Multiple sequence alignment - TraesCS7D01G024500

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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 TraesCS7D01G024500 chr7D 100.000 3548 0 0 1 3548 11490587 11487040 0.000000e+00 6553.0
1 TraesCS7D01G024500 chr7D 100.000 473 0 0 3076 3548 11475354 11474882 0.000000e+00 874.0
2 TraesCS7D01G024500 chr4A 89.374 2014 182 9 825 2831 726430428 726432416 0.000000e+00 2505.0
3 TraesCS7D01G024500 chr4A 89.467 1481 101 25 442 1893 726401263 726402717 0.000000e+00 1820.0
4 TraesCS7D01G024500 chr4A 93.827 567 32 3 2957 3522 726432915 726433479 0.000000e+00 850.0
5 TraesCS7D01G024500 chr4A 89.683 504 32 2 2356 2859 726402720 726403203 3.010000e-175 625.0
6 TraesCS7D01G024500 chr4A 88.248 468 17 17 1 441 726400710 726401166 3.140000e-145 525.0
7 TraesCS7D01G024500 chr4A 96.656 299 9 1 3144 3441 726412278 726412576 2.460000e-136 496.0
8 TraesCS7D01G024500 chr4A 93.960 298 14 2 2856 3153 726409565 726409858 6.990000e-122 448.0
9 TraesCS7D01G024500 chr4A 97.273 110 3 0 3439 3548 726414048 726414157 1.680000e-43 187.0
10 TraesCS7D01G024500 chrUn 100.000 473 0 0 3076 3548 335462590 335462118 0.000000e+00 874.0
11 TraesCS7D01G024500 chr7A 86.035 623 39 18 1 600 10978057 10977460 3.010000e-175 625.0
12 TraesCS7D01G024500 chr6B 97.059 34 1 0 2801 2834 1155377 1155410 1.380000e-04 58.4
13 TraesCS7D01G024500 chr3D 92.500 40 3 0 127 166 4871621 4871582 1.380000e-04 58.4
14 TraesCS7D01G024500 chr3A 94.595 37 2 0 127 163 10485569 10485533 1.380000e-04 58.4


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 TraesCS7D01G024500 chr7D 11487040 11490587 3547 True 6553.0 6553 100.000000 1 3548 1 chr7D.!!$R2 3547
1 TraesCS7D01G024500 chr4A 726430428 726433479 3051 False 1677.5 2505 91.600500 825 3522 2 chr4A.!!$F3 2697
2 TraesCS7D01G024500 chr4A 726400710 726403203 2493 False 990.0 1820 89.132667 1 2859 3 chr4A.!!$F1 2858
3 TraesCS7D01G024500 chr4A 726409565 726414157 4592 False 377.0 496 95.963000 2856 3548 3 chr4A.!!$F2 692
4 TraesCS7D01G024500 chr7A 10977460 10978057 597 True 625.0 625 86.035000 1 600 1 chr7A.!!$R1 599

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
131 136 0.889994 TAAGTCTTAACCGCTCGGCA 59.110 50.0 8.41 0.0 39.32 5.69 F
1155 1326 0.106918 TCGCCAACTGGAACAACCTT 60.107 50.0 0.00 0.0 38.70 3.50 F
1971 2142 0.172578 TCATCTACAACCTCGCCACG 59.827 55.0 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 2036 0.390998 GAAGTCAGTGGGCTCTCTGC 60.391 60.0 10.89 6.4 41.94 4.26 R
2231 2402 0.543749 CCACACCTCCTCCAATCTCC 59.456 60.0 0.00 0.0 0.00 3.71 R
3281 6253 1.294659 CCTTGAGGCTCACGCTTGTC 61.295 60.0 18.55 0.0 36.09 3.18 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
61 66 5.437191 AGGGGTACAAATCAAGTTAGGAG 57.563 43.478 0.00 0.00 0.00 3.69
64 69 4.501071 GGTACAAATCAAGTTAGGAGCGA 58.499 43.478 0.00 0.00 0.00 4.93
92 97 5.105063 TCAATTTATGCAGTCTCGTCTGAG 58.895 41.667 0.00 0.00 43.99 3.35
105 110 3.242518 TCGTCTGAGTCAATTAACGCAG 58.757 45.455 6.15 6.15 45.19 5.18
106 111 5.141097 CTCGTCTGAGTCAATTAACGCAGT 61.141 45.833 11.69 0.00 44.46 4.40
107 112 4.083164 TCGTCTGAGTCAATTAACGCAGTA 60.083 41.667 11.69 0.00 45.00 2.74
108 113 4.030306 CGTCTGAGTCAATTAACGCAGTAC 59.970 45.833 11.69 8.17 45.00 2.73
109 114 5.162075 GTCTGAGTCAATTAACGCAGTACT 58.838 41.667 11.69 0.00 45.00 2.73
