Multiple sequence alignment - TraesCS3D01G330000

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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 TraesCS3D01G330000 chr3D 100.000 3006 0 0 1 3006 442774207 442777212 0.000000e+00 5552
1 TraesCS3D01G330000 chr3D 96.740 859 11 5 2159 3004 511684797 511683943 0.000000e+00 1415
2 TraesCS3D01G330000 chr3B 88.397 1310 94 27 853 2119 580220178 580221472 0.000000e+00 1524
3 TraesCS3D01G330000 chr3B 86.232 414 19 9 2609 3006 10015896 10015505 6.000000e-112 414
4 TraesCS3D01G330000 chr6D 97.329 861 10 1 2159 3006 52828878 52828018 0.000000e+00 1450
5 TraesCS3D01G330000 chr6D 96.573 817 23 3 1 814 41923792 41924606 0.000000e+00 1349
6 TraesCS3D01G330000 chr6D 96.196 815 30 1 1 814 347439089 347439903 0.000000e+00 1332
7 TraesCS3D01G330000 chr2D 97.096 861 9 4 2159 3006 275176893 275177750 0.000000e+00 1437
8 TraesCS3D01G330000 chr4D 96.679 813 24 1 2 811 119368943 119369755 0.000000e+00 1349
9 TraesCS3D01G330000 chr4D 95.134 822 31 4 1 818 487122078 487121262 0.000000e+00 1288
10 TraesCS3D01G330000 chrUn 95.906 806 32 1 10 814 108803720 108802915 0.000000e+00 1304
11 TraesCS3D01G330000 chrUn 95.012 822 34 5 1 818 105335148 105335966 0.000000e+00 1284
12 TraesCS3D01G330000 chr5D 95.477 818 32 3 1 814 426403887 426404703 0.000000e+00 1301
13 TraesCS3D01G330000 chr5D 92.593 864 32 5 2159 3006 169968387 169969234 0.000000e+00 1212
14 TraesCS3D01G330000 chr7D 95.466 816 30 5 1 814 126989255 126988445 0.000000e+00 1295
15 TraesCS3D01G330000 chr1D 95.355 818 32 4 1 814 446541192 446540377 0.000000e+00 1295
16 TraesCS3D01G330000 chr4A 91.484 869 48 9 2157 3006 43267369 43268230 0.000000e+00 1171
17 TraesCS3D01G330000 chr4A 90.942 817 24 16 2206 3006 618263289 618264071 0.000000e+00 1053
18 TraesCS3D01G330000 chr1A 90.962 863 51 9 2160 3003 568651020 568651874 0.000000e+00 1136
19 TraesCS3D01G330000 chr2A 90.586 871 51 9 2160 3006 719697728 719698591 0.000000e+00 1125
20 TraesCS3D01G330000 chr5A 89.480 865 51 19 2159 3004 664545992 664545149 0.000000e+00 1057
21 TraesCS3D01G330000 chr5A 77.788 1103 158 50 984 2007 685870517 685869423 1.540000e-167 599
22 TraesCS3D01G330000 chr3A 90.401 573 44 5 911 1472 583978262 583978834 0.000000e+00 743
23 TraesCS3D01G330000 chr3A 81.073 354 47 12 1556 1894 584004113 584004461 6.390000e-67 265
24 TraesCS3D01G330000 chr3A 97.101 69 2 0 1468 1536 583983920 583983988 1.890000e-22 117


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 TraesCS3D01G330000 chr3D 442774207 442777212 3005 False 5552 5552 100.000 1 3006 1 chr3D.!!$F1 3005
1 TraesCS3D01G330000 chr3D 511683943 511684797 854 True 1415 1415 96.740 2159 3004 1 chr3D.!!$R1 845
2 TraesCS3D01G330000 chr3B 580220178 580221472 1294 False 1524 1524 88.397 853 2119 1 chr3B.!!$F1 1266
3 TraesCS3D01G330000 chr6D 52828018 52828878 860 True 1450 1450 97.329 2159 3006 1 chr6D.!!$R1 847
