Multiple sequence alignment - TraesCS7A01G419800

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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 TraesCS7A01G419800 chr7A 100.000 4972 0 0 1 4972 611465660 611470631 0.000000e+00 9182.0
1 TraesCS7A01G419800 chr7A 92.222 720 44 7 2499 3211 700977473 700978187 0.000000e+00 1009.0
2 TraesCS7A01G419800 chr7A 88.737 293 22 5 3661 3943 700978182 700978473 1.020000e-91 348.0
3 TraesCS7A01G419800 chr7A 95.370 216 10 0 2996 3211 700941427 700941642 1.330000e-90 344.0
4 TraesCS7A01G419800 chr7A 88.396 293 23 5 3661 3943 700941637 700941928 4.770000e-90 342.0
5 TraesCS7A01G419800 chr7A 91.919 198 15 1 2307 2504 700976397 700976593 4.900000e-70 276.0
6 TraesCS7A01G419800 chr7B 95.968 3447 119 11 723 4155 571256204 571259644 0.000000e+00 5578.0
7 TraesCS7A01G419800 chr7B 89.575 518 18 6 4458 4972 571259696 571260180 4.230000e-175 625.0
8 TraesCS7A01G419800 chr7B 80.278 360 57 7 109 465 590497687 590497339 4.940000e-65 259.0
9 TraesCS7A01G419800 chr7B 77.636 313 58 9 108 410 665672228 665672538 3.950000e-41 180.0
10 TraesCS7A01G419800 chr7B 75.549 364 72 11 110 466 167593910 167594263 3.980000e-36 163.0
11 TraesCS7A01G419800 chr7B 79.775 178 25 10 114 284 666311533 666311706 8.740000e-23 119.0
12 TraesCS7A01G419800 chr7B 98.246 57 1 0 4242 4298 571259639 571259695 3.170000e-17 100.0
13 TraesCS7A01G419800 chr7D 95.818 2678 98 8 1908 4581 530925210 530927877 0.000000e+00 4313.0
14 TraesCS7A01G419800 chr7D 95.147 1154 43 9 698 1840 530924034 530925185 0.000000e+00 1808.0
15 TraesCS7A01G419800 chr7D 90.722 485 31 2 2486 2970 611010910 611011380 7.020000e-178 634.0
16 TraesCS7A01G419800 chr7D 88.577 499 42 7 3597 4087 611011383 611011874 4.290000e-165 592.0
17 TraesCS7A01G419800 chr7D 87.526 489 41 10 213 695 530923261 530923735 9.410000e-152 547.0
18 TraesCS7A01G419800 chr7D 94.186 172 6 2 2280 2447 611008921 611009092 4.940000e-65 259.0
19 TraesCS7A01G419800 chr7D 92.366 131 8 1 4458 4586 611008127 611008257 8.500000e-43 185.0
20 TraesCS7A01G419800 chr7D 76.454 361 72 9 110 466 204026294 204026645 3.060000e-42 183.0
21 TraesCS7A01G419800 chr7D 92.857 126 8 1 4174 4298 611008003 611008128 1.100000e-41 182.0
22 TraesCS7A01G419800 chr7D 83.673 98 14 2 113 209 176923224 176923128 1.910000e-14 91.6
23 TraesCS7A01G419800 chr2B 86.014 286 35 4 133 415 636653666 636653383 8.090000e-78 302.0
24 TraesCS7A01G419800 chr2B 85.227 176 23 3 4297 4470 793278078 793277904 1.420000e-40 178.0
25 TraesCS7A01G419800 chr6D 82.749 342 49 8 129 466 451863605 451863270 3.760000e-76 296.0
26 TraesCS7A01G419800 chr6D 91.515 165 11 2 4458 4620 354603903 354603740 1.800000e-54 224.0
27 TraesCS7A01G419800 chr6D 87.273 165 20 1 4295 4459 426106893 426106730 2.360000e-43 187.0
28 TraesCS7A01G419800 chr3D 91.411 163 13 1 4294 4456 87925997 87926158 6.480000e-54 222.0
29 TraesCS7A01G419800 chr3D 92.661 109 7 1 1 108 453767633 453767741 6.660000e-34 156.0
30 TraesCS7A01G419800 chr3A 79.532 342 45 13 127 466 354859279 354859597 2.330000e-53 220.0
31 TraesCS7A01G419800 chr3A 90.909 165 9 4 4458 4620 293591468 293591628 3.010000e-52 217.0
32 TraesCS7A01G419800 chr3A 91.667 108 9 0 1 108 595753537 595753644 3.100000e-32 150.0
33 TraesCS7A01G419800 chr6A 90.909 165 12 2 4458 4620 487116315 487116478 8.380000e-53 219.0
34 TraesCS7A01G419800 chr6A 88.166 169 15 4 4295 4459 574574462 574574295 3.930000e-46 196.0
35 TraesCS7A01G419800 chr6A 86.982 169 18 3 4295 4460 574612008 574611841 2.360000e-43 187.0
36 TraesCS7A01G419800 chr4D 90.625 160 14 1 4297 4456 117421191 117421349 1.400000e-50 211.0
37 TraesCS7A01G419800 chr5D 89.697 165 14 2 4458 4620 515243803 515243640 1.810000e-49 207.0
38 TraesCS7A01G419800 chr4B 86.550 171 22 1 4292 4462 659784370 659784201 2.360000e-43 187.0
39 TraesCS7A01G419800 chr4B 80.368 163 28 2 4642 4800 546050836 546050674 2.430000e-23 121.0
40 TraesCS7A01G419800 chr4B 87.805 82 9 1 25 105 454315314 454315233 1.470000e-15 95.3
41 TraesCS7A01G419800 chr1B 87.273 165 19 2 4297 4460 533863225 533863062 2.360000e-43 187.0
42 TraesCS7A01G419800 chr1B 86.310 168 19 3 4458 4622 449710419 449710253 3.950000e-41 180.0
43 TraesCS7A01G419800 chrUn 85.802 162 16 5 4458 4615 189571265 189571107 1.110000e-36 165.0
44 TraesCS7A01G419800 chr2D 81.818 198 30 6 113 307 186993570 186993376 1.430000e-35 161.0
45 TraesCS7A01G419800 chr6B 94.286 105 4 1 4 108 478750778 478750676 5.150000e-35 159.0
46 TraesCS7A01G419800 chr6B 87.500 104 11 1 5 108 524338904 524339005 8.740000e-23 119.0
47 TraesCS7A01G419800 chr2A 90.196 102 9 1 7 108 724364418 724364318 1.120000e-26 132.0


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 TraesCS7A01G419800 chr7A 611465660 611470631 4971 False 9182.000000 9182 100.000000 1 4972 1 chr7A.!!$F1 4971
1 TraesCS7A01G419800 chr7A 700976397 700978473 2076 False 544.333333 1009 90.959333 2307 3943 3 chr7A.!!$F3 1636
2 TraesCS7A01G419800 chr7A 700941427 700941928 501 False 343.000000 344 91.883000 2996 3943 2 chr7A.!!$F2 947
