Multiple sequence alignment - TraesCS5A01G235500

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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 TraesCS5A01G235500 chr5A 100.000 4333 0 0 1 4333 451464671 451469003 0.000000e+00 8002
1 TraesCS5A01G235500 chr5D 93.786 2108 79 15 1896 3979 350997111 350999190 0.000000e+00 3120
2 TraesCS5A01G235500 chr5D 92.291 934 38 15 852 1777 350996083 350996990 0.000000e+00 1295
3 TraesCS5A01G235500 chr5D 91.189 715 31 12 136 823 350995375 350996084 0.000000e+00 942
4 TraesCS5A01G235500 chr5D 94.955 337 16 1 3996 4332 350999242 350999577 1.070000e-145 527
5 TraesCS5A01G235500 chr5D 97.115 104 2 1 1777 1879 350997021 350997124 1.600000e-39 174
6 TraesCS5A01G235500 chr5B 95.882 1360 51 5 2615 3972 411812916 411814272 0.000000e+00 2196
7 TraesCS5A01G235500 chr5B 92.066 1210 64 16 136 1325 411810455 411811652 0.000000e+00 1674
8 TraesCS5A01G235500 chr5B 82.822 652 60 19 1896 2513 411812304 411812937 1.770000e-148 536
9 TraesCS5A01G235500 chr5B 92.308 338 15 3 3996 4333 411814332 411814658 1.820000e-128 470
10 TraesCS5A01G235500 chr5B 88.073 109 6 1 1777 1878 411812208 411812316 5.880000e-24 122
11 TraesCS5A01G235500 chr3A 95.455 132 4 1 1 132 741395216 741395087 4.390000e-50 209
12 TraesCS5A01G235500 chr3A 95.455 132 4 1 1 132 741432234 741432105 4.390000e-50 209
13 TraesCS5A01G235500 chr3A 95.455 132 4 1 1 132 741501301 741501172 4.390000e-50 209
14 TraesCS5A01G235500 chr3A 95.455 132 5 1 1 132 741575479 741575349 4.390000e-50 209
15 TraesCS5A01G235500 chr3A 95.420 131 4 2 1 131 701344611 701344483 1.580000e-49 207
16 TraesCS5A01G235500 chr3A 94.697 132 5 1 1 132 741413516 741413387 2.040000e-48 204
17 TraesCS5A01G235500 chr3A 94.697 132 5 1 1 132 741556530 741556401 2.040000e-48 204
18 TraesCS5A01G235500 chr6A 95.420 131 4 1 1 131 7988514 7988642 1.580000e-49 207
19 TraesCS5A01G235500 chr1A 89.744 156 11 4 1 156 271887559 271887409 1.230000e-45 195


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 TraesCS5A01G235500 chr5A 451464671 451469003 4332 False 8002.0 8002 100.0000 1 4333 1 chr5A.!!$F1 4332
1 TraesCS5A01G235500 chr5D 350995375 350999577 4202 False 1211.6 3120 93.8672 136 4332 5 chr5D.!!$F1 4196
2 TraesCS5A01G235500 chr5B 411810455 411814658 4203 False 999.6 2196 90.2302 136 4333 5 chr5B.!!$F1 4197

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
838 866 0.108520 GGTTCCTCCGCGTAATGTGA 60.109 55.0 4.92 0.0 0.00 3.58 F
1431 1624 0.251297 CAGTGGCTGGATTGGGTTCA 60.251 55.0 0.00 0.0 0.00 3.18 F
2603 2884 0.741221 CACTAGGCTTCCTTCCACGC 60.741 60.0 0.00 0.0 34.61 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 2184 0.326595 TAAGGCGCCAGGACAAATCA 59.673 50.0 31.54 0.0 0.0 2.57 R
3101 3382 0.670546 ACGACCGGAGAAGTGCATTG 60.671 55.0 9.46 0.0 0.0 2.82 R
4261 4581 0.615850 AGGTAGCTCACTCCTTTGCC 59.384 55.0 0.00 0.0 0.0 4.52 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.692791 TGTCATTGATCCTACGTCGAG 57.307 47.619 0.00 0.00 0.00 4.04
21 22 3.275999 TGTCATTGATCCTACGTCGAGA 58.724 45.455 0.00 0.00 0.00 4.04
22 23 3.883489 TGTCATTGATCCTACGTCGAGAT 59.117 43.478 0.00 0.00 0.00 2.75
23 24 4.338400 TGTCATTGATCCTACGTCGAGATT 59.662 41.667 0.00 0.00 0.00 2.40
24 25 4.912766 GTCATTGATCCTACGTCGAGATTC 59.087 45.833 0.00 0.00 0.00 2.52
25 26 3.604065 TTGATCCTACGTCGAGATTCG 57.396 47.619 0.00 0.00 42.10 3.34
26 27 2.558378 TGATCCTACGTCGAGATTCGT 58.442 47.619 0.00 4.19 41.35 3.85
27 28 2.287103 TGATCCTACGTCGAGATTCGTG 59.713 50.000 8.84 0.36 41.35 4.35
28 29 1.730501 TCCTACGTCGAGATTCGTGT 58.269 50.000 8.84 2.15 41.35 4.49
29 30 1.395954 TCCTACGTCGAGATTCGTGTG 59.604 52.381 8.84 2.59 41.35 3.82
30 31 1.531264 CCTACGTCGAGATTCGTGTGG 60.531 57.143 8.84 7.24 41.35 4.17
31 32 1.395954 CTACGTCGAGATTCGTGTGGA 59.604 52.381 8.84 0.00 41.35 4.02
32 33 0.809385 ACGTCGAGATTCGTGTGGAT 59.191 50.000 0.00 0.00 41.35 3.41
33 34 2.011947 ACGTCGAGATTCGTGTGGATA 58.988 47.619 0.00 0.00 41.35 2.59
34 35 2.617308 ACGTCGAGATTCGTGTGGATAT 59.383 45.455 0.00 0.00 41.35 1.63
35 36 3.066342 ACGTCGAGATTCGTGTGGATATT 59.934 43.478 0.00 0.00 41.35 1.28
