Multiple sequence alignment - TraesCS6A01G027500

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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 TraesCS6A01G027500 chr6A 100.000 2357 0 0 1 2357 13879837 13877481 0.000000e+00 4353.0
1 TraesCS6A01G027500 chr6D 96.888 1189 37 0 627 1815 142136692 142135504 0.000000e+00 1991.0
2 TraesCS6A01G027500 chr6D 95.963 1189 47 1 627 1815 57791142 57789955 0.000000e+00 1929.0
3 TraesCS6A01G027500 chr6D 83.845 489 62 12 1880 2357 12338434 12338916 1.280000e-122 449.0
4 TraesCS6A01G027500 chr6D 85.149 101 14 1 55 155 12336078 12336177 4.140000e-18 102.0
5 TraesCS6A01G027500 chr2D 96.468 1189 42 0 627 1815 73126872 73125684 0.000000e+00 1964.0
6 TraesCS6A01G027500 chr2D 96.222 1191 43 2 626 1815 621748802 621749991 0.000000e+00 1949.0
7 TraesCS6A01G027500 chr2D 88.889 63 3 3 1 62 46297715 46297774 9.030000e-10 75.0
8 TraesCS6A01G027500 chr2D 87.692 65 4 3 1 64 221650791 221650730 3.250000e-09 73.1
9 TraesCS6A01G027500 chr1D 96.537 1184 40 1 632 1815 60171810 60170628 0.000000e+00 1958.0
10 TraesCS6A01G027500 chr1D 95.934 1205 40 5 612 1815 205134710 205133514 0.000000e+00 1945.0
11 TraesCS6A01G027500 chr1D 96.131 1189 45 1 627 1815 247505758 247504571 0.000000e+00 1940.0
12 TraesCS6A01G027500 chr1D 95.966 1190 45 3 626 1815 411532274 411531088 0.000000e+00 1929.0
13 TraesCS6A01G027500 chr3D 95.966 1190 48 0 626 1815 584701393 584700204 0.000000e+00 1932.0
14 TraesCS6A01G027500 chr3D 88.710 62 5 1 1 62 67481020 67480961 9.030000e-10 75.0
15 TraesCS6A01G027500 chr6B 81.233 373 65 5 1988 2357 22990888 22990518 1.770000e-76 296.0
16 TraesCS6A01G027500 chr6B 87.692 65 4 3 1 64 269946937 269946998 3.250000e-09 73.1
17 TraesCS6A01G027500 chr7D 92.857 56 2 1 1 56 375400863 375400916 1.940000e-11 80.5
18 TraesCS6A01G027500 chr7D 91.379 58 3 1 1 58 265693137 265693082 6.980000e-11 78.7
19 TraesCS6A01G027500 chr4D 90.000 60 3 2 1 60 4772185 4772129 9.030000e-10 75.0
20 TraesCS6A01G027500 chr5D 87.692 65 4 3 1 64 175300004 175300065 3.250000e-09 73.1
21 TraesCS6A01G027500 chr3A 87.692 65 4 3 1 64 251035815 251035754 3.250000e-09 73.1


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 TraesCS6A01G027500 chr6A 13877481 13879837 2356 True 4353.0 4353 100.000 1 2357 1 chr6A.!!$R1 2356
1 TraesCS6A01G027500 chr6D 142135504 142136692 1188 True 1991.0 1991 96.888 627 1815 1 chr6D.!!$R2 1188
2 TraesCS6A01G027500 chr6D 57789955 57791142 1187 True 1929.0 1929 95.963 627 1815 1 chr6D.!!$R1 1188
3 TraesCS6A01G027500 chr6D 12336078 12338916 2838 False 275.5 449 84.497 55 2357 2 chr6D.!!$F1 2302
4 TraesCS6A01G027500 chr2D 73125684 73126872 1188 True 1964.0 1964 96.468 627 1815 1 chr2D.!!$R1 1188
5 TraesCS6A01G027500 chr2D 621748802 621749991 1189 False 1949.0 1949 96.222 626 1815 1 chr2D.!!$F2 1189
6 TraesCS6A01G027500 chr1D 60170628 60171810 1182 True 1958.0 1958 96.537 632 1815 1 chr1D.!!$R1 1183
7 TraesCS6A01G027500 chr1D 205133514 205134710 1196 True 1945.0 1945 95.934 612 1815 1 chr1D.!!$R2 1203
8 TraesCS6A01G027500 chr1D 247504571 247505758 1187 True 1940.0 1940 96.131 627 1815 1 chr1D.!!$R3 1188
9 TraesCS6A01G027500 chr1D 411531088 411532274 1186 True 1929.0 1929 95.966 626 1815 1 chr1D.!!$R4 1189
10 TraesCS6A01G027500 chr3D 584700204 584701393 1189 True 1932.0 1932 95.966 626 1815 1 chr3D.!!$R2 1189

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
157 158 0.24746 GGGGGAAAGAAACATGCAGC 59.753 55.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 3731 0.039165 CTTTCTTGTTTGCCGGAGCC 60.039 55.0 5.05 0.0 38.69 4.7 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
50 51 9.528018 AACATTTATTATAATTGCAAACGGAGG 57.472 29.630 1.71 0.00 0.00 4.30
51 52 8.141268 ACATTTATTATAATTGCAAACGGAGGG 58.859 33.333 1.71 0.00 0.00 4.30
52 53 7.883391 TTTATTATAATTGCAAACGGAGGGA 57.117 32.000 1.71 0.00 0.00 4.20
53 54 7.504924 TTATTATAATTGCAAACGGAGGGAG 57.495 36.000 1.71 0.00 0.00 4.30
54 55 2.871096 TAATTGCAAACGGAGGGAGT 57.129 45.000 1.71 0.00 0.00 3.85