3 TraesCS7A01G419800 chr7B 571256204 571260180 3976 False 2101.000000 5578 94.596333 723 4972 3 chr7B.!!$F4 4249
4 TraesCS7A01G419800 chr7D 530923261 530927877 4616 False 2222.666667 4313 92.830333 213 4581 3 chr7D.!!$F2 4368
5 TraesCS7A01G419800 chr7D 611008003 611011874 3871 False 370.400000 634 91.741600 2280 4586 5 chr7D.!!$F3 2306

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
129 130 0.034896 TTGAAACAGGCTCTCGTCCC 59.965 55.000 0.00 0.0 0.00 4.46 F
364 367 0.037160 GGTTTTCACCCGAAGCCCTA 59.963 55.000 0.00 0.0 37.03 3.53 F
726 1032 0.172803 ACTCGAACCCACTCGCATAC 59.827 55.000 0.00 0.0 38.73 2.39 F
740 1046 0.463654 GCATACTCGCATTCCCACCA 60.464 55.000 0.00 0.0 0.00 4.17 F
1570 1884 0.741221 GTTGGTCACGGATGAGGAGC 60.741 60.000 0.00 0.0 34.75 4.70 F
1573 1887 1.064946 GTCACGGATGAGGAGCTCG 59.935 63.158 7.83 0.0 34.75 5.03 F
3371 6370 0.388907 CATCGCTTGGCAAACTTGGG 60.389 55.000 0.00 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1068 1382 2.066999 CCTGTACTCCCCCTCCAGC 61.067 68.421 0.00 0.0 0.00 4.85 R
1299 1613 2.099141 TCCAAAAGAGCTCCATGACG 57.901 50.000 10.93 0.0 0.00 4.35 R
1770 2084 2.107750 ATGAGCCACGCCTCATCG 59.892 61.111 7.71 0.0 46.75 3.84 R
1857 2171 2.414481 CAGCGATATTGTGATAGGCTGC 59.586 50.000 0.00 0.0 39.87 5.25 R
3343 6342 1.202114 TGCCAAGCGATGAAACCAATC 59.798 47.619 0.00 0.0 0.00 2.67 R
3429 6428 2.943653 CGGCGACCAAGAACCAAC 59.056 61.111 0.00 0.0 0.00 3.77 R
4634 7654 0.321346 TCCACGACATGCACAGATGT 59.679 50.000 0.00 0.0 39.34 3.06 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.912862 AATCCTCCCTGCTTACCCAT 58.087 50.000 0.00 0.00 0.00 4.00
21 22 0.253160 TCCTCCCTGCTTACCCATGT 60.253 55.000 0.00 0.00 0.00 3.21
22 23 0.107017 CCTCCCTGCTTACCCATGTG 60.107 60.000 0.00 0.00 0.00 3.21
23 24 0.107017 CTCCCTGCTTACCCATGTGG 60.107 60.000 0.00 0.00 41.37 4.17
24 25 0.548926 TCCCTGCTTACCCATGTGGA 60.549 55.000 0.00 0.00 37.39 4.02
25 26 0.552848 CCCTGCTTACCCATGTGGAT 59.447 55.000 0.00 0.00 37.39 3.41
26 27 1.683943 CCTGCTTACCCATGTGGATG 58.316 55.000 0.00 0.00 37.39 3.51
27 28 1.212688 CCTGCTTACCCATGTGGATGA 59.787 52.381 0.00 0.00 37.39 2.92
28 29 2.158564 CCTGCTTACCCATGTGGATGAT 60.159 50.000 0.00 0.00 37.39 2.45
29 30 3.144506 CTGCTTACCCATGTGGATGATC 58.855 50.000 0.00 0.00 37.39 2.92
30 31 2.779430 TGCTTACCCATGTGGATGATCT 59.221 45.455 0.00 0.00 37.39 2.75
31 32 3.202818 TGCTTACCCATGTGGATGATCTT 59.797 43.478 0.00 0.00 37.39 2.40
32 33 3.567164 GCTTACCCATGTGGATGATCTTG 59.433 47.826 0.00 0.00 37.39 3.02
33 34 4.785301 CTTACCCATGTGGATGATCTTGT 58.215 43.478 0.00 0.00 37.39 3.16
34 35 3.744940 ACCCATGTGGATGATCTTGTT 57.255 42.857 0.00 0.00 37.39 2.83
35 36 4.051661 ACCCATGTGGATGATCTTGTTT 57.948 40.909 0.00 0.00 37.39 2.83
37 38 5.579047 ACCCATGTGGATGATCTTGTTTAA 58.421 37.500 0.00 0.00 37.39 1.52
41 42 7.364056 CCCATGTGGATGATCTTGTTTAAATGT 60.364 37.037 0.00 0.00 37.39 2.71
42 43 7.490079 CCATGTGGATGATCTTGTTTAAATGTG 59.510 37.037 0.00 0.00 37.39 3.21
43 44 7.523293 TGTGGATGATCTTGTTTAAATGTGT 57.477 32.000 0.00 0.00 0.00 3.72
44 45 7.950512 TGTGGATGATCTTGTTTAAATGTGTT 58.049 30.769 0.00 0.00 0.00 3.32
45 46 7.866898 TGTGGATGATCTTGTTTAAATGTGTTG 59.133 33.333 0.00 0.00 0.00 3.33
47 48 8.081633 TGGATGATCTTGTTTAAATGTGTTGAC 58.918 33.333 0.00 0.00 0.00 3.18
48 49 7.542130 GGATGATCTTGTTTAAATGTGTTGACC 59.458 37.037 0.00 0.00 0.00 4.02
49 50 7.581213 TGATCTTGTTTAAATGTGTTGACCT 57.419 32.000 0.00 0.00 0.00 3.85
52 53 7.164230 TCTTGTTTAAATGTGTTGACCTTGT 57.836 32.000 0.00 0.00 0.00 3.16
53 54 7.607250 TCTTGTTTAAATGTGTTGACCTTGTT 58.393 30.769 0.00 0.00 0.00 2.83
54 55 8.091449 TCTTGTTTAAATGTGTTGACCTTGTTT 58.909 29.630 0.00 0.00 0.00 2.83
56 57 8.023050 TGTTTAAATGTGTTGACCTTGTTTTG 57.977 30.769 0.00 0.00 0.00 2.44
57 58 7.657761 TGTTTAAATGTGTTGACCTTGTTTTGT 59.342 29.630 0.00 0.00 0.00 2.83
58 59 7.588143 TTAAATGTGTTGACCTTGTTTTGTG 57.412 32.000 0.00 0.00 0.00 3.33
63 64 4.384547 GTGTTGACCTTGTTTTGTGAACAC 59.615 41.667 8.81 8.81 46.63 3.32
65 66 4.167554 TGACCTTGTTTTGTGAACACAC 57.832 40.909 7.16 0.00 41.67 3.82
67 68 5.004448 TGACCTTGTTTTGTGAACACACTA 58.996 37.500 7.16 0.00 41.67 2.74
69 70 6.151985 TGACCTTGTTTTGTGAACACACTATT 59.848 34.615 7.16 0.00 41.67 1.73
70 71 6.930731 ACCTTGTTTTGTGAACACACTATTT 58.069 32.000 7.16 0.00 41.67 1.40
71 72 7.382898 ACCTTGTTTTGTGAACACACTATTTT 58.617 30.769 7.16 0.00 41.67 1.82
72 73 7.330700 ACCTTGTTTTGTGAACACACTATTTTG 59.669 33.333 7.16 0.00 41.67 2.44
73 74 7.330700 CCTTGTTTTGTGAACACACTATTTTGT 59.669 33.333 7.16 0.00 41.67 2.83
74 75 7.804614 TGTTTTGTGAACACACTATTTTGTC 57.195 32.000 7.16 0.00 41.67 3.18
77 78 7.624360 TTTGTGAACACACTATTTTGTCTCT 57.376 32.000 7.16 0.00 41.67 3.10
79 80 6.345298 TGTGAACACACTATTTTGTCTCTCA 58.655 36.000 3.39 0.00 36.21 3.27
80 81 6.992123 TGTGAACACACTATTTTGTCTCTCAT 59.008 34.615 3.39 0.00 36.21 2.90
81 82 7.498900 TGTGAACACACTATTTTGTCTCTCATT 59.501 33.333 3.39 0.00 36.21 2.57
84 85 7.664082 ACACACTATTTTGTCTCTCATTCTG 57.336 36.000 0.00 0.00 0.00 3.02
86 87 7.716998 ACACACTATTTTGTCTCTCATTCTGTT 59.283 33.333 0.00 0.00 0.00 3.16
87 88 8.013947 CACACTATTTTGTCTCTCATTCTGTTG 58.986 37.037 0.00 0.00 0.00 3.33