36 37 4.042398 CGTCGAGATTCGTGTGGATATTT 58.958 43.478 0.00 0.00 41.35 1.40
37 38 4.503007 CGTCGAGATTCGTGTGGATATTTT 59.497 41.667 0.00 0.00 41.35 1.82
38 39 5.331607 CGTCGAGATTCGTGTGGATATTTTC 60.332 44.000 0.00 0.00 41.35 2.29
39 40 5.749109 GTCGAGATTCGTGTGGATATTTTCT 59.251 40.000 0.00 0.00 41.35 2.52
40 41 6.255887 GTCGAGATTCGTGTGGATATTTTCTT 59.744 38.462 0.00 0.00 41.35 2.52
41 42 6.816640 TCGAGATTCGTGTGGATATTTTCTTT 59.183 34.615 0.00 0.00 41.35 2.52
42 43 7.333423 TCGAGATTCGTGTGGATATTTTCTTTT 59.667 33.333 0.00 0.00 41.35 2.27
43 44 7.962918 CGAGATTCGTGTGGATATTTTCTTTTT 59.037 33.333 0.00 0.00 34.72 1.94
77 78 9.965824 TTCTTTTCCTCTTTATGTTTGATTCAC 57.034 29.630 0.00 0.00 0.00 3.18
78 79 9.354673 TCTTTTCCTCTTTATGTTTGATTCACT 57.645 29.630 0.00 0.00 0.00 3.41
79 80 9.617975 CTTTTCCTCTTTATGTTTGATTCACTC 57.382 33.333 0.00 0.00 0.00 3.51
80 81 8.690203 TTTCCTCTTTATGTTTGATTCACTCA 57.310 30.769 0.00 0.00 0.00 3.41
81 82 7.672983 TCCTCTTTATGTTTGATTCACTCAC 57.327 36.000 0.00 0.00 32.17 3.51
82 83 7.453393 TCCTCTTTATGTTTGATTCACTCACT 58.547 34.615 0.00 0.00 32.17 3.41
83 84 7.939039 TCCTCTTTATGTTTGATTCACTCACTT 59.061 33.333 0.00 0.00 32.17 3.16
84 85 8.019669 CCTCTTTATGTTTGATTCACTCACTTG 58.980 37.037 0.00 0.00 32.17 3.16
85 86 7.874940 TCTTTATGTTTGATTCACTCACTTGG 58.125 34.615 0.00 0.00 32.17 3.61
86 87 7.719193 TCTTTATGTTTGATTCACTCACTTGGA 59.281 33.333 0.00 0.00 32.17 3.53
87 88 8.408043 TTTATGTTTGATTCACTCACTTGGAT 57.592 30.769 0.00 0.00 32.17 3.41
88 89 5.694231 TGTTTGATTCACTCACTTGGATG 57.306 39.130 0.00 0.00 32.17 3.51
89 90 5.132502 TGTTTGATTCACTCACTTGGATGT 58.867 37.500 0.00 0.00 32.17 3.06
90 91 5.008911 TGTTTGATTCACTCACTTGGATGTG 59.991 40.000 0.00 0.00 39.15 3.21
91 92 3.076621 TGATTCACTCACTTGGATGTGC 58.923 45.455 0.00 0.00 37.81 4.57
92 93 2.636647 TTCACTCACTTGGATGTGCA 57.363 45.000 0.00 0.00 37.81 4.57
93 94 2.636647 TCACTCACTTGGATGTGCAA 57.363 45.000 0.00 0.00 37.81 4.08
94 95 3.144657 TCACTCACTTGGATGTGCAAT 57.855 42.857 0.00 0.00 37.81 3.56
95 96 4.284829 TCACTCACTTGGATGTGCAATA 57.715 40.909 0.00 0.00 37.81 1.90
96 97 4.650734 TCACTCACTTGGATGTGCAATAA 58.349 39.130 0.00 0.00 37.81 1.40
97 98 4.455533 TCACTCACTTGGATGTGCAATAAC 59.544 41.667 0.00 0.00 37.81 1.89
98 99 4.456911 CACTCACTTGGATGTGCAATAACT 59.543 41.667 0.00 0.00 37.81 2.24
99 100 5.643348 CACTCACTTGGATGTGCAATAACTA 59.357 40.000 0.00 0.00 37.81 2.24
100 101 5.877012 ACTCACTTGGATGTGCAATAACTAG 59.123 40.000 0.00 0.00 37.81 2.57
101 102 6.048732 TCACTTGGATGTGCAATAACTAGA 57.951 37.500 0.00 0.00 37.81 2.43
102 103 6.108687 TCACTTGGATGTGCAATAACTAGAG 58.891 40.000 0.00 0.00 37.81 2.43
103 104 4.878397 ACTTGGATGTGCAATAACTAGAGC 59.122 41.667 0.00 0.00 0.00 4.09
104 105 4.486125 TGGATGTGCAATAACTAGAGCA 57.514 40.909 0.00 0.00 34.10 4.26
126 127 4.250116 CATCTAGATGTGCCCTAGACAC 57.750 50.000 22.42 8.47 43.57 3.67
130 131 3.478780 TGTGCCCTAGACACACCC 58.521 61.111 12.81 0.00 42.88 4.61
131 132 1.460497 TGTGCCCTAGACACACCCA 60.460 57.895 12.81 0.00 42.88 4.51
132 133 1.057275 TGTGCCCTAGACACACCCAA 61.057 55.000 12.81 0.00 42.88 4.12
133 134 0.605589 GTGCCCTAGACACACCCAAC 60.606 60.000 10.07 0.00 37.96 3.77
134 135 1.057275 TGCCCTAGACACACCCAACA 61.057 55.000 0.00 0.00 0.00 3.33
138 139 2.422235 CCCTAGACACACCCAACAAACA 60.422 50.000 0.00 0.00 0.00 2.83
144 145 3.030291 ACACACCCAACAAACACATCAT 58.970 40.909 0.00 0.00 0.00 2.45
147 148 5.127845 ACACACCCAACAAACACATCATAAA 59.872 36.000 0.00 0.00 0.00 1.40
160 161 6.902341 ACACATCATAAATTCAGTGTGTGAC 58.098 36.000 15.64 0.00 45.75 3.67
227 236 8.603242 AACGTGTATATATTCAGGGTTCAATC 57.397 34.615 14.16 0.00 0.00 2.67
241 250 4.823989 GGGTTCAATCCAATCATCCACTAG 59.176 45.833 0.00 0.00 0.00 2.57
258 267 7.801893 TCCACTAGGAATTTCAGTAACCTAA 57.198 36.000 0.00 0.00 42.23 2.69
307 317 5.334435 TGAATTCAGCGATCAATTCGATC 57.666 39.130 3.38 7.45 44.62 3.69
447 457 0.305922 GCGAAGATCCCTGCAAATCG 59.694 55.000 0.00 0.00 0.00 3.34
460 470 1.079127 AAATCGCCCACAGAGACCG 60.079 57.895 0.00 0.00 0.00 4.79
726 737 3.682292 ATCCCCTCGCTTCGTTGCC 62.682 63.158 0.00 0.00 0.00 4.52
