Multiple sequence alignment - TraesCS6D01G216100

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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 TraesCS6D01G216100 chr6D 100.000 2621 0 0 1 2621 306128136 306130756 0.000000e+00 4841.0
1 TraesCS6D01G216100 chr6D 86.275 204 28 0 1142 1345 469205360 469205563 3.400000e-54 222.0
2 TraesCS6D01G216100 chr6D 82.377 244 39 4 271 511 144464730 144464972 2.640000e-50 209.0
3 TraesCS6D01G216100 chr6B 91.699 1783 83 32 869 2621 473055685 473057432 0.000000e+00 2412.0
4 TraesCS6D01G216100 chr6B 93.107 1030 42 9 1107 2119 563805962 563804945 0.000000e+00 1482.0
5 TraesCS6D01G216100 chr6B 88.971 272 18 8 1851 2119 563814508 563814246 2.520000e-85 326.0
6 TraesCS6D01G216100 chr6B 87.192 203 26 0 1142 1344 715448892 715449094 5.640000e-57 231.0
7 TraesCS6D01G216100 chr6A 91.546 1656 94 18 871 2512 441485984 441487607 0.000000e+00 2241.0
8 TraesCS6D01G216100 chr6A 92.630 692 38 9 7 696 441485312 441485992 0.000000e+00 983.0
9 TraesCS6D01G216100 chr6A 88.293 205 14 5 689 883 494463288 494463084 1.210000e-58 237.0
10 TraesCS6D01G216100 chr6A 87.255 204 26 0 1142 1345 614381579 614381782 1.570000e-57 233.0
11 TraesCS6D01G216100 chr6A 87.685 203 15 6 690 882 45782872 45782670 7.300000e-56 228.0
12 TraesCS6D01G216100 chr6A 94.286 35 2 0 225 259 201047374 201047408 1.000000e-03 54.7
13 TraesCS6D01G216100 chr2B 89.270 233 24 1 1142 1373 557227660 557227428 9.180000e-75 291.0
14 TraesCS6D01G216100 chr2A 88.841 233 25 1 1142 1373 618267349 618267117 4.270000e-73 285.0
15 TraesCS6D01G216100 chr2A 89.583 192 14 5 696 881 63803958 63803767 3.370000e-59 239.0
16 TraesCS6D01G216100 chr2D 87.983 233 27 1 1142 1373 476345879 476345647 9.240000e-70 274.0
17 TraesCS6D01G216100 chr2D 90.860 186 8 4 693 872 32641542 32641360 9.370000e-60 241.0
18 TraesCS6D01G216100 chr2D 82.329 249 40 4 264 510 374104086 374103840 2.040000e-51 213.0
19 TraesCS6D01G216100 chrUn 91.713 181 12 3 695 872 108762902 108763082 5.600000e-62 248.0
20 TraesCS6D01G216100 chr7D 89.899 198 11 5 685 874 452687998 452688194 2.010000e-61 246.0
21 TraesCS6D01G216100 chr5A 91.304 184 10 3 694 871 101083456 101083273 2.010000e-61 246.0
22 TraesCS6D01G216100 chr7A 85.124 242 32 4 271 510 293302632 293302393 7.250000e-61 244.0
23 TraesCS6D01G216100 chr3D 84.426 244 36 2 271 513 21798183 21798425 3.370000e-59 239.0
24 TraesCS6D01G216100 chr3D 90.659 182 11 3 695 870 533955696 533955515 1.210000e-58 237.0
25 TraesCS6D01G216100 chr5B 84.232 241 37 1 271 510 313380904 313381144 1.570000e-57 233.0
26 TraesCS6D01G216100 chr5D 88.265 196 17 3 690 879 348748661 348748466 2.030000e-56 230.0
27 TraesCS6D01G216100 chr5D 83.128 243 39 2 270 511 492185548 492185307 1.220000e-53 220.0
28 TraesCS6D01G216100 chr3B 83.607 244 34 5 269 510 665987461 665987700 9.440000e-55 224.0
29 TraesCS6D01G216100 chr1A 83.613 238 37 2 271 506 22387701 22387464 3.400000e-54 222.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G216100 chr6D 306128136 306130756 2620 False 4841 4841 100.000 1 2621 1 chr6D.!!$F2 2620