110 115 5.286558 GTCTGAGTCAATTAACGCAGTACTC 59.713 44.000 11.69 0.00 45.00 2.59
111 116 5.183331 TCTGAGTCAATTAACGCAGTACTCT 59.817 40.000 11.69 0.00 45.00 3.24
112 117 5.779922 TGAGTCAATTAACGCAGTACTCTT 58.220 37.500 0.00 0.00 45.00 2.85
113 118 6.916440 TGAGTCAATTAACGCAGTACTCTTA 58.084 36.000 0.00 0.00 45.00 2.10
114 119 7.372714 TGAGTCAATTAACGCAGTACTCTTAA 58.627 34.615 0.00 0.00 45.00 1.85
115 120 7.541091 TGAGTCAATTAACGCAGTACTCTTAAG 59.459 37.037 0.00 0.00 45.00 1.85
131 136 0.889994 TAAGTCTTAACCGCTCGGCA 59.110 50.000 8.41 0.00 39.32 5.69
202 207 2.632996 TGTGGACTGAGTTAACTCCTGG 59.367 50.000 28.43 20.72 42.20 4.45
247 252 3.242867 AGACTTGGACATCTCTGGTGAA 58.757 45.455 0.00 0.00 0.00 3.18
341 346 8.425577 AACATCTACTGTTGATAACTGCATAC 57.574 34.615 4.48 0.00 46.37 2.39
369 374 4.636249 CAAGACTGAACAAACTAGGAGCT 58.364 43.478 0.00 0.00 0.00 4.09
370 375 4.965200 AGACTGAACAAACTAGGAGCTT 57.035 40.909 0.00 0.00 0.00 3.74
371 376 4.888917 AGACTGAACAAACTAGGAGCTTC 58.111 43.478 0.00 0.00 0.00 3.86
384 409 9.628500 AAACTAGGAGCTTCCGAAAATTATTAT 57.372 29.630 0.00 0.00 42.75 1.28
472 596 6.493189 AGCAAAAGAAACATCCCCTAAAAA 57.507 33.333 0.00 0.00 0.00 1.94
495 622 5.975693 AAGGGCAAAAGAAATAATGACGA 57.024 34.783 0.00 0.00 0.00 4.20
528 655 9.520204 TTTTTCAGAATCAAAGATGACAAAGAC 57.480 29.630 0.00 0.00 38.69 3.01
533 660 8.824781 CAGAATCAAAGATGACAAAGACGATAT 58.175 33.333 0.00 0.00 38.69 1.63
554 681 7.173390 CGATATTCCCTCCATTCTTTTTACTCC 59.827 40.741 0.00 0.00 0.00 3.85
577 704 7.323420 TCCGCATATAAGATTCATCCTAAGTG 58.677 38.462 0.00 0.00 0.00 3.16
642 769 3.911964 GCTTGCAACACCTACGTAATTTG 59.088 43.478 0.00 0.00 0.00 2.32
643 770 4.555906 GCTTGCAACACCTACGTAATTTGT 60.556 41.667 0.00 0.00 0.00 2.83
649 776 7.012138 TGCAACACCTACGTAATTTGTTTTCTA 59.988 33.333 11.49 0.59 0.00 2.10
658 785 8.976715 ACGTAATTTGTTTTCTACGTAACTTG 57.023 30.769 4.46 0.00 46.10 3.16
659 786 7.583762 ACGTAATTTGTTTTCTACGTAACTTGC 59.416 33.333 4.46 0.00 46.10 4.01
660 787 7.583401 CGTAATTTGTTTTCTACGTAACTTGCA 59.417 33.333 0.00 0.00 34.02 4.08
662 789 7.673810 ATTTGTTTTCTACGTAACTTGCAAC 57.326 32.000 0.00 0.00 0.00 4.17
663 790 5.798015 TGTTTTCTACGTAACTTGCAACA 57.202 34.783 0.00 0.00 0.00 3.33
667 794 7.594015 TGTTTTCTACGTAACTTGCAACAAAAA 59.406 29.630 0.00 0.00 0.00 1.94
695 822 9.632638 TTTCCTAGTAATAGATAACGTAGGTGT 57.367 33.333 0.00 0.00 0.00 4.16
697 824 9.935241 TCCTAGTAATAGATAACGTAGGTGTAG 57.065 37.037 0.00 0.00 0.00 2.74
698 825 9.717942 CCTAGTAATAGATAACGTAGGTGTAGT 57.282 37.037 0.00 0.00 0.00 2.73
727 854 4.695455 TGATTCACGAGTTCCATTTTCCTC 59.305 41.667 0.00 0.00 0.00 3.71
728 855 3.053831 TCACGAGTTCCATTTTCCTCC 57.946 47.619 0.00 0.00 0.00 4.30
730 857 3.009033 TCACGAGTTCCATTTTCCTCCAT 59.991 43.478 0.00 0.00 0.00 3.41
731 858 3.758554 CACGAGTTCCATTTTCCTCCATT 59.241 43.478 0.00 0.00 0.00 3.16
732 859 4.218417 CACGAGTTCCATTTTCCTCCATTT 59.782 41.667 0.00 0.00 0.00 2.32
733 860 4.832823 ACGAGTTCCATTTTCCTCCATTTT 59.167 37.500 0.00 0.00 0.00 1.82
734 861 5.304357 ACGAGTTCCATTTTCCTCCATTTTT 59.696 36.000 0.00 0.00 0.00 1.94
782 912 2.857152 GAGTAGAGAGCGCAAAGATGTG 59.143 50.000 11.47 0.00 40.10 3.21
785 915 1.151668 GAGAGCGCAAAGATGTGTGT 58.848 50.000 11.47 0.00 39.31 3.72
792 922 2.413112 CGCAAAGATGTGTGTCTGGTAG 59.587 50.000 0.00 0.00 32.29 3.18
793 923 3.664107 GCAAAGATGTGTGTCTGGTAGA 58.336 45.455 0.00 0.00 0.00 2.59