776 803 4.216257 CCGATTTCCTCTTCTCTTTTTGCA 59.784 41.667 0.00 0.00 0.00 4.08
796 824 3.533697 CGAGAGGGGTTGGATAGGA 57.466 57.895 0.00 0.00 0.00 2.94
838 866 0.108520 GGTTCCTCCGCGTAATGTGA 60.109 55.000 4.92 0.00 0.00 3.58
843 871 1.794701 CCTCCGCGTAATGTGATGATG 59.205 52.381 4.92 0.00 0.00 3.07
849 877 3.611517 GCGTAATGTGATGATGTTCAGC 58.388 45.455 0.00 0.00 32.56 4.26
861 889 8.350722 GTGATGATGTTCAGCATTGATTAATCT 58.649 33.333 16.24 0.00 45.09 2.40
894 922 1.208535 CCTCACGTGTTAATGGGCCTA 59.791 52.381 16.51 0.00 0.00 3.93
895 923 2.277084 CTCACGTGTTAATGGGCCTAC 58.723 52.381 16.51 0.00 0.00 3.18
920 951 2.102578 CCGAAAAAGGATGGAGCCATT 58.897 47.619 3.11 0.00 36.70 3.16
922 953 2.159198 CGAAAAAGGATGGAGCCATTGG 60.159 50.000 3.11 0.00 36.70 3.16
923 954 2.629017 AAAAGGATGGAGCCATTGGT 57.371 45.000 4.26 0.00 36.70 3.67
936 967 1.247567 CATTGGTGTGGTGTTCCCTC 58.752 55.000 0.00 0.00 0.00 4.30
1057 1088 3.635191 TGCTGTGGTGGATGGCGA 61.635 61.111 0.00 0.00 0.00 5.54
1153 1184 2.705220 TCGTCATCGGCGACTACG 59.295 61.111 29.19 29.19 37.96 3.51
1311 1346 2.383298 ACGTTCAACACTGCGAAATG 57.617 45.000 0.00 0.00 0.00 2.32
1325 1360 3.129113 TGCGAAATGAATGATGAGGGTTG 59.871 43.478 0.00 0.00 0.00 3.77
1327 1362 3.067180 CGAAATGAATGATGAGGGTTGGG 59.933 47.826 0.00 0.00 0.00 4.12
1328 1363 3.763557 AATGAATGATGAGGGTTGGGT 57.236 42.857 0.00 0.00 0.00 4.51
1329 1364 3.763557 ATGAATGATGAGGGTTGGGTT 57.236 42.857 0.00 0.00 0.00 4.11
1330 1365 4.879295 ATGAATGATGAGGGTTGGGTTA 57.121 40.909 0.00 0.00 0.00 2.85
1331 1366 4.235079 TGAATGATGAGGGTTGGGTTAG 57.765 45.455 0.00 0.00 0.00 2.34
1332 1367 3.591527 TGAATGATGAGGGTTGGGTTAGT 59.408 43.478 0.00 0.00 0.00 2.24
1355 1390 2.696864 GGTGAACCATCTCCCCTCA 58.303 57.895 0.00 0.00 33.89 3.86
1359 1394 3.202151 GGTGAACCATCTCCCCTCATTTA 59.798 47.826 0.00 0.00 33.89 1.40
1404 1597 1.942657 TGCCGCTTTCATTGATAGCTC 59.057 47.619 21.59 15.17 35.15 4.09
1431 1624 0.251297 CAGTGGCTGGATTGGGTTCA 60.251 55.000 0.00 0.00 0.00 3.18
1437 1630 2.450476 GCTGGATTGGGTTCACATTCT 58.550 47.619 0.00 0.00 0.00 2.40
1438 1631 3.620488 GCTGGATTGGGTTCACATTCTA 58.380 45.455 0.00 0.00 0.00 2.10
1439 1632 3.629398 GCTGGATTGGGTTCACATTCTAG 59.371 47.826 6.14 6.14 34.48 2.43
1440 1633 4.848357 CTGGATTGGGTTCACATTCTAGT 58.152 43.478 0.00 0.00 29.93 2.57
1441 1634 5.629133 GCTGGATTGGGTTCACATTCTAGTA 60.629 44.000 10.36 0.00 34.12 1.82
1442 1635 6.381498 TGGATTGGGTTCACATTCTAGTAA 57.619 37.500 0.00 0.00 0.00 2.24
1443 1636 6.414732 TGGATTGGGTTCACATTCTAGTAAG 58.585 40.000 0.00 0.00 0.00 2.34
1471 1664 3.688694 TTCGATCGGAAAAGGGAGAAA 57.311 42.857 16.41 0.00 0.00 2.52
1487 1680 5.105063 GGGAGAAAGCAATGAATTTACAGC 58.895 41.667 0.00 0.00 0.00 4.40
1505 1698 1.079503 GCGACTGGGTTGATCTGTTC 58.920 55.000 0.00 0.00 0.00 3.18
1516 1709 4.521146 GTTGATCTGTTCATGGTGAGGAT 58.479 43.478 0.00 0.00 33.34 3.24
1601 1800 5.682943 TGGTAAAGTCGTCAGAAAATTGG 57.317 39.130 0.00 0.00 0.00 3.16
1612 1811 5.622378 GTCAGAAAATTGGAACGAGTCATC 58.378 41.667 0.00 0.00 0.00 2.92
1624 1823 3.364889 CGAGTCATCGGTGGCTATTAA 57.635 47.619 0.87 0.00 41.25 1.40
1627 1826 4.051922 GAGTCATCGGTGGCTATTAACAG 58.948 47.826 0.87 0.00 41.25 3.16
1630 1829 4.634443 GTCATCGGTGGCTATTAACAGTTT 59.366 41.667 0.00 0.00 0.00 2.66
1632 1831 3.340034 TCGGTGGCTATTAACAGTTTGG 58.660 45.455 0.00 0.00 0.00 3.28
1635 1834 4.216687 CGGTGGCTATTAACAGTTTGGAAA 59.783 41.667 0.00 0.00 0.00 3.13
1651 1850 6.596497 AGTTTGGAAATCATTGATTCATTGGC 59.404 34.615 12.15 3.39 30.29 4.52
1878 2120 6.916440 TCATCCTTCAACATTGAATTCACTG 58.084 36.000 20.70 20.70 45.26 3.66
1879 2121 6.491062 TCATCCTTCAACATTGAATTCACTGT 59.509 34.615 21.89 21.89 45.26 3.55
1880 2122 6.075762 TCCTTCAACATTGAATTCACTGTG 57.924 37.500 26.41 20.31 45.26 3.66
1881 2123 5.009911 TCCTTCAACATTGAATTCACTGTGG 59.990 40.000 26.41 23.96 45.26 4.17
1882 2124 5.221303 CCTTCAACATTGAATTCACTGTGGT 60.221 40.000 26.41 13.97 45.26 4.16
1883 2125 5.437289 TCAACATTGAATTCACTGTGGTC 57.563 39.130 26.41 4.27 39.28 4.02
1884 2126 4.886489 TCAACATTGAATTCACTGTGGTCA 59.114 37.500 26.41 10.41 39.28 4.02