1 TraesCS6D01G216100 chr6B 473055685 473057432 1747 False 2412 2412 91.699 869 2621 1 chr6B.!!$F1 1752
2 TraesCS6D01G216100 chr6B 563804945 563805962 1017 True 1482 1482 93.107 1107 2119 1 chr6B.!!$R1 1012
3 TraesCS6D01G216100 chr6A 441485312 441487607 2295 False 1612 2241 92.088 7 2512 2 chr6A.!!$F3 2505

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
309 311 0.090843 GTAGTGCGTTCGCGTTTCTC 59.909 55.0 5.77 0.0 43.62 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2116 0.108567 GACCGAGTGCTTCTTCCTCC 60.109 60.0 0.0 0.0 0.0 4.3 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
42 43 2.125106 GGATGGACACACGAGGCC 60.125 66.667 0.00 0.00 0.00 5.19
43 44 2.125106 GATGGACACACGAGGCCC 60.125 66.667 0.00 0.00 0.00 5.80
85 86 2.570135 GGGAGTATCGGAGTCTTACGT 58.430 52.381 0.00 0.00 34.37 3.57
137 139 3.490526 CCAAATTTGTTCGACTTTGCAGG 59.509 43.478 16.73 0.00 0.00 4.85
159 161 4.340263 GAAAAAGTGTGTTCGGACAAGTC 58.660 43.478 0.00 0.00 37.57 3.01
178 180 2.016704 GGTGGATCGATACAGCGCG 61.017 63.158 23.11 0.00 28.36 6.86
234 236 1.190763 CGAACAGTTACGGACGGTTTG 59.809 52.381 10.06 9.50 44.89 2.93
278 280 6.410504 GCCCTTCCATATTTTACTACTCCCTT 60.411 42.308 0.00 0.00 0.00 3.95
299 301 5.920273 CCTTCATTTCAAAATGTAGTGCGTT 59.080 36.000 16.16 0.00 44.66 4.84
301 303 5.143660 TCATTTCAAAATGTAGTGCGTTCG 58.856 37.500 13.57 0.00 44.66 3.95
304 306 0.863144 AAAATGTAGTGCGTTCGCGT 59.137 45.000 5.77 5.08 43.62 6.01
309 311 0.090843 GTAGTGCGTTCGCGTTTCTC 59.909 55.000 5.77 0.00 43.62 2.87
310 312 0.318022 TAGTGCGTTCGCGTTTCTCA 60.318 50.000 5.77 0.00 43.62 3.27
312 314 0.315544 GTGCGTTCGCGTTTCTCAAA 60.316 50.000 5.77 0.00 43.62 2.69
347 350 7.118680 TGACCGTAAATTTAACCAATGAGACTC 59.881 37.037 0.00 0.00 0.00 3.36
423 426 4.133820 CGGTGATATAATTGTTGCTCCCA 58.866 43.478 0.00 0.00 0.00 4.37
431 434 2.380084 TTGTTGCTCCCATCGTAGTC 57.620 50.000 0.00 0.00 0.00 2.59
459 462 8.067189 GTCTCGTTGGTTAAATTTACGGTTAAA 58.933 33.333 9.79 0.00 33.37 1.52
467 470 9.695526 GGTTAAATTTACGGTTAAACTTGGATT 57.304 29.630 0.00 0.00 29.77 3.01
478 481 3.643159 AACTTGGATTCCAGAAAACGC 57.357 42.857 5.36 0.00 33.81 4.84
493 496 2.583868 CGCGGGCGCACTACATTA 60.584 61.111 8.62 0.00 42.06 1.90
497 500 0.531974 CGGGCGCACTACATTATGGT 60.532 55.000 8.62 0.00 0.00 3.55
504 507 4.245660 CGCACTACATTATGGTATGGAGG 58.754 47.826 0.00 0.00 40.22 4.30
526 529 8.430431 GGAGGGAGTATAAAATTGCTTAGTAGT 58.570 37.037 0.00 0.00 0.00 2.73
594 603 8.841300 TCTACTACAATTGCACATAAACAAACA 58.159 29.630 5.05 0.00 0.00 2.83
695 704 5.994887 AGCAAACGGACGCATTATATAAA 57.005 34.783 0.00 0.00 0.00 1.40
696 705 5.985781 AGCAAACGGACGCATTATATAAAG 58.014 37.500 0.00 0.00 0.00 1.85
697 706 5.049680 AGCAAACGGACGCATTATATAAAGG 60.050 40.000 0.00 0.00 0.00 3.11
698 707 5.685841 CAAACGGACGCATTATATAAAGGG 58.314 41.667 11.82 11.82 0.00 3.95
699 708 4.612264 ACGGACGCATTATATAAAGGGT 57.388 40.909 17.20 17.20 33.69 4.34
700 709 4.563061 ACGGACGCATTATATAAAGGGTC 58.437 43.478 27.00 27.00 42.39 4.46
701 710 4.282703 ACGGACGCATTATATAAAGGGTCT 59.717 41.667 30.41 18.58 42.59 3.85
702 711 4.625742 CGGACGCATTATATAAAGGGTCTG 59.374 45.833 30.41 29.12 42.59 3.51