794 924 3.681897 GCAAAGATGTGTGTCTGGTAGAG 59.318 47.826 0.00 0.00 0.00 2.43
795 925 4.561530 GCAAAGATGTGTGTCTGGTAGAGA 60.562 45.833 0.00 0.00 0.00 3.10
796 926 5.167121 CAAAGATGTGTGTCTGGTAGAGAG 58.833 45.833 0.00 0.00 0.00 3.20
797 927 4.308526 AGATGTGTGTCTGGTAGAGAGA 57.691 45.455 0.00 0.00 0.00 3.10
798 928 4.269183 AGATGTGTGTCTGGTAGAGAGAG 58.731 47.826 0.00 0.00 0.00 3.20
799 929 3.790089 TGTGTGTCTGGTAGAGAGAGA 57.210 47.619 0.00 0.00 0.00 3.10
800 930 3.680490 TGTGTGTCTGGTAGAGAGAGAG 58.320 50.000 0.00 0.00 0.00 3.20
801 931 3.328050 TGTGTGTCTGGTAGAGAGAGAGA 59.672 47.826 0.00 0.00 0.00 3.10
802 932 3.938963 GTGTGTCTGGTAGAGAGAGAGAG 59.061 52.174 0.00 0.00 0.00 3.20
803 933 3.841255 TGTGTCTGGTAGAGAGAGAGAGA 59.159 47.826 0.00 0.00 0.00 3.10
804 934 4.081142 TGTGTCTGGTAGAGAGAGAGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
854 1018 1.633432 TGTCCTGTTATCCACCCCAAG 59.367 52.381 0.00 0.00 0.00 3.61
869 1033 2.373224 CCCAAGGAGGAAAAGCTGATC 58.627 52.381 0.00 0.00 41.22 2.92
902 1066 5.049818 CCAAGATCTTGTCAACTGTCTTGAC 60.050 44.000 29.03 5.82 46.57 3.18
1044 1212 4.436113 ACTACTACTCCTAGCACTACCC 57.564 50.000 0.00 0.00 0.00 3.69
1048 1219 2.162264 ACTCCTAGCACTACCCCTTC 57.838 55.000 0.00 0.00 0.00 3.46
1086 1257 6.690194 ATCAAATGTAGGAGATCAAGCAAC 57.310 37.500 0.00 0.00 0.00 4.17
1155 1326 0.106918 TCGCCAACTGGAACAACCTT 60.107 50.000 0.00 0.00 38.70 3.50
1305 1476 1.005394 CGCCAACTACGTCAAGGGT 60.005 57.895 0.00 0.00 0.00 4.34
1337 1508 1.255667 GCGGTCCTTGGACTACTGGA 61.256 60.000 17.99 0.00 0.00 3.86
1489 1660 1.105457 GCCATTGCTAAGCCACATGA 58.895 50.000 0.00 0.00 33.53 3.07
1550 1721 1.227089 GGCTCGTGCTCGACATCAT 60.227 57.895 6.80 0.00 41.35 2.45
1571 1742 3.694043 TGTGATAGCAGTGTTTGGCTA 57.306 42.857 0.00 0.00 45.75 3.93
1612 1783 1.302351 TCGATGCCACACATGCACA 60.302 52.632 0.00 0.00 42.38 4.57
1614 1785 0.248336 CGATGCCACACATGCACATC 60.248 55.000 0.00 0.00 42.38 3.06
1735 1906 2.304180 AGAAAGCTAGCAGAGGCAGAAA 59.696 45.455 18.83 0.00 44.61 2.52
1788 1959 1.227674 GAGAAAGATGGCCGGCGAT 60.228 57.895 25.12 25.12 0.00 4.58
1790 1961 3.186390 GAAAGATGGCCGGCGATGC 62.186 63.158 29.81 18.86 0.00 3.91
1812 1983 0.812811 CAGGCACCGAGGATGACATG 60.813 60.000 0.00 0.00 0.00 3.21
1824 1995 3.144506 GGATGACATGCTGTCCCATTAG 58.855 50.000 11.99 0.00 46.40 1.73
1831 2002 0.535335 GCTGTCCCATTAGGTCGACA 59.465 55.000 18.91 0.00 35.59 4.35
1908 2079 4.245660 TGATCAGGACGTTCATCAACTTC 58.754 43.478 0.00 0.00 31.40 3.01
1914 2085 3.120199 GGACGTTCATCAACTTCATGGTG 60.120 47.826 0.00 0.00 33.38 4.17
1917 2088 1.452110 TCATCAACTTCATGGTGGCG 58.548 50.000 0.00 0.00 32.15 5.69
1922 2093 0.608856 AACTTCATGGTGGCGATGCA 60.609 50.000 0.00 0.00 0.00 3.96
1965 2136 1.476891 TCGTGGCTCATCTACAACCTC 59.523 52.381 0.00 0.00 0.00 3.85
1971 2142 0.172578 TCATCTACAACCTCGCCACG 59.827 55.000 0.00 0.00 0.00 4.94
1974 2145 2.356553 TACAACCTCGCCACGCAC 60.357 61.111 0.00 0.00 0.00 5.34
2037 2208 3.788766 GCCGCACGACGCAAATCT 61.789 61.111 0.00 0.00 42.60 2.40
2039 2210 2.571611 CGCACGACGCAAATCTGC 60.572 61.111 0.00 0.00 45.75 4.26
2041 2212 2.965147 GCACGACGCAAATCTGCCA 61.965 57.895 0.00 0.00 46.56 4.92
2042 2213 1.133253 CACGACGCAAATCTGCCAG 59.867 57.895 0.00 0.00 46.56 4.85
2043 2214 2.034879 ACGACGCAAATCTGCCAGG 61.035 57.895 0.00 0.00 46.56 4.45
2061 2232 2.604174 GGGCGTCGTGGTGTTTGAG 61.604 63.158 0.00 0.00 0.00 3.02