1885 2127 4.836125 ACATTGAATTCACTGTGGTCAC 57.164 40.909 25.47 0.00 38.16 3.67
1886 2128 4.206375 ACATTGAATTCACTGTGGTCACA 58.794 39.130 25.47 3.64 38.16 3.58
1887 2129 4.644234 ACATTGAATTCACTGTGGTCACAA 59.356 37.500 25.47 10.10 41.33 3.33
1888 2130 5.126869 ACATTGAATTCACTGTGGTCACAAA 59.873 36.000 25.47 0.78 41.33 2.83
1889 2131 5.651387 TTGAATTCACTGTGGTCACAAAA 57.349 34.783 7.89 1.46 41.33 2.44
1890 2132 5.651387 TGAATTCACTGTGGTCACAAAAA 57.349 34.783 3.38 1.15 41.33 1.94
1936 2178 2.045561 TACATAATGGGGCACAACGG 57.954 50.000 0.00 0.00 0.00 4.44
2058 2301 7.332182 TGTTTGATTTTGGTTTTCACCTTGTAC 59.668 33.333 0.00 0.00 44.61 2.90
2123 2366 7.341512 TCCTGCATGTTCCATATCAAAAATACA 59.658 33.333 0.00 0.00 0.00 2.29
2137 2380 5.782845 TCAAAAATACATTGGCTAAAGGGGT 59.217 36.000 0.00 0.00 0.00 4.95
2248 2523 3.826157 CACCTTGAATTCCAGCCACTAAA 59.174 43.478 2.27 0.00 0.00 1.85
2445 2720 4.410099 GGAGGCATTGGAATTATGATCCA 58.590 43.478 0.00 0.00 45.09 3.41
2446 2721 4.219288 GGAGGCATTGGAATTATGATCCAC 59.781 45.833 0.00 0.00 46.37 4.02
2447 2722 4.154942 AGGCATTGGAATTATGATCCACC 58.845 43.478 0.00 0.00 46.37 4.61
2448 2723 4.140853 AGGCATTGGAATTATGATCCACCT 60.141 41.667 0.00 0.00 46.37 4.00
2449 2724 4.590222 GGCATTGGAATTATGATCCACCTT 59.410 41.667 0.00 0.00 46.37 3.50
2450 2725 5.510179 GGCATTGGAATTATGATCCACCTTG 60.510 44.000 0.00 0.00 46.37 3.61
2451 2726 5.302568 GCATTGGAATTATGATCCACCTTGA 59.697 40.000 0.00 0.00 46.37 3.02
2452 2727 6.736794 GCATTGGAATTATGATCCACCTTGAC 60.737 42.308 0.00 0.00 46.37 3.18
2519 2794 7.465989 TGCATCACATGATATTATTGCATACG 58.534 34.615 0.00 0.00 32.63 3.06
2534 2809 7.596749 ATTGCATACGTTATATTCCTGTAGC 57.403 36.000 0.00 0.00 0.00 3.58
2546 2825 1.134699 TCCTGTAGCTATGCAGTGTGC 60.135 52.381 9.74 0.00 45.29 4.57
2565 2844 1.741770 GTGTGCAAGGGCGGTAGAG 60.742 63.158 0.00 0.00 45.35 2.43
2603 2884 0.741221 CACTAGGCTTCCTTCCACGC 60.741 60.000 0.00 0.00 34.61 5.34
2623 2904 7.174253 TCCACGCTTTATCATTCAGTTTTAACT 59.826 33.333 0.00 0.00 40.60 2.24
2708 2989 9.384764 TCATTTGTATCCGTTTTGATGTACATA 57.615 29.630 8.71 0.00 0.00 2.29
2811 3092 6.320171 CACATCAGAAGCAGGAAATTACTTG 58.680 40.000 0.00 0.00 0.00 3.16
2851 3132 3.492337 GGTGATAACAAGGGTTTGGTGA 58.508 45.455 0.00 0.00 38.66 4.02
3003 3284 0.798776 CCTCGTTTGGATGACAGTGC 59.201 55.000 0.00 0.00 0.00 4.40
3025 3306 2.691409 TTCCTGAATAGGGAGTTGCG 57.309 50.000 0.00 0.00 44.70 4.85
3149 3430 7.192148 CATCAATTTTGTTGATGCCAAAAGA 57.808 32.000 15.31 0.00 46.03 2.52
3431 3712 7.765360 CCACAATGGATGTTAAGCAATTATGTT 59.235 33.333 0.00 0.00 41.46 2.71
3483 3764 4.156455 TCCCAAGTTCAGATAAGATGGC 57.844 45.455 0.00 0.00 0.00 4.40
3730 4011 3.128068 GCCCTCGTAACCAACCTTTTATG 59.872 47.826 0.00 0.00 0.00 1.90
3811 4092 1.227380 CAGGGACCAGCGATGTAGC 60.227 63.158 0.00 0.00 37.41 3.58
3832 4113 6.969828 AGCTAGTACAAATTCAAGTACAGC 57.030 37.500 18.79 18.79 42.26 4.40
3879 4160 4.636206 CCTTGCAGTAATACTTGGAAGGAC 59.364 45.833 24.34 1.43 41.99 3.85
3979 4264 4.028131 ACACATTCATGATTGGCCAAGAT 58.972 39.130 24.94 15.17 0.00 2.40
3980 4265 4.468510 ACACATTCATGATTGGCCAAGATT 59.531 37.500 24.94 7.11 0.00 2.40
3981 4266 5.047847 CACATTCATGATTGGCCAAGATTC 58.952 41.667 24.94 16.95 0.00 2.52
3982 4267 4.712829 ACATTCATGATTGGCCAAGATTCA 59.287 37.500 24.94 22.07 0.00 2.57
3986 4271 4.712829 TCATGATTGGCCAAGATTCACATT 59.287 37.500 24.94 2.80 0.00 2.71
3987 4272 4.724074 TGATTGGCCAAGATTCACATTC 57.276 40.909 24.94 13.23 0.00 2.67
3988 4273 4.087907 TGATTGGCCAAGATTCACATTCA 58.912 39.130 24.94 15.74 0.00 2.57
3989 4274 4.158949 TGATTGGCCAAGATTCACATTCAG 59.841 41.667 24.94 0.00 0.00 3.02
3990 4275 3.438216 TGGCCAAGATTCACATTCAGA 57.562 42.857 0.61 0.00 0.00 3.27
3991 4276 3.349927 TGGCCAAGATTCACATTCAGAG 58.650 45.455 0.61 0.00 0.00 3.35
3992 4277 3.009363 TGGCCAAGATTCACATTCAGAGA 59.991 43.478 0.61 0.00 0.00 3.10
4037 4357 6.446909 TTGGTGAAGTCATGCCCATATATA 57.553 37.500 0.00 0.00 0.00 0.86
4258 4578 1.670083 CGAACCACGAGGGGGAAAC 60.670 63.158 3.29 0.00 45.77 2.78
4285 4605 0.615850 AGGAGTGAGCTACCTTTGCC 59.384 55.000 0.00 0.00 0.00 4.52