55 56 2.871096 AATTGCAAACGGAGGGAGTA 57.129 45.000 1.71 0.00 0.00 2.59
56 57 2.871096 ATTGCAAACGGAGGGAGTAA 57.129 45.000 1.71 0.00 0.00 2.24
57 58 2.871096 TTGCAAACGGAGGGAGTAAT 57.129 45.000 0.00 0.00 0.00 1.89
58 59 3.985019 TTGCAAACGGAGGGAGTAATA 57.015 42.857 0.00 0.00 0.00 0.98
59 60 4.497291 TTGCAAACGGAGGGAGTAATAT 57.503 40.909 0.00 0.00 0.00 1.28
60 61 4.497291 TGCAAACGGAGGGAGTAATATT 57.503 40.909 0.00 0.00 0.00 1.28
61 62 4.850680 TGCAAACGGAGGGAGTAATATTT 58.149 39.130 0.00 0.00 0.00 1.40
62 63 5.258051 TGCAAACGGAGGGAGTAATATTTT 58.742 37.500 0.00 0.00 0.00 1.82
63 64 5.124776 TGCAAACGGAGGGAGTAATATTTTG 59.875 40.000 0.00 0.00 0.00 2.44
64 65 5.355910 GCAAACGGAGGGAGTAATATTTTGA 59.644 40.000 0.00 0.00 0.00 2.69
65 66 6.458342 GCAAACGGAGGGAGTAATATTTTGAG 60.458 42.308 0.00 0.00 0.00 3.02
66 67 6.555463 AACGGAGGGAGTAATATTTTGAGA 57.445 37.500 0.00 0.00 0.00 3.27
67 68 6.555463 ACGGAGGGAGTAATATTTTGAGAA 57.445 37.500 0.00 0.00 0.00 2.87
94 95 5.241662 GTGATAAGCACTGAAGAGAACCTT 58.758 41.667 0.00 0.00 44.27 3.50
95 96 5.703130 GTGATAAGCACTGAAGAGAACCTTT 59.297 40.000 0.00 0.00 44.27 3.11
96 97 5.702670 TGATAAGCACTGAAGAGAACCTTTG 59.297 40.000 0.00 0.00 34.68 2.77
102 103 3.135530 ACTGAAGAGAACCTTTGAGTGCT 59.864 43.478 0.00 0.00 34.68 4.40
106 107 2.891580 AGAGAACCTTTGAGTGCTCGTA 59.108 45.455 0.00 0.00 45.80 3.43
155 156 2.094100 TTGGGGGAAAGAAACATGCA 57.906 45.000 0.00 0.00 0.00 3.96
156 157 1.631405 TGGGGGAAAGAAACATGCAG 58.369 50.000 0.00 0.00 0.00 4.41
157 158 0.247460 GGGGGAAAGAAACATGCAGC 59.753 55.000 0.00 0.00 0.00 5.25
158 159 0.247460 GGGGAAAGAAACATGCAGCC 59.753 55.000 0.00 0.00 0.00 4.85
159 160 0.968405 GGGAAAGAAACATGCAGCCA 59.032 50.000 0.00 0.00 0.00 4.75
161 162 2.027837 GGGAAAGAAACATGCAGCCAAT 60.028 45.455 0.00 0.00 0.00 3.16
163 164 4.067192 GGAAAGAAACATGCAGCCAATTT 58.933 39.130 0.00 0.00 0.00 1.82
164 165 4.152938 GGAAAGAAACATGCAGCCAATTTC 59.847 41.667 0.00 0.00 33.56 2.17
167 168 5.664294 AGAAACATGCAGCCAATTTCATA 57.336 34.783 12.44 0.00 34.78 2.15
168 169 6.040209 AGAAACATGCAGCCAATTTCATAA 57.960 33.333 12.44 0.00 34.78 1.90
169 170 6.103997 AGAAACATGCAGCCAATTTCATAAG 58.896 36.000 12.44 0.00 34.78 1.73
170 171 5.664294 AACATGCAGCCAATTTCATAAGA 57.336 34.783 0.00 0.00 0.00 2.10
172 173 6.229936 ACATGCAGCCAATTTCATAAGAAT 57.770 33.333 0.00 0.00 32.89 2.40
173 174 6.046593 ACATGCAGCCAATTTCATAAGAATG 58.953 36.000 0.00 0.00 32.89 2.67
183 1973 7.652105 CCAATTTCATAAGAATGCCATCTTCTG 59.348 37.037 4.53 6.12 40.13 3.02
184 1974 5.762825 TTCATAAGAATGCCATCTTCTGC 57.237 39.130 4.53 0.00 40.13 4.26
188 1978 4.877378 AAGAATGCCATCTTCTGCAAAA 57.123 36.364 0.00 0.00 41.50 2.44
189 1979 5.416271 AAGAATGCCATCTTCTGCAAAAT 57.584 34.783 0.00 0.00 41.50 1.82
196 1986 5.105106 TGCCATCTTCTGCAAAATGATTCAT 60.105 36.000 0.00 0.00 33.87 2.57
203 1993 8.027189 TCTTCTGCAAAATGATTCATCTTTCAG 58.973 33.333 6.14 6.14 0.00 3.02
206 1996 8.145767 TCTGCAAAATGATTCATCTTTCAGTTT 58.854 29.630 10.73 0.06 39.81 2.66
208 1998 7.927092 TGCAAAATGATTCATCTTTCAGTTTCA 59.073 29.630 0.00 0.00 37.87 2.69
222 2012 8.773645 TCTTTCAGTTTCATACTTGTACACATG 58.226 33.333 0.00 0.00 33.85 3.21
232 2022 9.150348 TCATACTTGTACACATGTTTCATACAG 57.850 33.333 0.00 1.20 40.83 2.74
235 2025 7.861630 ACTTGTACACATGTTTCATACAGAAC 58.138 34.615 0.00 0.00 40.83 3.01
236 2026 7.715249 ACTTGTACACATGTTTCATACAGAACT 59.285 33.333 0.00 0.00 40.83 3.01
245 2035 9.486497 CATGTTTCATACAGAACTGATATAGCT 57.514 33.333 8.87 0.00 40.83 3.32
278 2068 5.880054 TTTCTCAAACACTTGCCTATAGC 57.120 39.130 0.00 0.00 44.14 2.97
292 2083 9.067986 ACTTGCCTATAGCCTAAATTAATCAAC 57.932 33.333 0.00 0.00 42.71 3.18
295 2086 8.846211 TGCCTATAGCCTAAATTAATCAACAAC 58.154 33.333 0.00 0.00 42.71 3.32
300 2091 6.608610 AGCCTAAATTAATCAACAACGTCAC 58.391 36.000 0.00 0.00 0.00 3.67
301 2092 5.798434 GCCTAAATTAATCAACAACGTCACC 59.202 40.000 0.00 0.00 0.00 4.02
309 2100 2.096819 TCAACAACGTCACCAAAGCTTC 59.903 45.455 0.00 0.00 0.00 3.86
321 2112 4.946157 CACCAAAGCTTCACTATCCTCAAT 59.054 41.667 0.00 0.00 0.00 2.57
