Multiple sequence alignment - TraesCS4A01G487800

Loading Multiple Alignment...

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 TraesCS4A01G487800 chr4A 100.000 2777 0 0 1 2777 739869131 739871907 0.000000e+00 5129
1 TraesCS4A01G487800 chr4A 88.719 1835 153 25 10 1799 741482718 741480893 0.000000e+00 2193
2 TraesCS4A01G487800 chr4A 86.211 1842 184 31 1 1795 741814108 741812290 0.000000e+00 1930
3 TraesCS4A01G487800 chr4A 86.076 1817 186 41 1 1779 740453896 740452109 0.000000e+00 1892
4 TraesCS4A01G487800 chr4A 87.807 1181 116 15 568 1732 739654185 739655353 0.000000e+00 1358
5 TraesCS4A01G487800 chr4A 86.904 1153 122 15 590 1725 739736416 739737556 0.000000e+00 1266
6 TraesCS4A01G487800 chr4A 87.770 1063 122 7 745 1800 740581393 740582454 0.000000e+00 1236
7 TraesCS4A01G487800 chr4A 86.787 1052 122 11 736 1777 740939982 740941026 0.000000e+00 1157
8 TraesCS4A01G487800 chr4A 86.444 1077 119 18 745 1800 741592696 741593766 0.000000e+00 1155
9 TraesCS4A01G487800 chr4A 90.305 557 50 4 2 556 739653587 739654141 0.000000e+00 726
10 TraesCS4A01G487800 chr4A 89.928 556 54 2 2 556 742058866 742059420 0.000000e+00 715
11 TraesCS4A01G487800 chr4A 91.485 505 43 0 1 505 741793043 741792539 0.000000e+00 695
12 TraesCS4A01G487800 chr4A 91.124 507 45 0 1 507 740939099 740939605 0.000000e+00 688
13 TraesCS4A01G487800 chr4A 82.985 670 67 34 1817 2475 741812163 741811530 1.870000e-156 562
14 TraesCS4A01G487800 chr4A 86.104 403 32 8 168 570 742132398 742132776 1.990000e-111 412
15 TraesCS4A01G487800 chr4A 85.432 405 31 11 168 570 739735904 739736282 2.000000e-106 396
16 TraesCS4A01G487800 chr4A 84.122 296 33 6 2491 2777 740943274 740943564 9.800000e-70 274
17 TraesCS4A01G487800 chr4A 92.810 153 6 4 1817 1969 740583412 740583559 1.670000e-52 217
18 TraesCS4A01G487800 chr4A 78.698 338 52 16 2443 2777 742062578 742062898 1.010000e-49 207
19 TraesCS4A01G487800 chr4A 98.361 61 1 0 2676 2736 739738523 739738583 1.050000e-19 108
20 TraesCS4A01G487800 chr4A 95.745 47 1 1 2553 2599 739738591 739738636 1.070000e-09 75
21 TraesCS4A01G487800 chr7A 88.072 1836 170 20 1 1800 2116014 2114192 0.000000e+00 2132
22 TraesCS4A01G487800 chr7A 88.081 1829 162 26 1 1799 1994981 1993179 0.000000e+00 2119
23 TraesCS4A01G487800 chr7A 87.921 1813 172 29 1 1779 3206490 3204691 0.000000e+00 2091
24 TraesCS4A01G487800 chr7A 79.114 632 81 17 2097 2717 3204223 3203632 3.350000e-104 388
25 TraesCS4A01G487800 chr7D 88.215 1748 178 16 1 1738 2562563 2560834 0.000000e+00 2061
26 TraesCS4A01G487800 chr7D 88.617 1063 105 11 745 1793 3784670 3783610 0.000000e+00 1279
27 TraesCS4A01G487800 chr7D 87.992 1066 109 14 745 1793 3630872 3629809 0.000000e+00 1242
28 TraesCS4A01G487800 chr7D 87.885 1040 119 5 745 1779 2607595 2606558 0.000000e+00 1216
29 TraesCS4A01G487800 chr7D 88.120 867 61 9 1944 2777 2606338 2605481 0.000000e+00 992
30 TraesCS4A01G487800 chr7D 89.229 687 55 11 2097 2777 3236959 3236286 0.000000e+00 841
31 TraesCS4A01G487800 chr7D 89.083 687 56 11 2097 2777 3221750 3221077 0.000000e+00 835