4 TraesCS3D01G330000 chr6D 41923792 41924606 814 False 1349 1349 96.573 1 814 1 chr6D.!!$F1 813
5 TraesCS3D01G330000 chr6D 347439089 347439903 814 False 1332 1332 96.196 1 814 1 chr6D.!!$F2 813
6 TraesCS3D01G330000 chr2D 275176893 275177750 857 False 1437 1437 97.096 2159 3006 1 chr2D.!!$F1 847
7 TraesCS3D01G330000 chr4D 119368943 119369755 812 False 1349 1349 96.679 2 811 1 chr4D.!!$F1 809
8 TraesCS3D01G330000 chr4D 487121262 487122078 816 True 1288 1288 95.134 1 818 1 chr4D.!!$R1 817
9 TraesCS3D01G330000 chrUn 108802915 108803720 805 True 1304 1304 95.906 10 814 1 chrUn.!!$R1 804
10 TraesCS3D01G330000 chrUn 105335148 105335966 818 False 1284 1284 95.012 1 818 1 chrUn.!!$F1 817
11 TraesCS3D01G330000 chr5D 426403887 426404703 816 False 1301 1301 95.477 1 814 1 chr5D.!!$F2 813
12 TraesCS3D01G330000 chr5D 169968387 169969234 847 False 1212 1212 92.593 2159 3006 1 chr5D.!!$F1 847
13 TraesCS3D01G330000 chr7D 126988445 126989255 810 True 1295 1295 95.466 1 814 1 chr7D.!!$R1 813
14 TraesCS3D01G330000 chr1D 446540377 446541192 815 True 1295 1295 95.355 1 814 1 chr1D.!!$R1 813
15 TraesCS3D01G330000 chr4A 43267369 43268230 861 False 1171 1171 91.484 2157 3006 1 chr4A.!!$F1 849
16 TraesCS3D01G330000 chr4A 618263289 618264071 782 False 1053 1053 90.942 2206 3006 1 chr4A.!!$F2 800
17 TraesCS3D01G330000 chr1A 568651020 568651874 854 False 1136 1136 90.962 2160 3003 1 chr1A.!!$F1 843
18 TraesCS3D01G330000 chr2A 719697728 719698591 863 False 1125 1125 90.586 2160 3006 1 chr2A.!!$F1 846
19 TraesCS3D01G330000 chr5A 664545149 664545992 843 True 1057 1057 89.480 2159 3004 1 chr5A.!!$R1 845
20 TraesCS3D01G330000 chr5A 685869423 685870517 1094 True 599 599 77.788 984 2007 1 chr5A.!!$R2 1023
21 TraesCS3D01G330000 chr3A 583978262 583978834 572 False 743 743 90.401 911 1472 1 chr3A.!!$F1 561

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
821 833 0.180406 ACCAAACACGCCTCAAGTCT 59.82 50.0 0.0 0.0 0.0 3.24 F
1759 1868 0.460311 ATTCTCGTCGCAGGGTAAGG 59.54 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2077 0.527565 GCAATAGCACCCAGTGGTTG 59.472 55.000 8.74 5.15 44.75 3.77 R
2713 2855 2.090719 CCTGGTAATCTCCTAGGGTCCA 60.091 54.545 9.46 7.90 0.00 4.02 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
148 149 1.372251 AGCACGACGAACAGCTCTG 60.372 57.895 0.00 0.00 30.05 3.35
168 169 0.959867 TGGTGCATGAACATGACCCG 60.960 55.000 17.40 0.00 41.20 5.28
261 262 1.299620 CGACGGTTCGTTCAGTGGT 60.300 57.895 0.00 0.00 41.37 4.16
560 571 1.681229 AGGGGGTGAGGCTAATTTGA 58.319 50.000 0.00 0.00 0.00 2.69
657 669 4.383861 CGCACTCAGCCTGGCTCA 62.384 66.667 20.49 4.68 41.38 4.26
691 703 2.657237 CGAGGGTTTCCTGCGAGT 59.343 61.111 0.00 0.00 45.05 4.18
693 705 1.446272 GAGGGTTTCCTGCGAGTCG 60.446 63.158 8.54 8.54 45.05 4.18
700 712 2.829003 CCTGCGAGTCGGGCTCTA 60.829 66.667 15.52 0.00 41.98 2.43
815 827 2.335011 GGCAACCAAACACGCCTC 59.665 61.111 0.00 0.00 41.50 4.70
817 829 1.435515 GCAACCAAACACGCCTCAA 59.564 52.632 0.00 0.00 0.00 3.02