703 712 5.548406 GGACGCATTATATAAAGGGTCTGT 58.452 41.667 30.41 12.62 42.59 3.41
704 713 5.638234 GGACGCATTATATAAAGGGTCTGTC 59.362 44.000 30.41 19.05 42.59 3.51
705 714 6.420913 ACGCATTATATAAAGGGTCTGTCT 57.579 37.500 12.93 0.00 0.00 3.41
706 715 7.309621 GGACGCATTATATAAAGGGTCTGTCTA 60.310 40.741 30.41 0.00 42.59 2.59
707 716 7.603651 ACGCATTATATAAAGGGTCTGTCTAG 58.396 38.462 12.93 0.00 0.00 2.43
708 717 7.450634 ACGCATTATATAAAGGGTCTGTCTAGA 59.549 37.037 12.93 0.00 0.00 2.43
709 718 8.304596 CGCATTATATAAAGGGTCTGTCTAGAA 58.695 37.037 0.00 0.00 34.01 2.10
710 719 9.425577 GCATTATATAAAGGGTCTGTCTAGAAC 57.574 37.037 0.00 0.00 40.04 3.01
713 722 7.973048 ATATAAAGGGTCTGTCTAGAACACA 57.027 36.000 0.00 0.00 42.67 3.72
714 723 6.875972 ATAAAGGGTCTGTCTAGAACACAT 57.124 37.500 0.00 0.00 42.67 3.21
715 724 4.810191 AAGGGTCTGTCTAGAACACATC 57.190 45.455 0.00 0.00 42.67 3.06
716 725 4.054359 AGGGTCTGTCTAGAACACATCT 57.946 45.455 0.00 0.00 42.67 2.90
717 726 5.194473 AGGGTCTGTCTAGAACACATCTA 57.806 43.478 0.00 0.00 42.67 1.98
747 756 7.348808 GACATATGTCACATCTAAGCTGATG 57.651 40.000 27.33 11.48 44.18 3.07
756 765 5.970140 CATCTAAGCTGATGTTCACTCTG 57.030 43.478 5.99 0.00 39.05 3.35
757 766 5.417811 CATCTAAGCTGATGTTCACTCTGT 58.582 41.667 5.99 0.00 39.05 3.41
758 767 5.474578 TCTAAGCTGATGTTCACTCTGTT 57.525 39.130 0.00 0.00 0.00 3.16
759 768 5.858381 TCTAAGCTGATGTTCACTCTGTTT 58.142 37.500 0.00 0.00 0.00 2.83
760 769 4.825546 AAGCTGATGTTCACTCTGTTTG 57.174 40.909 0.00 0.00 0.00 2.93
761 770 3.813443 AGCTGATGTTCACTCTGTTTGT 58.187 40.909 0.00 0.00 0.00 2.83
762 771 3.562973 AGCTGATGTTCACTCTGTTTGTG 59.437 43.478 0.00 0.00 36.82 3.33
763 772 3.561310 GCTGATGTTCACTCTGTTTGTGA 59.439 43.478 0.00 0.00 41.94 3.58
764 773 4.214971 GCTGATGTTCACTCTGTTTGTGAT 59.785 41.667 0.00 0.00 42.95 3.06
765 774 5.616424 GCTGATGTTCACTCTGTTTGTGATC 60.616 44.000 0.00 0.00 42.95 2.92
766 775 5.614308 TGATGTTCACTCTGTTTGTGATCT 58.386 37.500 0.00 0.00 42.95 2.75
767 776 6.758254 TGATGTTCACTCTGTTTGTGATCTA 58.242 36.000 0.00 0.00 42.95 1.98
768 777 7.389232 TGATGTTCACTCTGTTTGTGATCTAT 58.611 34.615 0.00 0.00 42.95 1.98
769 778 7.879677 TGATGTTCACTCTGTTTGTGATCTATT 59.120 33.333 0.00 0.00 42.95 1.73
770 779 8.627208 ATGTTCACTCTGTTTGTGATCTATTT 57.373 30.769 0.00 0.00 42.95 1.40
771 780 8.450578 TGTTCACTCTGTTTGTGATCTATTTT 57.549 30.769 0.00 0.00 42.95 1.82
772 781 8.902806 TGTTCACTCTGTTTGTGATCTATTTTT 58.097 29.630 0.00 0.00 42.95 1.94
813 822 9.687210 ATTTCTTGTTGCTGCATTATATATGTG 57.313 29.630 1.84 0.00 0.00 3.21
814 823 7.806409 TCTTGTTGCTGCATTATATATGTGT 57.194 32.000 1.84 0.00 0.00 3.72
815 824 7.641760 TCTTGTTGCTGCATTATATATGTGTG 58.358 34.615 1.84 0.00 0.00 3.82
816 825 6.316440 TGTTGCTGCATTATATATGTGTGG 57.684 37.500 1.84 0.00 0.00 4.17
817 826 5.241285 TGTTGCTGCATTATATATGTGTGGG 59.759 40.000 1.84 0.00 0.00 4.61
818 827 5.240013 TGCTGCATTATATATGTGTGGGA 57.760 39.130 0.00 0.00 0.00 4.37
819 828 5.247862 TGCTGCATTATATATGTGTGGGAG 58.752 41.667 0.00 0.00 0.00 4.30
820 829 4.095483 GCTGCATTATATATGTGTGGGAGC 59.905 45.833 0.00 0.00 0.00 4.70
821 830 5.494724 CTGCATTATATATGTGTGGGAGCT 58.505 41.667 0.00 0.00 0.00 4.09