325 2116 6.994496 CCAAAGCTTCACTATCCTCAATATCA 59.006 38.462 0.00 0.00 0.00 2.15
326 2117 7.172875 CCAAAGCTTCACTATCCTCAATATCAG 59.827 40.741 0.00 0.00 0.00 2.90
331 2122 8.364142 GCTTCACTATCCTCAATATCAGTTAGT 58.636 37.037 0.00 0.00 0.00 2.24
344 2135 3.338249 TCAGTTAGTGCAAGGAAGATGC 58.662 45.455 0.00 0.00 44.08 3.91
357 2148 1.863454 GAAGATGCGAGCAATCGACAT 59.137 47.619 0.57 4.79 34.48 3.06
370 2161 9.670719 CGAGCAATCGACATAGTATATATGAAT 57.329 33.333 2.05 0.00 34.64 2.57
485 2309 7.558161 TTGTTGATGAGCTACAATAATGGAG 57.442 36.000 0.00 0.00 40.82 3.86
486 2310 6.888105 TGTTGATGAGCTACAATAATGGAGA 58.112 36.000 0.00 0.00 40.23 3.71
487 2311 7.337938 TGTTGATGAGCTACAATAATGGAGAA 58.662 34.615 0.00 0.00 40.23 2.87
488 2312 7.828717 TGTTGATGAGCTACAATAATGGAGAAA 59.171 33.333 0.00 0.00 40.23 2.52
489 2313 8.844244 GTTGATGAGCTACAATAATGGAGAAAT 58.156 33.333 0.00 0.00 40.23 2.17
606 2430 6.966534 ATCCTTCACAATGAATATTGACCC 57.033 37.500 6.98 0.00 45.21 4.46
608 2432 4.640201 CCTTCACAATGAATATTGACCCGT 59.360 41.667 6.98 0.00 45.21 5.28
621 2445 8.740123 AATATTGACCCGTTACAATATGTTCA 57.260 30.769 14.32 0.00 43.97 3.18
624 2448 8.918202 ATTGACCCGTTACAATATGTTCATAT 57.082 30.769 0.00 0.09 35.39 1.78
771 2595 2.758423 TCTAGGCAACATCTGTCGCTAA 59.242 45.455 0.00 0.00 41.41 3.09
788 2612 2.711547 GCTAATCCTACCCCCTTGATGT 59.288 50.000 0.00 0.00 0.00 3.06
939 2763 4.394712 CGCCGCCTTCTTCCACCT 62.395 66.667 0.00 0.00 0.00 4.00
1048 2872 2.514592 CGTCCATCCAGCCGCATT 60.515 61.111 0.00 0.00 0.00 3.56
1055 2879 3.853330 CCAGCCGCATTCGTCGTG 61.853 66.667 0.00 0.00 0.00 4.35
1211 3035 1.981256 GAACAGCAGTTCCTCCCAAA 58.019 50.000 10.70 0.00 46.68 3.28
1214 3038 1.064017 ACAGCAGTTCCTCCCAAAACA 60.064 47.619 0.00 0.00 0.00 2.83
1242 3066 1.806461 ATGGAGGATACGACGCGCAT 61.806 55.000 5.73 0.00 46.39 4.73
1410 3236 1.082206 TTTCCTCCGGTCCCCATCT 59.918 57.895 0.00 0.00 0.00 2.90
1426 3252 3.099141 CCATCTTATGCCACCAAACCTT 58.901 45.455 0.00 0.00 0.00 3.50
1686 3512 3.196207 AACGCAGCCACCACCTCAT 62.196 57.895 0.00 0.00 0.00 2.90
1698 3524 0.603707 CACCTCATGACACGCAGGTT 60.604 55.000 0.00 0.00 37.13 3.50
1815 3641 2.125350 CCAGCCAAGACGGAGAGC 60.125 66.667 0.00 0.00 36.56 4.09
1816 3642 2.659016 CAGCCAAGACGGAGAGCA 59.341 61.111 0.00 0.00 36.56 4.26
1817 3643 1.447489 CAGCCAAGACGGAGAGCAG 60.447 63.158 0.00 0.00 36.56 4.24
1818 3644 2.125350 GCCAAGACGGAGAGCAGG 60.125 66.667 0.00 0.00 36.56 4.85
1819 3645 2.948720 GCCAAGACGGAGAGCAGGT 61.949 63.158 0.00 0.00 36.56 4.00
1820 3646 1.605058 GCCAAGACGGAGAGCAGGTA 61.605 60.000 0.00 0.00 36.56 3.08
1821 3647 0.173708 CCAAGACGGAGAGCAGGTAC 59.826 60.000 0.00 0.00 36.56 3.34
1822 3648 0.888619 CAAGACGGAGAGCAGGTACA 59.111 55.000 0.00 0.00 0.00 2.90
1823 3649 1.272490 CAAGACGGAGAGCAGGTACAA 59.728 52.381 0.00 0.00 0.00 2.41
1824 3650 1.853963 AGACGGAGAGCAGGTACAAT 58.146 50.000 0.00 0.00 0.00 2.71
1825 3651 3.014304 AGACGGAGAGCAGGTACAATA 57.986 47.619 0.00 0.00 0.00 1.90
1826 3652 3.567397 AGACGGAGAGCAGGTACAATAT 58.433 45.455 0.00 0.00 0.00 1.28
1827 3653 3.319405 AGACGGAGAGCAGGTACAATATG 59.681 47.826 0.00 0.00 0.00 1.78
1828 3654 3.031736 ACGGAGAGCAGGTACAATATGT 58.968 45.455 0.00 0.00 0.00 2.29
1829 3655 3.451178 ACGGAGAGCAGGTACAATATGTT 59.549 43.478 0.00 0.00 0.00 2.71
1830 3656 4.051922 CGGAGAGCAGGTACAATATGTTC 58.948 47.826 0.00 0.00 0.00 3.18
1831 3657 4.441495 CGGAGAGCAGGTACAATATGTTCA 60.441 45.833 0.00 0.00 0.00 3.18
1832 3658 5.615289 GGAGAGCAGGTACAATATGTTCAT 58.385 41.667 0.00 0.00 0.00 2.57
1833 3659 6.516693 CGGAGAGCAGGTACAATATGTTCATA 60.517 42.308 0.00 0.00 0.00 2.15
1834 3660 7.390027 GGAGAGCAGGTACAATATGTTCATAT 58.610 38.462 0.00 0.09 0.00 1.78
1835 3661 8.531982 GGAGAGCAGGTACAATATGTTCATATA 58.468 37.037 5.85 0.00 0.00 0.86
1858 3684 6.636454 ATTATCATATATGTTGACCCCCGT 57.364 37.500 12.42 0.00 0.00 5.28
1859 3685 4.993705 ATCATATATGTTGACCCCCGTT 57.006 40.909 12.42 0.00 0.00 4.44
1860 3686 7.556416 TTATCATATATGTTGACCCCCGTTA 57.444 36.000 12.42 0.00 0.00 3.18
1861 3687 5.217978 TCATATATGTTGACCCCCGTTAC 57.782 43.478 12.42 0.00 0.00 2.50