32 TraesCS4A01G487800 chr7D 82.748 313 24 16 1821 2129 2560686 2560400 4.590000e-63 252
33 TraesCS4A01G487800 chr7D 87.059 170 14 4 1817 1985 3228164 3228002 4.720000e-43 185
34 TraesCS4A01G487800 chr7D 86.471 170 15 4 1817 1985 3243374 3243212 2.200000e-41 180
35 TraesCS4A01G487800 chrUn 89.374 687 54 11 2097 2777 325095539 325094866 0.000000e+00 846
36 TraesCS4A01G487800 chrUn 89.229 687 55 11 2097 2777 340806433 340807106 0.000000e+00 841
37 TraesCS4A01G487800 chrUn 87.059 170 14 4 1817 1985 328674972 328674810 4.720000e-43 185
38 TraesCS4A01G487800 chr5A 88.727 275 16 6 2097 2365 464230986 464230721 3.450000e-84 322
39 TraesCS4A01G487800 chr6A 87.956 274 19 7 2097 2365 57063339 57063603 7.470000e-81 311
40 TraesCS4A01G487800 chr1A 87.956 274 20 6 2097 2365 48268210 48267945 7.470000e-81 311
41 TraesCS4A01G487800 chr1A 87.591 274 21 6 2097 2365 581407173 581406908 3.470000e-79 305
42 TraesCS4A01G487800 chr1A 87.500 272 21 6 2097 2363 370464079 370463816 4.490000e-78 302
43 TraesCS4A01G487800 chr1A 85.714 189 15 5 2097 2281 522014700 522014880 3.650000e-44 189
44 TraesCS4A01G487800 chr3A 87.591 274 20 8 2097 2365 130370688 130370424 3.470000e-79 305


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 TraesCS4A01G487800 chr4A 739869131 739871907 2776 False 5129.000000 5129 100.000000 1 2777 1 chr4A.!!$F1 2776
1 TraesCS4A01G487800 chr4A 741480893 741482718 1825 True 2193.000000 2193 88.719000 10 1799 1 chr4A.!!$R2 1789
2 TraesCS4A01G487800 chr4A 740452109 740453896 1787 True 1892.000000 1892 86.076000 1 1779 1 chr4A.!!$R1 1778
3 TraesCS4A01G487800 chr4A 741811530 741814108 2578 True 1246.000000 1930 84.598000 1 2475 2 chr4A.!!$R4 2474
4 TraesCS4A01G487800 chr4A 741592696 741593766 1070 False 1155.000000 1155 86.444000 745 1800 1 chr4A.!!$F2 1055
5 TraesCS4A01G487800 chr4A 739653587 739655353 1766 False 1042.000000 1358 89.056000 2 1732 2 chr4A.!!$F4 1730
6 TraesCS4A01G487800 chr4A 740581393 740583559 2166 False 726.500000 1236 90.290000 745 1969 2 chr4A.!!$F6 1224
7 TraesCS4A01G487800 chr4A 740939099 740943564 4465 False 706.333333 1157 87.344333 1 2777 3 chr4A.!!$F7 2776
8 TraesCS4A01G487800 chr4A 741792539 741793043 504 True 695.000000 695 91.485000 1 505 1 chr4A.!!$R3 504
9 TraesCS4A01G487800 chr4A 739735904 739738636 2732 False 461.250000 1266 91.610500 168 2736 4 chr4A.!!$F5 2568
10 TraesCS4A01G487800 chr4A 742058866 742062898 4032 False 461.000000 715 84.313000 2 2777 2 chr4A.!!$F8 2775
11 TraesCS4A01G487800 chr7A 2114192 2116014 1822 True 2132.000000 2132 88.072000 1 1800 1 chr7A.!!$R2 1799
12 TraesCS4A01G487800 chr7A 1993179 1994981 1802 True 2119.000000 2119 88.081000 1 1799 1 chr7A.!!$R1 1798
13 TraesCS4A01G487800 chr7A 3203632 3206490 2858 True 1239.500000 2091 83.517500 1 2717 2 chr7A.!!$R3 2716
14 TraesCS4A01G487800 chr7D 3783610 3784670 1060 True 1279.000000 1279 88.617000 745 1793 1 chr7D.!!$R6 1048
15 TraesCS4A01G487800 chr7D 3629809 3630872 1063 True 1242.000000 1242 87.992000 745 1793 1 chr7D.!!$R5 1048
16 TraesCS4A01G487800 chr7D 2560400 2562563 2163 True 1156.500000 2061 85.481500 1 2129 2 chr7D.!!$R7 2128