822 831 5.879763 TGCATTATATATGTGTGGGAGCTT 58.120 37.500 0.00 0.00 0.00 3.74
823 832 7.014988 TGCATTATATATGTGTGGGAGCTTA 57.985 36.000 0.00 0.00 0.00 3.09
824 833 7.105588 TGCATTATATATGTGTGGGAGCTTAG 58.894 38.462 0.00 0.00 0.00 2.18
825 834 7.038373 TGCATTATATATGTGTGGGAGCTTAGA 60.038 37.037 0.00 0.00 0.00 2.10
826 835 7.989741 GCATTATATATGTGTGGGAGCTTAGAT 59.010 37.037 0.00 0.00 0.00 1.98
827 836 9.322773 CATTATATATGTGTGGGAGCTTAGATG 57.677 37.037 0.00 0.00 0.00 2.90
828 837 6.942163 ATATATGTGTGGGAGCTTAGATGT 57.058 37.500 0.00 0.00 0.00 3.06
829 838 2.768253 TGTGTGGGAGCTTAGATGTG 57.232 50.000 0.00 0.00 0.00 3.21
830 839 2.256306 TGTGTGGGAGCTTAGATGTGA 58.744 47.619 0.00 0.00 0.00 3.58
831 840 2.028112 TGTGTGGGAGCTTAGATGTGAC 60.028 50.000 0.00 0.00 0.00 3.67
832 841 2.028112 GTGTGGGAGCTTAGATGTGACA 60.028 50.000 0.00 0.00 0.00 3.58
833 842 2.840038 TGTGGGAGCTTAGATGTGACAT 59.160 45.455 0.00 0.00 0.00 3.06
834 843 3.118629 TGTGGGAGCTTAGATGTGACATC 60.119 47.826 17.46 17.46 0.00 3.06
835 844 2.435805 TGGGAGCTTAGATGTGACATCC 59.564 50.000 21.05 6.28 0.00 3.51
836 845 2.703007 GGGAGCTTAGATGTGACATCCT 59.297 50.000 21.05 11.37 0.00 3.24
837 846 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
838 847 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
839 848 5.163301 GGGAGCTTAGATGTGACATCCTTAA 60.163 44.000 21.05 13.11 0.00 1.85
840 849 6.349300 GGAGCTTAGATGTGACATCCTTAAA 58.651 40.000 21.05 10.18 0.00 1.52
841 850 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
842 851 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
928 937 2.291741 GTCACCTCAAAGCCTCACAAAG 59.708 50.000 0.00 0.00 0.00 2.77
1383 1399 0.033405 CCTCCTCCTTCTCGTACCCA 60.033 60.000 0.00 0.00 0.00 4.51
1425 1441 2.875485 CGCGAGGAGGAGAACGAA 59.125 61.111 0.00 0.00 0.00 3.85
1515 1531 4.821589 GGGTTCTCGCCGCTGGAG 62.822 72.222 0.00 0.00 0.00 3.86
1671 1687 5.623956 TGTCTTTCTGTTTTGGGAGTCTA 57.376 39.130 0.00 0.00 0.00 2.59
1672 1688 6.187727 TGTCTTTCTGTTTTGGGAGTCTAT 57.812 37.500 0.00 0.00 0.00 1.98
1673 1689 6.601332 TGTCTTTCTGTTTTGGGAGTCTATT 58.399 36.000 0.00 0.00 0.00 1.73
1703 1719 2.532843 GGTGTACTTCCCTACCTGTCA 58.467 52.381 0.00 0.00 0.00 3.58
1772 1791 6.867662 ATCGGTTAAGATTTTCTATGGCAG 57.132 37.500 0.00 0.00 0.00 4.85
1823 1856 2.557924 CCCAGCTGCATGTGTTAGAAAA 59.442 45.455 8.66 0.00 0.00 2.29
1825 1858 4.418392 CCAGCTGCATGTGTTAGAAAATC 58.582 43.478 8.66 0.00 0.00 2.17
1868 1901 2.209838 AGTGGATCGTGTAATGCGAG 57.790 50.000 0.00 0.00 41.83 5.03
1873 1906 3.187700 GGATCGTGTAATGCGAGTTCTT 58.812 45.455 0.00 0.00 41.83 2.52
1905 1938 4.501071 GTTTCCCTTAGTATGCTCGTCAA 58.499 43.478 0.00 0.00 0.00 3.18
1918 1951 2.743183 GCTCGTCAATATGAGGCCAAGT 60.743 50.000 5.01 0.00 38.91 3.16
1936 1969 5.222631 CCAAGTCATTCAACAGCTAAAACC 58.777 41.667 0.00 0.00 0.00 3.27
1949 1982 4.941263 CAGCTAAAACCCAGTGTAGCATTA 59.059 41.667 11.11 0.00 41.17 1.90
1950 1983 5.414454 CAGCTAAAACCCAGTGTAGCATTAA 59.586 40.000 11.11 0.00 41.17 1.40
1951 1984 5.648092 AGCTAAAACCCAGTGTAGCATTAAG 59.352 40.000 11.11 0.00 41.17 1.85
1952 1985 4.783764 AAAACCCAGTGTAGCATTAAGC 57.216 40.909 0.00 0.00 46.19 3.09