818 830 0.594796 GCAACCAAACACGCCTCAAG 60.595 55.000 0.00 0.00 0.00 3.02
819 831 0.738389 CAACCAAACACGCCTCAAGT 59.262 50.000 0.00 0.00 0.00 3.16
820 832 1.021968 AACCAAACACGCCTCAAGTC 58.978 50.000 0.00 0.00 0.00 3.01
821 833 0.180406 ACCAAACACGCCTCAAGTCT 59.820 50.000 0.00 0.00 0.00 3.24
822 834 1.414919 ACCAAACACGCCTCAAGTCTA 59.585 47.619 0.00 0.00 0.00 2.59
823 835 2.038557 ACCAAACACGCCTCAAGTCTAT 59.961 45.455 0.00 0.00 0.00 1.98
824 836 3.074412 CCAAACACGCCTCAAGTCTATT 58.926 45.455 0.00 0.00 0.00 1.73
825 837 3.502211 CCAAACACGCCTCAAGTCTATTT 59.498 43.478 0.00 0.00 0.00 1.40
826 838 4.693566 CCAAACACGCCTCAAGTCTATTTA 59.306 41.667 0.00 0.00 0.00 1.40
827 839 5.390567 CCAAACACGCCTCAAGTCTATTTAC 60.391 44.000 0.00 0.00 0.00 2.01
828 840 3.508762 ACACGCCTCAAGTCTATTTACG 58.491 45.455 0.00 0.00 0.00 3.18
829 841 2.281762 CACGCCTCAAGTCTATTTACGC 59.718 50.000 0.00 0.00 0.00 4.42
830 842 2.094390 ACGCCTCAAGTCTATTTACGCA 60.094 45.455 0.00 0.00 0.00 5.24
831 843 2.927477 CGCCTCAAGTCTATTTACGCAA 59.073 45.455 0.00 0.00 0.00 4.85
833 845 3.242446 GCCTCAAGTCTATTTACGCAAGC 60.242 47.826 0.00 0.00 45.62 4.01
834 846 4.184629 CCTCAAGTCTATTTACGCAAGCT 58.815 43.478 0.00 0.00 45.62 3.74
835 847 5.348986 CCTCAAGTCTATTTACGCAAGCTA 58.651 41.667 0.00 0.00 45.62 3.32
836 848 5.986135 CCTCAAGTCTATTTACGCAAGCTAT 59.014 40.000 0.00 0.00 45.62 2.97
837 849 6.144724 CCTCAAGTCTATTTACGCAAGCTATC 59.855 42.308 0.00 0.00 45.62 2.08
838 850 6.569780 TCAAGTCTATTTACGCAAGCTATCA 58.430 36.000 0.00 0.00 45.62 2.15
839 851 6.475727 TCAAGTCTATTTACGCAAGCTATCAC 59.524 38.462 0.00 0.00 45.62 3.06
840 852 5.902681 AGTCTATTTACGCAAGCTATCACA 58.097 37.500 0.00 0.00 45.62 3.58
841 853 5.980116 AGTCTATTTACGCAAGCTATCACAG 59.020 40.000 0.00 0.00 45.62 3.66
842 854 5.749109 GTCTATTTACGCAAGCTATCACAGT 59.251 40.000 0.00 0.00 45.62 3.55
843 855 6.255887 GTCTATTTACGCAAGCTATCACAGTT 59.744 38.462 0.00 0.00 45.62 3.16
844 856 4.661993 TTTACGCAAGCTATCACAGTTG 57.338 40.909 0.00 0.00 45.62 3.16
845 857 2.455674 ACGCAAGCTATCACAGTTGA 57.544 45.000 0.00 0.00 45.62 3.18
846 858 2.069273 ACGCAAGCTATCACAGTTGAC 58.931 47.619 0.00 0.00 45.62 3.18
847 859 1.394917 CGCAAGCTATCACAGTTGACC 59.605 52.381 0.00 0.00 33.38 4.02
848 860 2.704572 GCAAGCTATCACAGTTGACCT 58.295 47.619 0.00 0.00 33.38 3.85
887 899 7.067251 TGTTGATCATATCAGCAAAGCATGTAA 59.933 33.333 0.00 0.00 45.52 2.41
905 918 9.238368 AGCATGTAATAGCTTGTTTTAAAGGTA 57.762 29.630 0.00 0.00 42.53 3.08
939 953 4.453480 AAAAAGGGTGTTGATCCAGAGA 57.547 40.909 0.00 0.00 0.00 3.10
951 965 2.154854 TCCAGAGAAACAAGACAGCG 57.845 50.000 0.00 0.00 0.00 5.18
974 990 6.514376 GCGTAATGTTATATCCAACCCAAAGG 60.514 42.308 0.00 0.00 40.04 3.11
1005 1025 1.605710 CTTGCAATGGGGTCGATGATC 59.394 52.381 0.00 0.00 0.00 2.92
1151 1194 2.278332 AACTGAACCTTCTTCTGGCC 57.722 50.000 0.00 0.00 0.00 5.36
1179 1241 3.683340 CCTTCGGCTAACCAAGAACTAAC 59.317 47.826 0.00 0.00 34.57 2.34