17 TraesCS4A01G487800 chr7D 2605481 2607595 2114 True 1104.000000 1216 88.002500 745 2777 2 chr7D.!!$R8 2032
18 TraesCS4A01G487800 chr7D 3236286 3236959 673 True 841.000000 841 89.229000 2097 2777 1 chr7D.!!$R3 680
19 TraesCS4A01G487800 chr7D 3221077 3221750 673 True 835.000000 835 89.083000 2097 2777 1 chr7D.!!$R1 680
20 TraesCS4A01G487800 chrUn 325094866 325095539 673 True 846.000000 846 89.374000 2097 2777 1 chrUn.!!$R1 680
21 TraesCS4A01G487800 chrUn 340806433 340807106 673 False 841.000000 841 89.229000 2097 2777 1 chrUn.!!$F1 680

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
489 505 0.392998 CTGGTGGATTCTGGTTCCCG 60.393 60.0 0.0 0.0 31.87 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2487 4601 0.321653 ATTTGTGGTCAGGACTCCGC 60.322 55.0 0.0 0.0 35.12 5.54 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
54 55 4.274459 GGATGGACTGTCAGTAAATGATGC 59.726 45.833 5.21 0.00 40.92 3.91
211 224 6.095440 GTGGAATAGCTTGGCTAAGATTTGAA 59.905 38.462 14.82 0.00 44.62 2.69
214 227 3.424703 AGCTTGGCTAAGATTTGAAGCA 58.575 40.909 14.82 0.00 36.99 3.91
286 299 2.031157 CCAAATGGACCAACGACTTGAC 60.031 50.000 0.00 0.00 37.39 3.18
303 316 1.209504 TGACCTTTATTCGGAGCCTGG 59.790 52.381 0.00 0.00 0.00 4.45
489 505 0.392998 CTGGTGGATTCTGGTTCCCG 60.393 60.000 0.00 0.00 31.87 5.14
622 803 2.286523 CGGAGTCCACTTCCTGCCT 61.287 63.158 10.49 0.00 0.00 4.75
646 838 4.201950 GCTGCATGTTCCAGGTATACTTTG 60.202 45.833 2.25 2.22 0.00 2.77
653 846 6.535540 TGTTCCAGGTATACTTTGCTAACAA 58.464 36.000 2.25 0.00 0.00 2.83
670 863 5.870978 GCTAACAAAGACAATTTGCCATCAT 59.129 36.000 0.00 0.00 32.93 2.45
829 1198 3.035305 TCCAGGTGGGAATATGGCA 57.965 52.632 0.00 0.00 44.80 4.92
934 1303 2.038295 GAGCATTGGATCTACCTCCCTG 59.962 54.545 0.00 0.00 39.86 4.45
1008 1380 2.036256 GTGCCCAAGATGCCACCT 59.964 61.111 0.00 0.00 0.00 4.00
1016 1388 1.614903 CAAGATGCCACCTGCTCAAAA 59.385 47.619 0.00 0.00 42.00 2.44
1035 1422 0.179100 ACGTCATCTGGGATTCGCTG 60.179 55.000 2.19 1.96 0.00 5.18
1039 1426 0.394192 CATCTGGGATTCGCTGGCTA 59.606 55.000 7.58 0.00 0.00 3.93
1053 1440 1.689273 CTGGCTATAGGAACCGAGCTT 59.311 52.381 1.04 0.00 35.23 3.74
1057 1444 2.864489 GCTATAGGAACCGAGCTTCTGC 60.864 54.545 1.04 0.00 40.05 4.26
1068 1455 2.261215 GCTTCTGCTGTTTGGGGAG 58.739 57.895 0.00 0.00 36.03 4.30
1072 1459 3.185203 TGCTGTTTGGGGAGGGCT 61.185 61.111 0.00 0.00 0.00 5.19
1075 1462 4.299796 TGTTTGGGGAGGGCTGGC 62.300 66.667 0.00 0.00 0.00 4.85
1118 1511 3.287867 CAATTCATGGACAGGGCTAGT 57.712 47.619 0.00 0.00 0.00 2.57
1119 1512 2.947652 CAATTCATGGACAGGGCTAGTG 59.052 50.000 0.00 0.00 0.00 2.74
1124 1535 0.042581 TGGACAGGGCTAGTGGATGA 59.957 55.000 0.00 0.00 0.00 2.92
1152 1563 2.356553 CCGCGGTTCTCGTTTGGA 60.357 61.111 19.50 0.00 41.72 3.53
1167 1578 0.961019 TTGGATCAGCAAGTGTTGGC 59.039 50.000 0.00 0.00 0.00 4.52
1340 1757 5.421056 AGTTCTATGTGATCGGTGGTCTTAA 59.579 40.000 0.00 0.00 0.00 1.85
1448 1883 4.464008 CTCAACAATATAGCCATGGGTGT 58.536 43.478 26.70 22.10 0.00 4.16
1463 1898 0.321653 GGTGTTCCTCCGCTCATTGT 60.322 55.000 0.00 0.00 0.00 2.71