2079 2250 0.318762 AGCCAGACGAGACCAAAGAC 59.681 55.000 0.00 0.00 0.00 3.01
2094 2265 0.531200 AAGACCTAGTGTACCAGCGC 59.469 55.000 0.00 0.00 0.00 5.92
2112 2283 2.434185 GCGGCCATGTTCGAGTCA 60.434 61.111 2.24 0.00 0.00 3.41
2169 2340 4.477975 GTCCTCGCCGACGACCTG 62.478 72.222 5.11 0.00 45.12 4.00
2217 2388 0.534652 GCAGCACCATCCTGATCTCC 60.535 60.000 0.00 0.00 32.03 3.71
2231 2402 1.071385 GATCTCCACCTACAGCATGGG 59.929 57.143 0.00 0.00 43.62 4.00
2242 2413 0.178998 CAGCATGGGGAGATTGGAGG 60.179 60.000 0.00 0.00 0.00 4.30
2256 2427 1.687493 GGAGGAGGTGTGGGGAGAG 60.687 68.421 0.00 0.00 0.00 3.20
2292 2463 2.997315 CCGGAGAGGTGGCTGTCA 60.997 66.667 0.00 0.00 34.51 3.58
2299 2470 1.003355 AGGTGGCTGTCATCCAACG 60.003 57.895 5.11 0.00 45.74 4.10
2300 2471 2.690778 GGTGGCTGTCATCCAACGC 61.691 63.158 0.00 0.00 35.01 4.84
2342 2513 2.432456 GCACGTGCCGTCTCATGA 60.432 61.111 30.12 0.00 38.32 3.07
2349 2520 0.109272 TGCCGTCTCATGAGTTCGTC 60.109 55.000 26.94 20.81 0.00 4.20
2352 2523 0.454452 CGTCTCATGAGTTCGTCGCA 60.454 55.000 21.92 0.00 0.00 5.10
2455 2626 1.364626 CTTCGATGTGGAGGTGCTGC 61.365 60.000 0.00 0.00 0.00 5.25
2475 2646 2.677037 GCATAGTAACACCGTGAAGCCT 60.677 50.000 5.28 0.00 0.00 4.58
2506 2677 4.631377 CGGTTATTCTGCAGATGAAGAACA 59.369 41.667 19.04 0.00 42.18 3.18
2551 2722 2.230189 ATCAGAGGGCGACTGAGGGA 62.230 60.000 15.15 0.00 45.49 4.20
2686 2857 2.691409 TATGTGACACCTAGCAAGCC 57.309 50.000 2.45 0.00 0.00 4.35
2694 2865 3.231818 ACACCTAGCAAGCCGTATATCT 58.768 45.455 0.00 0.00 0.00 1.98
2695 2866 3.256136 ACACCTAGCAAGCCGTATATCTC 59.744 47.826 0.00 0.00 0.00 2.75
2696 2867 2.826725 ACCTAGCAAGCCGTATATCTCC 59.173 50.000 0.00 0.00 0.00 3.71
2697 2868 2.166664 CCTAGCAAGCCGTATATCTCCC 59.833 54.545 0.00 0.00 0.00 4.30
2698 2869 1.717032 AGCAAGCCGTATATCTCCCA 58.283 50.000 0.00 0.00 0.00 4.37
2699 2870 2.047061 AGCAAGCCGTATATCTCCCAA 58.953 47.619 0.00 0.00 0.00 4.12
2700 2871 2.438021 AGCAAGCCGTATATCTCCCAAA 59.562 45.455 0.00 0.00 0.00 3.28
2701 2872 2.548480 GCAAGCCGTATATCTCCCAAAC 59.452 50.000 0.00 0.00 0.00 2.93
2702 2873 3.744530 GCAAGCCGTATATCTCCCAAACT 60.745 47.826 0.00 0.00 0.00 2.66
2703 2874 4.502604 GCAAGCCGTATATCTCCCAAACTA 60.503 45.833 0.00 0.00 0.00 2.24
2704 2875 5.230942 CAAGCCGTATATCTCCCAAACTAG 58.769 45.833 0.00 0.00 0.00 2.57
2705 2876 3.258622 AGCCGTATATCTCCCAAACTAGC 59.741 47.826 0.00 0.00 0.00 3.42
2706 2877 3.258622 GCCGTATATCTCCCAAACTAGCT 59.741 47.826 0.00 0.00 0.00 3.32
2707 2878 4.618693 GCCGTATATCTCCCAAACTAGCTC 60.619 50.000 0.00 0.00 0.00 4.09
2708 2879 4.523173 CCGTATATCTCCCAAACTAGCTCA 59.477 45.833 0.00 0.00 0.00 4.26
2709 2880 5.336055 CCGTATATCTCCCAAACTAGCTCAG 60.336 48.000 0.00 0.00 0.00 3.35
2710 2881 2.998316 ATCTCCCAAACTAGCTCAGC 57.002 50.000 0.00 0.00 0.00 4.26
2711 2882 1.644509 TCTCCCAAACTAGCTCAGCA 58.355 50.000 0.00 0.00 0.00 4.41
2744 2915 2.841215 TGTTACCTGAGGGAAACGTTG 58.159 47.619 0.00 0.00 36.25 4.10
2759 2930 5.062809 GGAAACGTTGCAAAAATTTGACTCA 59.937 36.000 8.91 0.00 40.55 3.41
2762 2933 3.862267 CGTTGCAAAAATTTGACTCACCA 59.138 39.130 0.00 0.00 40.55 4.17
2859 3030 0.517316 GTCTGTCAACCCGTGCATTC 59.483 55.000 0.00 0.00 0.00 2.67
3072 3615 3.306088 CCCTGCGTTAAGAAAGACAGAGA 60.306 47.826 0.00 0.00 0.00 3.10
3094 3637 2.630317 CGCCAGATCATGCGCTTC 59.370 61.111 9.73 0.13 44.64 3.86
3109 3652 1.795286 CGCTTCGAAGTTTGCTTCTCT 59.205 47.619 25.24 0.00 46.65 3.10