1862 3688 4.654724 TCATATATGTTGACCCCCGTTACA 59.345 41.667 12.42 0.00 0.00 2.41
1863 3689 5.130643 TCATATATGTTGACCCCCGTTACAA 59.869 40.000 12.42 0.00 0.00 2.41
1864 3690 2.891191 ATGTTGACCCCCGTTACAAT 57.109 45.000 0.00 0.00 0.00 2.71
1865 3691 5.633655 ATATGTTGACCCCCGTTACAATA 57.366 39.130 0.00 0.00 0.00 1.90
1866 3692 4.513406 ATGTTGACCCCCGTTACAATAT 57.487 40.909 0.00 0.00 0.00 1.28
1867 3693 3.611970 TGTTGACCCCCGTTACAATATG 58.388 45.455 0.00 0.00 0.00 1.78
1868 3694 3.009253 TGTTGACCCCCGTTACAATATGT 59.991 43.478 0.00 0.00 0.00 2.29
1869 3695 4.011698 GTTGACCCCCGTTACAATATGTT 58.988 43.478 0.00 0.00 0.00 2.71
1870 3696 3.876341 TGACCCCCGTTACAATATGTTC 58.124 45.455 0.00 0.00 0.00 3.18
1871 3697 3.263681 TGACCCCCGTTACAATATGTTCA 59.736 43.478 0.00 0.00 0.00 3.18
1872 3698 4.080243 TGACCCCCGTTACAATATGTTCAT 60.080 41.667 0.00 0.00 0.00 2.57
1873 3699 5.130643 TGACCCCCGTTACAATATGTTCATA 59.869 40.000 0.00 0.00 0.00 2.15
1874 3700 6.183361 TGACCCCCGTTACAATATGTTCATAT 60.183 38.462 0.09 0.09 0.00 1.78
1875 3701 7.016366 TGACCCCCGTTACAATATGTTCATATA 59.984 37.037 5.85 0.00 0.00 0.86
1876 3702 7.924541 ACCCCCGTTACAATATGTTCATATAT 58.075 34.615 5.85 1.69 0.00 0.86
1877 3703 7.827236 ACCCCCGTTACAATATGTTCATATATG 59.173 37.037 6.36 6.36 0.00 1.78
1878 3704 8.044309 CCCCCGTTACAATATGTTCATATATGA 58.956 37.037 11.49 11.49 34.44 2.15
1879 3705 9.613428 CCCCGTTACAATATGTTCATATATGAT 57.387 33.333 16.06 4.53 36.56 2.45
1906 3732 9.533253 AAAATAGAACACTTTTCAATGTGAAGG 57.467 29.630 11.43 0.00 37.70 3.46
1907 3733 4.936891 AGAACACTTTTCAATGTGAAGGC 58.063 39.130 11.43 0.00 37.70 4.35
1908 3734 4.646492 AGAACACTTTTCAATGTGAAGGCT 59.354 37.500 11.43 0.00 37.70 4.58
1909 3735 4.574599 ACACTTTTCAATGTGAAGGCTC 57.425 40.909 11.43 0.00 37.70 4.70
1910 3736 3.319122 ACACTTTTCAATGTGAAGGCTCC 59.681 43.478 11.43 0.00 37.70 4.70
1911 3737 2.554032 ACTTTTCAATGTGAAGGCTCCG 59.446 45.455 0.00 0.00 37.70 4.63
1912 3738 1.533625 TTTCAATGTGAAGGCTCCGG 58.466 50.000 0.00 0.00 37.70 5.14
1913 3739 0.960364 TTCAATGTGAAGGCTCCGGC 60.960 55.000 0.00 0.00 31.83 6.13
1914 3740 1.675310 CAATGTGAAGGCTCCGGCA 60.675 57.895 0.00 0.00 40.87 5.69
1915 3741 1.074775 AATGTGAAGGCTCCGGCAA 59.925 52.632 0.00 0.00 40.87 4.52
1916 3742 0.539438 AATGTGAAGGCTCCGGCAAA 60.539 50.000 0.00 0.00 40.87 3.68
1917 3743 1.244019 ATGTGAAGGCTCCGGCAAAC 61.244 55.000 0.00 0.00 40.87 2.93
1918 3744 1.896660 GTGAAGGCTCCGGCAAACA 60.897 57.895 0.00 0.00 40.87 2.83
1928 3754 2.218603 TCCGGCAAACAAGAAAGACTC 58.781 47.619 0.00 0.00 0.00 3.36
1930 3756 2.224314 CCGGCAAACAAGAAAGACTCTC 59.776 50.000 0.00 0.00 31.02 3.20
1933 3759 3.304324 GGCAAACAAGAAAGACTCTCAGC 60.304 47.826 0.00 0.00 31.02 4.26
1934 3760 3.563390 GCAAACAAGAAAGACTCTCAGCT 59.437 43.478 0.00 0.00 31.02 4.24
1944 3770 4.799564 AGACTCTCAGCTCTACCAAAAG 57.200 45.455 0.00 0.00 0.00 2.27
1947 3773 4.100373 ACTCTCAGCTCTACCAAAAGGAT 58.900 43.478 0.00 0.00 0.00 3.24
1951 3778 6.644347 TCTCAGCTCTACCAAAAGGATTTAG 58.356 40.000 0.00 0.00 37.28 1.85
1953 3780 7.399191 TCTCAGCTCTACCAAAAGGATTTAGTA 59.601 37.037 0.00 0.00 37.28 1.82
1958 3785 7.418712 GCTCTACCAAAAGGATTTAGTAGCCTA 60.419 40.741 3.14 0.00 41.31 3.93
1961 3788 7.698506 ACCAAAAGGATTTAGTAGCCTAAAC 57.301 36.000 0.00 0.00 43.91 2.01
1969 3796 6.542735 GGATTTAGTAGCCTAAACCTTCAAGG 59.457 42.308 0.22 0.22 43.91 3.61
1988 3816 7.676683 TCAAGGTAGAATATAGGAGCTTTGT 57.323 36.000 0.00 0.00 0.00 2.83
2009 3841 8.722342 TTTGTTTTGCGAAGATGTAAAGATAC 57.278 30.769 0.00 0.00 0.00 2.24
2013 3845 6.662414 TTGCGAAGATGTAAAGATACCAAG 57.338 37.500 0.00 0.00 0.00 3.61
2014 3846 4.570772 TGCGAAGATGTAAAGATACCAAGC 59.429 41.667 0.00 0.00 0.00 4.01
2015 3847 4.570772 GCGAAGATGTAAAGATACCAAGCA 59.429 41.667 0.00 0.00 0.00 3.91
2016 3848 5.237344 GCGAAGATGTAAAGATACCAAGCAT 59.763 40.000 0.00 0.00 0.00 3.79
2018 3850 7.118390 GCGAAGATGTAAAGATACCAAGCATAT 59.882 37.037 0.00 0.00 0.00 1.78
2019 3851 9.639601 CGAAGATGTAAAGATACCAAGCATATA 57.360 33.333 0.00 0.00 0.00 0.86