88 89 7.933577 ACACTATTTTGTCTCTCATTCTGTTGA 59.066 33.333 0.00 0.00 0.00 3.18
89 90 8.944029 CACTATTTTGTCTCTCATTCTGTTGAT 58.056 33.333 0.00 0.00 0.00 2.57
118 119 7.353414 TGATATAGTCTCCTCCTTGAAACAG 57.647 40.000 0.00 0.00 0.00 3.16
119 120 6.325028 TGATATAGTCTCCTCCTTGAAACAGG 59.675 42.308 0.00 0.00 34.86 4.00
120 121 1.349357 AGTCTCCTCCTTGAAACAGGC 59.651 52.381 0.00 0.00 33.35 4.85
121 122 1.349357 GTCTCCTCCTTGAAACAGGCT 59.651 52.381 0.00 0.00 33.35 4.58
122 123 1.625818 TCTCCTCCTTGAAACAGGCTC 59.374 52.381 0.00 0.00 33.35 4.70
123 124 1.627834 CTCCTCCTTGAAACAGGCTCT 59.372 52.381 0.00 0.00 33.35 4.09
124 125 1.625818 TCCTCCTTGAAACAGGCTCTC 59.374 52.381 0.00 0.00 33.35 3.20
125 126 1.674221 CCTCCTTGAAACAGGCTCTCG 60.674 57.143 0.00 0.00 33.35 4.04
127 128 1.000955 TCCTTGAAACAGGCTCTCGTC 59.999 52.381 0.00 0.00 33.35 4.20
128 129 1.433534 CTTGAAACAGGCTCTCGTCC 58.566 55.000 0.00 0.00 0.00 4.79
129 130 0.034896 TTGAAACAGGCTCTCGTCCC 59.965 55.000 0.00 0.00 0.00 4.46
130 131 1.446272 GAAACAGGCTCTCGTCCCG 60.446 63.158 0.00 0.00 0.00 5.14
131 132 3.591254 AAACAGGCTCTCGTCCCGC 62.591 63.158 0.00 0.00 0.00 6.13
133 134 3.764466 CAGGCTCTCGTCCCGCTT 61.764 66.667 0.00 0.00 0.00 4.68
135 136 1.681327 AGGCTCTCGTCCCGCTTTA 60.681 57.895 0.00 0.00 0.00 1.85
136 137 1.043673 AGGCTCTCGTCCCGCTTTAT 61.044 55.000 0.00 0.00 0.00 1.40
137 138 0.672342 GGCTCTCGTCCCGCTTTATA 59.328 55.000 0.00 0.00 0.00 0.98
139 140 2.490903 GGCTCTCGTCCCGCTTTATATA 59.509 50.000 0.00 0.00 0.00 0.86
140 141 3.130693 GGCTCTCGTCCCGCTTTATATAT 59.869 47.826 0.00 0.00 0.00 0.86
163 164 3.398954 AGCAACACAACAAAGTACACG 57.601 42.857 0.00 0.00 0.00 4.49
164 165 2.096819 AGCAACACAACAAAGTACACGG 59.903 45.455 0.00 0.00 0.00 4.94
165 166 2.446282 CAACACAACAAAGTACACGGC 58.554 47.619 0.00 0.00 0.00 5.68
166 167 1.018910 ACACAACAAAGTACACGGCC 58.981 50.000 0.00 0.00 0.00 6.13
167 168 0.041663 CACAACAAAGTACACGGCCG 60.042 55.000 26.86 26.86 0.00 6.13
168 169 0.179078 ACAACAAAGTACACGGCCGA 60.179 50.000 35.90 6.51 0.00 5.54
169 170 0.938713 CAACAAAGTACACGGCCGAA 59.061 50.000 35.90 14.32 0.00 4.30
170 171 0.939419 AACAAAGTACACGGCCGAAC 59.061 50.000 35.90 25.10 0.00 3.95
171 172 1.216941 ACAAAGTACACGGCCGAACG 61.217 55.000 35.90 21.75 40.31 3.95
172 173 0.940519 CAAAGTACACGGCCGAACGA 60.941 55.000 35.90 11.21 37.61 3.85
173 174 0.037975 AAAGTACACGGCCGAACGAT 60.038 50.000 35.90 16.97 37.61 3.73
174 175 0.810648 AAGTACACGGCCGAACGATA 59.189 50.000 35.90 13.09 37.61 2.92
175 176 0.099436 AGTACACGGCCGAACGATAC 59.901 55.000 35.90 23.14 37.61 2.24
177 178 0.099259 TACACGGCCGAACGATACAG 59.901 55.000 35.90 11.48 37.61 2.74
179 180 1.153901 ACGGCCGAACGATACAGTG 60.154 57.895 35.90 0.00 37.61 3.66
180 181 1.153901 CGGCCGAACGATACAGTGT 60.154 57.895 24.07 0.00 35.47 3.55
181 182 1.410737 CGGCCGAACGATACAGTGTG 61.411 60.000 24.07 0.00 35.47 3.82
182 183 1.082117 GGCCGAACGATACAGTGTGG 61.082 60.000 5.88 0.00 0.00 4.17
185 186 1.068125 CCGAACGATACAGTGTGGTGA 60.068 52.381 5.88 0.00 0.00 4.02
186 187 2.251040 CGAACGATACAGTGTGGTGAG 58.749 52.381 5.88 0.00 0.00 3.51
187 188 2.607187 GAACGATACAGTGTGGTGAGG 58.393 52.381 5.88 0.00 0.00 3.86
189 190 1.819288 ACGATACAGTGTGGTGAGGAG 59.181 52.381 5.88 0.00 0.00 3.69
190 191 1.135139 CGATACAGTGTGGTGAGGAGG 59.865 57.143 5.88 0.00 0.00 4.30
191 192 0.905357 ATACAGTGTGGTGAGGAGGC 59.095 55.000 5.88 0.00 0.00 4.70
192 193 1.192146 TACAGTGTGGTGAGGAGGCC 61.192 60.000 5.88 0.00 0.00 5.19
193 194 2.930562 AGTGTGGTGAGGAGGCCC 60.931 66.667 0.00 0.00 0.00 5.80
204 205 0.621082 AGGAGGCCCTCTTACAAAGC 59.379 55.000 11.29 0.00 38.86 3.51
206 207 1.680249 GGAGGCCCTCTTACAAAGCAG 60.680 57.143 11.29 0.00 0.00 4.24
207 208 1.279271 GAGGCCCTCTTACAAAGCAGA 59.721 52.381 2.64 0.00 0.00 4.26
208 209 1.918957 AGGCCCTCTTACAAAGCAGAT 59.081 47.619 0.00 0.00 0.00 2.90
209 210 2.310052 AGGCCCTCTTACAAAGCAGATT 59.690 45.455 0.00 0.00 0.00 2.40
210 211 3.523564 AGGCCCTCTTACAAAGCAGATTA 59.476 43.478 0.00 0.00 0.00 1.75
224 225 8.730680 ACAAAGCAGATTAAAAGATACGACATT 58.269 29.630 0.00 0.00 0.00 2.71
249 250 3.056749 CCTAGAACAAGCTAACACCTCGT 60.057 47.826 0.00 0.00 0.00 4.18
251 252 2.364324 AGAACAAGCTAACACCTCGTCA 59.636 45.455 0.00 0.00 0.00 4.35
277 278 1.984321 GACCGACGACTCCTGAGCTC 61.984 65.000 6.82 6.82 0.00 4.09
295 296 3.353836 CACGACAACGCCCCAAGG 61.354 66.667 0.00 0.00 43.96 3.61
302 303 3.507377 AACGCCCCAAGGAAGGTGG 62.507 63.158 0.00 0.00 38.00 4.61
311 314 4.699522 GGAAGGTGGCGGCGAAGT 62.700 66.667 12.98 0.00 0.00 3.01
312 315 2.263540 GAAGGTGGCGGCGAAGTA 59.736 61.111 12.98 0.00 0.00 2.24
315 318 1.895020 AAGGTGGCGGCGAAGTATCA 61.895 55.000 12.98 0.00 0.00 2.15
324 327 1.331756 GGCGAAGTATCACCATTGCTG 59.668 52.381 0.00 0.00 0.00 4.41
340 343 0.595095 GCTGAGTCCAAGCAAACAGG 59.405 55.000 0.00 0.00 0.00 4.00
364 367 0.037160 GGTTTTCACCCGAAGCCCTA 59.963 55.000 0.00 0.00 37.03 3.53
366 369 0.322187 TTTTCACCCGAAGCCCTAGC 60.322 55.000 0.00 0.00 40.32 3.42
369 372 0.397957 TCACCCGAAGCCCTAGCATA 60.398 55.000 0.00 0.00 43.56 3.14
