCCG 57.113 45.000 0.00 0.00 40.13 6.13
170 171 0.388659 TATCAAATTGCATGGGCCGC 59.611 50.000 0.00 0.00 40.13 6.53
171 172 1.332144 ATCAAATTGCATGGGCCGCT 61.332 50.000 0.00 0.00 40.13 5.52
172 173 1.812093 CAAATTGCATGGGCCGCTG 60.812 57.895 0.00 0.00 40.13 5.18
173 174 1.983481 AAATTGCATGGGCCGCTGA 60.983 52.632 9.87 0.00 40.13 4.26
174 175 1.332144 AAATTGCATGGGCCGCTGAT 61.332 50.000 9.87 0.00 40.13 2.90
175 176 2.023414 AATTGCATGGGCCGCTGATG 62.023 55.000 9.87 3.78 40.13 3.07
178 179 3.214123 CATGGGCCGCTGATGGTG 61.214 66.667 0.00 0.00 0.00 4.17
179 180 3.731728 ATGGGCCGCTGATGGTGT 61.732 61.111 0.00 0.00 0.00 4.16
180 181 3.286694 ATGGGCCGCTGATGGTGTT 62.287 57.895 0.00 0.00 0.00 3.32
181 182 2.676471 GGGCCGCTGATGGTGTTT 60.676 61.111 0.00 0.00 0.00 2.83
182 183 2.275380 GGGCCGCTGATGGTGTTTT 61.275 57.895 0.00 0.00 0.00 2.43
183 184 1.080569 GGCCGCTGATGGTGTTTTG 60.081 57.895 0.00 0.00 0.00 2.44
184 185 1.080569 GCCGCTGATGGTGTTTTGG 60.081 57.895 0.00 0.00 0.00 3.28
185 186 1.523154 GCCGCTGATGGTGTTTTGGA 61.523 55.000 0.00 0.00 0.00 3.53
186 187 1.176527 CCGCTGATGGTGTTTTGGAT 58.823 50.000 0.00 0.00 0.00 3.41
187 188 1.135315 CCGCTGATGGTGTTTTGGATG 60.135 52.381 0.00 0.00 0.00 3.51
188 189 1.135315 CGCTGATGGTGTTTTGGATGG 60.135 52.381 0.00 0.00 0.00 3.51
189 190 1.205417 GCTGATGGTGTTTTGGATGGG 59.795 52.381 0.00 0.00 0.00 4.00
190 191 1.205417 CTGATGGTGTTTTGGATGGGC 59.795 52.381 0.00 0.00 0.00 5.36
191 192 0.536724 GATGGTGTTTTGGATGGGCC 59.463 55.000 0.00 0.00 37.10 5.80
192 193 0.909133 ATGGTGTTTTGGATGGGCCC 60.909 55.000 17.59 17.59 34.97 5.80
193 194 2.645192 GGTGTTTTGGATGGGCCCG 61.645 63.158 19.37 0.00 34.97 6.13
194 195 1.605165 GTGTTTTGGATGGGCCCGA 60.605 57.895 19.37 6.86 34.97 5.14
195 196 1.304052 TGTTTTGGATGGGCCCGAG 60.304 57.895 19.37 0.00 34.97 4.63
196 197 2.052104 GTTTTGGATGGGCCCGAGG 61.052 63.158 19.37 0.00 34.97 4.63
197 198 2.543797 TTTTGGATGGGCCCGAGGT 61.544 57.895 19.37 2.29 34.97 3.85
198 199 2.779742 TTTTGGATGGGCCCGAGGTG 62.780 60.000 19.37 0.00 34.97 4.00
1111 1169 4.254492 GGTACGCCTTTGATTTCTCTCTT 58.746 43.478 0.00 0.00 0.00 2.85
1127 1196 6.365970 TCTCTCTTTGTCTCTTTATTGGCT 57.634 37.500 0.00 0.00 0.00 4.75
1162 1231 9.295825 TCTTTTGGCATTTTTAGTATCTTCTGA 57.704 29.630 0.00 0.00 0.00 3.27
1190 1259 3.868077 ACGTATTTCTGATCTGCTTCTGC 59.132 43.478 0.00 0.00 40.20 4.26
1295 1364 0.535102 AAGAAGGTCAAGGTGCGTGG 60.535 55.000 0.00 0.00 0.00 4.94
1298 1367 0.250166 AAGGTCAAGGTGCGTGGTAC 60.250 55.000 0.00 0.00 0.00 3.34
1306 1375 3.975168 AGGTGCGTGGTACTCTATTTT 57.025 42.857 0.00 0.00 0.00 1.82
1307 1376 4.281898 AGGTGCGTGGTACTCTATTTTT 57.718 40.909 0.00 0.00 0.00 1.94
1354 1423 6.466812 CCCAGTGGCAATCTTAATTTCTTTT 58.533 36.000 2.61 0.00 0.00 2.27
1356 1425 6.128472 CCAGTGGCAATCTTAATTTCTTTTGC 60.128 38.462 0.00 0.00 38.90 3.68
1452 1521 2.599281 TCCTCGGAGAACGTGCCA 60.599 61.111 6.58 0.00 44.69 4.92
1455 1524 2.027625 CTCGGAGAACGTGCCAACC 61.028 63.158 0.00 0.00 44.69 3.77