1468 1903 3.244422 TGTTCCTCCGCTCATTGTAGTTT 60.244 43.478 0.00 0.00 0.00 2.66
1592 2036 5.625150 ACAGTCTAAGAACAAAGATGGCTT 58.375 37.500 0.00 0.00 35.37 4.35
1629 2073 1.741770 GTGTGGTGACCGGCTGATC 60.742 63.158 0.00 0.00 0.00 2.92
1732 2176 1.202475 GGAATTTGTTTGCCACACGGT 60.202 47.619 0.00 0.00 33.98 4.83
1754 2201 3.118038 TCATACAGGGGTAACTGGATTGC 60.118 47.826 0.00 0.00 38.94 3.56
1756 2206 0.251916 CAGGGGTAACTGGATTGCGA 59.748 55.000 0.00 0.00 34.84 5.10
1784 2234 0.773644 ATGGGTTGCTGAGTTGGTCT 59.226 50.000 0.00 0.00 0.00 3.85
1803 2256 5.012664 TGGTCTACTGAATAAAGGTTGCTGA 59.987 40.000 0.00 0.00 0.00 4.26
1805 2258 6.166982 GTCTACTGAATAAAGGTTGCTGAGT 58.833 40.000 0.00 0.00 0.00 3.41
1809 2262 3.058293 TGAATAAAGGTTGCTGAGTTGCG 60.058 43.478 0.00 0.00 35.36 4.85
1810 2263 0.591170 TAAAGGTTGCTGAGTTGCGC 59.409 50.000 0.00 0.00 35.36 6.09
1811 2264 2.075426 AAAGGTTGCTGAGTTGCGCC 62.075 55.000 4.18 0.00 35.36 6.53
1812 2265 2.965716 AAGGTTGCTGAGTTGCGCCT 62.966 55.000 4.18 0.00 40.70 5.52
1813 2266 2.253452 GTTGCTGAGTTGCGCCTG 59.747 61.111 4.18 0.00 35.36 4.85
1815 2268 2.545596 TTGCTGAGTTGCGCCTGTG 61.546 57.895 4.18 0.00 35.36 3.66
1855 2443 2.582728 TTCAACTTTGGCTGCAACAG 57.417 45.000 0.50 0.00 34.12 3.16
1858 2446 1.035139 AACTTTGGCTGCAACAGAGG 58.965 50.000 0.50 1.51 32.44 3.69
1859 2447 1.288127 CTTTGGCTGCAACAGAGGC 59.712 57.895 0.50 0.00 32.44 4.70
1879 2470 3.929610 GGCGCATGTCTTCTCTATTATCC 59.070 47.826 10.83 0.00 0.00 2.59
1914 2594 7.327275 CGCACCTCATATTCTGTAGTCTATTTC 59.673 40.741 0.00 0.00 0.00 2.17
1928 2612 7.664318 TGTAGTCTATTTCTTTTTCCCCAGTTC 59.336 37.037 0.00 0.00 0.00 3.01
1933 2617 2.774687 TCTTTTTCCCCAGTTCGCTAC 58.225 47.619 0.00 0.00 0.00 3.58
1937 2621 1.271856 TTCCCCAGTTCGCTACATGA 58.728 50.000 0.00 0.00 0.00 3.07
1939 2623 2.673258 TCCCCAGTTCGCTACATGATA 58.327 47.619 0.00 0.00 0.00 2.15
1940 2624 2.364324 TCCCCAGTTCGCTACATGATAC 59.636 50.000 0.00 0.00 0.00 2.24
1941 2625 2.365617 CCCCAGTTCGCTACATGATACT 59.634 50.000 0.00 0.00 0.00 2.12
1942 2626 3.384668 CCCAGTTCGCTACATGATACTG 58.615 50.000 0.00 3.53 34.32 2.74
1957 2641 7.530010 ACATGATACTGTATGCTTTTGTTCAC 58.470 34.615 4.79 0.00 0.00 3.18
1971 2660 6.385649 TTTTGTTCACTTCTGTTATCACCC 57.614 37.500 0.00 0.00 0.00 4.61
1983 2810 5.724370 TCTGTTATCACCCTCTGAATGGTAA 59.276 40.000 0.00 0.00 32.32 2.85
1984 2811 6.386927 TCTGTTATCACCCTCTGAATGGTAAT 59.613 38.462 0.00 0.00 32.32 1.89
1985 2812 6.356556 TGTTATCACCCTCTGAATGGTAATG 58.643 40.000 0.00 0.00 32.32 1.90
1986 2813 6.157820 TGTTATCACCCTCTGAATGGTAATGA 59.842 38.462 0.00 0.00 32.32 2.57
1987 2814 5.919348 ATCACCCTCTGAATGGTAATGAT 57.081 39.130 0.00 0.00 32.32 2.45
1988 2815 8.375506 GTTATCACCCTCTGAATGGTAATGATA 58.624 37.037 0.00 0.00 32.32 2.15
1989 2816 7.579940 ATCACCCTCTGAATGGTAATGATAT 57.420 36.000 0.00 0.00 32.32 1.63
1990 2817 7.392766 TCACCCTCTGAATGGTAATGATATT 57.607 36.000 0.00 0.00 32.32 1.28
1991 2818 8.504811 TCACCCTCTGAATGGTAATGATATTA 57.495 34.615 0.00 0.00 32.32 0.98
1992 2819 9.116080 TCACCCTCTGAATGGTAATGATATTAT 57.884 33.333 0.00 0.00 32.32 1.28