1247 1317 3.256960 ACCCAGGTGTCGGCCATT 61.257 61.111 2.24 0.00 0.00 3.16
1253 1323 2.038426 CCAGGTGTCGGCCATTATCATA 59.962 50.000 2.24 0.00 0.00 2.15
1259 1329 3.243336 GTCGGCCATTATCATAGACGAC 58.757 50.000 2.24 1.07 41.79 4.34
1346 1416 2.430694 CGTCTTCTCCACCATCCATGTA 59.569 50.000 0.00 0.00 0.00 2.29
1349 1419 4.346418 GTCTTCTCCACCATCCATGTATCT 59.654 45.833 0.00 0.00 0.00 1.98
1431 1501 4.371417 ACCTCGCCCCCTACGTCA 62.371 66.667 0.00 0.00 0.00 4.35
1577 1662 1.920574 CTCTTCGTCATAACCGCTGTG 59.079 52.381 0.00 0.00 0.00 3.66
1636 1745 6.151648 TCCATTCCTTGTATGCTTTCTCTTTG 59.848 38.462 0.00 0.00 0.00 2.77
1646 1755 2.868899 CTTTCTCTTTGGTGGCTTCCT 58.131 47.619 1.63 0.00 0.00 3.36
1648 1757 4.398319 CTTTCTCTTTGGTGGCTTCCTTA 58.602 43.478 1.63 0.00 0.00 2.69
1649 1758 3.703001 TCTCTTTGGTGGCTTCCTTAG 57.297 47.619 1.63 0.00 0.00 2.18
1671 1780 3.304659 GCTAGCTAGTGATCTCAGCTGTC 60.305 52.174 21.62 4.61 45.04 3.51
1676 1785 4.499019 GCTAGTGATCTCAGCTGTCTTACC 60.499 50.000 14.67 0.00 32.46 2.85
1687 1796 5.767665 TCAGCTGTCTTACCAAAATGCTTAA 59.232 36.000 14.67 0.00 0.00 1.85
1688 1797 6.434028 TCAGCTGTCTTACCAAAATGCTTAAT 59.566 34.615 14.67 0.00 0.00 1.40
1689 1798 7.039784 TCAGCTGTCTTACCAAAATGCTTAATT 60.040 33.333 14.67 0.00 0.00 1.40
1690 1799 8.243426 CAGCTGTCTTACCAAAATGCTTAATTA 58.757 33.333 5.25 0.00 0.00 1.40
1751 1860 4.307443 AGTGATGAATATTCTCGTCGCA 57.693 40.909 16.24 3.43 42.06 5.10
1759 1868 0.460311 ATTCTCGTCGCAGGGTAAGG 59.540 55.000 0.00 0.00 0.00 2.69
1771 1880 3.451178 GCAGGGTAAGGAGAATCTGTGTA 59.549 47.826 0.00 0.00 33.73 2.90
1772 1881 4.680975 GCAGGGTAAGGAGAATCTGTGTAC 60.681 50.000 0.00 0.00 33.73 2.90
1774 1883 5.129485 CAGGGTAAGGAGAATCTGTGTACAT 59.871 44.000 0.00 0.00 33.73 2.29
1775 1884 6.323996 CAGGGTAAGGAGAATCTGTGTACATA 59.676 42.308 0.00 0.00 33.73 2.29
1776 1885 6.324254 AGGGTAAGGAGAATCTGTGTACATAC 59.676 42.308 0.00 0.00 33.73 2.39
1777 1886 6.097839 GGGTAAGGAGAATCTGTGTACATACA 59.902 42.308 0.00 0.00 33.73 2.29
1778 1887 7.202011 GGGTAAGGAGAATCTGTGTACATACAT 60.202 40.741 0.00 0.00 35.06 2.29
1822 1944 1.748493 TGTTGGTTCCAAGCTGAACAC 59.252 47.619 16.28 9.00 45.12 3.32
1826 1948 2.024414 GGTTCCAAGCTGAACACACTT 58.976 47.619 16.28 0.00 45.12 3.16
1833 1955 5.239306 TCCAAGCTGAACACACTTCTATTTG 59.761 40.000 0.00 0.00 0.00 2.32
1835 1957 6.460123 CCAAGCTGAACACACTTCTATTTGTT 60.460 38.462 0.00 0.00 34.88 2.83
1837 1959 5.009010 AGCTGAACACACTTCTATTTGTTGG 59.991 40.000 0.00 0.00 32.34 3.77
1839 1961 4.887071 TGAACACACTTCTATTTGTTGGCT 59.113 37.500 0.00 0.00 32.34 4.75
1842 1964 4.887071 ACACACTTCTATTTGTTGGCTTCA 59.113 37.500 0.00 0.00 0.00 3.02
1847 1972 7.986889 ACACTTCTATTTGTTGGCTTCAAAAAT 59.013 29.630 10.44 0.31 38.11 1.82
1864 1989 0.622136 AATCTGTGAGCAGGCCATCA 59.378 50.000 5.01 2.88 42.78 3.07
1906 2031 2.952783 CGTACGATTGGACCGGCG 60.953 66.667 10.44 0.00 0.00 6.46
1952 2077 2.507407 TTGGGTTTATCTGGTGGCTC 57.493 50.000 0.00 0.00 0.00 4.70