381 384 1.040646 CTAGCATAACGAGCCCCTCA 58.959 55.000 0.00 0.00 0.00 3.86
465 468 2.437343 GCTTTCGCTCGGACACTCG 61.437 63.158 0.00 0.00 0.00 4.18
476 479 1.334243 CGGACACTCGGGAATAGTCTC 59.666 57.143 0.00 0.00 0.00 3.36
477 480 2.657143 GGACACTCGGGAATAGTCTCT 58.343 52.381 0.00 0.00 0.00 3.10
479 482 3.447944 GGACACTCGGGAATAGTCTCTTT 59.552 47.826 0.00 0.00 0.00 2.52
527 531 6.385033 GCTGCAGAAGTGTCTTCAATAAAAT 58.615 36.000 20.43 0.00 28.78 1.82
558 562 5.906073 AGAAATTTGTGTCCCTCTTGTTTG 58.094 37.500 0.00 0.00 0.00 2.93
572 576 9.807921 TCCCTCTTGTTTGTCTTCTAATAATTT 57.192 29.630 0.00 0.00 0.00 1.82
663 670 5.695818 ACGTAATTGGTCATTGTTTAGTGC 58.304 37.500 0.00 0.00 0.00 4.40
695 702 5.683681 TCATGCTTATTGCTATCCAGTTCA 58.316 37.500 0.00 0.00 43.37 3.18
696 703 6.301486 TCATGCTTATTGCTATCCAGTTCAT 58.699 36.000 0.00 0.00 43.37 2.57
702 1005 8.233190 GCTTATTGCTATCCAGTTCATCATTAC 58.767 37.037 0.00 0.00 38.95 1.89
709 1012 3.587061 TCCAGTTCATCATTACCCACACT 59.413 43.478 0.00 0.00 0.00 3.55
711 1014 3.618594 CAGTTCATCATTACCCACACTCG 59.381 47.826 0.00 0.00 0.00 4.18
712 1015 3.513912 AGTTCATCATTACCCACACTCGA 59.486 43.478 0.00 0.00 0.00 4.04
726 1032 0.172803 ACTCGAACCCACTCGCATAC 59.827 55.000 0.00 0.00 38.73 2.39
740 1046 0.463654 GCATACTCGCATTCCCACCA 60.464 55.000 0.00 0.00 0.00 4.17
831 1144 2.531942 ACGGCTTTCCCCTTCCCT 60.532 61.111 0.00 0.00 0.00 4.20
860 1174 2.364324 CCCTCATCCCATTTGCTTGATG 59.636 50.000 0.00 0.00 36.73 3.07
964 1278 2.606308 CGCAATCCATTGGCAGCTTATC 60.606 50.000 0.00 0.00 38.21 1.75
1102 1416 3.455469 GGATGCACAAGGGCCTGC 61.455 66.667 6.92 8.30 0.00 4.85
1236 1550 2.765699 GAGGGAGATGGCCTATGAGATC 59.234 54.545 3.32 0.00 0.00 2.75
1270 1584 2.930040 GACAGGTACATGAATCACCACG 59.070 50.000 15.54 0.00 34.62 4.94
1299 1613 2.588856 ATCCGGACAAGCCTAACGCC 62.589 60.000 6.12 0.00 38.78 5.68
1434 1748 1.797025 GTGACAGGTACAGGCTTGAC 58.203 55.000 1.40 0.00 0.00 3.18
1466 1780 3.109612 CTGCGAGCTCCAATGCTGC 62.110 63.158 8.47 4.26 44.17 5.25
1570 1884 0.741221 GTTGGTCACGGATGAGGAGC 60.741 60.000 0.00 0.00 34.75 4.70
1573 1887 1.064946 GTCACGGATGAGGAGCTCG 59.935 63.158 7.83 0.00 34.75 5.03
1770 2084 1.338337 TCTCCCATTTCTCGATCGAGC 59.662 52.381 34.92 0.00 41.71 5.03
1929 2252 6.748333 TTCAGCTTGAGATTTATGGTTCTG 57.252 37.500 0.00 0.00 0.00 3.02
2441 3196 4.402616 TGTGGAGGAAATGGAAAGGATT 57.597 40.909 0.00 0.00 0.00 3.01
2578 5570 6.715347 AGCAGAAAGATTTGTTAAGGTTGT 57.285 33.333 0.00 0.00 0.00 3.32
2775 5774 3.347216 AGTGGTCATCAAACACATAGCC 58.653 45.455 0.00 0.00 37.58 3.93
2780 5779 3.758554 GTCATCAAACACATAGCCTGGTT 59.241 43.478 0.00 0.00 0.00 3.67
2958 5957 2.136298 TGCTCTAGACAGGAGTGAGG 57.864 55.000 0.00 0.00 33.73 3.86
3171 6170 1.851658 ACTTGTTGATGGCGCAAAAC 58.148 45.000 10.83 8.24 0.00 2.43
3219 6218 1.804372 GCCTAGAGGAACTGTCATGCG 60.804 57.143 0.00 0.00 41.55 4.73
3224 6223 2.563179 AGAGGAACTGTCATGCGTAACT 59.437 45.455 0.00 0.00 41.55 2.24
3267 6266 1.434188 TCTCTTGCAGGAGTTGGGAA 58.566 50.000 23.56 2.23 35.11 3.97
3332 6331 2.224079 CGCACATAAGACAAGCACAAGT 59.776 45.455 0.00 0.00 0.00 3.16
3371 6370 0.388907 CATCGCTTGGCAAACTTGGG 60.389 55.000 0.00 0.00 0.00 4.12
3394 6393 0.676184 TCTCAGCTTGAGCGTCTGTT 59.324 50.000 7.94 0.00 43.95 3.16
3429 6428 2.415893 GGCCGTTTGATTGACATTCCAG 60.416 50.000 0.00 0.00 0.00 3.86
3443 6442 1.961793 TTCCAGTTGGTTCTTGGTCG 58.038 50.000 0.00 0.00 36.34 4.79
3587 6586 1.122019 AGACCCTTCTCGTGCTTGGT 61.122 55.000 0.00 0.00 0.00 3.67
3731 6736 1.531578 GGTCTTCTGACGTTTGAAGCC 59.468 52.381 19.89 19.16 43.79 4.35
3755 6761 1.421382 CCATGCCAAAACTCAAAGCG 58.579 50.000 0.00 0.00 0.00 4.68
3836 6845 1.228367 CAGCAACCTCTGTGCCCTT 60.228 57.895 0.00 0.00 0.00 3.95
3878 6887 2.203625 TGCCAGGGTGAAAAGGCC 60.204 61.111 0.00 0.00 46.45 5.19
3915 6924 0.747283 GCTGGAGTCTGCAATCAGGG 60.747 60.000 0.00 0.00 40.69 4.45
3950 6959 1.818959 TTCCCAACCGTCCTACACCG 61.819 60.000 0.00 0.00 0.00 4.94
3974 6983 6.073222 CGTATTTCCATAGGTTGTATTGAGGC 60.073 42.308 0.00 0.00 0.00 4.70
4001 7010 0.526211 AGAACGACTGATGCAGCGTA 59.474 50.000 13.93 0.00 40.82 4.42
4096 7112 6.069381 ACAATCCAAGAAGCTATCTAGGGTTT 60.069 38.462 0.00 0.00 37.42 3.27
4104 7120 7.787028 AGAAGCTATCTAGGGTTTCTGTAAAG 58.213 38.462 0.00 0.00 36.32 1.85
4311 7331 7.850935 TCAATAATATACTCCCTTCGTTCCT 57.149 36.000 0.00 0.00 0.00 3.36
4450 7470 9.844790 TCTAAAAAGACTTATATTGACGAACGA 57.155 29.630 0.14 0.00 0.00 3.85
4473 7493 8.316214 ACGAAGGGACTATATTTGTTTGACTTA 58.684 33.333 0.00 0.00 38.49 2.24
4585 7605 3.559655 GTCAAAGTTGAATTTTGGGGTGC 59.440 43.478 12.27 0.00 39.21 5.01
4613 7633 4.023707 GCGTCTTATTCATTGGAATGGAGG 60.024 45.833 0.00 5.73 43.47 4.30
4614 7634 4.516698 CGTCTTATTCATTGGAATGGAGGG 59.483 45.833 0.00 0.00 43.47 4.30
4615 7635 5.687441 CGTCTTATTCATTGGAATGGAGGGA 60.687 44.000 0.00 0.00 43.47 4.20
4616 7636 5.767168 GTCTTATTCATTGGAATGGAGGGAG 59.233 44.000 0.00 0.00 43.47 4.30
4617 7637 5.433051 TCTTATTCATTGGAATGGAGGGAGT 59.567 40.000 0.00 0.00 43.47 3.85
4618 7638 6.619437 TCTTATTCATTGGAATGGAGGGAGTA 59.381 38.462 0.00 0.00 43.47 2.59
4619 7639 5.937492 ATTCATTGGAATGGAGGGAGTAT 57.063 39.130 0.00 0.00 42.10 2.12