1993 2820 9.745018 CACCCTCTGAATGGTAATGATATTATT 57.255 33.333 0.00 0.00 32.32 1.40
2004 2831 9.859152 TGGTAATGATATTATTTGTGATGGTCA 57.141 29.630 0.00 0.00 0.00 4.02
2013 2840 7.715266 TTATTTGTGATGGTCAATTCATGGA 57.285 32.000 0.00 0.00 0.00 3.41
2014 2841 6.801718 ATTTGTGATGGTCAATTCATGGAT 57.198 33.333 0.00 0.00 0.00 3.41
2015 2842 6.608539 TTTGTGATGGTCAATTCATGGATT 57.391 33.333 0.00 0.00 0.00 3.01
2016 2843 6.608539 TTGTGATGGTCAATTCATGGATTT 57.391 33.333 0.00 0.00 0.00 2.17
2017 2844 5.968254 TGTGATGGTCAATTCATGGATTTG 58.032 37.500 0.00 0.00 0.00 2.32
2018 2845 5.481122 TGTGATGGTCAATTCATGGATTTGT 59.519 36.000 0.00 0.00 0.00 2.83
2019 2846 6.014413 TGTGATGGTCAATTCATGGATTTGTT 60.014 34.615 0.00 0.00 0.00 2.83
2020 2847 6.875195 GTGATGGTCAATTCATGGATTTGTTT 59.125 34.615 0.00 0.00 0.00 2.83
2021 2848 6.874664 TGATGGTCAATTCATGGATTTGTTTG 59.125 34.615 0.00 0.00 0.00 2.93
2022 2849 6.416631 TGGTCAATTCATGGATTTGTTTGA 57.583 33.333 0.00 0.00 0.00 2.69
2027 2854 7.816031 GTCAATTCATGGATTTGTTTGACTGAT 59.184 33.333 9.31 0.00 37.57 2.90
2039 2866 7.624360 TTGTTTGACTGATACTGTGTTTCTT 57.376 32.000 0.00 0.00 0.00 2.52
2041 2868 7.693952 TGTTTGACTGATACTGTGTTTCTTTC 58.306 34.615 0.00 0.00 0.00 2.62
2054 2881 7.233348 ACTGTGTTTCTTTCCATATTTCCATGT 59.767 33.333 0.00 0.00 0.00 3.21
2078 2905 1.739562 CTGCTGGAACGTCTGCCTC 60.740 63.158 0.00 0.00 0.00 4.70
2095 2954 2.903798 CCTCTGCCTCATTCTCAAGTC 58.096 52.381 0.00 0.00 0.00 3.01
2100 2959 2.278854 GCCTCATTCTCAAGTCTGCTC 58.721 52.381 0.00 0.00 0.00 4.26
2129 2990 6.402222 AGAGAAGACATGTATGAGTTTGGAC 58.598 40.000 0.00 0.00 0.00 4.02
2130 2991 6.212388 AGAGAAGACATGTATGAGTTTGGACT 59.788 38.462 0.00 0.00 39.32 3.85
2131 2992 6.773638 AGAAGACATGTATGAGTTTGGACTT 58.226 36.000 0.00 0.00 35.88 3.01
2132 2993 7.227156 AGAAGACATGTATGAGTTTGGACTTT 58.773 34.615 0.00 0.00 35.88 2.66
2133 2994 6.808008 AGACATGTATGAGTTTGGACTTTG 57.192 37.500 0.00 0.00 35.88 2.77
2134 2995 5.707298 AGACATGTATGAGTTTGGACTTTGG 59.293 40.000 0.00 0.00 35.88 3.28
2135 2996 5.630121 ACATGTATGAGTTTGGACTTTGGA 58.370 37.500 0.00 0.00 35.88 3.53
2157 3028 5.220835 GGAGAAAGTGCCAATTTGGTTTTTG 60.221 40.000 16.62 0.00 40.46 2.44
2158 3029 5.495640 AGAAAGTGCCAATTTGGTTTTTGA 58.504 33.333 16.62 0.00 40.46 2.69
2170 3042 8.938906 CAATTTGGTTTTTGATTTGCTAGCTAT 58.061 29.630 17.23 9.41 0.00 2.97
2171 3043 7.887996 TTTGGTTTTTGATTTGCTAGCTATG 57.112 32.000 17.23 0.00 0.00 2.23
2173 3045 7.408756 TGGTTTTTGATTTGCTAGCTATGAT 57.591 32.000 17.23 4.43 0.00 2.45
2181 3056 7.198390 TGATTTGCTAGCTATGATTTTCTTGC 58.802 34.615 17.23 0.00 0.00 4.01
2197 3072 4.439305 TCTTGCTTCAATTTGGATTCCG 57.561 40.909 0.00 0.00 0.00 4.30
2507 5918 1.882352 GCGGAGTCCTGACCACAAATT 60.882 52.381 7.77 0.00 0.00 1.82
2547 5958 9.234384 CTATCACAACTACTGTAAATAGTTCGG 57.766 37.037 0.00 0.00 40.18 4.30
2759 6261 5.980116 CCTTTAGTGATGGACTGTATCTTCG 59.020 44.000 0.00 0.00 35.96 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 174 3.995199 TGAACCTCAGCTTCAAGTACTG 58.005 45.455 0.00 0.00 0.00 2.74
211 224 1.134280 AGATTAGGCATTGCGTCTGCT 60.134 47.619 7.19 0.00 43.34 4.24