1471 1540 1.833630 CAACCAGGATCAGCAGGTCTA 59.166 52.381 0.00 0.00 32.05 2.59
1480 1549 5.902431 AGGATCAGCAGGTCTAAATTCTACT 59.098 40.000 0.00 0.00 0.00 2.57
1481 1550 6.041523 AGGATCAGCAGGTCTAAATTCTACTC 59.958 42.308 0.00 0.00 0.00 2.59
1482 1551 5.599999 TCAGCAGGTCTAAATTCTACTCC 57.400 43.478 0.00 0.00 0.00 3.85
1483 1552 4.406003 TCAGCAGGTCTAAATTCTACTCCC 59.594 45.833 0.00 0.00 0.00 4.30
1484 1553 4.407296 CAGCAGGTCTAAATTCTACTCCCT 59.593 45.833 0.00 0.00 0.00 4.20
1485 1554 4.651962 AGCAGGTCTAAATTCTACTCCCTC 59.348 45.833 0.00 0.00 0.00 4.30
1486 1555 4.651962 GCAGGTCTAAATTCTACTCCCTCT 59.348 45.833 0.00 0.00 0.00 3.69
1487 1556 5.452636 GCAGGTCTAAATTCTACTCCCTCTG 60.453 48.000 0.00 0.00 0.00 3.35
1488 1557 5.659079 CAGGTCTAAATTCTACTCCCTCTGT 59.341 44.000 0.00 0.00 0.00 3.41
1489 1558 6.834451 CAGGTCTAAATTCTACTCCCTCTGTA 59.166 42.308 0.00 0.00 0.00 2.74
1490 1559 7.342284 CAGGTCTAAATTCTACTCCCTCTGTAA 59.658 40.741 0.00 0.00 0.00 2.41
1491 1560 7.899709 AGGTCTAAATTCTACTCCCTCTGTAAA 59.100 37.037 0.00 0.00 0.00 2.01
1492 1561 8.198778 GGTCTAAATTCTACTCCCTCTGTAAAG 58.801 40.741 0.00 0.00 0.00 1.85
1493 1562 8.968969 GTCTAAATTCTACTCCCTCTGTAAAGA 58.031 37.037 0.00 0.00 0.00 2.52
1494 1563 9.543231 TCTAAATTCTACTCCCTCTGTAAAGAA 57.457 33.333 0.00 0.00 0.00 2.52
1504 1573 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
1505 1574 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
1506 1575 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
1507 1576 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
1508 1577 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
1523 1592 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
1524 1593 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
1580 1649 1.470098 CTGCAATGTCCAAGTACTGCC 59.530 52.381 0.00 0.00 0.00 4.85
1582 1651 1.614317 GCAATGTCCAAGTACTGCCCT 60.614 52.381 0.00 0.00 0.00 5.19
1583 1652 2.355716 GCAATGTCCAAGTACTGCCCTA 60.356 50.000 0.00 0.00 0.00 3.53
1584 1653 3.685550 GCAATGTCCAAGTACTGCCCTAT 60.686 47.826 0.00 0.00 0.00 2.57
1585 1654 3.845781 ATGTCCAAGTACTGCCCTATG 57.154 47.619 0.00 0.00 0.00 2.23
1606 1680 3.763360 TGGGGAACTAGACGTCGATTAAA 59.237 43.478 10.46 0.00 0.00 1.52
1607 1681 4.142315 TGGGGAACTAGACGTCGATTAAAG 60.142 45.833 10.46 4.92 0.00 1.85
1626 1700 0.104120 GCCGGTGCCTTTTCTTGTTT 59.896 50.000 1.90 0.00 0.00 2.83
1627 1701 1.338655 GCCGGTGCCTTTTCTTGTTTA 59.661 47.619 1.90 0.00 0.00 2.01
1789 1865 2.964438 TTCGTTCACGCGTGCTTCCT 62.964 55.000 33.63 0.00 39.60 3.36
1842 1918 3.791245 AGAAGATCTCGAGTGAATTGCC 58.209 45.455 13.13 0.00 0.00 4.52
1871 1947 4.740268 AGGTGTTCTTCGTTTTTGGTTTC 58.260 39.130 0.00 0.00 0.00 2.78
1872 1948 4.218852 AGGTGTTCTTCGTTTTTGGTTTCA 59.781 37.500 0.00 0.00 0.00 2.69
1949 2025 1.493022 TGTGGCCTGTTCCTTACTTGT 59.507 47.619 3.32 0.00 0.00 3.16
2020 2177 5.221441 GGAAATTGAAGGCCTTAACAACAGT 60.221 40.000 20.54 5.60 0.00 3.55
2064 2221 2.033194 CGAGGCAGTTCCGTTTCCC 61.033 63.158 0.00 0.00 40.77 3.97
2139 2318 2.047179 GCCTTTCCTCCGCTCGTT 60.047 61.111 0.00 0.00 0.00 3.85