4620 7640 8.518720 TTATTCATTGGAATGGAGGGAGTATA 57.481 34.615 0.00 0.00 43.47 1.47
4621 7641 7.594849 ATTCATTGGAATGGAGGGAGTATAT 57.405 36.000 0.00 0.00 42.10 0.86
4622 7642 8.700145 ATTCATTGGAATGGAGGGAGTATATA 57.300 34.615 0.00 0.00 42.10 0.86
4623 7643 8.518720 TTCATTGGAATGGAGGGAGTATATAA 57.481 34.615 0.00 0.00 37.03 0.98
4624 7644 7.918076 TCATTGGAATGGAGGGAGTATATAAC 58.082 38.462 0.00 0.00 37.03 1.89
4625 7645 6.697641 TTGGAATGGAGGGAGTATATAACC 57.302 41.667 0.00 0.00 0.00 2.85
4626 7646 5.733000 TGGAATGGAGGGAGTATATAACCA 58.267 41.667 8.76 0.00 0.00 3.67
4627 7647 6.339220 TGGAATGGAGGGAGTATATAACCAT 58.661 40.000 0.00 0.00 38.12 3.55
4628 7648 6.797540 TGGAATGGAGGGAGTATATAACCATT 59.202 38.462 0.00 0.00 45.30 3.16
4630 7650 7.888514 AATGGAGGGAGTATATAACCATTCA 57.111 36.000 0.00 5.66 40.95 2.57
4631 7651 7.888514 ATGGAGGGAGTATATAACCATTCAA 57.111 36.000 6.86 1.21 33.67 2.69
4632 7652 7.699709 TGGAGGGAGTATATAACCATTCAAA 57.300 36.000 8.76 0.00 0.00 2.69
4633 7653 8.287904 TGGAGGGAGTATATAACCATTCAAAT 57.712 34.615 8.76 0.00 0.00 2.32
4634 7654 9.400208 TGGAGGGAGTATATAACCATTCAAATA 57.600 33.333 8.76 0.00 0.00 1.40
4635 7655 9.668497 GGAGGGAGTATATAACCATTCAAATAC 57.332 37.037 8.76 0.00 0.00 1.89
4654 7674 1.065926 ACATCTGTGCATGTCGTGGAT 60.066 47.619 0.00 0.00 30.76 3.41
4700 7720 9.586150 GCATCAATGTATAAAAGTTCATACTCG 57.414 33.333 8.33 0.00 31.99 4.18
4707 7727 9.811995 TGTATAAAAGTTCATACTCGTATGCTT 57.188 29.630 11.29 7.76 41.92 3.91
4710 7730 6.408858 AAAGTTCATACTCGTATGCTTGTG 57.591 37.500 11.29 0.00 41.92 3.33
4740 7760 4.277476 ACACTTGACCATCCAAACAAGAA 58.723 39.130 0.00 0.00 41.16 2.52
4804 7827 2.423538 CCTCCAATCACCAAAATCGACC 59.576 50.000 0.00 0.00 0.00 4.79
4813 7836 4.755629 TCACCAAAATCGACCGTGAATTTA 59.244 37.500 0.00 0.00 30.83 1.40
4852 7875 3.911661 AACAATGTTGAAGAGCTCAGC 57.088 42.857 17.77 7.72 34.81 4.26
4927 7950 5.277974 GCACTGAGAAACTTTTGTATGCTCA 60.278 40.000 0.00 0.00 34.84 4.26
4928 7951 6.369005 CACTGAGAAACTTTTGTATGCTCAG 58.631 40.000 13.57 13.57 46.15 3.35
4929 7952 6.203530 CACTGAGAAACTTTTGTATGCTCAGA 59.796 38.462 19.98 0.00 45.03 3.27
4930 7953 6.767902 ACTGAGAAACTTTTGTATGCTCAGAA 59.232 34.615 19.98 0.00 45.03 3.02
4931 7954 6.959361 TGAGAAACTTTTGTATGCTCAGAAC 58.041 36.000 0.00 0.00 32.75 3.01
4932 7955 6.767902 TGAGAAACTTTTGTATGCTCAGAACT 59.232 34.615 0.00 0.00 32.75 3.01
4933 7956 7.041780 TGAGAAACTTTTGTATGCTCAGAACTC 60.042 37.037 0.00 0.00 32.75 3.01
4934 7957 6.767902 AGAAACTTTTGTATGCTCAGAACTCA 59.232 34.615 0.00 0.00 0.00 3.41
4948 7971 4.590647 TCAGAACTCAGAAGACACCTCATT 59.409 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.496429 CATGGGTAAGCAGGGAGGATT 59.504 52.381 0.00 0.00 0.00 3.01
3 4 0.107017 CACATGGGTAAGCAGGGAGG 60.107 60.000 0.00 0.00 0.00 4.30
4 5 0.107017 CCACATGGGTAAGCAGGGAG 60.107 60.000 0.00 0.00 0.00 4.30
5 6 0.548926 TCCACATGGGTAAGCAGGGA 60.549 55.000 0.00 0.00 38.11 4.20
6 7 0.552848 ATCCACATGGGTAAGCAGGG 59.447 55.000 0.00 0.00 38.11 4.45
7 8 1.212688 TCATCCACATGGGTAAGCAGG 59.787 52.381 0.00 0.00 38.11 4.85
8 9 2.715749 TCATCCACATGGGTAAGCAG 57.284 50.000 0.00 0.00 38.11 4.24
9 10 2.779430 AGATCATCCACATGGGTAAGCA 59.221 45.455 0.00 0.00 38.11 3.91
10 11 3.498774 AGATCATCCACATGGGTAAGC 57.501 47.619 0.00 0.00 38.11 3.09
11 12 4.785301 ACAAGATCATCCACATGGGTAAG 58.215 43.478 0.00 0.00 38.11 2.34
12 13 4.860802 ACAAGATCATCCACATGGGTAA 57.139 40.909 0.00 0.00 38.11 2.85
13 14 4.860802 AACAAGATCATCCACATGGGTA 57.139 40.909 0.00 0.00 38.11 3.69
14 15 3.744940 AACAAGATCATCCACATGGGT 57.255 42.857 0.00 0.00 38.11 4.51
16 17 7.490079 CACATTTAAACAAGATCATCCACATGG 59.510 37.037 0.00 0.00 0.00 3.66
17 18 8.030692 ACACATTTAAACAAGATCATCCACATG 58.969 33.333 0.00 0.00 0.00 3.21
19 20 7.523293 ACACATTTAAACAAGATCATCCACA 57.477 32.000 0.00 0.00 0.00 4.17
21 22 8.081633 GTCAACACATTTAAACAAGATCATCCA 58.918 33.333 0.00 0.00 0.00 3.41
22 23 7.542130 GGTCAACACATTTAAACAAGATCATCC 59.458 37.037 0.00 0.00 0.00 3.51
23 24 8.299570 AGGTCAACACATTTAAACAAGATCATC 58.700 33.333 0.00 0.00 0.00 2.92
24 25 8.181904 AGGTCAACACATTTAAACAAGATCAT 57.818 30.769 0.00 0.00 0.00 2.45
25 26 7.581213 AGGTCAACACATTTAAACAAGATCA 57.419 32.000 0.00 0.00 0.00 2.92
26 27 7.920682 ACAAGGTCAACACATTTAAACAAGATC 59.079 33.333 0.00 0.00 0.00 2.75
27 28 7.781056 ACAAGGTCAACACATTTAAACAAGAT 58.219 30.769 0.00 0.00 0.00 2.40
28 29 7.164230 ACAAGGTCAACACATTTAAACAAGA 57.836 32.000 0.00 0.00 0.00 3.02
29 30 7.826260 AACAAGGTCAACACATTTAAACAAG 57.174 32.000 0.00 0.00 0.00 3.16
30 31 8.499162 CAAAACAAGGTCAACACATTTAAACAA 58.501 29.630 0.00 0.00 0.00 2.83
31 32 7.657761 ACAAAACAAGGTCAACACATTTAAACA 59.342 29.630 0.00 0.00 0.00 2.83
32 33 7.954786 CACAAAACAAGGTCAACACATTTAAAC 59.045 33.333 0.00 0.00 0.00 2.01
33 34 7.872993 TCACAAAACAAGGTCAACACATTTAAA 59.127 29.630 0.00 0.00 0.00 1.52
34 35 7.378966 TCACAAAACAAGGTCAACACATTTAA 58.621 30.769 0.00 0.00 0.00 1.52
35 36 6.925211 TCACAAAACAAGGTCAACACATTTA 58.075 32.000 0.00 0.00 0.00 1.40
37 38 5.398603 TCACAAAACAAGGTCAACACATT 57.601 34.783 0.00 0.00 0.00 2.71