2021 3853 9.442047 AAGATGTAAAGATACCAAGCATATAGC 57.558 33.333 0.00 0.00 46.19 2.97
2037 3869 7.681125 GCATATAGCTGGTCACGTATATAAC 57.319 40.000 0.00 0.00 41.15 1.89
2057 3894 4.675190 ACGAGACAGAAAAATGCTGATG 57.325 40.909 0.00 0.00 36.86 3.07
2086 3923 0.107410 ACCGTCTTTGCTGGTGACAA 60.107 50.000 0.00 0.00 42.06 3.18
2087 3924 0.588252 CCGTCTTTGCTGGTGACAAG 59.412 55.000 0.00 0.00 42.06 3.16
2091 3928 3.607775 CGTCTTTGCTGGTGACAAGAATG 60.608 47.826 0.00 0.00 42.06 2.67
2093 3930 0.592637 TTGCTGGTGACAAGAATGCG 59.407 50.000 0.00 0.00 42.06 4.73
2099 3936 2.147958 GGTGACAAGAATGCGTACCAA 58.852 47.619 0.00 0.00 31.23 3.67
2101 3938 3.190535 GGTGACAAGAATGCGTACCAATT 59.809 43.478 0.00 0.00 31.23 2.32
2154 3991 3.314635 CAGCTCTGGGCAATCAAGAATAC 59.685 47.826 0.74 0.00 44.79 1.89
2168 4005 4.157289 TCAAGAATACACACGGACTCTACC 59.843 45.833 0.00 0.00 0.00 3.18
2192 4029 1.543429 GCAACTGCTACTGAACCACCT 60.543 52.381 0.00 0.00 38.21 4.00
2217 4054 3.937706 GGATCTGAGGATTGAACAGTGTG 59.062 47.826 0.00 0.00 33.93 3.82
2233 4070 6.655078 ACAGTGTGCTATTTTCAATTCCTT 57.345 33.333 0.00 0.00 0.00 3.36
2236 4073 7.147312 CAGTGTGCTATTTTCAATTCCTTCAA 58.853 34.615 0.00 0.00 0.00 2.69
2237 4074 7.816031 CAGTGTGCTATTTTCAATTCCTTCAAT 59.184 33.333 0.00 0.00 0.00 2.57
2276 4113 0.924090 GACGAATGTCGATGGACTGC 59.076 55.000 9.41 0.00 43.74 4.40
2297 4134 3.250744 CATGCTTTGACATGCTTCCAAG 58.749 45.455 0.00 0.00 40.89 3.61
2298 4135 2.309613 TGCTTTGACATGCTTCCAAGT 58.690 42.857 0.00 0.00 0.00 3.16
2299 4136 2.694628 TGCTTTGACATGCTTCCAAGTT 59.305 40.909 0.00 0.00 0.00 2.66
2303 4140 4.572985 TTGACATGCTTCCAAGTTGAAG 57.427 40.909 3.87 7.46 43.71 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.528018 CCTCCGTTTGCAATTATAATAAATGTT 57.472 29.630 0.00 0.00 0.00 2.71
25 26 8.141268 CCCTCCGTTTGCAATTATAATAAATGT 58.859 33.333 0.00 0.00 0.00 2.71
26 27 8.356657 TCCCTCCGTTTGCAATTATAATAAATG 58.643 33.333 0.00 2.06 0.00 2.32
27 28 8.472007 TCCCTCCGTTTGCAATTATAATAAAT 57.528 30.769 0.00 0.00 0.00 1.40
28 29 7.558444 ACTCCCTCCGTTTGCAATTATAATAAA 59.442 33.333 0.00 0.00 0.00 1.40
29 30 7.057894 ACTCCCTCCGTTTGCAATTATAATAA 58.942 34.615 0.00 0.00 0.00 1.40
30 31 6.597562 ACTCCCTCCGTTTGCAATTATAATA 58.402 36.000 0.00 0.00 0.00 0.98
31 32 5.445964 ACTCCCTCCGTTTGCAATTATAAT 58.554 37.500 0.00 0.00 0.00 1.28
32 33 4.850680 ACTCCCTCCGTTTGCAATTATAA 58.149 39.130 0.00 0.00 0.00 0.98
33 34 4.497291 ACTCCCTCCGTTTGCAATTATA 57.503 40.909 0.00 0.00 0.00 0.98
34 35 3.366052 ACTCCCTCCGTTTGCAATTAT 57.634 42.857 0.00 0.00 0.00 1.28
35 36 2.871096 ACTCCCTCCGTTTGCAATTA 57.129 45.000 0.00 0.00 0.00 1.40
36 37 2.871096 TACTCCCTCCGTTTGCAATT 57.129 45.000 0.00 0.00 0.00 2.32
37 38 2.871096 TTACTCCCTCCGTTTGCAAT 57.129 45.000 0.00 0.00 0.00 3.56
38 39 2.871096 ATTACTCCCTCCGTTTGCAA 57.129 45.000 0.00 0.00 0.00 4.08
39 40 4.497291 AATATTACTCCCTCCGTTTGCA 57.503 40.909 0.00 0.00 0.00 4.08
40 41 5.355910 TCAAAATATTACTCCCTCCGTTTGC 59.644 40.000 0.00 0.00 0.00 3.68
41 42 6.821665 TCTCAAAATATTACTCCCTCCGTTTG 59.178 38.462 0.00 0.00 0.00 2.93
42 43 6.954232 TCTCAAAATATTACTCCCTCCGTTT 58.046 36.000 0.00 0.00 0.00 3.60
43 44 6.555463 TCTCAAAATATTACTCCCTCCGTT 57.445 37.500 0.00 0.00 0.00 4.44
44 45 6.555463 TTCTCAAAATATTACTCCCTCCGT 57.445 37.500 0.00 0.00 0.00 4.69
45 46 7.859325 TTTTCTCAAAATATTACTCCCTCCG 57.141 36.000 0.00 0.00 0.00 4.63
46 47 9.190317 ACATTTTCTCAAAATATTACTCCCTCC 57.810 33.333 0.00 0.00 38.97 4.30
48 49 9.753674 TCACATTTTCTCAAAATATTACTCCCT 57.246 29.630 0.00 0.00 38.97 4.20
75 76 5.163301 ACTCAAAGGTTCTCTTCAGTGCTTA 60.163 40.000 0.00 0.00 33.94 3.09
85 86 1.689273 ACGAGCACTCAAAGGTTCTCT 59.311 47.619 0.00 0.00 29.67 3.10
102 103 6.336842 ACTTTACTAGGTTTTGCTCTACGA 57.663 37.500 0.00 0.00 0.00 3.43
106 107 5.932883 GCAGTACTTTACTAGGTTTTGCTCT 59.067 40.000 0.00 0.00 37.23 4.09
114 115 6.823689 CCAATCATTGCAGTACTTTACTAGGT 59.176 38.462 0.00 0.00 37.23 3.08
116 117 6.260936 CCCCAATCATTGCAGTACTTTACTAG 59.739 42.308 0.00 0.00 37.23 2.57
118 119 4.949856 CCCCAATCATTGCAGTACTTTACT 59.050 41.667 0.00 0.00 40.28 2.24