3114 3657 4.073293 TCGAAGTTTGCTTCTCTTCCTT 57.927 40.909 5.91 0.00 46.65 3.36
3143 3686 4.574599 AACTCCTGAATCAACAAAGTGC 57.425 40.909 0.00 0.00 0.00 4.40
3144 3687 3.825328 ACTCCTGAATCAACAAAGTGCT 58.175 40.909 0.00 0.00 0.00 4.40
3187 6159 4.043200 GTGCCGCAACTCCCAAGC 62.043 66.667 0.00 0.00 0.00 4.01
3258 6230 0.383590 CACTCGAGCGATGGAGATGT 59.616 55.000 19.84 0.00 34.40 3.06
3433 6407 0.247814 CGCATCCACGTTGATCTTGC 60.248 55.000 0.00 1.55 0.00 4.01
3511 7959 6.047870 GCATGATTCTTCTTCTCTCTTGCTA 58.952 40.000 0.00 0.00 35.39 3.49
3543 7991 7.845037 TCTCAAGATCTTCTAAGAGCATTTGA 58.155 34.615 4.57 10.37 43.60 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 24 7.073208 TGTACCCCTATCTGATAGATCAACAA 58.927 38.462 23.04 3.73 36.20 2.83
61 66 4.331168 AGACTGCATAAATTGAGTCTTCGC 59.669 41.667 0.00 0.00 38.54 4.70
64 69 5.482908 ACGAGACTGCATAAATTGAGTCTT 58.517 37.500 0.00 0.00 40.16 3.01
92 97 7.541437 AGACTTAAGAGTACTGCGTTAATTGAC 59.459 37.037 10.09 0.00 35.88 3.18
105 110 5.027099 CGAGCGGTTAAGACTTAAGAGTAC 58.973 45.833 10.09 0.00 35.88 2.73
106 111 4.095483 CCGAGCGGTTAAGACTTAAGAGTA 59.905 45.833 10.09 0.00 35.88 2.59
107 112 3.119566 CCGAGCGGTTAAGACTTAAGAGT 60.120 47.826 10.09 0.00 39.32 3.24
108 113 3.436496 CCGAGCGGTTAAGACTTAAGAG 58.564 50.000 10.09 6.57 0.00 2.85
109 114 2.416431 GCCGAGCGGTTAAGACTTAAGA 60.416 50.000 10.09 0.00 37.65 2.10
110 115 1.925185 GCCGAGCGGTTAAGACTTAAG 59.075 52.381 7.93 0.00 37.65 1.85
111 116 1.273048 TGCCGAGCGGTTAAGACTTAA 59.727 47.619 10.94 3.44 37.65 1.85
112 117 0.889994 TGCCGAGCGGTTAAGACTTA 59.110 50.000 10.94 0.00 37.65 2.24
113 118 0.249398 ATGCCGAGCGGTTAAGACTT 59.751 50.000 10.94 0.00 37.65 3.01
114 119 0.460284 CATGCCGAGCGGTTAAGACT 60.460 55.000 10.94 0.00 37.65 3.24
115 120 0.459585 TCATGCCGAGCGGTTAAGAC 60.460 55.000 10.94 0.00 37.65 3.01
202 207 1.673920 TCTTCGTTGTTTGTTGGGCTC 59.326 47.619 0.00 0.00 0.00 4.70
247 252 2.092429 TGTTGCTCAGGAAAAGGACTGT 60.092 45.455 0.00 0.00 36.17 3.55
276 281 2.412870 TGGTTGACTCGTGTAATGCTG 58.587 47.619 0.00 0.00 0.00 4.41
341 346 2.549754 AGTTTGTTCAGTCTTGCATCGG 59.450 45.455 0.00 0.00 0.00 4.18
356 361 3.764237 TTTCGGAAGCTCCTAGTTTGT 57.236 42.857 0.00 0.00 33.30 2.83
369 374 9.936759 AGCTTTCCAAAATAATAATTTTCGGAA 57.063 25.926 15.59 15.59 42.18 4.30
370 375 9.936759 AAGCTTTCCAAAATAATAATTTTCGGA 57.063 25.926 0.00 9.03 42.18 4.55
417 445 2.105006 TTGCAGCTGTTTGCCAAAAA 57.895 40.000 16.64 0.00 43.43 1.94
472 596 6.339587 TCGTCATTATTTCTTTTGCCCTTT 57.660 33.333 0.00 0.00 0.00 3.11
475 601 4.105486 GCTCGTCATTATTTCTTTTGCCC 58.895 43.478 0.00 0.00 0.00 5.36
476 602 4.986622 AGCTCGTCATTATTTCTTTTGCC 58.013 39.130 0.00 0.00 0.00 4.52
490 617 7.433708 TGATTCTGAAAAATTAAGCTCGTCA 57.566 32.000 0.00 0.00 0.00 4.35
528 655 7.173390 GGAGTAAAAAGAATGGAGGGAATATCG 59.827 40.741 0.00 0.00 0.00 2.92
533 660 4.585879 CGGAGTAAAAAGAATGGAGGGAA 58.414 43.478 0.00 0.00 0.00 3.97
554 681 8.763049 TTCACTTAGGATGAATCTTATATGCG 57.237 34.615 0.00 0.00 31.11 4.73
589 716 7.487484 TGTTTGCTAATGTTCTTGATCAAACA 58.513 30.769 13.84 13.84 45.19 2.83
596 723 6.587226 GCATGATTGTTTGCTAATGTTCTTGA 59.413 34.615 0.00 0.00 35.95 3.02
642 769 7.495339 TTTTGTTGCAAGTTACGTAGAAAAC 57.505 32.000 0.00 0.00 0.00 2.43
669 796 9.632638 ACACCTACGTTATCTATTACTAGGAAA 57.367 33.333 0.00 0.00 0.00 3.13