41 42 4.038042 TGTGTTCACAAAACAAGGTCAACA 59.962 37.500 2.99 0.00 31.20 3.33
42 43 4.384547 GTGTGTTCACAAAACAAGGTCAAC 59.615 41.667 7.22 0.00 43.37 3.18
43 44 4.279671 AGTGTGTTCACAAAACAAGGTCAA 59.720 37.500 7.22 0.00 46.01 3.18
44 45 3.823873 AGTGTGTTCACAAAACAAGGTCA 59.176 39.130 7.22 0.00 46.01 4.02
45 46 4.434713 AGTGTGTTCACAAAACAAGGTC 57.565 40.909 7.22 0.00 46.01 3.85
47 48 7.330700 ACAAAATAGTGTGTTCACAAAACAAGG 59.669 33.333 7.22 0.00 46.01 3.61
48 49 8.238481 ACAAAATAGTGTGTTCACAAAACAAG 57.762 30.769 7.22 0.00 46.01 3.16
49 50 8.085296 AGACAAAATAGTGTGTTCACAAAACAA 58.915 29.630 7.22 0.00 46.01 2.83
52 53 8.050778 AGAGACAAAATAGTGTGTTCACAAAA 57.949 30.769 7.22 0.00 46.01 2.44
53 54 7.335673 TGAGAGACAAAATAGTGTGTTCACAAA 59.664 33.333 7.22 0.04 46.01 2.83
54 55 6.821160 TGAGAGACAAAATAGTGTGTTCACAA 59.179 34.615 7.22 0.00 46.01 3.33
56 57 6.844696 TGAGAGACAAAATAGTGTGTTCAC 57.155 37.500 0.00 0.00 44.15 3.18
57 58 7.933577 AGAATGAGAGACAAAATAGTGTGTTCA 59.066 33.333 0.00 0.00 0.00 3.18
58 59 8.226448 CAGAATGAGAGACAAAATAGTGTGTTC 58.774 37.037 0.00 0.00 39.69 3.18
63 64 8.315391 TCAACAGAATGAGAGACAAAATAGTG 57.685 34.615 0.00 0.00 39.69 2.74
92 93 9.083422 CTGTTTCAAGGAGGAGACTATATCATA 57.917 37.037 0.00 0.00 44.43 2.15
94 95 6.325028 CCTGTTTCAAGGAGGAGACTATATCA 59.675 42.308 0.00 0.00 44.43 2.15
95 96 6.740122 GCCTGTTTCAAGGAGGAGACTATATC 60.740 46.154 0.00 0.00 44.43 1.63
97 98 4.406003 GCCTGTTTCAAGGAGGAGACTATA 59.594 45.833 0.00 0.00 44.43 1.31
98 99 3.198853 GCCTGTTTCAAGGAGGAGACTAT 59.801 47.826 0.00 0.00 44.43 2.12
101 102 1.349357 AGCCTGTTTCAAGGAGGAGAC 59.651 52.381 0.00 0.00 40.02 3.36
102 103 1.625818 GAGCCTGTTTCAAGGAGGAGA 59.374 52.381 0.00 0.00 40.02 3.71
103 104 1.627834 AGAGCCTGTTTCAAGGAGGAG 59.372 52.381 0.00 0.00 40.02 3.69
104 105 1.625818 GAGAGCCTGTTTCAAGGAGGA 59.374 52.381 0.00 0.00 40.02 3.71
105 106 1.674221 CGAGAGCCTGTTTCAAGGAGG 60.674 57.143 0.00 0.00 40.02 4.30
106 107 1.001406 ACGAGAGCCTGTTTCAAGGAG 59.999 52.381 0.00 0.00 40.02 3.69
107 108 1.000955 GACGAGAGCCTGTTTCAAGGA 59.999 52.381 0.00 0.00 40.02 3.36
108 109 1.433534 GACGAGAGCCTGTTTCAAGG 58.566 55.000 0.00 0.00 40.63 3.61
109 110 1.433534 GGACGAGAGCCTGTTTCAAG 58.566 55.000 0.00 0.00 0.00 3.02
112 113 4.600207 GGGACGAGAGCCTGTTTC 57.400 61.111 0.00 0.00 0.00 2.78
137 138 7.801315 CGTGTACTTTGTTGTGTTGCTTTATAT 59.199 33.333 0.00 0.00 0.00 0.86
139 140 5.968848 CGTGTACTTTGTTGTGTTGCTTTAT 59.031 36.000 0.00 0.00 0.00 1.40
140 141 5.325494 CGTGTACTTTGTTGTGTTGCTTTA 58.675 37.500 0.00 0.00 0.00 1.85
144 145 2.446282 CCGTGTACTTTGTTGTGTTGC 58.554 47.619 0.00 0.00 0.00 4.17
145 146 2.446282 GCCGTGTACTTTGTTGTGTTG 58.554 47.619 0.00 0.00 0.00 3.33
146 147 1.402613 GGCCGTGTACTTTGTTGTGTT 59.597 47.619 0.00 0.00 0.00 3.32
148 149 0.041663 CGGCCGTGTACTTTGTTGTG 60.042 55.000 19.50 0.00 0.00 3.33
151 152 0.939419 GTTCGGCCGTGTACTTTGTT 59.061 50.000 27.15 0.00 0.00 2.83
153 154 0.940519 TCGTTCGGCCGTGTACTTTG 60.941 55.000 27.15 9.45 0.00 2.77
154 155 0.037975 ATCGTTCGGCCGTGTACTTT 60.038 50.000 27.15 8.89 0.00 2.66
155 156 0.810648 TATCGTTCGGCCGTGTACTT 59.189 50.000 27.15 13.43 0.00 2.24
157 158 0.179166 TGTATCGTTCGGCCGTGTAC 60.179 55.000 27.15 19.67 0.00 2.90
158 159 0.099259 CTGTATCGTTCGGCCGTGTA 59.901 55.000 27.15 9.28 0.00 2.90
161 162 1.153901 CACTGTATCGTTCGGCCGT 60.154 57.895 27.15 7.91 0.00 5.68
162 163 1.153901 ACACTGTATCGTTCGGCCG 60.154 57.895 22.12 22.12 0.00 6.13
163 164 1.082117 CCACACTGTATCGTTCGGCC 61.082 60.000 0.00 0.00 0.00 6.13
164 165 0.389426 ACCACACTGTATCGTTCGGC 60.389 55.000 0.00 0.00 0.00 5.54
165 166 1.068125 TCACCACACTGTATCGTTCGG 60.068 52.381 0.00 0.00 0.00 4.30
166 167 2.251040 CTCACCACACTGTATCGTTCG 58.749 52.381 0.00 0.00 0.00 3.95
167 168 2.230508 TCCTCACCACACTGTATCGTTC 59.769 50.000 0.00 0.00 0.00 3.95
168 169 2.231478 CTCCTCACCACACTGTATCGTT 59.769 50.000 0.00 0.00 0.00 3.85
169 170 1.819288 CTCCTCACCACACTGTATCGT 59.181 52.381 0.00 0.00 0.00 3.73
170 171 1.135139 CCTCCTCACCACACTGTATCG 59.865 57.143 0.00 0.00 0.00 2.92
171 172 1.134670 GCCTCCTCACCACACTGTATC 60.135 57.143 0.00 0.00 0.00 2.24
172 173 0.905357 GCCTCCTCACCACACTGTAT 59.095 55.000 0.00 0.00 0.00 2.29
173 174 1.192146 GGCCTCCTCACCACACTGTA 61.192 60.000 0.00 0.00 0.00 2.74
174 175 2.520536 GGCCTCCTCACCACACTGT 61.521 63.158 0.00 0.00 0.00 3.55
175 176 2.348998 GGCCTCCTCACCACACTG 59.651 66.667 0.00 0.00 0.00 3.66
177 178 2.930562 AGGGCCTCCTCACCACAC 60.931 66.667 0.00 0.00 39.80 3.82
186 187 0.328258 TGCTTTGTAAGAGGGCCTCC 59.672 55.000 29.62 15.26 0.00 4.30
187 188 1.279271 TCTGCTTTGTAAGAGGGCCTC 59.721 52.381 26.42 26.42 0.00 4.70
189 190 2.426842 ATCTGCTTTGTAAGAGGGCC 57.573 50.000 0.00 0.00 0.00 5.80
190 191 5.897377 TTTAATCTGCTTTGTAAGAGGGC 57.103 39.130 0.00 0.00 0.00 5.19
191 192 7.687941 TCTTTTAATCTGCTTTGTAAGAGGG 57.312 36.000 0.00 0.00 0.00 4.30
193 194 9.907576 CGTATCTTTTAATCTGCTTTGTAAGAG 57.092 33.333 0.00 0.00 0.00 2.85
195 196 9.690434 GTCGTATCTTTTAATCTGCTTTGTAAG 57.310 33.333 0.00 0.00 0.00 2.34
197 198 8.766000 TGTCGTATCTTTTAATCTGCTTTGTA 57.234 30.769 0.00 0.00 0.00 2.41