2034 2166 5.796350 ATATGCACACGAAAAGGAGTTAC 57.204 39.130 0.00 0.00 0.00 2.50
2035 2167 3.188159 TGCACACGAAAAGGAGTTACT 57.812 42.857 0.00 0.00 0.00 2.24
2036 2168 4.325028 TGCACACGAAAAGGAGTTACTA 57.675 40.909 0.00 0.00 0.00 1.82
2109 2242 2.631418 CAGGAACATTTGCTGCTCTG 57.369 50.000 0.00 0.00 42.18 3.35
2115 2248 2.579873 ACATTTGCTGCTCTGTTCACT 58.420 42.857 0.00 0.00 0.00 3.41
2119 2252 0.533531 TGCTGCTCTGTTCACTGGTG 60.534 55.000 0.00 0.00 0.00 4.17
2120 2253 0.533755 GCTGCTCTGTTCACTGGTGT 60.534 55.000 0.00 0.00 0.00 4.16
2121 2254 1.224075 CTGCTCTGTTCACTGGTGTG 58.776 55.000 0.53 0.00 45.07 3.82
2122 2255 0.815213 TGCTCTGTTCACTGGTGTGC 60.815 55.000 0.53 0.00 43.49 4.57
2123 2256 0.533755 GCTCTGTTCACTGGTGTGCT 60.534 55.000 0.53 0.00 43.49 4.40
2124 2257 1.959042 CTCTGTTCACTGGTGTGCTT 58.041 50.000 0.53 0.00 43.49 3.91
2125 2258 2.806745 GCTCTGTTCACTGGTGTGCTTA 60.807 50.000 0.53 0.00 43.49 3.09
2126 2259 3.062763 CTCTGTTCACTGGTGTGCTTAG 58.937 50.000 0.53 0.00 43.49 2.18
2127 2260 2.698274 TCTGTTCACTGGTGTGCTTAGA 59.302 45.455 0.53 0.00 43.49 2.10
2128 2261 3.062763 CTGTTCACTGGTGTGCTTAGAG 58.937 50.000 0.53 0.00 43.49 2.43
2129 2262 2.698274 TGTTCACTGGTGTGCTTAGAGA 59.302 45.455 0.53 0.00 43.49 3.10
2130 2263 3.133901 TGTTCACTGGTGTGCTTAGAGAA 59.866 43.478 0.53 0.00 43.49 2.87
2131 2264 4.202357 TGTTCACTGGTGTGCTTAGAGAAT 60.202 41.667 0.53 0.00 43.49 2.40
2132 2265 4.193826 TCACTGGTGTGCTTAGAGAATC 57.806 45.455 0.53 0.00 43.49 2.52
2133 2266 3.834813 TCACTGGTGTGCTTAGAGAATCT 59.165 43.478 0.53 0.00 45.92 2.40
2134 2267 4.081972 TCACTGGTGTGCTTAGAGAATCTC 60.082 45.833 1.19 1.19 44.16 2.75
2135 2268 4.081752 CACTGGTGTGCTTAGAGAATCTCT 60.082 45.833 17.67 17.67 40.54 3.10
2136 2269 5.126222 CACTGGTGTGCTTAGAGAATCTCTA 59.874 44.000 15.47 15.47 40.54 2.43
2137 2270 6.183360 CACTGGTGTGCTTAGAGAATCTCTAT 60.183 42.308 19.49 0.00 40.54 1.98
2138 2271 7.946917 CACTGGTGTGCTTAGAGAATCTCTATC 60.947 44.444 19.49 14.59 40.54 2.08
2145 2278 2.734276 GAGAATCTCTATCGCACCCC 57.266 55.000 2.45 0.00 0.00 4.95
2146 2279 2.243810 GAGAATCTCTATCGCACCCCT 58.756 52.381 2.45 0.00 0.00 4.79
2147 2280 3.422796 GAGAATCTCTATCGCACCCCTA 58.577 50.000 2.45 0.00 0.00 3.53
2148 2281 4.020543 GAGAATCTCTATCGCACCCCTAT 58.979 47.826 2.45 0.00 0.00 2.57
2149 2282 4.020543 AGAATCTCTATCGCACCCCTATC 58.979 47.826 0.00 0.00 0.00 2.08
2150 2283 2.971901 TCTCTATCGCACCCCTATCA 57.028 50.000 0.00 0.00 0.00 2.15
2151 2284 3.458044 TCTCTATCGCACCCCTATCAT 57.542 47.619 0.00 0.00 0.00 2.45
2152 2285 3.779444 TCTCTATCGCACCCCTATCATT 58.221 45.455 0.00 0.00 0.00 2.57
2153 2286 4.160329 TCTCTATCGCACCCCTATCATTT 58.840 43.478 0.00 0.00 0.00 2.32
2154 2287 5.330233 TCTCTATCGCACCCCTATCATTTA 58.670 41.667 0.00 0.00 0.00 1.40
2155 2288 5.778241 TCTCTATCGCACCCCTATCATTTAA 59.222 40.000 0.00 0.00 0.00 1.52
2206 2342 1.001633 GTGGGGCGAAGTCTCACTAAA 59.998 52.381 0.00 0.00 0.00 1.85
2241 2378 4.631377 TGCGAATCAAAGGAGTCAATACAG 59.369 41.667 0.00 0.00 38.00 2.74