4287 4607 1.677217 GGAGTGAGCTACCTTTGCCAG 60.677 57.143 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.275999 TCTCGACGTAGGATCAATGACA 58.724 45.455 0.00 0.00 0.00 3.58
1 2 3.965292 TCTCGACGTAGGATCAATGAC 57.035 47.619 0.00 0.00 0.00 3.06
2 3 4.319549 CGAATCTCGACGTAGGATCAATGA 60.320 45.833 0.00 0.00 43.74 2.57
3 4 3.908978 CGAATCTCGACGTAGGATCAATG 59.091 47.826 0.00 0.00 43.74 2.82
4 5 3.564644 ACGAATCTCGACGTAGGATCAAT 59.435 43.478 2.59 0.00 43.74 2.57
5 6 2.941064 ACGAATCTCGACGTAGGATCAA 59.059 45.455 2.59 0.00 43.74 2.57
6 7 2.287103 CACGAATCTCGACGTAGGATCA 59.713 50.000 2.59 0.00 43.74 2.92
7 8 2.287373 ACACGAATCTCGACGTAGGATC 59.713 50.000 2.59 0.00 43.74 3.36
8 9 2.031807 CACACGAATCTCGACGTAGGAT 59.968 50.000 2.59 0.00 43.74 3.24
9 10 1.395954 CACACGAATCTCGACGTAGGA 59.604 52.381 2.59 0.00 43.74 2.94
10 11 1.531264 CCACACGAATCTCGACGTAGG 60.531 57.143 2.59 1.36 43.74 3.18
11 12 1.395954 TCCACACGAATCTCGACGTAG 59.604 52.381 2.59 0.00 43.74 3.51
12 13 1.441738 TCCACACGAATCTCGACGTA 58.558 50.000 2.59 0.00 43.74 3.57
13 14 0.809385 ATCCACACGAATCTCGACGT 59.191 50.000 2.59 0.00 43.74 4.34
14 15 2.750301 TATCCACACGAATCTCGACG 57.250 50.000 2.59 0.00 43.74 5.12
15 16 5.749109 AGAAAATATCCACACGAATCTCGAC 59.251 40.000 2.59 0.00 43.74 4.20
16 17 5.902681 AGAAAATATCCACACGAATCTCGA 58.097 37.500 2.59 0.00 43.74 4.04
17 18 6.589830 AAGAAAATATCCACACGAATCTCG 57.410 37.500 0.00 0.00 46.93 4.04
51 52 9.965824 GTGAATCAAACATAAAGAGGAAAAGAA 57.034 29.630 0.00 0.00 0.00 2.52
52 53 9.354673 AGTGAATCAAACATAAAGAGGAAAAGA 57.645 29.630 0.00 0.00 0.00 2.52
53 54 9.617975 GAGTGAATCAAACATAAAGAGGAAAAG 57.382 33.333 0.00 0.00 0.00 2.27
54 55 9.130661 TGAGTGAATCAAACATAAAGAGGAAAA 57.869 29.630 0.00 0.00 34.02 2.29
55 56 8.567948 GTGAGTGAATCAAACATAAAGAGGAAA 58.432 33.333 0.00 0.00 40.43 3.13
56 57 7.939039 AGTGAGTGAATCAAACATAAAGAGGAA 59.061 33.333 0.00 0.00 40.43 3.36
57 58 7.453393 AGTGAGTGAATCAAACATAAAGAGGA 58.547 34.615 0.00 0.00 40.43 3.71
58 59 7.678947 AGTGAGTGAATCAAACATAAAGAGG 57.321 36.000 0.00 0.00 40.43 3.69
59 60 8.019669 CCAAGTGAGTGAATCAAACATAAAGAG 58.980 37.037 0.00 0.00 40.43 2.85
60 61 7.719193 TCCAAGTGAGTGAATCAAACATAAAGA 59.281 33.333 0.00 0.00 40.43 2.52
61 62 7.874940 TCCAAGTGAGTGAATCAAACATAAAG 58.125 34.615 0.00 0.00 40.43 1.85
62 63 7.815840 TCCAAGTGAGTGAATCAAACATAAA 57.184 32.000 0.00 0.00 40.43 1.40
63 64 7.448161 ACATCCAAGTGAGTGAATCAAACATAA 59.552 33.333 0.00 0.00 40.43 1.90
64 65 6.942005 ACATCCAAGTGAGTGAATCAAACATA 59.058 34.615 0.00 0.00 40.43 2.29
65 66 5.771666 ACATCCAAGTGAGTGAATCAAACAT 59.228 36.000 0.00 0.00 40.43 2.71
66 67 5.008911 CACATCCAAGTGAGTGAATCAAACA 59.991 40.000 0.00 0.00 42.05 2.83
67 68 5.455392 CACATCCAAGTGAGTGAATCAAAC 58.545 41.667 0.00 0.00 42.05 2.93
68 69 4.022935 GCACATCCAAGTGAGTGAATCAAA 60.023 41.667 0.00 0.00 42.05 2.69
69 70 3.503363 GCACATCCAAGTGAGTGAATCAA 59.497 43.478 0.00 0.00 42.05 2.57
70 71 3.076621 GCACATCCAAGTGAGTGAATCA 58.923 45.455 0.00 0.00 42.05 2.57
71 72 3.076621 TGCACATCCAAGTGAGTGAATC 58.923 45.455 0.00 0.00 42.05 2.52
72 73 3.144657 TGCACATCCAAGTGAGTGAAT 57.855 42.857 0.00 0.00 42.05 2.57
73 74 2.636647 TGCACATCCAAGTGAGTGAA 57.363 45.000 0.00 0.00 42.05 3.18
74 75 2.636647 TTGCACATCCAAGTGAGTGA 57.363 45.000 0.00 0.00 42.05 3.41
75 76 4.456911 AGTTATTGCACATCCAAGTGAGTG 59.543 41.667 0.00 0.00 42.05 3.51
76 77 4.655963 AGTTATTGCACATCCAAGTGAGT 58.344 39.130 0.00 0.00 42.05 3.41
77 78 6.108687 TCTAGTTATTGCACATCCAAGTGAG 58.891 40.000 0.00 0.00 42.05 3.51
78 79 6.048732 TCTAGTTATTGCACATCCAAGTGA 57.951 37.500 0.00 0.00 42.05 3.41
79 80 5.220739 GCTCTAGTTATTGCACATCCAAGTG 60.221 44.000 0.00 0.00 42.37 3.16
80 81 4.878397 GCTCTAGTTATTGCACATCCAAGT 59.122 41.667 0.00 0.00 0.00 3.16
81 82 4.877823 TGCTCTAGTTATTGCACATCCAAG 59.122 41.667 0.00 0.00 0.00 3.61
82 83 4.842574 TGCTCTAGTTATTGCACATCCAA 58.157 39.130 0.00 0.00 0.00 3.53
83 84 4.486125 TGCTCTAGTTATTGCACATCCA 57.514 40.909 0.00 0.00 0.00 3.41
105 106 3.638627 TGTGTCTAGGGCACATCTAGATG 59.361 47.826 27.63 27.63 43.25 2.90
106 107 3.639094 GTGTGTCTAGGGCACATCTAGAT 59.361 47.826 18.92 0.00 46.66 1.98