1966 1999 3.709987 CATTAAGCCATTAACCAGCTGC 58.290 45.455 8.66 0.00 36.84 5.25
1972 2005 2.398554 ATTAACCAGCTGCGCCGTG 61.399 57.895 8.66 0.00 0.00 4.94
1978 2011 1.439353 CCAGCTGCGCCGTGATTATT 61.439 55.000 8.66 0.00 0.00 1.40
2032 2067 0.798776 CGGGAGCATGAAACTGTGTC 59.201 55.000 0.00 0.00 0.00 3.67
2036 2073 2.821969 GGAGCATGAAACTGTGTCCAAT 59.178 45.455 0.00 0.00 0.00 3.16
2037 2074 3.366679 GGAGCATGAAACTGTGTCCAATG 60.367 47.826 0.00 0.00 0.00 2.82
2038 2075 3.489355 AGCATGAAACTGTGTCCAATGA 58.511 40.909 0.00 0.00 0.00 2.57
2039 2076 3.504906 AGCATGAAACTGTGTCCAATGAG 59.495 43.478 0.00 0.00 0.00 2.90
2055 2092 4.327898 CCAATGAGCCATTTTTCGATTGTG 59.672 41.667 0.00 0.00 31.05 3.33
2066 2103 4.733972 TTTCGATTGTGCGTTGATTGTA 57.266 36.364 0.00 0.00 0.00 2.41
2074 2112 3.007074 TGTGCGTTGATTGTAAGGTAGGA 59.993 43.478 0.00 0.00 0.00 2.94
2078 2116 5.041940 GCGTTGATTGTAAGGTAGGAGTAG 58.958 45.833 0.00 0.00 0.00 2.57
2157 2196 2.287915 GCGGATTGCAGAATGATAACGT 59.712 45.455 0.00 0.00 45.45 3.99
2183 2222 1.450669 GCGAAACCGCCCTGGATTA 60.451 57.895 0.00 0.00 46.48 1.75
2213 2258 1.672881 CCCATGGATTCTCGCTTGAAC 59.327 52.381 15.22 0.00 0.00 3.18
2223 2268 2.174349 GCTTGAACTGGCTTCGCG 59.826 61.111 0.00 0.00 0.00 5.87
2225 2270 1.941812 CTTGAACTGGCTTCGCGTT 59.058 52.632 5.77 0.00 0.00 4.84
2254 2299 4.559063 CATGCTCCGAGGGCAGGG 62.559 72.222 4.76 0.00 43.15 4.45
2325 2374 2.748843 GCGCTCTGAGAAAGGCTGC 61.749 63.158 9.28 0.00 0.00 5.25
2500 2553 6.982141 CCACTGTTGACTGTTTACTAGTAACA 59.018 38.462 14.96 14.14 0.00 2.41
2502 2555 6.694411 ACTGTTGACTGTTTACTAGTAACACG 59.306 38.462 14.96 13.23 0.00 4.49
2504 2557 7.035004 TGTTGACTGTTTACTAGTAACACGTT 58.965 34.615 14.96 7.53 0.00 3.99
2505 2558 7.009448 TGTTGACTGTTTACTAGTAACACGTTG 59.991 37.037 14.96 11.78 0.00 4.10
2506 2559 5.459762 TGACTGTTTACTAGTAACACGTTGC 59.540 40.000 14.96 8.17 0.00 4.17
2507 2560 5.350633 ACTGTTTACTAGTAACACGTTGCA 58.649 37.500 14.96 5.39 0.00 4.08
2508 2561 5.987347 ACTGTTTACTAGTAACACGTTGCAT 59.013 36.000 14.96 0.00 0.00 3.96
2534 2590 4.587211 TGGTAATTTAACTGCGCGTTAG 57.413 40.909 18.95 9.59 39.15 2.34
2535 2591 3.995705 TGGTAATTTAACTGCGCGTTAGT 59.004 39.130 18.95 10.31 39.15 2.24
2540 2596 4.388189 TTTAACTGCGCGTTAGTAAACC 57.612 40.909 18.95 0.00 39.15 3.27
2582 2638 8.083462 GGTGATATTCAGCATAAATTCGTGTA 57.917 34.615 2.04 0.00 43.79 2.90
2599 2655 1.275291 TGTAGCGGAGGACTGGAAAAG 59.725 52.381 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.383552 CCCATCTTTCTCTGAATCCGTTCT 60.384 45.833 0.00 0.00 35.33 3.01
2 3 3.519510 TCCCATCTTTCTCTGAATCCGTT 59.480 43.478 0.00 0.00 0.00 4.44
3 4 3.107601 TCCCATCTTTCTCTGAATCCGT 58.892 45.455 0.00 0.00 0.00 4.69
4 5 3.494048 CCTCCCATCTTTCTCTGAATCCG 60.494 52.174 0.00 0.00 0.00 4.18
5 6 3.713764 TCCTCCCATCTTTCTCTGAATCC 59.286 47.826 0.00 0.00 0.00 3.01
42 43 1.303806 CACCCAAAACCCCTACCGG 60.304 63.158 0.00 0.00 0.00 5.28
43 44 1.303806 CCACCCAAAACCCCTACCG 60.304 63.158 0.00 0.00 0.00 4.02
46 47 2.855597 GCCCACCCAAAACCCCTA 59.144 61.111 0.00 0.00 0.00 3.53
85 86 1.194781 GGGAGTCCAGACAGAAGCCA 61.195 60.000 12.30 0.00 0.00 4.75