2713 2855 3.745797 GCAGAGGAGTGGTTCAGAGTTTT 60.746 47.826 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 149 0.527565 GGGTCATGTTCATGCACCAC 59.472 55.000 22.57 12.03 0.00 4.16
168 169 4.256920 ACTGATTAGTGTGATTCAGGCAC 58.743 43.478 4.06 0.35 39.89 5.01
261 262 7.828508 TTAAGCTAGGTGTAGGATCGATTTA 57.171 36.000 0.00 0.00 0.00 1.40
405 408 2.373707 GGCTGATCTGGTGCTCCCT 61.374 63.158 1.59 0.00 0.00 4.20
657 669 1.153823 CGGATCGGCAGTTTCTCGT 60.154 57.895 0.00 0.00 0.00 4.18
691 703 1.990060 AAAGCAGCCTAGAGCCCGA 60.990 57.895 0.00 0.00 45.47 5.14
693 705 0.463474 CTCAAAGCAGCCTAGAGCCC 60.463 60.000 0.00 0.00 45.47 5.19
814 826 6.475727 GTGATAGCTTGCGTAAATAGACTTGA 59.524 38.462 0.00 0.00 0.00 3.02
815 827 6.255670 TGTGATAGCTTGCGTAAATAGACTTG 59.744 38.462 0.00 0.00 0.00 3.16
817 829 5.902681 TGTGATAGCTTGCGTAAATAGACT 58.097 37.500 0.00 0.00 0.00 3.24
818 830 5.749109 ACTGTGATAGCTTGCGTAAATAGAC 59.251 40.000 0.00 0.00 0.00 2.59
819 831 5.902681 ACTGTGATAGCTTGCGTAAATAGA 58.097 37.500 0.00 0.00 0.00 1.98
820 832 6.255670 TCAACTGTGATAGCTTGCGTAAATAG 59.744 38.462 0.00 0.00 0.00 1.73
821 833 6.035650 GTCAACTGTGATAGCTTGCGTAAATA 59.964 38.462 0.00 0.00 35.80 1.40
822 834 4.935205 TCAACTGTGATAGCTTGCGTAAAT 59.065 37.500 0.00 0.00 0.00 1.40
823 835 4.151689 GTCAACTGTGATAGCTTGCGTAAA 59.848 41.667 0.00 0.00 35.80 2.01
824 836 3.678072 GTCAACTGTGATAGCTTGCGTAA 59.322 43.478 0.00 0.00 35.80 3.18
825 837 3.250744 GTCAACTGTGATAGCTTGCGTA 58.749 45.455 0.00 0.00 35.80 4.42
826 838 2.069273 GTCAACTGTGATAGCTTGCGT 58.931 47.619 0.00 0.00 35.80 5.24
827 839 1.394917 GGTCAACTGTGATAGCTTGCG 59.605 52.381 0.00 0.00 35.80 4.85
828 840 2.417933 CAGGTCAACTGTGATAGCTTGC 59.582 50.000 0.00 0.00 42.42 4.01
840 852 4.879545 ACAATAAACAACGACAGGTCAACT 59.120 37.500 0.00 0.00 0.00 3.16
841 853 5.164606 ACAATAAACAACGACAGGTCAAC 57.835 39.130 0.00 0.00 0.00 3.18
842 854 5.354513 TCAACAATAAACAACGACAGGTCAA 59.645 36.000 0.00 0.00 0.00 3.18
843 855 4.876679 TCAACAATAAACAACGACAGGTCA 59.123 37.500 0.00 0.00 0.00 4.02
844 856 5.412526 TCAACAATAAACAACGACAGGTC 57.587 39.130 0.00 0.00 0.00 3.85
845 857 5.529430 TGATCAACAATAAACAACGACAGGT 59.471 36.000 0.00 0.00 0.00 4.00
846 858 5.996219 TGATCAACAATAAACAACGACAGG 58.004 37.500 0.00 0.00 0.00 4.00
847 859 9.425893 GATATGATCAACAATAAACAACGACAG 57.574 33.333 0.00 0.00 0.00 3.51
848 860 8.940952 TGATATGATCAACAATAAACAACGACA 58.059 29.630 0.00 0.00 36.11 4.35
849 861 9.425893 CTGATATGATCAACAATAAACAACGAC 57.574 33.333 0.00 0.00 39.11 4.34
850 862 8.122330 GCTGATATGATCAACAATAAACAACGA 58.878 33.333 0.00 0.00 39.11 3.85
851 863 7.909641 TGCTGATATGATCAACAATAAACAACG 59.090 33.333 0.00 0.00 39.11 4.10
887 899 8.520351 GTGGTCAATACCTTTAAAACAAGCTAT 58.480 33.333 0.00 0.00 46.91 2.97
905 918 3.573967 CACCCTTTTTAGCTGTGGTCAAT 59.426 43.478 0.00 0.00 0.00 2.57
939 953 7.551262 TGGATATAACATTACGCTGTCTTGTTT 59.449 33.333 11.39 6.03 33.03 2.83