203 204 8.827677 AGGTTAATGTCGTATCTTTTAATCTGC 58.172 33.333 0.00 0.00 0.00 4.26
210 211 9.715121 TTGTTCTAGGTTAATGTCGTATCTTTT 57.285 29.630 0.00 0.00 0.00 2.27
224 225 5.336213 CGAGGTGTTAGCTTGTTCTAGGTTA 60.336 44.000 0.00 0.00 0.00 2.85
249 250 0.536687 AGTCGTCGGTCAGGTCTTGA 60.537 55.000 0.00 0.00 0.00 3.02
251 252 1.242665 GGAGTCGTCGGTCAGGTCTT 61.243 60.000 0.00 0.00 0.00 3.01
261 262 2.041115 TGGAGCTCAGGAGTCGTCG 61.041 63.158 17.19 0.00 0.00 5.12
277 278 3.353836 CTTGGGGCGTTGTCGTGG 61.354 66.667 0.00 0.00 39.49 4.94
295 296 1.152383 GATACTTCGCCGCCACCTTC 61.152 60.000 0.00 0.00 0.00 3.46
311 314 3.877559 CTTGGACTCAGCAATGGTGATA 58.122 45.455 15.87 0.67 39.36 2.15
312 315 2.719739 CTTGGACTCAGCAATGGTGAT 58.280 47.619 15.87 6.36 39.36 3.06
315 318 0.111061 TGCTTGGACTCAGCAATGGT 59.889 50.000 0.00 0.00 35.46 3.55
324 327 1.251251 ATGCCTGTTTGCTTGGACTC 58.749 50.000 0.00 0.00 0.00 3.36
340 343 1.132453 GCTTCGGGTGAAAACCTATGC 59.868 52.381 0.00 0.00 32.66 3.14
364 367 0.107654 GTTGAGGGGCTCGTTATGCT 60.108 55.000 0.00 0.00 32.35 3.79
366 369 0.174845 TCGTTGAGGGGCTCGTTATG 59.825 55.000 0.00 0.00 32.35 1.90
369 372 2.035237 TTGTCGTTGAGGGGCTCGTT 62.035 55.000 0.00 0.00 32.35 3.85
381 384 2.325583 TGCTTCTTGGAGTTGTCGTT 57.674 45.000 0.00 0.00 0.00 3.85
426 429 2.098233 CGTGCTATTTGGCGTCGGT 61.098 57.895 0.00 0.00 34.52 4.69
452 455 1.721664 TATTCCCGAGTGTCCGAGCG 61.722 60.000 0.00 0.00 0.00 5.03
465 468 7.286313 AGGATCAAATGAAAGAGACTATTCCC 58.714 38.462 0.00 0.00 0.00 3.97
476 479 7.414540 CCCTACTTCGAAAGGATCAAATGAAAG 60.415 40.741 16.06 0.00 34.58 2.62
477 480 6.374333 CCCTACTTCGAAAGGATCAAATGAAA 59.626 38.462 16.06 0.00 34.58 2.69
479 482 5.428253 CCCTACTTCGAAAGGATCAAATGA 58.572 41.667 16.06 0.00 34.58 2.57
493 496 0.460987 CTTCTGCAGCCCCTACTTCG 60.461 60.000 9.47 0.00 0.00 3.79
527 531 9.807921 AAGAGGGACACAAATTTCTCTATTTTA 57.192 29.630 5.53 0.00 32.12 1.52
533 537 5.053978 ACAAGAGGGACACAAATTTCTCT 57.946 39.130 0.28 0.28 33.58 3.10
540 544 3.963129 AGACAAACAAGAGGGACACAAA 58.037 40.909 0.00 0.00 0.00 2.83
591 595 9.539825 TGCACTTTTTAAAACATTCACATATGT 57.460 25.926 1.41 1.41 40.37 2.29
592 596 9.796062 GTGCACTTTTTAAAACATTCACATATG 57.204 29.630 10.32 0.00 0.00 1.78
593 597 9.762933 AGTGCACTTTTTAAAACATTCACATAT 57.237 25.926 15.25 0.00 0.00 1.78
594 598 9.593134 AAGTGCACTTTTTAAAACATTCACATA 57.407 25.926 26.36 0.00 30.82 2.29
608 612 5.359576 TGAGTAACATGGAAGTGCACTTTTT 59.640 36.000 31.58 20.31 36.11 1.94
609 613 4.887071 TGAGTAACATGGAAGTGCACTTTT 59.113 37.500 31.58 22.76 36.11 2.27
610 614 4.460263 TGAGTAACATGGAAGTGCACTTT 58.540 39.130 31.58 17.73 36.11 2.66
615 619 3.609853 TGGATGAGTAACATGGAAGTGC 58.390 45.455 0.00 0.00 39.56 4.40
695 702 2.093128 GGGTTCGAGTGTGGGTAATGAT 60.093 50.000 0.00 0.00 0.00 2.45
696 703 1.276989 GGGTTCGAGTGTGGGTAATGA 59.723 52.381 0.00 0.00 0.00 2.57
702 1005 1.004918 GAGTGGGTTCGAGTGTGGG 60.005 63.158 0.00 0.00 0.00 4.61
709 1012 0.454600 GAGTATGCGAGTGGGTTCGA 59.545 55.000 0.00 0.00 43.03 3.71
711 1014 1.146358 GCGAGTATGCGAGTGGGTTC 61.146 60.000 0.00 0.00 0.00 3.62
712 1015 1.153628 GCGAGTATGCGAGTGGGTT 60.154 57.895 0.00 0.00 0.00 4.11
726 1032 1.302431 TGTGTGGTGGGAATGCGAG 60.302 57.895 0.00 0.00 0.00 5.03
831 1144 0.649992 ATGGGATGAGGGAGGGAAGA 59.350 55.000 0.00 0.00 0.00 2.87
860 1174 5.504853 AGGAAATGGATCTGGAGAAGTTTC 58.495 41.667 0.00 0.00 0.00 2.78
964 1278 4.862574 CACTTGTGCAGAATCAATGGAATG 59.137 41.667 0.00 0.00 0.00 2.67
1068 1382 2.066999 CCTGTACTCCCCCTCCAGC 61.067 68.421 0.00 0.00 0.00 4.85
1236 1550 3.314357 TGTACCTGTCGATGTAATCCTCG 59.686 47.826 0.00 0.00 41.39 4.63
1299 1613 2.099141 TCCAAAAGAGCTCCATGACG 57.901 50.000 10.93 0.00 0.00 4.35
1365 1679 4.936891 ACTTGAGTTCTTTGATTTGCACC 58.063 39.130 0.00 0.00 0.00 5.01
1434 1748 2.792290 CGCAGAACAGACCATCGCG 61.792 63.158 0.00 0.00 34.38 5.87
1521 1835 4.275810 ACTCATCCTTTGGACCATCAATG 58.724 43.478 0.00 0.00 32.98 2.82
1527 1841 7.466804 ACTTAATTAACTCATCCTTTGGACCA 58.533 34.615 0.00 0.00 32.98 4.02
1570 1884 2.213499 AGAAACAACCTTCAGTGCGAG 58.787 47.619 0.00 0.00 0.00 5.03
1573 1887 3.206150 TGAGAGAAACAACCTTCAGTGC 58.794 45.455 0.00 0.00 0.00 4.40
1770 2084 2.107750 ATGAGCCACGCCTCATCG 59.892 61.111 7.71 0.00 46.75 3.84
1857 2171 2.414481 CAGCGATATTGTGATAGGCTGC 59.586 50.000 0.00 0.00 39.87 5.25
2062 2386 3.557054 GGCACACTTGATAGTCTTCCACA 60.557 47.826 0.00 0.00 30.26 4.17
2354 2678 3.567585 TGATCCAGTCTTCTCTGCTATCG 59.432 47.826 0.00 0.00 33.26 2.92
2578 5570 7.338710 TGTGTCAAATAAATTTTTCCCACCAA 58.661 30.769 0.00 0.00 0.00 3.67
2775 5774 4.466828 CGAACTTTATGCTGTGAAACCAG 58.533 43.478 0.00 0.00 34.36 4.00
2780 5779 1.463056 CGGCGAACTTTATGCTGTGAA 59.537 47.619 0.00 0.00 0.00 3.18
2924 5923 1.379576 AGCAAGCATTCTCAGGGCC 60.380 57.895 0.00 0.00 0.00 5.80
3171 6170 1.750778 GTTCCCAATGCCATGTGGTAG 59.249 52.381 0.35 0.00 37.57 3.18
3224 6223 1.694844 TTGAGGTACTGTCGTCCACA 58.305 50.000 0.00 0.00 41.55 4.17
3236 6235 4.471025 TCCTGCAAGAGATTGATTGAGGTA 59.529 41.667 0.00 0.00 34.07 3.08
3332 6331 6.204688 GCGATGAAACCAATCTATCCACATAA 59.795 38.462 0.00 0.00 0.00 1.90