2142 2321 2.358247 TTTCCTCCGCTCGTTGCC 60.358 61.111 0.00 0.00 38.78 4.52
2146 2325 4.697756 CTCCGCTCGTTGCCCCAA 62.698 66.667 0.00 0.00 38.78 4.12
2229 4576 1.202758 TGTTCAGGTGCCGATGTCTTT 60.203 47.619 0.00 0.00 0.00 2.52
2252 4599 4.077108 GTCAGGAATAAAAGTTTCCGGGT 58.923 43.478 0.00 0.00 45.99 5.28
2417 4767 2.129607 GTCACGAAGCCGAAAGTGTTA 58.870 47.619 0.00 0.00 39.50 2.41
2431 4781 2.404559 AGTGTTAGTGTTGGAGGTGGA 58.595 47.619 0.00 0.00 0.00 4.02
2464 4814 3.305471 GCGGTGGTCTCATCTAAGGTATC 60.305 52.174 0.00 0.00 0.00 2.24
2488 4838 5.057149 GTGCACCTAGAGTTTCTTCAAAGA 58.943 41.667 5.22 0.00 0.00 2.52
2491 4841 5.934625 GCACCTAGAGTTTCTTCAAAGATGA 59.065 40.000 0.00 0.00 34.49 2.92
2508 4858 4.154942 AGATGAAAGATGGTTGCTGGTTT 58.845 39.130 0.00 0.00 0.00 3.27
2595 4945 1.739371 GCTCCGGTAGACAATCCACAC 60.739 57.143 0.00 0.00 0.00 3.82
2596 4946 0.528924 TCCGGTAGACAATCCACACG 59.471 55.000 0.00 0.00 0.00 4.49
2603 4957 1.289109 GACAATCCACACGGACACGG 61.289 60.000 0.00 0.00 46.79 4.94
2663 5017 3.656559 CAGTTTTGCTGCTATGGCTTTT 58.343 40.909 1.68 0.00 38.52 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.471815 TTGTCCTACTGGATCCGGAT 57.528 50.000 27.90 19.21 45.29 4.18
1 2 2.471815 ATTGTCCTACTGGATCCGGA 57.528 50.000 27.90 14.70 45.29 5.14
2 3 3.244112 GGTTATTGTCCTACTGGATCCGG 60.244 52.174 19.66 19.66 45.29 5.14
3 4 3.641906 AGGTTATTGTCCTACTGGATCCG 59.358 47.826 7.39 4.62 45.29 4.18
4 5 5.130477 TGAAGGTTATTGTCCTACTGGATCC 59.870 44.000 4.20 4.20 45.29 3.36
5 6 6.235231 TGAAGGTTATTGTCCTACTGGATC 57.765 41.667 0.00 0.00 45.29 3.36
6 7 6.443849 TCTTGAAGGTTATTGTCCTACTGGAT 59.556 38.462 0.00 0.00 45.29 3.41
7 8 5.783360 TCTTGAAGGTTATTGTCCTACTGGA 59.217 40.000 0.00 0.00 40.69 3.86
8 9 6.049955 TCTTGAAGGTTATTGTCCTACTGG 57.950 41.667 0.00 0.00 34.56 4.00
9 10 6.540189 CCATCTTGAAGGTTATTGTCCTACTG 59.460 42.308 0.00 0.00 34.56 2.74
10 11 6.353082 CCCATCTTGAAGGTTATTGTCCTACT 60.353 42.308 0.00 0.00 34.56 2.57
11 12 5.823045 CCCATCTTGAAGGTTATTGTCCTAC 59.177 44.000 0.00 0.00 34.56 3.18
12 13 5.631481 GCCCATCTTGAAGGTTATTGTCCTA 60.631 44.000 0.00 0.00 34.56 2.94
13 14 4.860022 CCCATCTTGAAGGTTATTGTCCT 58.140 43.478 0.00 0.00 36.81 3.85
14 15 3.381590 GCCCATCTTGAAGGTTATTGTCC 59.618 47.826 0.00 0.00 0.00 4.02
15 16 4.096984 CAGCCCATCTTGAAGGTTATTGTC 59.903 45.833 0.00 0.00 0.00 3.18
16 17 4.019174 CAGCCCATCTTGAAGGTTATTGT 58.981 43.478 0.00 0.00 0.00 2.71
17 18 3.181483 GCAGCCCATCTTGAAGGTTATTG 60.181 47.826 0.00 0.00 0.00 1.90
18 19 3.026694 GCAGCCCATCTTGAAGGTTATT 58.973 45.455 0.00 0.00 0.00 1.40
19 20 2.659428 GCAGCCCATCTTGAAGGTTAT 58.341 47.619 0.00 0.00 0.00 1.89
20 21 1.678728 CGCAGCCCATCTTGAAGGTTA 60.679 52.381 0.00 0.00 0.00 2.85
21 22 0.962356 CGCAGCCCATCTTGAAGGTT 60.962 55.000 0.00 0.00 0.00 3.50
22 23 1.377725 CGCAGCCCATCTTGAAGGT 60.378 57.895 0.00 0.00 0.00 3.50
23 24 0.465097 ATCGCAGCCCATCTTGAAGG 60.465 55.000 0.00 0.00 0.00 3.46
24 25 0.661552 CATCGCAGCCCATCTTGAAG 59.338 55.000 0.00 0.00 0.00 3.02