123 124 1.922447 TCCCCCAATCATTGCAGTACT 59.078 47.619 0.00 0.00 0.00 2.73
155 156 5.601313 AGATGGCATTCTTATGAAATTGGCT 59.399 36.000 0.00 5.67 38.08 4.75
156 157 5.850614 AGATGGCATTCTTATGAAATTGGC 58.149 37.500 0.00 10.04 37.88 4.52
157 158 7.652105 CAGAAGATGGCATTCTTATGAAATTGG 59.348 37.037 20.09 2.16 44.08 3.16
158 159 7.169308 GCAGAAGATGGCATTCTTATGAAATTG 59.831 37.037 24.93 7.22 44.08 2.32
159 160 7.147794 TGCAGAAGATGGCATTCTTATGAAATT 60.148 33.333 24.93 2.59 44.08 1.82
161 162 5.653330 TGCAGAAGATGGCATTCTTATGAAA 59.347 36.000 24.93 15.51 44.08 2.69
163 164 4.784177 TGCAGAAGATGGCATTCTTATGA 58.216 39.130 24.93 14.34 44.08 2.15
164 165 5.509716 TTGCAGAAGATGGCATTCTTATG 57.490 39.130 20.28 20.28 44.14 1.90
167 168 4.877378 TTTTGCAGAAGATGGCATTCTT 57.123 36.364 0.00 6.66 40.17 2.52
168 169 4.464951 TCATTTTGCAGAAGATGGCATTCT 59.535 37.500 0.00 0.00 40.17 2.40
169 170 4.751060 TCATTTTGCAGAAGATGGCATTC 58.249 39.130 0.00 0.00 40.17 2.67
170 171 4.811969 TCATTTTGCAGAAGATGGCATT 57.188 36.364 0.00 0.00 40.17 3.56
172 173 4.221041 TGAATCATTTTGCAGAAGATGGCA 59.779 37.500 0.00 0.00 38.46 4.92
173 174 4.751060 TGAATCATTTTGCAGAAGATGGC 58.249 39.130 0.00 0.00 0.00 4.40
183 1973 8.301730 TGAAACTGAAAGATGAATCATTTTGC 57.698 30.769 0.00 0.00 37.43 3.68
189 1979 9.288576 ACAAGTATGAAACTGAAAGATGAATCA 57.711 29.630 0.00 0.00 38.88 2.57
196 1986 8.773645 CATGTGTACAAGTATGAAACTGAAAGA 58.226 33.333 0.00 0.00 38.88 2.52
206 1996 9.150348 CTGTATGAAACATGTGTACAAGTATGA 57.850 33.333 17.81 2.09 37.50 2.15
208 1998 9.719355 TTCTGTATGAAACATGTGTACAAGTAT 57.281 29.630 0.00 0.00 37.50 2.12
261 2051 6.699575 ATTTAGGCTATAGGCAAGTGTTTG 57.300 37.500 26.41 0.00 44.01 2.93
265 2055 8.621532 TGATTAATTTAGGCTATAGGCAAGTG 57.378 34.615 26.41 0.00 44.01 3.16
278 2068 6.904498 TGGTGACGTTGTTGATTAATTTAGG 58.096 36.000 0.00 0.00 0.00 2.69
292 2083 1.670811 AGTGAAGCTTTGGTGACGTTG 59.329 47.619 0.00 0.00 0.00 4.10
295 2086 2.673368 GGATAGTGAAGCTTTGGTGACG 59.327 50.000 0.00 0.00 0.00 4.35
300 2091 6.994496 TGATATTGAGGATAGTGAAGCTTTGG 59.006 38.462 0.00 0.00 0.00 3.28
301 2092 7.714377 ACTGATATTGAGGATAGTGAAGCTTTG 59.286 37.037 0.00 0.00 0.00 2.77
309 2100 7.436933 TGCACTAACTGATATTGAGGATAGTG 58.563 38.462 16.66 16.66 37.67 2.74
321 2112 5.118990 GCATCTTCCTTGCACTAACTGATA 58.881 41.667 0.00 0.00 39.90 2.15
325 2116 2.028112 TCGCATCTTCCTTGCACTAACT 60.028 45.455 0.00 0.00 40.14 2.24
326 2117 2.346803 TCGCATCTTCCTTGCACTAAC 58.653 47.619 0.00 0.00 40.14 2.34
331 2122 0.606130 TTGCTCGCATCTTCCTTGCA 60.606 50.000 0.00 0.00 40.14 4.08
344 2135 9.670719 ATTCATATATACTATGTCGATTGCTCG 57.329 33.333 0.00 0.00 46.41 5.03
458 2282 8.970020 TCCATTATTGTAGCTCATCAACAATTT 58.030 29.630 15.12 3.75 42.31 1.82
459 2283 8.523915 TCCATTATTGTAGCTCATCAACAATT 57.476 30.769 15.12 0.00 42.31 2.32
460 2284 7.994911 TCTCCATTATTGTAGCTCATCAACAAT 59.005 33.333 14.49 14.49 44.01 2.71
461 2285 7.337938 TCTCCATTATTGTAGCTCATCAACAA 58.662 34.615 1.66 1.66 37.51 2.83
462 2286 6.888105 TCTCCATTATTGTAGCTCATCAACA 58.112 36.000 0.00 0.00 0.00 3.33
463 2287 7.792374 TTCTCCATTATTGTAGCTCATCAAC 57.208 36.000 0.00 0.00 0.00 3.18
464 2288 8.985315 ATTTCTCCATTATTGTAGCTCATCAA 57.015 30.769 0.00 0.00 0.00 2.57
585 2409 4.640201 ACGGGTCAATATTCATTGTGAAGG 59.360 41.667 0.00 0.00 40.05 3.46
588 2412 6.174049 TGTAACGGGTCAATATTCATTGTGA 58.826 36.000 0.00 0.00 41.96 3.58
589 2413 6.429791 TGTAACGGGTCAATATTCATTGTG 57.570 37.500 0.00 0.00 41.96 3.33
630 2454 3.696548 GGGTGCATCCTCCTTTTCTAAAG 59.303 47.826 9.39 0.00 36.25 1.85
705 2529 8.212312 TGATGTACCACTTTGTAAGGTCTTTTA 58.788 33.333 0.00 0.00 36.87 1.52
771 2595 3.318313 CACTACATCAAGGGGGTAGGAT 58.682 50.000 0.00 0.00 38.99 3.24
788 2612 1.216977 CGGACATTCGGCACCACTA 59.783 57.895 0.00 0.00 0.00 2.74
939 2763 2.783379 ACCTGCTCTGGAGATGGATA 57.217 50.000 13.27 0.00 0.00 2.59
1048 2872 0.249031 CAGCTGCATATCCACGACGA 60.249 55.000 0.00 0.00 0.00 4.20
1076 2900 2.094757 ATTGACGACGAGTGGTGGCA 62.095 55.000 0.00 0.00 0.00 4.92
1211 3035 2.270205 CTCCATGGAGGCGCTGTT 59.730 61.111 31.14 0.00 38.51 3.16