214 227 2.484417 CCAGAGATTAGGCATTGCGTCT 60.484 50.000 7.19 5.74 0.00 4.18
286 299 0.819666 GGCCAGGCTCCGAATAAAGG 60.820 60.000 12.43 0.00 0.00 3.11
303 316 3.006940 TGTCGATATTGTTTCCACTGGC 58.993 45.455 0.00 0.00 0.00 4.85
379 392 0.320946 CAGCTGCACCCCCAAATTTG 60.321 55.000 11.40 11.40 0.00 2.32
489 505 3.681593 TGGCACTACCTTTTATCACCAC 58.318 45.455 0.00 0.00 40.22 4.16
622 803 2.505407 AGTATACCTGGAACATGCAGCA 59.495 45.455 0.00 0.00 38.20 4.41
646 838 5.229423 TGATGGCAAATTGTCTTTGTTAGC 58.771 37.500 0.00 0.00 0.00 3.09
653 846 4.020928 TGAAGCATGATGGCAAATTGTCTT 60.021 37.500 0.00 0.00 35.83 3.01
670 863 4.196193 CGGGTAATTTATCACCTGAAGCA 58.804 43.478 0.00 0.00 42.85 3.91
829 1198 2.670148 GGTTCAGGGAGGCGATGGT 61.670 63.158 0.00 0.00 0.00 3.55
879 1248 2.104331 CGACGCAGGCGGTAGATT 59.896 61.111 18.63 0.00 44.69 2.40
918 1287 0.694444 GGCCAGGGAGGTAGATCCAA 60.694 60.000 0.00 0.00 41.52 3.53
934 1303 2.108362 CTCGTGGGGATTACGGCC 59.892 66.667 0.00 0.00 41.58 6.13
961 1333 2.268920 CCCAGTGGACGGGTCATG 59.731 66.667 11.95 0.00 39.05 3.07
1008 1380 1.071542 TCCCAGATGACGTTTTGAGCA 59.928 47.619 0.00 0.00 0.00 4.26
1016 1388 0.179100 CAGCGAATCCCAGATGACGT 60.179 55.000 0.00 0.00 0.00 4.34
1035 1422 1.964933 AGAAGCTCGGTTCCTATAGCC 59.035 52.381 5.33 0.00 35.54 3.93
1053 1440 3.170362 CCCTCCCCAAACAGCAGA 58.830 61.111 0.00 0.00 0.00 4.26
1057 1444 2.036256 CCAGCCCTCCCCAAACAG 59.964 66.667 0.00 0.00 0.00 3.16
1068 1455 1.137872 CTATATCTCATCCGCCAGCCC 59.862 57.143 0.00 0.00 0.00 5.19
1072 1459 2.432146 GGATGCTATATCTCATCCGCCA 59.568 50.000 16.02 0.00 46.23 5.69
1078 1465 8.829746 TGAATTGGTAAGGATGCTATATCTCAT 58.170 33.333 0.00 0.00 0.00 2.90
1116 1509 1.561542 GGGGTGTTCATCTCATCCACT 59.438 52.381 0.00 0.00 37.78 4.00
1118 1511 0.541392 CGGGGTGTTCATCTCATCCA 59.459 55.000 0.00 0.00 37.78 3.41
1119 1512 0.815615 GCGGGGTGTTCATCTCATCC 60.816 60.000 0.00 0.00 35.52 3.51
1152 1563 1.317613 TTTCGCCAACACTTGCTGAT 58.682 45.000 0.00 0.00 0.00 2.90
1167 1578 0.368907 CCACGACATACGCCTTTTCG 59.631 55.000 0.00 0.00 46.94 3.46
1340 1757 2.165845 GTCAATACCTCGTGGCTACTGT 59.834 50.000 2.76 0.00 36.63 3.55
1448 1883 3.695830 AAACTACAATGAGCGGAGGAA 57.304 42.857 0.00 0.00 0.00 3.36
1463 1898 7.538575 GGCATAAAGCTCATTCTTCAAAACTA 58.461 34.615 0.00 0.00 44.79 2.24
1468 1903 3.181497 GCGGCATAAAGCTCATTCTTCAA 60.181 43.478 0.00 0.00 44.79 2.69
1518 1953 7.712639 CACTTATTGTCCAGCTTATCATACTGT 59.287 37.037 0.00 0.00 0.00 3.55
1592 2036 0.893270 CGCTTGGAAACCCATGTCCA 60.893 55.000 0.00 0.00 42.27 4.02
1732 2176 3.118038 GCAATCCAGTTACCCCTGTATGA 60.118 47.826 0.00 0.00 0.00 2.15
1784 2234 5.181245 GCAACTCAGCAACCTTTATTCAGTA 59.819 40.000 0.00 0.00 0.00 2.74
1810 2263 1.392589 ACAGTGAAAAGCCACACAGG 58.607 50.000 0.00 0.00 39.42 4.00
1811 2264 2.423185 TCAACAGTGAAAAGCCACACAG 59.577 45.455 0.00 0.00 39.42 3.66
1812 2265 2.441410 TCAACAGTGAAAAGCCACACA 58.559 42.857 0.00 0.00 39.42 3.72
1813 2266 3.066621 TCATCAACAGTGAAAAGCCACAC 59.933 43.478 0.00 0.00 39.42 3.82
1815 2268 3.988379 TCATCAACAGTGAAAAGCCAC 57.012 42.857 0.00 0.00 37.30 5.01