126 127 3.108144 CACACTTTTTCCTGCAAAGTCG 58.892 45.455 0.00 0.00 41.58 4.18
137 139 4.340263 GACTTGTCCGAACACACTTTTTC 58.660 43.478 0.00 0.00 34.35 2.29
159 161 2.016704 GCGCTGTATCGATCCACCG 61.017 63.158 0.00 0.40 0.00 4.94
178 180 2.340337 ACGTATTTAGCCGTCCAACAC 58.660 47.619 0.00 0.00 30.05 3.32
234 236 1.742268 GCATCTTCAAAGCAGACCCTC 59.258 52.381 0.00 0.00 0.00 4.30
278 280 5.143660 CGAACGCACTACATTTTGAAATGA 58.856 37.500 20.04 6.11 46.72 2.57
288 290 0.437295 GAAACGCGAACGCACTACAT 59.563 50.000 15.93 0.00 45.53 2.29
299 301 5.974158 TCAAATTGAATTTTGAGAAACGCGA 59.026 32.000 15.93 0.00 39.91 5.87
301 303 6.354858 GGTCAAATTGAATTTTGAGAAACGC 58.645 36.000 0.00 0.00 44.06 4.84
304 306 9.587772 TTTACGGTCAAATTGAATTTTGAGAAA 57.412 25.926 0.00 0.00 44.06 2.52
312 314 9.765795 TGGTTAAATTTACGGTCAAATTGAATT 57.234 25.926 0.00 0.00 37.97 2.17
347 350 2.285827 TTTTTATTCCCGCCGCAATG 57.714 45.000 0.00 0.00 0.00 2.82
423 426 0.731417 CCAACGAGACCGACTACGAT 59.269 55.000 0.00 0.00 42.66 3.73
431 434 4.434593 CCGTAAATTTAACCAACGAGACCG 60.435 45.833 11.09 1.83 42.50 4.79
459 462 1.535462 CGCGTTTTCTGGAATCCAAGT 59.465 47.619 2.61 0.00 30.80 3.16
478 481 0.531974 ACCATAATGTAGTGCGCCCG 60.532 55.000 4.18 0.00 0.00 6.13
486 489 7.979786 ATACTCCCTCCATACCATAATGTAG 57.020 40.000 0.00 0.00 0.00 2.74
493 496 6.948309 GCAATTTTATACTCCCTCCATACCAT 59.052 38.462 0.00 0.00 0.00 3.55
497 500 8.945193 ACTAAGCAATTTTATACTCCCTCCATA 58.055 33.333 0.00 0.00 0.00 2.74
504 507 9.819267 AGACACTACTAAGCAATTTTATACTCC 57.181 33.333 0.00 0.00 0.00 3.85
552 555 7.770801 TGTAGTAGAATGTGTGTAATCATGC 57.229 36.000 0.00 0.00 0.00 4.06
622 631 8.273557 GCGCTAGATTTTTCGAGTTTTCATATA 58.726 33.333 0.00 0.00 0.00 0.86
695 704 4.054359 AGATGTGTTCTAGACAGACCCT 57.946 45.455 0.00 0.00 39.39 4.34
722 731 6.927381 CATCAGCTTAGATGTGACATATGTCA 59.073 38.462 30.29 30.29 42.91 3.58
723 732 7.348808 CATCAGCTTAGATGTGACATATGTC 57.651 40.000 25.95 25.95 40.35 3.06
735 744 5.674052 ACAGAGTGAACATCAGCTTAGAT 57.326 39.130 0.00 0.00 0.00 1.98
736 745 5.474578 AACAGAGTGAACATCAGCTTAGA 57.525 39.130 0.00 0.00 0.00 2.10
737 746 5.468072 ACAAACAGAGTGAACATCAGCTTAG 59.532 40.000 0.00 0.00 0.00 2.18
738 747 5.237127 CACAAACAGAGTGAACATCAGCTTA 59.763 40.000 0.00 0.00 39.30 3.09
739 748 4.036027 CACAAACAGAGTGAACATCAGCTT 59.964 41.667 0.00 0.00 39.30 3.74
740 749 3.562973 CACAAACAGAGTGAACATCAGCT 59.437 43.478 0.00 0.00 39.30 4.24
741 750 3.561310 TCACAAACAGAGTGAACATCAGC 59.439 43.478 0.00 0.00 42.57 4.26
787 796 9.687210 CACATATATAATGCAGCAACAAGAAAT 57.313 29.630 0.00 0.00 0.00 2.17
788 797 8.685427 ACACATATATAATGCAGCAACAAGAAA 58.315 29.630 0.00 0.00 0.00 2.52
789 798 8.130469 CACACATATATAATGCAGCAACAAGAA 58.870 33.333 0.00 0.00 0.00 2.52
790 799 7.255208 CCACACATATATAATGCAGCAACAAGA 60.255 37.037 0.00 0.00 0.00 3.02
791 800 6.859508 CCACACATATATAATGCAGCAACAAG 59.140 38.462 0.00 0.00 0.00 3.16
792 801 6.238981 CCCACACATATATAATGCAGCAACAA 60.239 38.462 0.00 0.00 0.00 2.83
793 802 5.241285 CCCACACATATATAATGCAGCAACA 59.759 40.000 0.00 0.00 0.00 3.33
794 803 5.473162 TCCCACACATATATAATGCAGCAAC 59.527 40.000 0.00 0.00 0.00 4.17
795 804 5.629125 TCCCACACATATATAATGCAGCAA 58.371 37.500 0.00 0.00 0.00 3.91