1410 3236 1.883275 CACGAAGGTTTGGTGGCATAA 59.117 47.619 0.00 0.00 35.97 1.90
1426 3252 3.817787 CGGATCCGGAGTACACGA 58.182 61.111 26.95 0.00 35.56 4.35
1512 3338 6.019748 TGGAGATCTACAAGGAGTTCTTCTT 58.980 40.000 4.73 0.00 32.41 2.52
1596 3422 4.219070 TGGATCTTTTCTTCGAACTCCGTA 59.781 41.667 0.00 0.00 39.75 4.02
1686 3512 2.899838 GTGGCAACCTGCGTGTCA 60.900 61.111 0.00 0.00 46.21 3.58
1832 3658 9.442062 ACGGGGGTCAACATATATGATAATATA 57.558 33.333 19.63 0.00 0.00 0.86
1833 3659 8.331931 ACGGGGGTCAACATATATGATAATAT 57.668 34.615 19.63 0.00 0.00 1.28
1834 3660 7.743116 ACGGGGGTCAACATATATGATAATA 57.257 36.000 19.63 0.00 0.00 0.98
1835 3661 6.636454 ACGGGGGTCAACATATATGATAAT 57.364 37.500 19.63 0.06 0.00 1.28
1836 3662 6.442541 AACGGGGGTCAACATATATGATAA 57.557 37.500 19.63 1.08 0.00 1.75
1837 3663 6.497606 TGTAACGGGGGTCAACATATATGATA 59.502 38.462 19.63 1.40 0.00 2.15
1838 3664 4.993705 AACGGGGGTCAACATATATGAT 57.006 40.909 19.63 4.54 0.00 2.45
1839 3665 4.654724 TGTAACGGGGGTCAACATATATGA 59.345 41.667 19.63 0.00 0.00 2.15
1840 3666 4.963373 TGTAACGGGGGTCAACATATATG 58.037 43.478 11.29 11.29 0.00 1.78
1841 3667 5.633655 TTGTAACGGGGGTCAACATATAT 57.366 39.130 0.00 0.00 0.00 0.86
1842 3668 5.633655 ATTGTAACGGGGGTCAACATATA 57.366 39.130 0.00 0.00 0.00 0.86
1843 3669 4.513406 ATTGTAACGGGGGTCAACATAT 57.487 40.909 0.00 0.00 0.00 1.78
1844 3670 5.104444 ACATATTGTAACGGGGGTCAACATA 60.104 40.000 0.00 0.00 0.00 2.29
1845 3671 2.891191 ATTGTAACGGGGGTCAACAT 57.109 45.000 0.00 0.00 0.00 2.71
1846 3672 3.009253 ACATATTGTAACGGGGGTCAACA 59.991 43.478 0.00 0.00 0.00 3.33
1847 3673 3.613030 ACATATTGTAACGGGGGTCAAC 58.387 45.455 0.00 0.00 0.00 3.18
1848 3674 4.263374 TGAACATATTGTAACGGGGGTCAA 60.263 41.667 0.00 0.00 0.00 3.18
1849 3675 3.263681 TGAACATATTGTAACGGGGGTCA 59.736 43.478 0.00 0.00 0.00 4.02
1850 3676 3.876341 TGAACATATTGTAACGGGGGTC 58.124 45.455 0.00 0.00 0.00 4.46
1851 3677 4.513406 ATGAACATATTGTAACGGGGGT 57.487 40.909 0.00 0.00 0.00 4.95
1852 3678 8.044309 TCATATATGAACATATTGTAACGGGGG 58.956 37.037 13.12 0.00 35.71 5.40
1853 3679 9.613428 ATCATATATGAACATATTGTAACGGGG 57.387 33.333 19.03 0.00 40.69 5.73
1880 3706 9.533253 CCTTCACATTGAAAAGTGTTCTATTTT 57.467 29.630 0.00 0.00 35.73 1.82
1881 3707 7.653311 GCCTTCACATTGAAAAGTGTTCTATTT 59.347 33.333 0.00 0.00 35.73 1.40
1882 3708 7.014615 AGCCTTCACATTGAAAAGTGTTCTATT 59.985 33.333 0.00 0.00 35.73 1.73
1883 3709 6.491403 AGCCTTCACATTGAAAAGTGTTCTAT 59.509 34.615 0.00 0.00 35.73 1.98
1884 3710 5.827797 AGCCTTCACATTGAAAAGTGTTCTA 59.172 36.000 0.00 0.00 35.73 2.10
1885 3711 4.646492 AGCCTTCACATTGAAAAGTGTTCT 59.354 37.500 0.00 0.00 35.73 3.01
1886 3712 4.936891 AGCCTTCACATTGAAAAGTGTTC 58.063 39.130 0.00 0.00 35.73 3.18
1887 3713 4.202151 GGAGCCTTCACATTGAAAAGTGTT 60.202 41.667 0.00 0.00 35.73 3.32
1888 3714 3.319122 GGAGCCTTCACATTGAAAAGTGT 59.681 43.478 0.00 0.00 35.73 3.55
1889 3715 3.610114 CGGAGCCTTCACATTGAAAAGTG 60.610 47.826 0.00 0.00 35.73 3.16
1890 3716 2.554032 CGGAGCCTTCACATTGAAAAGT 59.446 45.455 0.00 0.00 35.73 2.66
1891 3717 2.095059 CCGGAGCCTTCACATTGAAAAG 60.095 50.000 0.00 0.00 35.73 2.27
1892 3718 1.885887 CCGGAGCCTTCACATTGAAAA 59.114 47.619 0.00 0.00 35.73 2.29
1893 3719 1.533625 CCGGAGCCTTCACATTGAAA 58.466 50.000 0.00 0.00 35.73 2.69
1894 3720 0.960364 GCCGGAGCCTTCACATTGAA 60.960 55.000 5.05 0.00 34.79 2.69
1895 3721 1.377202 GCCGGAGCCTTCACATTGA 60.377 57.895 5.05 0.00 0.00 2.57
1896 3722 1.243342 TTGCCGGAGCCTTCACATTG 61.243 55.000 5.05 0.00 38.69 2.82
1897 3723 0.539438 TTTGCCGGAGCCTTCACATT 60.539 50.000 5.05 0.00 38.69 2.71
1898 3724 1.074775 TTTGCCGGAGCCTTCACAT 59.925 52.632 5.05 0.00 38.69 3.21
1899 3725 1.896660 GTTTGCCGGAGCCTTCACA 60.897 57.895 5.05 0.00 38.69 3.58
1900 3726 1.452145 TTGTTTGCCGGAGCCTTCAC 61.452 55.000 5.05 0.00 38.69 3.18
1901 3727 1.152860 TTGTTTGCCGGAGCCTTCA 60.153 52.632 5.05 0.00 38.69 3.02
1902 3728 0.889186 TCTTGTTTGCCGGAGCCTTC 60.889 55.000 5.05 0.00 38.69 3.46
1903 3729 0.467290 TTCTTGTTTGCCGGAGCCTT 60.467 50.000 5.05 0.00 38.69 4.35