951 965 6.322712 TGCCTTTGGGTTGGATATAACATTAC 59.677 38.462 0.00 0.00 34.45 1.89
1129 1167 3.481453 GCCAGAAGAAGGTTCAGTTTCT 58.519 45.455 0.00 0.00 35.25 2.52
1179 1241 2.949678 CGTCGCCTGATCGAACCG 60.950 66.667 0.00 0.00 40.43 4.44
1247 1317 2.289820 GTCGTGCTGGTCGTCTATGATA 59.710 50.000 0.00 0.00 0.00 2.15
1253 1323 4.039357 CCGTCGTGCTGGTCGTCT 62.039 66.667 0.00 0.00 0.00 4.18
1346 1416 1.380302 GTTCAGGTGGCACCCAGAT 59.620 57.895 32.30 11.99 39.75 2.90
1577 1662 2.592861 GCATGAGGATCCGTGGCC 60.593 66.667 5.98 0.00 0.00 5.36
1621 1730 3.084786 AGCCACCAAAGAGAAAGCATAC 58.915 45.455 0.00 0.00 0.00 2.39
1625 1734 1.270826 GGAAGCCACCAAAGAGAAAGC 59.729 52.381 0.00 0.00 0.00 3.51
1646 1755 4.518590 CAGCTGAGATCACTAGCTAGCTAA 59.481 45.833 24.20 11.24 45.37 3.09
1648 1757 2.886523 CAGCTGAGATCACTAGCTAGCT 59.113 50.000 23.12 23.12 45.37 3.32
1649 1758 2.622942 ACAGCTGAGATCACTAGCTAGC 59.377 50.000 23.35 6.62 45.37 3.42
1671 1780 9.921637 TTTCACCTAATTAAGCATTTTGGTAAG 57.078 29.630 0.00 0.00 32.41 2.34
1676 1785 9.696917 AGTTCTTTCACCTAATTAAGCATTTTG 57.303 29.630 0.00 0.00 0.00 2.44
1687 1796 3.865745 CGCGATCAGTTCTTTCACCTAAT 59.134 43.478 0.00 0.00 0.00 1.73
1688 1797 3.250744 CGCGATCAGTTCTTTCACCTAA 58.749 45.455 0.00 0.00 0.00 2.69
1689 1798 2.416836 CCGCGATCAGTTCTTTCACCTA 60.417 50.000 8.23 0.00 0.00 3.08
1690 1799 1.673033 CCGCGATCAGTTCTTTCACCT 60.673 52.381 8.23 0.00 0.00 4.00
1721 1830 2.394545 TATTCATCACTACCGTCGCG 57.605 50.000 0.00 0.00 0.00 5.87
1727 1836 4.617645 GCGACGAGAATATTCATCACTACC 59.382 45.833 17.56 0.00 0.00 3.18
1751 1860 4.684724 TGTACACAGATTCTCCTTACCCT 58.315 43.478 0.00 0.00 0.00 4.34
1778 1887 9.679661 ACACAGAAATGAACCACAATATATACA 57.320 29.630 0.00 0.00 0.00 2.29
1799 1918 1.679139 TCAGCTTGGAACCAACACAG 58.321 50.000 1.83 0.00 0.00 3.66
1803 1922 1.748493 TGTGTTCAGCTTGGAACCAAC 59.252 47.619 12.87 7.25 45.12 3.77
1822 1944 7.769272 TTTTTGAAGCCAACAAATAGAAGTG 57.231 32.000 0.00 0.00 37.15 3.16
1826 1948 7.652909 CACAGATTTTTGAAGCCAACAAATAGA 59.347 33.333 0.00 0.00 37.15 1.98
1833 1955 3.737774 GCTCACAGATTTTTGAAGCCAAC 59.262 43.478 0.00 0.00 30.88 3.77
1835 1957 2.957680 TGCTCACAGATTTTTGAAGCCA 59.042 40.909 0.00 0.00 32.95 4.75
1864 1989 2.578021 AGGGTTCATAGATGCACCTGTT 59.422 45.455 10.54 0.00 42.61 3.16
1885 2010 2.580276 GGTCCAATCGTACGCCCA 59.420 61.111 11.24 0.00 0.00 5.36
1887 2012 2.584143 CCGGTCCAATCGTACGCC 60.584 66.667 11.24 3.68 0.00 5.68
1906 2031 4.761975 TGTTGTATCTCCCCGTAACAATC 58.238 43.478 0.00 0.00 33.10 2.67
1952 2077 0.527565 GCAATAGCACCCAGTGGTTG 59.472 55.000 8.74 5.15 44.75 3.77
2109 2242 9.612692 AGAGATTCTCTAAGCACACCAGTGAAC 62.613 44.444 14.61 0.00 42.74 3.18
2115 2248 5.009110 CGATAGAGATTCTCTAAGCACACCA 59.991 44.000 23.62 3.84 44.76 4.17
2119 2252 5.114785 TGCGATAGAGATTCTCTAAGCAC 57.885 43.478 31.58 20.46 45.78 4.40
2120 2253 4.022762 GGTGCGATAGAGATTCTCTAAGCA 60.023 45.833 31.58 31.58 46.98 3.91
2121 2254 4.481463 GGTGCGATAGAGATTCTCTAAGC 58.519 47.826 28.87 28.87 44.76 3.09