107 108 3.024547 GTGTGTCTAGGGCACATCTAGA 58.975 50.000 18.92 0.00 46.66 2.43
108 109 2.101582 GGTGTGTCTAGGGCACATCTAG 59.898 54.545 18.92 0.00 46.66 2.43
109 110 2.108168 GGTGTGTCTAGGGCACATCTA 58.892 52.381 18.92 0.21 46.66 1.98
110 111 0.905357 GGTGTGTCTAGGGCACATCT 59.095 55.000 18.92 0.00 46.66 2.90
111 112 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.000 18.92 18.25 46.66 3.06
112 113 0.840288 TGGGTGTGTCTAGGGCACAT 60.840 55.000 18.92 0.00 46.66 3.21
113 114 1.057275 TTGGGTGTGTCTAGGGCACA 61.057 55.000 14.22 14.22 43.60 4.57
114 115 0.605589 GTTGGGTGTGTCTAGGGCAC 60.606 60.000 10.20 10.20 37.37 5.01
115 116 1.057275 TGTTGGGTGTGTCTAGGGCA 61.057 55.000 0.00 0.00 0.00 5.36
116 117 0.109723 TTGTTGGGTGTGTCTAGGGC 59.890 55.000 0.00 0.00 0.00 5.19
117 118 2.227194 GTTTGTTGGGTGTGTCTAGGG 58.773 52.381 0.00 0.00 0.00 3.53
118 119 2.616842 GTGTTTGTTGGGTGTGTCTAGG 59.383 50.000 0.00 0.00 0.00 3.02
119 120 3.275143 TGTGTTTGTTGGGTGTGTCTAG 58.725 45.455 0.00 0.00 0.00 2.43
120 121 3.351794 TGTGTTTGTTGGGTGTGTCTA 57.648 42.857 0.00 0.00 0.00 2.59
121 122 2.208132 TGTGTTTGTTGGGTGTGTCT 57.792 45.000 0.00 0.00 0.00 3.41
122 123 2.425312 TGATGTGTTTGTTGGGTGTGTC 59.575 45.455 0.00 0.00 0.00 3.67
123 124 2.451490 TGATGTGTTTGTTGGGTGTGT 58.549 42.857 0.00 0.00 0.00 3.72
124 125 3.731652 ATGATGTGTTTGTTGGGTGTG 57.268 42.857 0.00 0.00 0.00 3.82
125 126 5.860941 TTTATGATGTGTTTGTTGGGTGT 57.139 34.783 0.00 0.00 0.00 4.16
126 127 6.927936 TGAATTTATGATGTGTTTGTTGGGTG 59.072 34.615 0.00 0.00 0.00 4.61
127 128 7.060383 TGAATTTATGATGTGTTTGTTGGGT 57.940 32.000 0.00 0.00 0.00 4.51
128 129 7.116662 CACTGAATTTATGATGTGTTTGTTGGG 59.883 37.037 0.00 0.00 0.00 4.12
129 130 7.652909 ACACTGAATTTATGATGTGTTTGTTGG 59.347 33.333 0.00 0.00 35.47 3.77
130 131 8.481641 CACACTGAATTTATGATGTGTTTGTTG 58.518 33.333 0.00 0.00 36.65 3.33
131 132 8.196771 ACACACTGAATTTATGATGTGTTTGTT 58.803 29.630 2.11 0.00 46.28 2.83
132 133 7.648908 CACACACTGAATTTATGATGTGTTTGT 59.351 33.333 5.14 0.00 46.28 2.83
133 134 7.861872 TCACACACTGAATTTATGATGTGTTTG 59.138 33.333 5.14 0.00 46.28 2.93
134 135 7.862372 GTCACACACTGAATTTATGATGTGTTT 59.138 33.333 5.14 0.00 46.28 2.83
138 139 7.692460 ATGTCACACACTGAATTTATGATGT 57.308 32.000 0.00 0.00 0.00 3.06
147 148 8.054152 TGCAATTATAATGTCACACACTGAAT 57.946 30.769 0.00 0.00 0.00 2.57
190 192 1.769733 TACACGTTAACTGCACGACC 58.230 50.000 3.71 0.00 40.20 4.79
227 236 6.125029 ACTGAAATTCCTAGTGGATGATTGG 58.875 40.000 0.00 0.00 42.81 3.16
241 250 8.349568 ACCAAAGATTAGGTTACTGAAATTCC 57.650 34.615 0.00 0.00 33.39 3.01
275 285 5.521372 TGATCGCTGAATTCAAGATACTGTG 59.479 40.000 19.82 9.85 0.00 3.66
276 286 5.664457 TGATCGCTGAATTCAAGATACTGT 58.336 37.500 19.82 5.21 0.00 3.55
282 292 5.147767 CGAATTGATCGCTGAATTCAAGA 57.852 39.130 9.88 12.04 45.89 3.02
307 317 0.109597 GCTCGATTTGGCACCAGTTG 60.110 55.000 0.00 0.00 0.00 3.16
447 457 2.185310 ATTGACCGGTCTCTGTGGGC 62.185 60.000 33.39 6.67 0.00 5.36
578 589 3.608662 TTCTGGGTCGACGCCGTT 61.609 61.111 27.39 0.00 37.05 4.44
726 737 2.027653 AGAAAAGGCGAGAAGGAAGGAG 60.028 50.000 0.00 0.00 0.00 3.69
776 803 0.398664 CCTATCCAACCCCTCTCGGT 60.399 60.000 0.00 0.00 37.93 4.69
796 824 0.400213 TCCGAGTCAAAGCCCAACAT 59.600 50.000 0.00 0.00 0.00 2.71
831 859 7.576861 ATCAATGCTGAACATCATCACATTA 57.423 32.000 0.00 0.00 38.34 1.90
832 860 5.907866 TCAATGCTGAACATCATCACATT 57.092 34.783 0.00 0.00 38.34 2.71
833 861 6.465439 AATCAATGCTGAACATCATCACAT 57.535 33.333 0.00 0.00 38.34 3.21
834 862 5.907866 AATCAATGCTGAACATCATCACA 57.092 34.783 0.00 0.00 38.34 3.58
835 863 8.350722 AGATTAATCAATGCTGAACATCATCAC 58.649 33.333 17.56 0.00 38.34 3.06
838 866 7.658261 CCAGATTAATCAATGCTGAACATCAT 58.342 34.615 17.56 0.00 38.34 2.45
843 871 4.500375 GGGCCAGATTAATCAATGCTGAAC 60.500 45.833 17.56 4.40 34.49 3.18
849 877 4.262721 CCCATTGGGCCAGATTAATCAATG 60.263 45.833 17.56 15.51 40.33 2.82
880 908 2.052782 CCCAGTAGGCCCATTAACAC 57.947 55.000 0.00 0.00 0.00 3.32
894 922 0.611896 CCATCCTTTTTCGGCCCAGT 60.612 55.000 0.00 0.00 0.00 4.00
895 923 0.323360 TCCATCCTTTTTCGGCCCAG 60.323 55.000 0.00 0.00 0.00 4.45