25 26 0.252761 TCATCGCAGCCCATCTTGAA 59.747 50.000 0.00 0.00 0.00 2.69
26 27 0.179065 CTCATCGCAGCCCATCTTGA 60.179 55.000 0.00 0.00 0.00 3.02
27 28 0.463295 ACTCATCGCAGCCCATCTTG 60.463 55.000 0.00 0.00 0.00 3.02
28 29 0.179062 GACTCATCGCAGCCCATCTT 60.179 55.000 0.00 0.00 0.00 2.40
29 30 1.445095 GACTCATCGCAGCCCATCT 59.555 57.895 0.00 0.00 0.00 2.90
30 31 1.596477 GGACTCATCGCAGCCCATC 60.596 63.158 0.00 0.00 0.00 3.51
31 32 1.703014 ATGGACTCATCGCAGCCCAT 61.703 55.000 0.00 0.00 0.00 4.00
32 33 2.315781 GATGGACTCATCGCAGCCCA 62.316 60.000 0.00 0.00 40.15 5.36
33 34 1.596477 GATGGACTCATCGCAGCCC 60.596 63.158 0.00 0.00 40.15 5.19
34 35 4.040068 GATGGACTCATCGCAGCC 57.960 61.111 0.00 0.00 40.15 4.85
40 41 1.592669 CCACCGCGATGGACTCATC 60.593 63.158 16.88 0.00 43.02 2.92
41 42 2.501128 CCACCGCGATGGACTCAT 59.499 61.111 16.88 0.00 43.02 2.90
42 43 4.451150 GCCACCGCGATGGACTCA 62.451 66.667 27.82 0.00 43.02 3.41
61 62 4.400961 AGGCCTTCCGCTGTCTGC 62.401 66.667 0.00 0.00 37.74 4.26
62 63 2.125350 GAGGCCTTCCGCTGTCTG 60.125 66.667 6.77 0.00 37.74 3.51
63 64 3.764466 CGAGGCCTTCCGCTGTCT 61.764 66.667 6.77 0.00 37.74 3.41
64 65 2.781595 TTTCGAGGCCTTCCGCTGTC 62.782 60.000 6.77 0.00 37.74 3.51
65 66 2.391724 TTTTCGAGGCCTTCCGCTGT 62.392 55.000 6.77 0.00 37.74 4.40
66 67 1.026718 ATTTTCGAGGCCTTCCGCTG 61.027 55.000 6.77 0.00 37.74 5.18
67 68 1.026718 CATTTTCGAGGCCTTCCGCT 61.027 55.000 6.77 0.00 37.74 5.52
68 69 1.429423 CATTTTCGAGGCCTTCCGC 59.571 57.895 6.77 0.00 37.47 5.54
69 70 0.392461 TCCATTTTCGAGGCCTTCCG 60.392 55.000 6.77 7.22 37.47 4.30
70 71 1.678101 CATCCATTTTCGAGGCCTTCC 59.322 52.381 6.77 0.00 0.00 3.46
71 72 1.678101 CCATCCATTTTCGAGGCCTTC 59.322 52.381 6.77 0.00 0.00 3.46
72 73 1.686115 CCCATCCATTTTCGAGGCCTT 60.686 52.381 6.77 0.00 0.00 4.35
73 74 0.106519 CCCATCCATTTTCGAGGCCT 60.107 55.000 3.86 3.86 0.00 5.19
74 75 1.109323 CCCCATCCATTTTCGAGGCC 61.109 60.000 0.00 0.00 0.00 5.19
75 76 1.109323 CCCCCATCCATTTTCGAGGC 61.109 60.000 0.00 0.00 0.00 4.70
76 77 1.109323 GCCCCCATCCATTTTCGAGG 61.109 60.000 0.00 0.00 0.00 4.63
77 78 1.447317 CGCCCCCATCCATTTTCGAG 61.447 60.000 0.00 0.00 0.00 4.04
78 79 1.453015 CGCCCCCATCCATTTTCGA 60.453 57.895 0.00 0.00 0.00 3.71
79 80 2.489275 CCGCCCCCATCCATTTTCG 61.489 63.158 0.00 0.00 0.00 3.46
80 81 2.796193 GCCGCCCCCATCCATTTTC 61.796 63.158 0.00 0.00 0.00 2.29
81 82 2.763710 GCCGCCCCCATCCATTTT 60.764 61.111 0.00 0.00 0.00 1.82
95 96 2.187599 CTTTCCACCAAGCTTCGCCG 62.188 60.000 0.00 0.00 0.00 6.46
96 97 0.889186 TCTTTCCACCAAGCTTCGCC 60.889 55.000 0.00 0.00 0.00 5.54
97 98 0.519077 CTCTTTCCACCAAGCTTCGC 59.481 55.000 0.00 0.00 0.00 4.70
98 99 1.160137 CCTCTTTCCACCAAGCTTCG 58.840 55.000 0.00 0.00 0.00 3.79
99 100 0.884514 GCCTCTTTCCACCAAGCTTC 59.115 55.000 0.00 0.00 0.00 3.86
100 101 0.480252 AGCCTCTTTCCACCAAGCTT 59.520 50.000 0.00 0.00 0.00 3.74
101 102 0.251077 CAGCCTCTTTCCACCAAGCT 60.251 55.000 0.00 0.00 0.00 3.74
102 103 1.246737 CCAGCCTCTTTCCACCAAGC 61.247 60.000 0.00 0.00 0.00 4.01