796 805 5.240013 TCCCACACATATATAATGCAGCA 57.760 39.130 0.00 0.00 0.00 4.41
797 806 4.095483 GCTCCCACACATATATAATGCAGC 59.905 45.833 0.00 0.00 0.00 5.25
798 807 5.494724 AGCTCCCACACATATATAATGCAG 58.505 41.667 0.00 0.00 0.00 4.41
799 808 5.503634 AGCTCCCACACATATATAATGCA 57.496 39.130 0.00 0.00 0.00 3.96
800 809 7.331026 TCTAAGCTCCCACACATATATAATGC 58.669 38.462 0.00 0.00 0.00 3.56
801 810 9.322773 CATCTAAGCTCCCACACATATATAATG 57.677 37.037 0.00 0.00 0.00 1.90
802 811 9.051259 ACATCTAAGCTCCCACACATATATAAT 57.949 33.333 0.00 0.00 0.00 1.28
803 812 8.314021 CACATCTAAGCTCCCACACATATATAA 58.686 37.037 0.00 0.00 0.00 0.98
804 813 7.673926 TCACATCTAAGCTCCCACACATATATA 59.326 37.037 0.00 0.00 0.00 0.86
805 814 6.498303 TCACATCTAAGCTCCCACACATATAT 59.502 38.462 0.00 0.00 0.00 0.86
806 815 5.838521 TCACATCTAAGCTCCCACACATATA 59.161 40.000 0.00 0.00 0.00 0.86
807 816 4.655649 TCACATCTAAGCTCCCACACATAT 59.344 41.667 0.00 0.00 0.00 1.78
808 817 4.030216 TCACATCTAAGCTCCCACACATA 58.970 43.478 0.00 0.00 0.00 2.29
809 818 2.840038 TCACATCTAAGCTCCCACACAT 59.160 45.455 0.00 0.00 0.00 3.21
810 819 2.028112 GTCACATCTAAGCTCCCACACA 60.028 50.000 0.00 0.00 0.00 3.72
811 820 2.028112 TGTCACATCTAAGCTCCCACAC 60.028 50.000 0.00 0.00 0.00 3.82
812 821 2.256306 TGTCACATCTAAGCTCCCACA 58.744 47.619 0.00 0.00 0.00 4.17
813 822 3.462021 GATGTCACATCTAAGCTCCCAC 58.538 50.000 10.81 0.00 0.00 4.61
814 823 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
815 824 2.703007 AGGATGTCACATCTAAGCTCCC 59.297 50.000 17.46 0.00 0.00 4.30
816 825 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
817 826 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
863 872 8.508875 CGGCGGATAGGTTTATATAACAATTTT 58.491 33.333 0.00 0.00 0.00 1.82
864 873 7.662669 ACGGCGGATAGGTTTATATAACAATTT 59.337 33.333 13.24 0.00 0.00 1.82
865 874 7.118680 CACGGCGGATAGGTTTATATAACAATT 59.881 37.037 13.24 0.00 0.00 2.32
866 875 6.592607 CACGGCGGATAGGTTTATATAACAAT 59.407 38.462 13.24 0.00 0.00 2.71
867 876 5.927689 CACGGCGGATAGGTTTATATAACAA 59.072 40.000 13.24 0.00 0.00 2.83
868 877 5.010922 ACACGGCGGATAGGTTTATATAACA 59.989 40.000 13.24 0.00 0.00 2.41
869 878 5.473039 ACACGGCGGATAGGTTTATATAAC 58.527 41.667 13.24 0.00 0.00 1.89
870 879 5.336690 GGACACGGCGGATAGGTTTATATAA 60.337 44.000 13.24 0.00 0.00 0.98
871 880 4.158394 GGACACGGCGGATAGGTTTATATA 59.842 45.833 13.24 0.00 0.00 0.86
872 881 3.056322 GGACACGGCGGATAGGTTTATAT 60.056 47.826 13.24 0.00 0.00 0.86
873 882 2.297033 GGACACGGCGGATAGGTTTATA 59.703 50.000 13.24 0.00 0.00 0.98
874 883 1.069668 GGACACGGCGGATAGGTTTAT 59.930 52.381 13.24 0.00 0.00 1.40
875 884 0.461135 GGACACGGCGGATAGGTTTA 59.539 55.000 13.24 0.00 0.00 2.01
876 885 1.219935 GGACACGGCGGATAGGTTT 59.780 57.895 13.24 0.00 0.00 3.27
958 967 1.874345 CGCTGTACGTTGGAGGGAGT 61.874 60.000 0.00 0.00 36.87 3.85
1383 1399 2.847234 TTGCCGAGGAGGGTGTGT 60.847 61.111 0.00 0.00 41.48 3.72
1444 1460 2.030562 CCAGAAGGCCGACGTTGT 59.969 61.111 0.00 0.00 0.00 3.32
1671 1687 3.974642 GGAAGTACACCCAGGATCCTAAT 59.025 47.826 15.67 0.00 0.00 1.73