1855 2443 2.810439 ATAGAGAAGACATGCGCCTC 57.190 50.000 4.18 1.62 0.00 4.70
1858 2446 4.560128 TGGATAATAGAGAAGACATGCGC 58.440 43.478 0.00 0.00 0.00 6.09
1859 2447 6.393171 TGATGGATAATAGAGAAGACATGCG 58.607 40.000 0.00 0.00 0.00 4.73
1914 2594 2.500229 TGTAGCGAACTGGGGAAAAAG 58.500 47.619 0.00 0.00 0.00 2.27
1920 2604 2.365617 AGTATCATGTAGCGAACTGGGG 59.634 50.000 0.00 0.00 0.00 4.96
1928 2612 6.018751 ACAAAAGCATACAGTATCATGTAGCG 60.019 38.462 0.00 0.00 38.96 4.26
1933 2617 7.755591 AGTGAACAAAAGCATACAGTATCATG 58.244 34.615 0.00 0.00 0.00 3.07
1937 2621 7.445402 ACAGAAGTGAACAAAAGCATACAGTAT 59.555 33.333 0.00 0.00 0.00 2.12
1939 2623 5.590259 ACAGAAGTGAACAAAAGCATACAGT 59.410 36.000 0.00 0.00 0.00 3.55
1940 2624 6.064846 ACAGAAGTGAACAAAAGCATACAG 57.935 37.500 0.00 0.00 0.00 2.74
1941 2625 6.449635 AACAGAAGTGAACAAAAGCATACA 57.550 33.333 0.00 0.00 0.00 2.29
1942 2626 8.289618 TGATAACAGAAGTGAACAAAAGCATAC 58.710 33.333 0.00 0.00 0.00 2.39
1957 2641 5.121811 CCATTCAGAGGGTGATAACAGAAG 58.878 45.833 0.00 0.00 34.17 2.85
1987 2814 9.418839 TCCATGAATTGACCATCACAAATAATA 57.581 29.630 0.00 0.00 0.00 0.98
1988 2815 8.308851 TCCATGAATTGACCATCACAAATAAT 57.691 30.769 0.00 0.00 0.00 1.28
1989 2816 7.715266 TCCATGAATTGACCATCACAAATAA 57.285 32.000 0.00 0.00 0.00 1.40
1990 2817 7.901283 ATCCATGAATTGACCATCACAAATA 57.099 32.000 0.00 0.00 0.00 1.40
1991 2818 6.801718 ATCCATGAATTGACCATCACAAAT 57.198 33.333 0.00 0.00 0.00 2.32
1992 2819 6.608539 AATCCATGAATTGACCATCACAAA 57.391 33.333 0.00 0.00 0.00 2.83
1993 2820 6.014413 ACAAATCCATGAATTGACCATCACAA 60.014 34.615 10.70 0.00 0.00 3.33
1994 2821 5.481122 ACAAATCCATGAATTGACCATCACA 59.519 36.000 10.70 0.00 0.00 3.58
1995 2822 5.969423 ACAAATCCATGAATTGACCATCAC 58.031 37.500 10.70 0.00 0.00 3.06
1996 2823 6.608539 AACAAATCCATGAATTGACCATCA 57.391 33.333 10.70 0.00 0.00 3.07
1997 2824 7.063780 GTCAAACAAATCCATGAATTGACCATC 59.936 37.037 10.70 0.00 40.52 3.51
1998 2825 6.875195 GTCAAACAAATCCATGAATTGACCAT 59.125 34.615 10.70 0.00 40.52 3.55
1999 2826 6.041865 AGTCAAACAAATCCATGAATTGACCA 59.958 34.615 17.99 0.00 43.45 4.02
2000 2827 6.366877 CAGTCAAACAAATCCATGAATTGACC 59.633 38.462 17.99 8.24 43.45 4.02
2001 2828 7.147312 TCAGTCAAACAAATCCATGAATTGAC 58.853 34.615 15.82 15.82 43.15 3.18
2002 2829 7.287512 TCAGTCAAACAAATCCATGAATTGA 57.712 32.000 10.70 0.00 31.93 2.57
2003 2830 9.079833 GTATCAGTCAAACAAATCCATGAATTG 57.920 33.333 0.00 0.00 0.00 2.32
2004 2831 9.028284 AGTATCAGTCAAACAAATCCATGAATT 57.972 29.630 0.00 0.00 0.00 2.17
2005 2832 8.464404 CAGTATCAGTCAAACAAATCCATGAAT 58.536 33.333 0.00 0.00 0.00 2.57
2006 2833 7.448161 ACAGTATCAGTCAAACAAATCCATGAA 59.552 33.333 0.00 0.00 0.00 2.57
2007 2834 6.942005 ACAGTATCAGTCAAACAAATCCATGA 59.058 34.615 0.00 0.00 0.00 3.07
2008 2835 7.025365 CACAGTATCAGTCAAACAAATCCATG 58.975 38.462 0.00 0.00 0.00 3.66
2009 2836 6.716628 ACACAGTATCAGTCAAACAAATCCAT 59.283 34.615 0.00 0.00 0.00 3.41
2010 2837 6.061441 ACACAGTATCAGTCAAACAAATCCA 58.939 36.000 0.00 0.00 0.00 3.41
2011 2838 6.560253 ACACAGTATCAGTCAAACAAATCC 57.440 37.500 0.00 0.00 0.00 3.01