1904 3730 0.467290 TTTCTTGTTTGCCGGAGCCT 60.467 50.000 5.05 0.00 38.69 4.58
1905 3731 0.039165 CTTTCTTGTTTGCCGGAGCC 60.039 55.000 5.05 0.00 38.69 4.70
1906 3732 0.951558 TCTTTCTTGTTTGCCGGAGC 59.048 50.000 5.05 0.00 40.48 4.70
1907 3733 2.222027 AGTCTTTCTTGTTTGCCGGAG 58.778 47.619 5.05 0.00 0.00 4.63
1908 3734 2.158813 AGAGTCTTTCTTGTTTGCCGGA 60.159 45.455 5.05 0.00 29.61 5.14
1909 3735 2.222027 AGAGTCTTTCTTGTTTGCCGG 58.778 47.619 0.00 0.00 29.61 6.13
1910 3736 2.872245 TGAGAGTCTTTCTTGTTTGCCG 59.128 45.455 0.00 0.00 35.87 5.69
1911 3737 3.304324 GCTGAGAGTCTTTCTTGTTTGCC 60.304 47.826 0.00 0.00 35.87 4.52
1912 3738 3.563390 AGCTGAGAGTCTTTCTTGTTTGC 59.437 43.478 0.00 0.00 35.87 3.68
1913 3739 5.055812 AGAGCTGAGAGTCTTTCTTGTTTG 58.944 41.667 0.00 0.00 35.87 2.93
1914 3740 5.289083 AGAGCTGAGAGTCTTTCTTGTTT 57.711 39.130 0.00 0.00 35.87 2.83
1915 3741 4.953940 AGAGCTGAGAGTCTTTCTTGTT 57.046 40.909 0.00 0.00 35.87 2.83
1916 3742 4.219725 GGTAGAGCTGAGAGTCTTTCTTGT 59.780 45.833 0.00 0.00 35.87 3.16
1917 3743 4.219507 TGGTAGAGCTGAGAGTCTTTCTTG 59.780 45.833 0.00 0.00 35.87 3.02
1918 3744 4.411927 TGGTAGAGCTGAGAGTCTTTCTT 58.588 43.478 0.00 0.00 35.87 2.52
1928 3754 6.410540 ACTAAATCCTTTTGGTAGAGCTGAG 58.589 40.000 0.00 0.00 41.38 3.35
1944 3770 6.542735 CCTTGAAGGTTTAGGCTACTAAATCC 59.457 42.308 2.25 8.13 46.72 3.01
1961 3788 6.926630 AGCTCCTATATTCTACCTTGAAGG 57.073 41.667 10.24 10.24 42.49 3.46
1969 3796 7.011109 TCGCAAAACAAAGCTCCTATATTCTAC 59.989 37.037 0.00 0.00 0.00 2.59
1973 3800 6.374333 TCTTCGCAAAACAAAGCTCCTATATT 59.626 34.615 0.00 0.00 0.00 1.28
1977 3804 3.472652 TCTTCGCAAAACAAAGCTCCTA 58.527 40.909 0.00 0.00 0.00 2.94
1979 3806 2.774439 TCTTCGCAAAACAAAGCTCC 57.226 45.000 0.00 0.00 0.00 4.70
1988 3816 7.441890 TTGGTATCTTTACATCTTCGCAAAA 57.558 32.000 0.00 0.00 0.00 2.44
2013 3845 6.414109 CGTTATATACGTGACCAGCTATATGC 59.586 42.308 0.00 0.00 45.14 3.14
2014 3846 7.894013 CGTTATATACGTGACCAGCTATATG 57.106 40.000 0.00 0.00 45.14 1.78
2031 3863 8.554528 CATCAGCATTTTTCTGTCTCGTTATAT 58.445 33.333 0.00 0.00 33.48 0.86
2037 3869 3.423571 GCATCAGCATTTTTCTGTCTCG 58.576 45.455 0.00 0.00 41.58 4.04
2070 3907 3.854784 GCATTCTTGTCACCAGCAAAGAC 60.855 47.826 0.00 0.00 0.00 3.01
2072 3909 2.669364 GCATTCTTGTCACCAGCAAAG 58.331 47.619 0.00 0.00 0.00 2.77
2074 3911 0.592637 CGCATTCTTGTCACCAGCAA 59.407 50.000 0.00 0.00 0.00 3.91
2075 3912 0.534877 ACGCATTCTTGTCACCAGCA 60.535 50.000 0.00 0.00 0.00 4.41
2076 3913 1.128692 GTACGCATTCTTGTCACCAGC 59.871 52.381 0.00 0.00 0.00 4.85
2086 3923 2.936498 CGAGGAAATTGGTACGCATTCT 59.064 45.455 0.00 0.00 0.00 2.40
2087 3924 2.676342 ACGAGGAAATTGGTACGCATTC 59.324 45.455 0.00 0.00 0.00 2.67
2091 3928 0.643820 CGACGAGGAAATTGGTACGC 59.356 55.000 0.00 0.00 0.00 4.42
2093 3930 3.841643 TCTTCGACGAGGAAATTGGTAC 58.158 45.455 7.27 0.00 0.00 3.34
2117 3954 4.484236 CAGAGCTGACAGAAGTAAGACAG 58.516 47.826 6.65 0.00 0.00 3.51
2154 3991 0.171455 GCTCAGGTAGAGTCCGTGTG 59.829 60.000 0.00 0.00 46.47 3.82
2192 4029 5.426509 ACACTGTTCAATCCTCAGATCCATA 59.573 40.000 0.00 0.00 33.93 2.74
2205 4042 7.599998 GGAATTGAAAATAGCACACTGTTCAAT 59.400 33.333 4.11 4.11 40.82 2.57
2217 4054 6.257193 CCAGCATTGAAGGAATTGAAAATAGC 59.743 38.462 0.00 0.00 0.00 2.97
2233 4070 2.307153 GGGGGTACTCCAGCATTGA 58.693 57.895 15.36 0.00 37.22 2.57
2258 4095 0.246360 TGCAGTCCATCGACATTCGT 59.754 50.000 0.00 0.00 41.87 3.85
2276 4113 3.250744 CTTGGAAGCATGTCAAAGCATG 58.749 45.455 0.00 2.06 46.50 4.06
2297 4134 1.625818 TCCTCCCTCAAGAGCTTCAAC 59.374 52.381 0.00 0.00 32.17 3.18
2298 4135 2.030027 TCCTCCCTCAAGAGCTTCAA 57.970 50.000 0.00 0.00 32.17 2.69
2299 4136 1.836166 CATCCTCCCTCAAGAGCTTCA 59.164 52.381 0.00 0.00 32.17 3.02
2303 4140 1.794714 TACCATCCTCCCTCAAGAGC 58.205 55.000 0.00 0.00 32.17 4.09
2304 4141 3.713764 ACATTACCATCCTCCCTCAAGAG 59.286 47.826 0.00 0.00 0.00 2.85
2309 4146 5.011840 GGTACTAACATTACCATCCTCCCTC 59.988 48.000 0.00 0.00 39.17 4.30


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

AutoCloner maintained by Alex Coulton.