671 798 9.935241 CTACACCTACGTTATCTATTACTAGGA 57.065 37.037 0.00 0.00 0.00 2.94
672 799 9.717942 ACTACACCTACGTTATCTATTACTAGG 57.282 37.037 0.00 0.00 0.00 3.02
684 811 9.926158 TGAATCAAAAATACTACACCTACGTTA 57.074 29.630 0.00 0.00 0.00 3.18
686 813 7.062605 CGTGAATCAAAAATACTACACCTACGT 59.937 37.037 0.00 0.00 0.00 3.57
687 814 7.274033 TCGTGAATCAAAAATACTACACCTACG 59.726 37.037 0.00 0.00 0.00 3.51
688 815 8.470040 TCGTGAATCAAAAATACTACACCTAC 57.530 34.615 0.00 0.00 0.00 3.18
689 816 8.308931 ACTCGTGAATCAAAAATACTACACCTA 58.691 33.333 0.00 0.00 0.00 3.08
690 817 7.159372 ACTCGTGAATCAAAAATACTACACCT 58.841 34.615 0.00 0.00 0.00 4.00
691 818 7.360575 ACTCGTGAATCAAAAATACTACACC 57.639 36.000 0.00 0.00 0.00 4.16
692 819 7.955864 GGAACTCGTGAATCAAAAATACTACAC 59.044 37.037 0.00 0.00 0.00 2.90
693 820 7.658167 TGGAACTCGTGAATCAAAAATACTACA 59.342 33.333 0.00 0.00 0.00 2.74
694 821 8.025243 TGGAACTCGTGAATCAAAAATACTAC 57.975 34.615 0.00 0.00 0.00 2.73
695 822 8.786826 ATGGAACTCGTGAATCAAAAATACTA 57.213 30.769 0.00 0.00 0.00 1.82
696 823 7.687941 ATGGAACTCGTGAATCAAAAATACT 57.312 32.000 0.00 0.00 0.00 2.12
697 824 8.742554 AAATGGAACTCGTGAATCAAAAATAC 57.257 30.769 0.00 0.00 0.00 1.89
698 825 9.405587 GAAAATGGAACTCGTGAATCAAAAATA 57.594 29.630 0.00 0.00 0.00 1.40
699 826 7.384932 GGAAAATGGAACTCGTGAATCAAAAAT 59.615 33.333 0.00 0.00 0.00 1.82
700 827 6.699642 GGAAAATGGAACTCGTGAATCAAAAA 59.300 34.615 0.00 0.00 0.00 1.94
701 828 6.040391 AGGAAAATGGAACTCGTGAATCAAAA 59.960 34.615 0.00 0.00 0.00 2.44
702 829 5.534654 AGGAAAATGGAACTCGTGAATCAAA 59.465 36.000 0.00 0.00 0.00 2.69
703 830 5.070001 AGGAAAATGGAACTCGTGAATCAA 58.930 37.500 0.00 0.00 0.00 2.57
704 831 4.651778 AGGAAAATGGAACTCGTGAATCA 58.348 39.130 0.00 0.00 0.00 2.57
705 832 4.095036 GGAGGAAAATGGAACTCGTGAATC 59.905 45.833 0.00 0.00 0.00 2.52
706 833 4.010349 GGAGGAAAATGGAACTCGTGAAT 58.990 43.478 0.00 0.00 0.00 2.57
707 834 3.181449 TGGAGGAAAATGGAACTCGTGAA 60.181 43.478 0.00 0.00 0.00 3.18
731 858 6.472016 GGGGCTTCTTCAAATGGAATAAAAA 58.528 36.000 0.00 0.00 34.32 1.94
732 859 5.045942 GGGGGCTTCTTCAAATGGAATAAAA 60.046 40.000 0.00 0.00 34.32 1.52
733 860 4.469586 GGGGGCTTCTTCAAATGGAATAAA 59.530 41.667 0.00 0.00 34.32 1.40
734 861 4.030216 GGGGGCTTCTTCAAATGGAATAA 58.970 43.478 0.00 0.00 34.32 1.40
735 862 3.272020 AGGGGGCTTCTTCAAATGGAATA 59.728 43.478 0.00 0.00 34.32 1.75
736 863 2.044908 AGGGGGCTTCTTCAAATGGAAT 59.955 45.455 0.00 0.00 34.32 3.01
737 864 1.432807 AGGGGGCTTCTTCAAATGGAA 59.567 47.619 0.00 0.00 0.00 3.53
738 865 1.005924 GAGGGGGCTTCTTCAAATGGA 59.994 52.381 0.00 0.00 0.00 3.41
739 866 1.478631 GAGGGGGCTTCTTCAAATGG 58.521 55.000 0.00 0.00 0.00 3.16
740 867 1.478631 GGAGGGGGCTTCTTCAAATG 58.521 55.000 0.00 0.00 0.00 2.32
741 868 0.034089 CGGAGGGGGCTTCTTCAAAT 60.034 55.000 0.00 0.00 0.00 2.32
742 869 1.378762 CGGAGGGGGCTTCTTCAAA 59.621 57.895 0.00 0.00 0.00 2.69
743 870 3.077907 CGGAGGGGGCTTCTTCAA 58.922 61.111 0.00 0.00 0.00 2.69
782 912 4.161565 TCTCTCTCTCTCTCTACCAGACAC 59.838 50.000 0.00 0.00 0.00 3.67
785 915 4.878968 TCTCTCTCTCTCTCTCTACCAGA 58.121 47.826 0.00 0.00 0.00 3.86
792 922 5.304101 ACATCTCTCTCTCTCTCTCTCTCTC 59.696 48.000 0.00 0.00 0.00 3.20
793 923 5.215069 ACATCTCTCTCTCTCTCTCTCTCT 58.785 45.833 0.00 0.00 0.00 3.10
794 924 5.543507 ACATCTCTCTCTCTCTCTCTCTC 57.456 47.826 0.00 0.00 0.00 3.20