902 930 2.833943 ACCAATGGCTCCATCCTTTTTC 59.166 45.455 0.00 0.00 35.31 2.29
904 932 2.181975 CACCAATGGCTCCATCCTTTT 58.818 47.619 0.00 0.00 35.31 2.27
907 935 0.033796 CACACCAATGGCTCCATCCT 60.034 55.000 0.00 0.00 35.31 3.24
920 951 0.626382 TTTGAGGGAACACCACACCA 59.374 50.000 0.00 0.00 39.69 4.17
943 974 1.767681 CCTCCTTCCTCTCCCAGATTG 59.232 57.143 0.00 0.00 0.00 2.67
1223 1254 1.597663 GTTCGGGCGGAGTATGAAATG 59.402 52.381 0.00 0.00 0.00 2.32
1224 1255 1.805120 CGTTCGGGCGGAGTATGAAAT 60.805 52.381 0.00 0.00 0.00 2.17
1226 1257 1.140161 CGTTCGGGCGGAGTATGAA 59.860 57.895 0.00 0.00 0.00 2.57
1227 1258 1.105167 ATCGTTCGGGCGGAGTATGA 61.105 55.000 0.00 0.00 0.00 2.15
1311 1346 4.200092 GACTAACCCAACCCTCATCATTC 58.800 47.826 0.00 0.00 0.00 2.67
1325 1360 1.739196 GTTCACCCGCGACTAACCC 60.739 63.158 8.23 0.00 0.00 4.11
1327 1362 0.390735 ATGGTTCACCCGCGACTAAC 60.391 55.000 8.23 6.36 35.15 2.34
1328 1363 0.108520 GATGGTTCACCCGCGACTAA 60.109 55.000 8.23 0.00 35.15 2.24
1329 1364 0.968901 AGATGGTTCACCCGCGACTA 60.969 55.000 8.23 0.00 35.15 2.59
1330 1365 2.227089 GAGATGGTTCACCCGCGACT 62.227 60.000 8.23 0.00 35.15 4.18
1331 1366 1.810030 GAGATGGTTCACCCGCGAC 60.810 63.158 8.23 0.00 35.15 5.19
1332 1367 2.577059 GAGATGGTTCACCCGCGA 59.423 61.111 8.23 0.00 35.15 5.87
1353 1388 6.654161 CCTGCCATGTTTTTCCAAATAAATGA 59.346 34.615 0.00 0.00 0.00 2.57
1354 1389 6.654161 TCCTGCCATGTTTTTCCAAATAAATG 59.346 34.615 0.00 0.00 0.00 2.32
1355 1390 6.654582 GTCCTGCCATGTTTTTCCAAATAAAT 59.345 34.615 0.00 0.00 0.00 1.40
1359 1394 3.647590 AGTCCTGCCATGTTTTTCCAAAT 59.352 39.130 0.00 0.00 0.00 2.32
1388 1581 8.915871 TGTAAATTTGAGCTATCAATGAAAGC 57.084 30.769 0.00 0.00 44.75 3.51
1404 1597 4.497300 CCAATCCAGCCACTGTAAATTTG 58.503 43.478 0.00 0.00 0.00 2.32
1439 1632 9.339492 CCTTTTCCGATCGAATATACTACTTAC 57.661 37.037 18.66 0.00 0.00 2.34
1440 1633 8.517878 CCCTTTTCCGATCGAATATACTACTTA 58.482 37.037 18.66 0.00 0.00 2.24
1441 1634 7.232127 TCCCTTTTCCGATCGAATATACTACTT 59.768 37.037 18.66 0.00 0.00 2.24
1442 1635 6.718454 TCCCTTTTCCGATCGAATATACTACT 59.282 38.462 18.66 0.00 0.00 2.57
1443 1636 6.917533 TCCCTTTTCCGATCGAATATACTAC 58.082 40.000 18.66 0.00 0.00 2.73
1471 1664 3.127548 CCAGTCGCTGTAAATTCATTGCT 59.872 43.478 6.19 0.00 0.00 3.91
1487 1680 2.455674 TGAACAGATCAACCCAGTCG 57.544 50.000 0.00 0.00 34.30 4.18
1505 1698 2.133281 TGCAAAGGATCCTCACCATG 57.867 50.000 16.52 10.45 0.00 3.66
1535 1728 6.286758 ACTCGTTCAATATTCTCATCTGCAT 58.713 36.000 0.00 0.00 0.00 3.96
1601 1800 0.454600 TAGCCACCGATGACTCGTTC 59.545 55.000 0.00 0.00 43.49 3.95
1612 1811 3.340034 TCCAAACTGTTAATAGCCACCG 58.660 45.455 0.00 0.00 0.00 4.94
1624 1823 7.604927 CCAATGAATCAATGATTTCCAAACTGT 59.395 33.333 10.09 0.00 31.89 3.55
1627 1826 6.372103 TGCCAATGAATCAATGATTTCCAAAC 59.628 34.615 10.09 0.00 31.89 2.93
1630 1829 5.678955 TGCCAATGAATCAATGATTTCCA 57.321 34.783 10.09 4.97 31.89 3.53
1632 1831 9.355215 GAGATATGCCAATGAATCAATGATTTC 57.645 33.333 10.09 4.52 31.89 2.17
1635 1834 9.175312 GTAGAGATATGCCAATGAATCAATGAT 57.825 33.333 0.00 0.00 0.00 2.45
1651 1850 5.189342 AGCCCCAGATCAATGTAGAGATATG 59.811 44.000 0.00 0.00 34.23 1.78
1902 2144 9.573166 CCCCATTATGTATTCTATTTCAGTGAA 57.427 33.333 0.08 0.08 0.00 3.18
1914 2156 3.004315 CCGTTGTGCCCCATTATGTATTC 59.996 47.826 0.00 0.00 0.00 1.75
1936 2178 2.867429 CGCCAGGACAAATCAAATCAC 58.133 47.619 0.00 0.00 0.00 3.06
1942 2184 0.326595 TAAGGCGCCAGGACAAATCA 59.673 50.000 31.54 0.00 0.00 2.57
1943 2185 1.604278 GATAAGGCGCCAGGACAAATC 59.396 52.381 31.54 15.30 0.00 2.17
2028 2271 6.374053 AGGTGAAAACCAAAATCAAACAAAGG 59.626 34.615 0.00 0.00 0.00 3.11
2058 2301 6.780457 ACTATCAACTCCAATTTTCATGGG 57.220 37.500 0.00 0.00 38.54 4.00
2123 2366 2.923629 TGGACTTACCCCTTTAGCCAAT 59.076 45.455 0.00 0.00 38.00 3.16
2151 2412 6.605471 TTGCAGAGAGGTCTCACTTTTATA 57.395 37.500 9.64 0.00 45.21 0.98
2191 2452 1.595993 CGTGTCGGACTCAGATGGGT 61.596 60.000 9.88 0.00 0.00 4.51
2248 2523 2.573462 TGCTTGAGAATTCAGCCCTAGT 59.427 45.455 8.44 0.00 34.15 2.57
2410 2685 0.326595 TGCCTCCCAATTCGCAAGTA 59.673 50.000 0.00 0.00 39.48 2.24