1672 1688 3.381335 GGAAGTACACCCAGGATCCTAA 58.619 50.000 15.67 0.00 0.00 2.69
1673 1689 2.359994 GGGAAGTACACCCAGGATCCTA 60.360 54.545 15.67 0.00 46.05 2.94
1772 1791 5.497635 AGTACTCCTAAGTAAGCGCTTAC 57.502 43.478 40.34 40.34 44.22 2.34
1823 1856 5.537300 AGCCAACGACAGATACTAATGAT 57.463 39.130 0.00 0.00 0.00 2.45
1825 1858 7.277981 ACTTAAAGCCAACGACAGATACTAATG 59.722 37.037 0.00 0.00 0.00 1.90
1882 1915 3.114065 GACGAGCATACTAAGGGAAACG 58.886 50.000 0.00 0.00 0.00 3.60
1888 1921 6.096036 CCTCATATTGACGAGCATACTAAGG 58.904 44.000 0.00 0.00 0.00 2.69
1905 1938 4.858850 TGTTGAATGACTTGGCCTCATAT 58.141 39.130 3.32 0.00 0.00 1.78
1918 1951 4.278170 CACTGGGTTTTAGCTGTTGAATGA 59.722 41.667 0.00 0.00 0.00 2.57
1936 1969 5.221048 GGTTAATGGCTTAATGCTACACTGG 60.221 44.000 0.00 0.00 42.39 4.00
1949 1982 2.183409 CGCAGCTGGTTAATGGCTT 58.817 52.632 17.12 0.00 33.74 4.35
1950 1983 3.909662 CGCAGCTGGTTAATGGCT 58.090 55.556 17.12 0.00 36.70 4.75
1966 1999 3.484683 ACAAACGAAAATAATCACGGCG 58.515 40.909 4.80 4.80 0.00 6.46
1972 2005 9.569212 GTATGATCGAGACAAACGAAAATAATC 57.431 33.333 0.00 0.00 42.80 1.75
1978 2011 6.096695 TGATGTATGATCGAGACAAACGAAA 58.903 36.000 0.00 0.00 42.80 3.46
2032 2067 4.327898 CACAATCGAAAAATGGCTCATTGG 59.672 41.667 0.00 0.00 34.04 3.16
2036 2073 2.668001 CGCACAATCGAAAAATGGCTCA 60.668 45.455 0.00 0.00 0.00 4.26
2037 2074 1.913403 CGCACAATCGAAAAATGGCTC 59.087 47.619 0.00 0.00 0.00 4.70
2038 2075 1.269448 ACGCACAATCGAAAAATGGCT 59.731 42.857 0.00 0.00 0.00 4.75
2039 2076 1.696988 ACGCACAATCGAAAAATGGC 58.303 45.000 0.00 0.00 0.00 4.40
2055 2092 3.858247 ACTCCTACCTTACAATCAACGC 58.142 45.455 0.00 0.00 0.00 4.84
2066 2103 4.874199 CTTCTTCCTCCTACTCCTACCTT 58.126 47.826 0.00 0.00 0.00 3.50
2074 2112 2.096248 CGAGTGCTTCTTCCTCCTACT 58.904 52.381 0.00 0.00 0.00 2.57
2078 2116 0.108567 GACCGAGTGCTTCTTCCTCC 60.109 60.000 0.00 0.00 0.00 4.30
2183 2222 3.474000 TCCATGGGGAAACGACGT 58.526 55.556 13.02 0.00 41.32 4.34
2223 2268 2.190578 CATGGAGAGGCCGGGAAC 59.809 66.667 2.18 0.00 40.66 3.62
2225 2270 4.804420 AGCATGGAGAGGCCGGGA 62.804 66.667 2.18 0.00 40.66 5.14
2325 2374 3.254654 CTACATGCACGACGGCGG 61.255 66.667 18.49 4.93 43.17 6.13
2500 2553 7.753132 CAGTTAAATTACCAATACATGCAACGT 59.247 33.333 0.00 0.00 0.00 3.99
2502 2555 7.253618 CGCAGTTAAATTACCAATACATGCAAC 60.254 37.037 0.00 0.00 0.00 4.17
2504 2557 6.261859 CGCAGTTAAATTACCAATACATGCA 58.738 36.000 0.00 0.00 0.00 3.96
2505 2558 5.173131 GCGCAGTTAAATTACCAATACATGC 59.827 40.000 0.30 0.00 0.00 4.06
2506 2559 5.395195 CGCGCAGTTAAATTACCAATACATG 59.605 40.000 8.75 0.00 0.00 3.21
2507 2560 5.065474 ACGCGCAGTTAAATTACCAATACAT 59.935 36.000 5.73 0.00 0.00 2.29
2508 2561 4.392445 ACGCGCAGTTAAATTACCAATACA 59.608 37.500 5.73 0.00 0.00 2.29
2534 2590 6.084925 CCATCATATCGTACTCTCGGTTTAC 58.915 44.000 0.00 0.00 0.00 2.01
2535 2591 5.766670 ACCATCATATCGTACTCTCGGTTTA 59.233 40.000 0.00 0.00 0.00 2.01
2540 2596 5.553290 ATCACCATCATATCGTACTCTCG 57.447 43.478 0.00 0.00 0.00 4.04
2582 2638 0.836400 TCCTTTTCCAGTCCTCCGCT 60.836 55.000 0.00 0.00 0.00 5.52
2599 2655 3.339141 GGACCTTCTGACATTTCACTCC 58.661 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.