795 925 5.965033 AACATCTCTCTCTCTCTCTCTCT 57.035 43.478 0.00 0.00 0.00 3.10
796 926 6.037610 GTGAAACATCTCTCTCTCTCTCTCTC 59.962 46.154 0.00 0.00 36.32 3.20
797 927 5.882557 GTGAAACATCTCTCTCTCTCTCTCT 59.117 44.000 0.00 0.00 36.32 3.10
798 928 5.220662 CGTGAAACATCTCTCTCTCTCTCTC 60.221 48.000 0.00 0.00 35.74 3.20
799 929 4.635765 CGTGAAACATCTCTCTCTCTCTCT 59.364 45.833 0.00 0.00 35.74 3.10
800 930 4.634004 TCGTGAAACATCTCTCTCTCTCTC 59.366 45.833 0.00 0.00 35.74 3.20
801 931 4.584874 TCGTGAAACATCTCTCTCTCTCT 58.415 43.478 0.00 0.00 35.74 3.10
802 932 4.955925 TCGTGAAACATCTCTCTCTCTC 57.044 45.455 0.00 0.00 35.74 3.20
803 933 4.338118 GGATCGTGAAACATCTCTCTCTCT 59.662 45.833 0.00 0.00 35.74 3.10
804 934 4.499019 GGGATCGTGAAACATCTCTCTCTC 60.499 50.000 0.00 0.00 35.74 3.20
869 1033 0.807667 CAAGATCTTGGACCGGAGCG 60.808 60.000 25.14 0.00 36.95 5.03
902 1066 6.093633 AGCTAAAATTAGTTAGAACTTGCCCG 59.906 38.462 0.00 0.00 40.37 6.13
914 1078 7.670140 ACTCCTAAAAGGCAGCTAAAATTAGTT 59.330 33.333 0.00 0.00 34.61 2.24
1044 1212 3.954904 TGATAAGGAAGACGAGGAGAAGG 59.045 47.826 0.00 0.00 0.00 3.46
1048 1219 5.665459 ACATTTGATAAGGAAGACGAGGAG 58.335 41.667 0.00 0.00 0.00 3.69
1086 1257 1.606885 ATTCCGTTGGCAGCAATGGG 61.607 55.000 12.39 0.00 40.65 4.00
1155 1326 2.202743 GCTGCGGCGTAGTCATGA 60.203 61.111 25.23 0.00 0.00 3.07
1337 1508 2.577059 CGGTGACTATGGTGCCGT 59.423 61.111 11.89 0.00 36.51 5.68
1426 1597 3.866582 GCAGCAGCGGGATAGGGT 61.867 66.667 0.00 0.00 0.00 4.34
1550 1721 2.862541 AGCCAAACACTGCTATCACAA 58.137 42.857 0.00 0.00 35.69 3.33
1735 1906 1.300080 CGAACCCGTACAACACCGT 60.300 57.895 0.00 0.00 0.00 4.83
1758 1929 4.767478 CCATCTTTCTCTGAATGCTCTCA 58.233 43.478 0.00 0.00 0.00 3.27
1790 1961 2.124983 CATCCTCGGTGCCTGTGG 60.125 66.667 0.00 0.00 0.00 4.17
1794 1965 1.524002 CATGTCATCCTCGGTGCCT 59.476 57.895 0.00 0.00 0.00 4.75
1851 2022 1.700739 TCTCTGCCCCGGTTAAGAAAA 59.299 47.619 0.00 0.00 0.00 2.29
1865 2036 0.390998 GAAGTCAGTGGGCTCTCTGC 60.391 60.000 10.89 6.40 41.94 4.26
1896 2067 2.414559 CGCCACCATGAAGTTGATGAAC 60.415 50.000 3.63 0.00 0.00 3.18
1908 2079 1.357690 GTCATGCATCGCCACCATG 59.642 57.895 0.00 0.00 38.10 3.66
1914 2085 2.281070 ATCGGGTCATGCATCGCC 60.281 61.111 0.00 1.31 0.00 5.54
1917 2088 1.601759 CCCCATCGGGTCATGCATC 60.602 63.158 0.00 0.00 45.50 3.91
1941 2112 0.817654 TGTAGATGAGCCACGACAGG 59.182 55.000 0.00 0.00 0.00 4.00
1942 2113 2.263077 GTTGTAGATGAGCCACGACAG 58.737 52.381 0.00 0.00 0.00 3.51
1954 2125 1.153628 GCGTGGCGAGGTTGTAGAT 60.154 57.895 0.00 0.00 0.00 1.98
2041 2212 3.868985 AAACACCACGACGCCCCT 61.869 61.111 0.00 0.00 0.00 4.79
2042 2213 3.656045 CAAACACCACGACGCCCC 61.656 66.667 0.00 0.00 0.00 5.80
2043 2214 2.589442 TCAAACACCACGACGCCC 60.589 61.111 0.00 0.00 0.00 6.13
2046 2217 1.831389 CTGGCTCAAACACCACGACG 61.831 60.000 0.00 0.00 0.00 5.12
2049 2220 1.831389 CGTCTGGCTCAAACACCACG 61.831 60.000 0.00 0.00 0.00 4.94
2061 2232 0.670854 GGTCTTTGGTCTCGTCTGGC 60.671 60.000 0.00 0.00 0.00 4.85
2079 2250 2.582498 GCGCGCTGGTACACTAGG 60.582 66.667 26.67 0.00 0.00 3.02
2094 2265 3.554692 GACTCGAACATGGCCGCG 61.555 66.667 0.00 0.00 0.00 6.46
2112 2283 1.384989 CGATCGGGTACAGCCTCAGT 61.385 60.000 7.38 0.00 37.43 3.41
2217 2388 1.135094 ATCTCCCCATGCTGTAGGTG 58.865 55.000 0.00 0.00 0.00 4.00
2231 2402 0.543749 CCACACCTCCTCCAATCTCC 59.456 60.000 0.00 0.00 0.00 3.71