103 104 0.610232 CCCAGCCTCTTTCCACCAAG 60.610 60.000 0.00 0.00 0.00 3.61
104 105 1.460255 CCCAGCCTCTTTCCACCAA 59.540 57.895 0.00 0.00 0.00 3.67
105 106 2.538141 CCCCAGCCTCTTTCCACCA 61.538 63.158 0.00 0.00 0.00 4.17
106 107 2.081585 AACCCCAGCCTCTTTCCACC 62.082 60.000 0.00 0.00 0.00 4.61
107 108 0.178961 AAACCCCAGCCTCTTTCCAC 60.179 55.000 0.00 0.00 0.00 4.02
108 109 0.178964 CAAACCCCAGCCTCTTTCCA 60.179 55.000 0.00 0.00 0.00 3.53
109 110 0.112412 TCAAACCCCAGCCTCTTTCC 59.888 55.000 0.00 0.00 0.00 3.13
110 111 1.248486 GTCAAACCCCAGCCTCTTTC 58.752 55.000 0.00 0.00 0.00 2.62
111 112 0.555769 TGTCAAACCCCAGCCTCTTT 59.444 50.000 0.00 0.00 0.00 2.52
112 113 0.779997 ATGTCAAACCCCAGCCTCTT 59.220 50.000 0.00 0.00 0.00 2.85
113 114 0.038744 CATGTCAAACCCCAGCCTCT 59.961 55.000 0.00 0.00 0.00 3.69
114 115 0.967380 CCATGTCAAACCCCAGCCTC 60.967 60.000 0.00 0.00 0.00 4.70
115 116 1.077265 CCATGTCAAACCCCAGCCT 59.923 57.895 0.00 0.00 0.00 4.58
116 117 1.984026 CCCATGTCAAACCCCAGCC 60.984 63.158 0.00 0.00 0.00 4.85
117 118 0.541764 TTCCCATGTCAAACCCCAGC 60.542 55.000 0.00 0.00 0.00 4.85
118 119 1.256812 GTTCCCATGTCAAACCCCAG 58.743 55.000 0.00 0.00 0.00 4.45
119 120 0.558220 TGTTCCCATGTCAAACCCCA 59.442 50.000 0.00 0.00 0.00 4.96
120 121 1.710816 TTGTTCCCATGTCAAACCCC 58.289 50.000 0.00 0.00 0.00 4.95
121 122 2.028203 CCATTGTTCCCATGTCAAACCC 60.028 50.000 0.00 0.00 0.00 4.11
122 123 2.612721 GCCATTGTTCCCATGTCAAACC 60.613 50.000 0.00 0.00 0.00 3.27
123 124 2.036992 TGCCATTGTTCCCATGTCAAAC 59.963 45.455 0.00 0.00 0.00 2.93
124 125 2.323599 TGCCATTGTTCCCATGTCAAA 58.676 42.857 0.00 0.00 0.00 2.69
125 126 2.006805 TGCCATTGTTCCCATGTCAA 57.993 45.000 0.00 0.00 0.00 3.18
126 127 2.006805 TTGCCATTGTTCCCATGTCA 57.993 45.000 0.00 0.00 0.00 3.58
127 128 3.399440 TTTTGCCATTGTTCCCATGTC 57.601 42.857 0.00 0.00 0.00 3.06
128 129 3.853355 TTTTTGCCATTGTTCCCATGT 57.147 38.095 0.00 0.00 0.00 3.21
129 130 5.708877 AAATTTTTGCCATTGTTCCCATG 57.291 34.783 0.00 0.00 0.00 3.66
130 131 7.173722 TGATAAATTTTTGCCATTGTTCCCAT 58.826 30.769 0.00 0.00 0.00 4.00
131 132 6.537355 TGATAAATTTTTGCCATTGTTCCCA 58.463 32.000 0.00 0.00 0.00 4.37
132 133 7.446001 TTGATAAATTTTTGCCATTGTTCCC 57.554 32.000 0.00 0.00 0.00 3.97
133 134 9.911138 AATTTGATAAATTTTTGCCATTGTTCC 57.089 25.926 0.00 0.00 37.84 3.62
135 136 9.194271 GCAATTTGATAAATTTTTGCCATTGTT 57.806 25.926 10.55 0.00 38.97 2.83
136 137 8.358148 TGCAATTTGATAAATTTTTGCCATTGT 58.642 25.926 16.42 0.00 38.97 2.71
137 138 8.744008 TGCAATTTGATAAATTTTTGCCATTG 57.256 26.923 16.42 11.64 38.97 2.82
138 139 9.360093 CATGCAATTTGATAAATTTTTGCCATT 57.640 25.926 16.42 3.71 38.97 3.16
139 140 7.976734 CCATGCAATTTGATAAATTTTTGCCAT 59.023 29.630 16.42 9.67 38.97 4.40
140 141 7.313646 CCATGCAATTTGATAAATTTTTGCCA 58.686 30.769 16.42 8.27 38.97 4.92
141 142 6.752815 CCCATGCAATTTGATAAATTTTTGCC 59.247 34.615 16.42 4.13 38.97 4.52
142 143 6.253942 GCCCATGCAATTTGATAAATTTTTGC 59.746 34.615 13.57 13.57 38.97 3.68