2416 2691 1.473258 TTCCAATGCCTCCCAATTCG 58.527 50.000 0.00 0.00 0.00 3.34
2445 2720 8.611051 AATAGAATAGTAGAAGGTGTCAAGGT 57.389 34.615 0.00 0.00 0.00 3.50
2447 2722 9.685828 GCTAATAGAATAGTAGAAGGTGTCAAG 57.314 37.037 0.00 0.00 41.47 3.02
2448 2723 9.422681 AGCTAATAGAATAGTAGAAGGTGTCAA 57.577 33.333 0.00 0.00 41.47 3.18
2449 2724 8.851145 CAGCTAATAGAATAGTAGAAGGTGTCA 58.149 37.037 0.00 0.00 41.47 3.58
2450 2725 8.852135 ACAGCTAATAGAATAGTAGAAGGTGTC 58.148 37.037 0.00 0.00 41.47 3.67
2451 2726 8.770010 ACAGCTAATAGAATAGTAGAAGGTGT 57.230 34.615 0.00 0.00 41.47 4.16
2483 2758 3.947196 TCATGTGATGCAACTATGGAACC 59.053 43.478 0.00 0.00 0.00 3.62
2519 2794 7.116948 CACACTGCATAGCTACAGGAATATAAC 59.883 40.741 14.07 0.00 38.25 1.89
2533 2808 1.133253 CACACGCACACTGCATAGC 59.867 57.895 0.00 0.00 45.36 2.97
2534 2809 1.133253 GCACACGCACACTGCATAG 59.867 57.895 0.00 0.00 45.36 2.23
2546 2825 3.118454 CTACCGCCCTTGCACACG 61.118 66.667 0.00 0.00 37.32 4.49
2811 3092 1.069227 CCGTCAACTGTAAAGCAAGCC 60.069 52.381 0.00 0.00 0.00 4.35
3003 3284 3.282885 GCAACTCCCTATTCAGGAAAGG 58.717 50.000 0.00 0.00 45.91 3.11
3025 3306 6.727824 TCATCAAGCTTAAACAACTCTAGC 57.272 37.500 0.00 0.00 0.00 3.42
3101 3382 0.670546 ACGACCGGAGAAGTGCATTG 60.671 55.000 9.46 0.00 0.00 2.82
3141 3422 3.681417 ACGGAATAGTTACGTCTTTTGGC 59.319 43.478 0.00 0.00 35.77 4.52
3168 3449 8.411683 GGATTCTCTGCATCAAGAACAATATTT 58.588 33.333 8.09 0.00 34.52 1.40
3181 3462 3.058450 CTCATGTCGGATTCTCTGCATC 58.942 50.000 0.00 0.00 0.00 3.91
3326 3607 9.625747 CTGCAGAGGAGTATATAATCTCAGATA 57.374 37.037 8.42 0.00 32.93 1.98
3431 3712 9.481340 GTGAGAACATGCTATCATTTATCTGTA 57.519 33.333 0.00 0.00 0.00 2.74
3438 3719 7.446625 GGATTAGGTGAGAACATGCTATCATTT 59.553 37.037 0.00 0.00 0.00 2.32
3483 3764 0.803117 CATGAAGAGTGGCAGCAGTG 59.197 55.000 0.00 0.00 0.00 3.66
3578 3859 7.227512 AGTGATTACAGAGAGTTTCTTTGGTTG 59.772 37.037 2.31 0.00 33.35 3.77
3637 3918 6.158023 TCAAGAGTAACTTCGGAAAGAACT 57.842 37.500 0.00 0.00 36.61 3.01
3811 4092 7.622256 GCAGTGCTGTACTTGAATTTGTACTAG 60.622 40.741 8.18 0.00 37.60 2.57
3832 4113 3.542712 ATAACAGAAACGCAAGCAGTG 57.457 42.857 0.00 0.00 45.62 3.66
3842 4123 5.438761 ACTGCAAGGTGAATAACAGAAAC 57.561 39.130 0.00 0.00 39.30 2.78
3879 4160 5.027206 CTTGTTGTCAAGTGCATCTACAG 57.973 43.478 0.00 0.00 44.09 2.74
3901 4182 5.637387 GGTGATTTTGAAGAGTCTCTGAGAC 59.363 44.000 26.43 26.43 45.38 3.36
3979 4264 3.708403 ATGGCAGTCTCTGAATGTGAA 57.292 42.857 0.00 0.00 32.44 3.18
3980 4265 3.008266 TCAATGGCAGTCTCTGAATGTGA 59.992 43.478 0.00 0.00 32.44 3.58
3981 4266 3.340928 TCAATGGCAGTCTCTGAATGTG 58.659 45.455 0.00 0.00 32.44 3.21
3982 4267 3.008813 ACTCAATGGCAGTCTCTGAATGT 59.991 43.478 0.00 0.00 32.44 2.71
3986 4271 3.405831 CAAACTCAATGGCAGTCTCTGA 58.594 45.455 0.00 0.00 32.44 3.27
3987 4272 2.095364 GCAAACTCAATGGCAGTCTCTG 60.095 50.000 0.00 0.00 34.12 3.35
3988 4273 2.157738 GCAAACTCAATGGCAGTCTCT 58.842 47.619 0.00 0.00 0.00 3.10
3989 4274 2.157738 AGCAAACTCAATGGCAGTCTC 58.842 47.619 0.00 0.00 0.00 3.36
3990 4275 2.283145 AGCAAACTCAATGGCAGTCT 57.717 45.000 0.00 0.00 0.00 3.24
3991 4276 3.503748 AGTAAGCAAACTCAATGGCAGTC 59.496 43.478 0.00 0.00 0.00 3.51
3992 4277 3.490348 AGTAAGCAAACTCAATGGCAGT 58.510 40.909 0.00 0.00 0.00 4.40
4037 4357 1.081892 CGCTCTGCAGTTACAAGCAT 58.918 50.000 20.46 0.00 40.42 3.79
4133 4453 1.372128 GTACGACGCCAAGAACGGT 60.372 57.895 0.00 0.00 34.00 4.83
4241 4561 1.303074 GGTTTCCCCCTCGTGGTTC 60.303 63.158 2.33 0.00 0.00 3.62
4242 4562 2.841317 GGTTTCCCCCTCGTGGTT 59.159 61.111 2.33 0.00 0.00 3.67
4252 4572 1.977009 CTCCTTTGCCGGGTTTCCC 60.977 63.158 2.18 0.00 41.09 3.97
4258 4578 1.899437 TAGCTCACTCCTTTGCCGGG 61.899 60.000 2.18 0.00 0.00 5.73
4261 4581 0.615850 AGGTAGCTCACTCCTTTGCC 59.384 55.000 0.00 0.00 0.00 4.52
4285 4605 6.204882 AGTCATTTTTCTTCCGTTTCTACCTG 59.795 38.462 0.00 0.00 0.00 4.00
4287 4607 6.204108 TCAGTCATTTTTCTTCCGTTTCTACC 59.796 38.462 0.00 0.00 0.00 3.18
4293 4613 5.126384 TGGTTTCAGTCATTTTTCTTCCGTT 59.874 36.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.