2242 2413 1.079438 AGTCCTCTCCCCACACCTC 59.921 63.158 0.00 0.00 0.00 3.85
2256 2427 2.722201 CCTGTACTCCCGGCAGTCC 61.722 68.421 0.00 0.00 0.00 3.85
2292 2463 2.579201 CTCCCGTCTGCGTTGGAT 59.421 61.111 0.00 0.00 36.15 3.41
2340 2511 1.525197 GTGTTGAATGCGACGAACTCA 59.475 47.619 0.00 0.00 0.00 3.41
2342 2513 0.865769 GGTGTTGAATGCGACGAACT 59.134 50.000 0.00 0.00 0.00 3.01
2349 2520 2.867472 GGTCCGGTGTTGAATGCG 59.133 61.111 0.00 0.00 0.00 4.73
2352 2523 1.295423 CCTCGGTCCGGTGTTGAAT 59.705 57.895 12.29 0.00 0.00 2.57
2455 2626 3.247006 AGGCTTCACGGTGTTACTATG 57.753 47.619 8.17 0.00 0.00 2.23
2475 2646 3.194755 TCTGCAGAATAACCGACAGCTTA 59.805 43.478 15.67 0.00 0.00 3.09
2551 2722 6.208599 AGTGACAATTAATTTGGATCGGTGTT 59.791 34.615 0.00 0.00 39.80 3.32
2686 2857 5.704888 CTGAGCTAGTTTGGGAGATATACG 58.295 45.833 0.00 0.00 0.00 3.06
2694 2865 1.210478 GGATGCTGAGCTAGTTTGGGA 59.790 52.381 5.83 0.00 0.00 4.37
2695 2866 1.673168 GGATGCTGAGCTAGTTTGGG 58.327 55.000 5.83 0.00 0.00 4.12
2696 2867 1.065199 TGGGATGCTGAGCTAGTTTGG 60.065 52.381 5.83 0.00 0.00 3.28
2697 2868 2.408271 TGGGATGCTGAGCTAGTTTG 57.592 50.000 5.83 0.00 0.00 2.93
2698 2869 3.084786 GTTTGGGATGCTGAGCTAGTTT 58.915 45.455 5.83 0.00 0.00 2.66
2699 2870 2.307098 AGTTTGGGATGCTGAGCTAGTT 59.693 45.455 5.83 0.00 0.00 2.24
2700 2871 1.912043 AGTTTGGGATGCTGAGCTAGT 59.088 47.619 5.83 0.00 0.00 2.57
2701 2872 2.706339 AGTTTGGGATGCTGAGCTAG 57.294 50.000 5.83 0.00 0.00 3.42
2702 2873 5.307976 ACATATAGTTTGGGATGCTGAGCTA 59.692 40.000 5.83 0.00 0.00 3.32
2703 2874 4.103785 ACATATAGTTTGGGATGCTGAGCT 59.896 41.667 5.83 0.00 0.00 4.09
2704 2875 4.392940 ACATATAGTTTGGGATGCTGAGC 58.607 43.478 0.00 0.00 0.00 4.26
2705 2876 6.428159 GGTAACATATAGTTTGGGATGCTGAG 59.572 42.308 0.00 0.00 41.64 3.35
2706 2877 6.101150 AGGTAACATATAGTTTGGGATGCTGA 59.899 38.462 0.00 0.00 41.64 4.26
2707 2878 6.205464 CAGGTAACATATAGTTTGGGATGCTG 59.795 42.308 0.00 0.00 41.64 4.41
2708 2879 6.101150 TCAGGTAACATATAGTTTGGGATGCT 59.899 38.462 0.00 0.00 41.64 3.79
2709 2880 6.296026 TCAGGTAACATATAGTTTGGGATGC 58.704 40.000 0.00 0.00 41.64 3.91
2710 2881 6.936900 CCTCAGGTAACATATAGTTTGGGATG 59.063 42.308 0.00 0.00 41.64 3.51
2711 2882 6.044404 CCCTCAGGTAACATATAGTTTGGGAT 59.956 42.308 0.00 0.00 41.64 3.85
2744 2915 3.245990 GTGCTGGTGAGTCAAATTTTTGC 59.754 43.478 0.00 0.00 38.05 3.68
2960 3503 4.717313 GGTGGCGACCCCTCCAAC 62.717 72.222 6.63 0.00 44.96 3.77
2964 3507 4.699522 GTGTGGTGGCGACCCCTC 62.700 72.222 16.02 0.56 42.34 4.30
2972 3515 2.295909 TGCTTGAATAAAGTGTGGTGGC 59.704 45.455 0.00 0.00 38.25 5.01
3058 3601 4.038763 TGGCGAAAGTCTCTGTCTTTCTTA 59.961 41.667 13.78 1.60 44.69 2.10
3109 3652 8.089625 TGATTCAGGAGTTATACATGAAGGAA 57.910 34.615 0.00 0.00 40.37 3.36
3114 3657 9.166173 CTTTGTTGATTCAGGAGTTATACATGA 57.834 33.333 0.00 0.00 0.00 3.07
3143 3686 5.010112 TCGGGATACTAAGAAGAGAATGCAG 59.990 44.000 0.00 0.00 0.00 4.41
3144 3687 4.893524 TCGGGATACTAAGAAGAGAATGCA 59.106 41.667 0.00 0.00 0.00 3.96
3258 6230 1.304381 GGCATTCTCCCTGGCACAA 60.304 57.895 0.00 0.00 38.70 3.33
3281 6253 1.294659 CCTTGAGGCTCACGCTTGTC 61.295 60.000 18.55 0.00 36.09 3.18
3433 6407 4.462483 GCTAGAAGGATCTGATGGAGTAGG 59.538 50.000 0.00 0.00 37.10 3.18
3511 7959 5.660417 TCTTAGAAGATCTTGAGATGGTGCT 59.340 40.000 14.00 2.75 34.37 4.40


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

AutoCloner maintained by Alex Coulton.