143 144 6.752815 GGCCCATGCAATTTGATAAATTTTTG 59.247 34.615 0.00 0.00 38.97 2.44
144 145 6.404513 CGGCCCATGCAATTTGATAAATTTTT 60.405 34.615 0.00 0.00 38.97 1.94
145 146 5.066246 CGGCCCATGCAATTTGATAAATTTT 59.934 36.000 0.00 0.00 38.97 1.82
146 147 4.575645 CGGCCCATGCAATTTGATAAATTT 59.424 37.500 0.00 0.00 38.97 1.82
147 148 4.128643 CGGCCCATGCAATTTGATAAATT 58.871 39.130 0.00 0.00 41.57 1.82
148 149 3.731089 CGGCCCATGCAATTTGATAAAT 58.269 40.909 0.00 0.00 40.13 1.40
149 150 2.741228 GCGGCCCATGCAATTTGATAAA 60.741 45.455 0.00 0.00 40.13 1.40
150 151 1.202510 GCGGCCCATGCAATTTGATAA 60.203 47.619 0.00 0.00 40.13 1.75
151 152 0.388659 GCGGCCCATGCAATTTGATA 59.611 50.000 0.00 0.00 40.13 2.15
152 153 1.144496 GCGGCCCATGCAATTTGAT 59.856 52.632 0.00 0.00 40.13 2.57
153 154 1.983481 AGCGGCCCATGCAATTTGA 60.983 52.632 0.00 0.00 40.13 2.69
154 155 1.812093 CAGCGGCCCATGCAATTTG 60.812 57.895 0.00 0.00 40.13 2.32
155 156 1.332144 ATCAGCGGCCCATGCAATTT 61.332 50.000 0.00 0.00 40.13 1.82
156 157 1.759299 ATCAGCGGCCCATGCAATT 60.759 52.632 0.00 0.00 40.13 2.32
157 158 2.123597 ATCAGCGGCCCATGCAAT 60.124 55.556 0.00 0.00 40.13 3.56
158 159 3.142162 CATCAGCGGCCCATGCAA 61.142 61.111 0.00 0.00 40.13 4.08
161 162 3.214123 CACCATCAGCGGCCCATG 61.214 66.667 0.00 0.00 0.00 3.66
162 163 2.786512 AAACACCATCAGCGGCCCAT 62.787 55.000 0.00 0.00 0.00 4.00
163 164 2.992817 AAAACACCATCAGCGGCCCA 62.993 55.000 0.00 0.00 0.00 5.36
164 165 2.275380 AAAACACCATCAGCGGCCC 61.275 57.895 0.00 0.00 0.00 5.80
165 166 1.080569 CAAAACACCATCAGCGGCC 60.081 57.895 0.00 0.00 0.00 6.13
166 167 1.080569 CCAAAACACCATCAGCGGC 60.081 57.895 0.00 0.00 0.00 6.53
167 168 1.135315 CATCCAAAACACCATCAGCGG 60.135 52.381 0.00 0.00 0.00 5.52
168 169 1.135315 CCATCCAAAACACCATCAGCG 60.135 52.381 0.00 0.00 0.00 5.18
169 170 1.205417 CCCATCCAAAACACCATCAGC 59.795 52.381 0.00 0.00 0.00 4.26
170 171 1.205417 GCCCATCCAAAACACCATCAG 59.795 52.381 0.00 0.00 0.00 2.90
171 172 1.265236 GCCCATCCAAAACACCATCA 58.735 50.000 0.00 0.00 0.00 3.07
172 173 0.536724 GGCCCATCCAAAACACCATC 59.463 55.000 0.00 0.00 34.01 3.51
173 174 0.909133 GGGCCCATCCAAAACACCAT 60.909 55.000 19.95 0.00 36.21 3.55
174 175 1.535202 GGGCCCATCCAAAACACCA 60.535 57.895 19.95 0.00 36.21 4.17
175 176 2.645192 CGGGCCCATCCAAAACACC 61.645 63.158 24.92 0.00 36.21 4.16
176 177 1.595093 CTCGGGCCCATCCAAAACAC 61.595 60.000 24.92 0.00 36.21 3.32
177 178 1.304052 CTCGGGCCCATCCAAAACA 60.304 57.895 24.92 0.00 36.21 2.83
178 179 2.052104 CCTCGGGCCCATCCAAAAC 61.052 63.158 24.92 0.00 36.21 2.43
179 180 2.358619 CCTCGGGCCCATCCAAAA 59.641 61.111 24.92 0.00 36.21 2.44
180 181 2.938798 ACCTCGGGCCCATCCAAA 60.939 61.111 24.92 0.00 36.21 3.28
181 182 3.727258 CACCTCGGGCCCATCCAA 61.727 66.667 24.92 0.00 36.21 3.53
1111 1169 9.109393 GATTACATACAGCCAATAAAGAGACAA 57.891 33.333 0.00 0.00 0.00 3.18
1157 1226 9.952188 CAGATCAGAAATACGTACTATTCAGAA 57.048 33.333 15.73 0.00 0.00 3.02
1162 1231 8.634444 AGAAGCAGATCAGAAATACGTACTATT 58.366 33.333 0.00 0.00 0.00 1.73