2122 2255 4.082463 GGGGTGCGATAGAGATTCTCTAAG 60.082 50.000 23.62 20.42 44.76 2.18
2123 2256 3.827302 GGGGTGCGATAGAGATTCTCTAA 59.173 47.826 23.62 7.88 44.76 2.10
2124 2257 3.074687 AGGGGTGCGATAGAGATTCTCTA 59.925 47.826 22.42 22.42 45.52 2.43
2125 2258 2.158385 AGGGGTGCGATAGAGATTCTCT 60.158 50.000 19.64 19.64 43.83 3.10
2126 2259 2.243810 AGGGGTGCGATAGAGATTCTC 58.756 52.381 5.49 5.49 39.76 2.87
2127 2260 2.390225 AGGGGTGCGATAGAGATTCT 57.610 50.000 0.00 0.00 39.76 2.40
2128 2261 3.764434 TGATAGGGGTGCGATAGAGATTC 59.236 47.826 0.00 0.00 39.76 2.52
2129 2262 3.779444 TGATAGGGGTGCGATAGAGATT 58.221 45.455 0.00 0.00 39.76 2.40
2130 2263 3.458044 TGATAGGGGTGCGATAGAGAT 57.542 47.619 0.00 0.00 39.76 2.75
2131 2264 2.971901 TGATAGGGGTGCGATAGAGA 57.028 50.000 0.00 0.00 39.76 3.10
2132 2265 4.543590 AAATGATAGGGGTGCGATAGAG 57.456 45.455 0.00 0.00 39.76 2.43
2133 2266 5.542635 AGTTAAATGATAGGGGTGCGATAGA 59.457 40.000 0.00 0.00 39.76 1.98
2134 2267 5.794894 AGTTAAATGATAGGGGTGCGATAG 58.205 41.667 0.00 0.00 0.00 2.08
2135 2268 5.305902 TGAGTTAAATGATAGGGGTGCGATA 59.694 40.000 0.00 0.00 0.00 2.92
2136 2269 4.102524 TGAGTTAAATGATAGGGGTGCGAT 59.897 41.667 0.00 0.00 0.00 4.58
2137 2270 3.452990 TGAGTTAAATGATAGGGGTGCGA 59.547 43.478 0.00 0.00 0.00 5.10
2138 2271 3.804036 TGAGTTAAATGATAGGGGTGCG 58.196 45.455 0.00 0.00 0.00 5.34
2139 2272 5.036117 TCTGAGTTAAATGATAGGGGTGC 57.964 43.478 0.00 0.00 0.00 5.01
2140 2273 5.615289 CCTCTGAGTTAAATGATAGGGGTG 58.385 45.833 3.66 0.00 0.00 4.61
2141 2274 4.103311 GCCTCTGAGTTAAATGATAGGGGT 59.897 45.833 3.66 0.00 0.00 4.95
2142 2275 4.646572 GCCTCTGAGTTAAATGATAGGGG 58.353 47.826 3.66 0.00 0.00 4.79
2143 2276 4.310769 CGCCTCTGAGTTAAATGATAGGG 58.689 47.826 3.66 0.00 0.00 3.53
2144 2277 4.039245 TCCGCCTCTGAGTTAAATGATAGG 59.961 45.833 3.66 0.00 0.00 2.57
2145 2278 4.985409 GTCCGCCTCTGAGTTAAATGATAG 59.015 45.833 3.66 0.00 0.00 2.08
2146 2279 4.202223 GGTCCGCCTCTGAGTTAAATGATA 60.202 45.833 3.66 0.00 0.00 2.15
2147 2280 3.432326 GGTCCGCCTCTGAGTTAAATGAT 60.432 47.826 3.66 0.00 0.00 2.45
2148 2281 2.093658 GGTCCGCCTCTGAGTTAAATGA 60.094 50.000 3.66 0.00 0.00 2.57
2149 2282 2.280628 GGTCCGCCTCTGAGTTAAATG 58.719 52.381 3.66 0.00 0.00 2.32
2150 2283 1.906574 TGGTCCGCCTCTGAGTTAAAT 59.093 47.619 3.66 0.00 35.27 1.40
2151 2284 1.001633 GTGGTCCGCCTCTGAGTTAAA 59.998 52.381 3.66 0.00 35.27 1.52
2152 2285 0.606604 GTGGTCCGCCTCTGAGTTAA 59.393 55.000 3.66 0.00 35.27 2.01
2153 2286 1.592400 CGTGGTCCGCCTCTGAGTTA 61.592 60.000 3.66 0.00 35.27 2.24
2154 2287 2.932234 CGTGGTCCGCCTCTGAGTT 61.932 63.158 3.66 0.00 35.27 3.01
2155 2288 3.374402 CGTGGTCCGCCTCTGAGT 61.374 66.667 3.66 0.00 35.27 3.41
2241 2378 6.898041 TCATTTGTAGTGTGCATTGTTAGTC 58.102 36.000 0.00 0.00 0.00 2.59
2713 2855 2.090719 CCTGGTAATCTCCTAGGGTCCA 60.091 54.545 9.46 7.90 0.00 4.02


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

AutoCloner maintained by Alex Coulton.