2012 2839 8.345565 AGAAACACAGTATCAGTCAAACAAATC 58.654 33.333 0.00 0.00 0.00 2.17
2013 2840 8.225603 AGAAACACAGTATCAGTCAAACAAAT 57.774 30.769 0.00 0.00 0.00 2.32
2014 2841 7.624360 AGAAACACAGTATCAGTCAAACAAA 57.376 32.000 0.00 0.00 0.00 2.83
2015 2842 7.624360 AAGAAACACAGTATCAGTCAAACAA 57.376 32.000 0.00 0.00 0.00 2.83
2016 2843 7.201696 GGAAAGAAACACAGTATCAGTCAAACA 60.202 37.037 0.00 0.00 0.00 2.83
2017 2844 7.132863 GGAAAGAAACACAGTATCAGTCAAAC 58.867 38.462 0.00 0.00 0.00 2.93
2018 2845 6.826231 TGGAAAGAAACACAGTATCAGTCAAA 59.174 34.615 0.00 0.00 0.00 2.69
2019 2846 6.353323 TGGAAAGAAACACAGTATCAGTCAA 58.647 36.000 0.00 0.00 0.00 3.18
2020 2847 5.924356 TGGAAAGAAACACAGTATCAGTCA 58.076 37.500 0.00 0.00 0.00 3.41
2021 2848 8.723942 ATATGGAAAGAAACACAGTATCAGTC 57.276 34.615 0.00 0.00 0.00 3.51
2022 2849 9.520515 AAATATGGAAAGAAACACAGTATCAGT 57.479 29.630 0.00 0.00 0.00 3.41
2027 2854 8.739039 CATGGAAATATGGAAAGAAACACAGTA 58.261 33.333 0.00 0.00 0.00 2.74
2054 2881 1.185618 AGACGTTCCAGCAGCCACTA 61.186 55.000 0.00 0.00 0.00 2.74
2078 2905 2.008329 GCAGACTTGAGAATGAGGCAG 58.992 52.381 0.00 0.00 0.00 4.85
2095 2954 5.686159 ACATGTCTTCTCTTTTTGAGCAG 57.314 39.130 0.00 0.00 42.38 4.24
2100 2959 9.390795 CAAACTCATACATGTCTTCTCTTTTTG 57.609 33.333 0.00 0.08 0.00 2.44
2129 2990 4.060205 CCAAATTGGCACTTTCTCCAAAG 58.940 43.478 0.00 0.00 44.55 2.77
2130 2991 3.454082 ACCAAATTGGCACTTTCTCCAAA 59.546 39.130 12.67 0.00 44.55 3.28
2131 2992 3.037549 ACCAAATTGGCACTTTCTCCAA 58.962 40.909 12.67 0.00 42.67 3.53
2132 2993 2.676748 ACCAAATTGGCACTTTCTCCA 58.323 42.857 12.67 0.00 42.67 3.86
2133 2994 3.751479 AACCAAATTGGCACTTTCTCC 57.249 42.857 12.67 0.00 42.67 3.71
2134 2995 5.584251 TCAAAAACCAAATTGGCACTTTCTC 59.416 36.000 12.67 0.00 42.67 2.87
2135 2996 5.495640 TCAAAAACCAAATTGGCACTTTCT 58.504 33.333 12.67 0.00 42.67 2.52
2157 3028 7.424001 AGCAAGAAAATCATAGCTAGCAAATC 58.576 34.615 18.83 3.59 0.00 2.17
2158 3029 7.344095 AGCAAGAAAATCATAGCTAGCAAAT 57.656 32.000 18.83 7.15 0.00 2.32
2170 3042 7.388500 GGAATCCAAATTGAAGCAAGAAAATCA 59.612 33.333 0.00 0.00 0.00 2.57
2171 3043 7.412237 CGGAATCCAAATTGAAGCAAGAAAATC 60.412 37.037 0.00 0.00 0.00 2.17
2173 3045 5.695816 CGGAATCCAAATTGAAGCAAGAAAA 59.304 36.000 0.00 0.00 0.00 2.29
2181 3056 5.723295 ACATTTCCGGAATCCAAATTGAAG 58.277 37.500 19.62 0.00 0.00 3.02
2197 3072 8.870879 GTCATAGTAACTGACAGTAACATTTCC 58.129 37.037 8.91 0.00 42.08 3.13
2336 3255 5.774690 ACTCATGTGCTCCTTTCCAAATAAA 59.225 36.000 0.00 0.00 0.00 1.40
2349 3268 7.413475 AATACGAAATGATACTCATGTGCTC 57.587 36.000 0.00 0.00 37.15 4.26
2375 3294 9.531942 AAGATATTCGATCATATTCATCTGAGC 57.468 33.333 0.00 0.00 0.00 4.26
2487 4601 0.321653 ATTTGTGGTCAGGACTCCGC 60.322 55.000 0.00 0.00 35.12 5.54
2507 5918 4.042271 TGTGATAGTAGAGTCACCACCA 57.958 45.455 3.38 0.00 43.09 4.17
2547 5958 6.382570 AGGATATCTGTACATAGGAGGCAATC 59.617 42.308 2.05 0.00 0.00 2.67
2608 6019 3.040795 GCGATATCTACGTCTGCGAAAA 58.959 45.455 0.00 0.00 42.00 2.29


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

AutoCloner maintained by Alex Coulton.