1190 1259 3.192922 GGACGCGATCCCCAAACG 61.193 66.667 15.93 0.00 42.46 3.60
1306 1375 5.067805 GCAGGAGTTTTGGAGAAGAAGAAAA 59.932 40.000 0.00 0.00 0.00 2.29
1307 1376 4.580580 GCAGGAGTTTTGGAGAAGAAGAAA 59.419 41.667 0.00 0.00 0.00 2.52
1308 1377 4.137543 GCAGGAGTTTTGGAGAAGAAGAA 58.862 43.478 0.00 0.00 0.00 2.52
1309 1378 3.496870 GGCAGGAGTTTTGGAGAAGAAGA 60.497 47.826 0.00 0.00 0.00 2.87
1345 1414 6.993902 AGATGTGATTTGTGGCAAAAGAAATT 59.006 30.769 0.00 0.00 0.00 1.82
1346 1415 6.527423 AGATGTGATTTGTGGCAAAAGAAAT 58.473 32.000 0.00 0.00 0.00 2.17
1354 1423 5.121611 CGTAAACTAGATGTGATTTGTGGCA 59.878 40.000 0.00 0.00 0.00 4.92
1356 1425 6.036083 CCTCGTAAACTAGATGTGATTTGTGG 59.964 42.308 0.00 0.00 0.00 4.17
1357 1426 6.455646 GCCTCGTAAACTAGATGTGATTTGTG 60.456 42.308 0.00 0.00 0.00 3.33
1358 1427 5.581085 GCCTCGTAAACTAGATGTGATTTGT 59.419 40.000 0.00 0.00 0.00 2.83
1408 1477 1.299648 CCACGGGGATCTGCTTCAA 59.700 57.895 0.00 0.00 35.59 2.69
1452 1521 2.254152 TAGACCTGCTGATCCTGGTT 57.746 50.000 0.00 0.00 37.20 3.67
1455 1524 5.033589 AGAATTTAGACCTGCTGATCCTG 57.966 43.478 0.00 0.00 0.00 3.86
1480 1549 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
1481 1550 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
1482 1551 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
1497 1566 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
1498 1567 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
1499 1568 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
1500 1569 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
1537 1606 9.525409 GCAGTACTCTCCGTAAAGAAATATAAA 57.475 33.333 0.00 0.00 0.00 1.40
1538 1607 8.689061 TGCAGTACTCTCCGTAAAGAAATATAA 58.311 33.333 0.00 0.00 0.00 0.98
1539 1608 8.229253 TGCAGTACTCTCCGTAAAGAAATATA 57.771 34.615 0.00 0.00 0.00 0.86
1540 1609 7.108841 TGCAGTACTCTCCGTAAAGAAATAT 57.891 36.000 0.00 0.00 0.00 1.28
1541 1610 6.519679 TGCAGTACTCTCCGTAAAGAAATA 57.480 37.500 0.00 0.00 0.00 1.40
1542 1611 5.401531 TGCAGTACTCTCCGTAAAGAAAT 57.598 39.130 0.00 0.00 0.00 2.17
1543 1612 4.859304 TGCAGTACTCTCCGTAAAGAAA 57.141 40.909 0.00 0.00 0.00 2.52
1544 1613 4.859304 TTGCAGTACTCTCCGTAAAGAA 57.141 40.909 0.00 0.00 0.00 2.52
1545 1614 4.219944 ACATTGCAGTACTCTCCGTAAAGA 59.780 41.667 0.00 0.00 0.00 2.52
1546 1615 4.495422 ACATTGCAGTACTCTCCGTAAAG 58.505 43.478 0.00 0.00 0.00 1.85
1547 1616 4.491676 GACATTGCAGTACTCTCCGTAAA 58.508 43.478 0.00 0.00 0.00 2.01
1548 1617 3.119245 GGACATTGCAGTACTCTCCGTAA 60.119 47.826 0.00 0.00 0.00 3.18
1549 1618 2.426024 GGACATTGCAGTACTCTCCGTA 59.574 50.000 0.00 0.00 0.00 4.02
1550 1619 1.204941 GGACATTGCAGTACTCTCCGT 59.795 52.381 0.00 0.00 0.00 4.69
1551 1620 1.204704 TGGACATTGCAGTACTCTCCG 59.795 52.381 0.00 0.00 0.00 4.63
1552 1621 3.265791 CTTGGACATTGCAGTACTCTCC 58.734 50.000 0.00 0.00 0.00 3.71
1553 1622 3.931578 ACTTGGACATTGCAGTACTCTC 58.068 45.455 0.00 0.00 0.00 3.20
1554 1623 4.528596 AGTACTTGGACATTGCAGTACTCT 59.471 41.667 8.14 0.00 38.28 3.24
1555 1624 4.627467 CAGTACTTGGACATTGCAGTACTC 59.373 45.833 10.17 0.00 39.96 2.59