3343 6342 1.202114 TGCCAAGCGATGAAACCAATC 59.798 47.619 0.00 0.00 0.00 2.67
3394 6393 3.975246 GGCCATCCGTTTTGACGA 58.025 55.556 0.00 0.00 34.64 4.20
3410 6409 4.229096 CAACTGGAATGTCAATCAAACGG 58.771 43.478 0.00 0.00 0.00 4.44
3429 6428 2.943653 CGGCGACCAAGAACCAAC 59.056 61.111 0.00 0.00 0.00 3.77
3581 6580 1.109323 AGACAGGCAAACCACCAAGC 61.109 55.000 0.00 0.00 39.06 4.01
3587 6586 4.072131 GAGATAACAAGACAGGCAAACCA 58.928 43.478 0.00 0.00 39.06 3.67
3731 6736 1.243342 TGAGTTTTGGCATGGCTCCG 61.243 55.000 21.08 0.00 0.00 4.63
3755 6761 2.789092 CGCCACAATCTGAAATTCGAGC 60.789 50.000 0.00 0.00 0.00 5.03
3836 6845 4.897670 TCAATCCAGATGCAGAGATCACTA 59.102 41.667 0.00 0.00 0.00 2.74
3878 6887 2.678934 TCGTGAACCCCCTCCTCG 60.679 66.667 0.00 0.00 0.00 4.63
3915 6924 2.359975 AAGTAGGCTGGCCGCAAC 60.360 61.111 18.87 15.56 41.67 4.17
3950 6959 6.073222 CGCCTCAATACAACCTATGGAAATAC 60.073 42.308 0.00 0.00 0.00 1.89
3974 6983 2.725490 CATCAGTCGTTCTCATCTCCG 58.275 52.381 0.00 0.00 0.00 4.63
4001 7010 1.147817 AGACAATCTGGGTTGGGCTTT 59.852 47.619 0.00 0.00 33.40 3.51
4060 7076 0.770499 TTGGATTGTCAGACCCAGCA 59.230 50.000 0.00 0.00 0.00 4.41
4172 7188 7.664318 TCTTACCTTTTCCTCTGTTTTCCATAC 59.336 37.037 0.00 0.00 0.00 2.39
4216 7233 7.254421 GGAAACTCTGTTGCGATTTCAATTTTT 60.254 33.333 0.00 0.00 32.13 1.94
4217 7234 6.200854 GGAAACTCTGTTGCGATTTCAATTTT 59.799 34.615 0.00 0.00 32.13 1.82
4218 7235 5.691754 GGAAACTCTGTTGCGATTTCAATTT 59.308 36.000 0.00 0.00 32.13 1.82
4219 7236 5.221224 TGGAAACTCTGTTGCGATTTCAATT 60.221 36.000 0.00 0.00 32.13 2.32
4220 7237 4.278170 TGGAAACTCTGTTGCGATTTCAAT 59.722 37.500 0.00 0.00 32.13 2.57
4236 7256 8.598041 GTGATATAGTGAGGGATTATGGAAACT 58.402 37.037 0.00 0.00 0.00 2.66
4357 7377 8.997621 TTAGAGCGTAGATTCACTTATTTTGT 57.002 30.769 0.00 0.00 0.00 2.83
4364 7384 7.256286 ACGTATTTTAGAGCGTAGATTCACTT 58.744 34.615 0.00 0.00 35.71 3.16
4366 7386 6.911511 AGACGTATTTTAGAGCGTAGATTCAC 59.088 38.462 0.00 0.00 37.71 3.18
4376 7396 9.435802 CGGATGTATATAGACGTATTTTAGAGC 57.564 37.037 0.00 0.00 0.00 4.09
4442 7462 5.346522 ACAAATATAGTCCCTTCGTTCGTC 58.653 41.667 0.00 0.00 0.00 4.20
4444 7464 6.311935 TCAAACAAATATAGTCCCTTCGTTCG 59.688 38.462 0.00 0.00 0.00 3.95
4585 7605 4.201812 ATTCCAATGAATAAGACGCACACG 60.202 41.667 0.00 0.00 41.52 4.49
4618 7638 9.353431 TGCACAGATGTATTTGAATGGTTATAT 57.647 29.630 0.00 0.00 0.00 0.86
4619 7639 8.744568 TGCACAGATGTATTTGAATGGTTATA 57.255 30.769 0.00 0.00 0.00 0.98
4620 7640 7.643569 TGCACAGATGTATTTGAATGGTTAT 57.356 32.000 0.00 0.00 0.00 1.89
4621 7641 7.122501 ACATGCACAGATGTATTTGAATGGTTA 59.877 33.333 0.00 0.00 34.69 2.85
4622 7642 5.981088 TGCACAGATGTATTTGAATGGTT 57.019 34.783 0.00 0.00 0.00 3.67
4623 7643 5.419788 ACATGCACAGATGTATTTGAATGGT 59.580 36.000 0.00 0.00 34.69 3.55
4624 7644 5.898174 ACATGCACAGATGTATTTGAATGG 58.102 37.500 0.00 0.00 34.69 3.16
4625 7645 5.679792 CGACATGCACAGATGTATTTGAATG 59.320 40.000 0.00 0.00 36.67 2.67
4626 7646 5.355071 ACGACATGCACAGATGTATTTGAAT 59.645 36.000 0.00 0.00 36.67 2.57
4627 7647 4.694982 ACGACATGCACAGATGTATTTGAA 59.305 37.500 0.00 0.00 36.67 2.69
4628 7648 4.093261 CACGACATGCACAGATGTATTTGA 59.907 41.667 0.00 0.00 36.67 2.69
4629 7649 4.336932 CACGACATGCACAGATGTATTTG 58.663 43.478 0.00 0.00 36.67 2.32
4630 7650 3.374988 CCACGACATGCACAGATGTATTT 59.625 43.478 0.00 0.00 36.67 1.40
4631 7651 2.938451 CCACGACATGCACAGATGTATT 59.062 45.455 0.00 0.00 36.67 1.89
4632 7652 2.168313 TCCACGACATGCACAGATGTAT 59.832 45.455 0.00 0.00 36.67 2.29
4633 7653 1.548269 TCCACGACATGCACAGATGTA 59.452 47.619 0.00 0.00 36.67 2.29
4634 7654 0.321346 TCCACGACATGCACAGATGT 59.679 50.000 0.00 0.00 39.34 3.06
4635 7655 1.660167 ATCCACGACATGCACAGATG 58.340 50.000 0.00 0.00 0.00 2.90
4636 7656 3.541996 TTATCCACGACATGCACAGAT 57.458 42.857 0.00 0.00 0.00 2.90
4654 7674 7.432059 TGATGCACATGTTTCAAGTTGAATTA 58.568 30.769 18.69 11.19 36.11 1.40
4700 7720 7.224513 TCAAGTGTTGAATTGCACAAGCATAC 61.225 38.462 0.00 0.00 43.31 2.39
4707 7727 2.757314 TGGTCAAGTGTTGAATTGCACA 59.243 40.909 0.00 0.00 42.15 4.57
4710 7730 3.005684 TGGATGGTCAAGTGTTGAATTGC 59.994 43.478 0.00 0.00 42.15 3.56
4740 7760 8.125978 TGGAATTCAAGAGCAACAATTCTAAT 57.874 30.769 7.93 0.00 36.11 1.73
4769 7792 7.004086 GGTGATTGGAGGTTCATATATTTGGA 58.996 38.462 0.00 0.00 0.00 3.53
4804 7827 5.687730 AGCTATCGAGTCATGTAAATTCACG 59.312 40.000 0.00 0.00 0.00 4.35
4813 7836 4.820897 TGTTTTCAGCTATCGAGTCATGT 58.179 39.130 0.00 0.00 0.00 3.21
4852 7875 4.516365 AGAGACGGTTAGTAACAACTGG 57.484 45.455 14.81 1.49 38.81 4.00
4927 7950 5.559148 AAATGAGGTGTCTTCTGAGTTCT 57.441 39.130 0.00 0.00 0.00 3.01
4928 7951 5.529060 ACAAAATGAGGTGTCTTCTGAGTTC 59.471 40.000 0.00 0.00 0.00 3.01
4929 7952 5.440610 ACAAAATGAGGTGTCTTCTGAGTT 58.559 37.500 0.00 0.00 0.00 3.01
4930 7953 5.041191 ACAAAATGAGGTGTCTTCTGAGT 57.959 39.130 0.00 0.00 0.00 3.41
4931 7954 5.604010 GACAAAATGAGGTGTCTTCTGAG 57.396 43.478 0.00 0.00 40.82 3.35
4948 7971 1.760613 AGAACCAGTGGACGAGACAAA 59.239 47.619 18.40 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.