1556 1625 4.569943 CAGTACTTGGACATTGCAGTACT 58.430 43.478 8.14 8.14 41.83 2.73
1557 1626 3.125316 GCAGTACTTGGACATTGCAGTAC 59.875 47.826 0.00 0.00 34.19 2.73
1558 1627 3.334691 GCAGTACTTGGACATTGCAGTA 58.665 45.455 0.00 0.00 0.00 2.74
1559 1628 2.154462 GCAGTACTTGGACATTGCAGT 58.846 47.619 0.00 0.00 0.00 4.40
1560 1629 1.470098 GGCAGTACTTGGACATTGCAG 59.530 52.381 0.00 0.00 33.42 4.41
1561 1630 1.533625 GGCAGTACTTGGACATTGCA 58.466 50.000 0.00 0.00 33.42 4.08
1562 1631 0.811281 GGGCAGTACTTGGACATTGC 59.189 55.000 0.00 0.00 0.00 3.56
1580 1649 1.607628 CGACGTCTAGTTCCCCATAGG 59.392 57.143 14.70 0.00 0.00 2.57
1582 1651 2.715749 TCGACGTCTAGTTCCCCATA 57.284 50.000 14.70 0.00 0.00 2.74
1583 1652 2.068834 ATCGACGTCTAGTTCCCCAT 57.931 50.000 14.70 0.00 0.00 4.00
1584 1653 1.843368 AATCGACGTCTAGTTCCCCA 58.157 50.000 14.70 0.00 0.00 4.96
1585 1654 4.357996 CTTTAATCGACGTCTAGTTCCCC 58.642 47.826 14.70 0.00 0.00 4.81
1606 1680 0.755327 AACAAGAAAAGGCACCGGCT 60.755 50.000 0.00 0.00 41.24 5.52
1607 1681 0.104120 AAACAAGAAAAGGCACCGGC 59.896 50.000 0.00 0.00 40.13 6.13
1626 1700 5.513788 GCCTTCCTCCAAGCATCTGATTATA 60.514 44.000 0.00 0.00 0.00 0.98
1627 1701 4.749166 GCCTTCCTCCAAGCATCTGATTAT 60.749 45.833 0.00 0.00 0.00 1.28
1745 1821 4.715523 ACCGCATCCCCACCAACG 62.716 66.667 0.00 0.00 0.00 4.10
1746 1822 3.061848 CACCGCATCCCCACCAAC 61.062 66.667 0.00 0.00 0.00 3.77
1756 1832 1.199097 GAACGAATGGTTTCACCGCAT 59.801 47.619 0.00 0.00 42.58 4.73
1799 1875 5.008613 TCTCTGTTTAAACATGACACAAGGC 59.991 40.000 20.83 0.00 38.41 4.35
1838 1914 3.211045 GAAGAACACCTACTGTTGGCAA 58.789 45.455 8.22 0.00 43.60 4.52
1842 1918 5.479716 AAAACGAAGAACACCTACTGTTG 57.520 39.130 0.00 0.00 43.60 3.33
2020 2177 7.201609 GCGTTGTTTATAAGGAGATCATGAACA 60.202 37.037 0.00 0.00 0.00 3.18
2086 2243 2.359967 GGCCTAGGAACTGCCTCGT 61.360 63.158 14.75 0.00 46.97 4.18
2163 2342 2.014033 AAAAGAAACCGGGGCTCCCA 62.014 55.000 6.32 0.00 45.83 4.37
2177 4262 1.968493 ACCTAGACACGAGCCAAAAGA 59.032 47.619 0.00 0.00 0.00 2.52
2229 4576 4.076394 CCCGGAAACTTTTATTCCTGACA 58.924 43.478 0.73 0.00 43.43 3.58
2274 4621 2.322830 CGACTCCTCGACACCGTCA 61.323 63.158 0.00 0.00 43.06 4.35
2318 4665 1.122019 AGACCTCCACCGCTGTCTTT 61.122 55.000 0.00 0.00 34.53 2.52
2393 4743 1.217882 CTTTCGGCTTCGTGACAACT 58.782 50.000 0.00 0.00 35.06 3.16
2417 4767 1.764854 ACCGTCCACCTCCAACACT 60.765 57.895 0.00 0.00 0.00 3.55
2464 4814 3.026630 TGAAGAAACTCTAGGTGCACG 57.973 47.619 11.45 0.00 0.00 5.34
2488 4838 4.503643 CCAAAACCAGCAACCATCTTTCAT 60.504 41.667 0.00 0.00 0.00 2.57
2491 4841 3.037549 TCCAAAACCAGCAACCATCTTT 58.962 40.909 0.00 0.00 0.00 2.52
2508 4858 4.039092 GCTGCTGAGGGGCTCCAA 62.039 66.667 4.79 0.00 34.83 3.53
2625 4979 1.202580 ACTGTGTTGTGAGCCTCTGAC 60.203 52.381 0.00 0.00 0.00 3.51
2663 5017 1.484240 CACCAAGCCAAGGTCCAAAAA 59.516 47.619 0.00 0.00 37.23 1.94
2671 5025 0.038744 ACATCTCCACCAAGCCAAGG 59.961 55.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.