Multiple sequence alignment - TraesCS3D01G220300

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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 TraesCS3D01G220300 chr3D 100.000 2784 0 0 1 2784 300682632 300679849 0.000000e+00 5142.0
1 TraesCS3D01G220300 chr3D 90.788 749 44 7 1 739 531450005 531450738 0.000000e+00 977.0
2 TraesCS3D01G220300 chr3D 96.507 544 13 2 1988 2525 23089051 23089594 0.000000e+00 894.0
3 TraesCS3D01G220300 chr3D 86.739 739 64 19 1039 1773 300582749 300583457 0.000000e+00 791.0
4 TraesCS3D01G220300 chr3D 90.769 455 41 1 288 741 13266764 13267218 8.530000e-170 606.0
5 TraesCS3D01G220300 chr5A 96.750 800 23 2 1988 2784 700670943 700671742 0.000000e+00 1330.0
6 TraesCS3D01G220300 chr5A 94.022 552 31 1 1988 2537 510491606 510491055 0.000000e+00 835.0
7 TraesCS3D01G220300 chr2A 95.500 800 35 1 1986 2784 29273411 29274210 0.000000e+00 1277.0
8 TraesCS3D01G220300 chr2A 90.727 798 66 2 1988 2784 166634835 166635625 0.000000e+00 1057.0
9 TraesCS3D01G220300 chr3A 86.124 1254 86 41 772 1991 434786688 434787887 0.000000e+00 1271.0
10 TraesCS3D01G220300 chr3A 87.615 759 78 9 1 743 709502471 709503229 0.000000e+00 867.0
11 TraesCS3D01G220300 chr3A 86.939 758 84 8 1 743 709536867 709537624 0.000000e+00 837.0
12 TraesCS3D01G220300 chr3A 89.167 600 56 4 1048 1647 434822465 434821875 0.000000e+00 739.0
13 TraesCS3D01G220300 chr3A 86.875 160 9 3 772 930 434822721 434822573 4.770000e-38 169.0
14 TraesCS3D01G220300 chr4A 96.042 758 25 5 1988 2740 65715137 65714380 0.000000e+00 1229.0
15 TraesCS3D01G220300 chr4A 92.593 108 8 0 2674 2781 563213503 563213610 3.710000e-34 156.0
16 TraesCS3D01G220300 chr1D 94.587 739 37 3 1 739 307838465 307837730 0.000000e+00 1140.0
17 TraesCS3D01G220300 chr1D 90.885 746 58 5 1 739 426189918 426190660 0.000000e+00 992.0
18 TraesCS3D01G220300 chr3B 87.055 1012 54 35 772 1772 420419149 420420094 0.000000e+00 1072.0
19 TraesCS3D01G220300 chr3B 86.567 737 67 19 1039 1773 420776882 420776176 0.000000e+00 784.0
20 TraesCS3D01G220300 chr3B 90.832 469 42 1 276 743 119310952 119310484 6.550000e-176 627.0
21 TraesCS3D01G220300 chr6A 92.818 738 32 2 1988 2723 546926608 546925890 0.000000e+00 1050.0
22 TraesCS3D01G220300 chr6A 93.421 76 4 1 2710 2784 546925065 546924990 8.150000e-21 111.0
23 TraesCS3D01G220300 chr7D 92.297 740 51 6 1 739 259362761 259362027 0.000000e+00 1046.0
24 TraesCS3D01G220300 chr7D 87.129 101 12 1 1812 1912 450758907 450758808 2.270000e-21 113.0
25 TraesCS3D01G220300 chr4D 91.644 730 54 4 19 742 508246417 508247145 0.000000e+00 1003.0
26 TraesCS3D01G220300 chr4D 96.674 451 13 2 1988 2437 465183409 465182960 0.000000e+00 749.0
27 TraesCS3D01G220300 chr4D 91.837 441 30 2 1 435 505153543 505153103 6.590000e-171 610.0
28 TraesCS3D01G220300 chr4D 92.593 108 8 0 2674 2781 8622413 8622520 3.710000e-34 156.0
29 TraesCS3D01G220300 chr4D 81.905 105 13 6 1812 1913 24864673 24864774 1.780000e-12 84.2
30 TraesCS3D01G220300 chr5B 89.986 739 73 1 1 739 683086114 683085377 0.000000e+00 953.0
31 TraesCS3D01G220300 chr5B 87.755 98 12 0 1816 1913 352488715 352488618 6.300000e-22 115.0
32 TraesCS3D01G220300 chr4B 86.156 679 85 8 1 674 384286735 384287409 0.000000e+00 725.0
33 TraesCS3D01G220300 chr2B 91.209 455 36 3 287 739 138438679 138438227 1.420000e-172 616.0
34 TraesCS3D01G220300 chr2B 86.940 536 47 13 1988 2500 214319619 214320154 5.170000e-162 580.0
35 TraesCS3D01G220300 chr2B 86.611 239 29 2 2457 2692 612094906 612095144 7.650000e-66 261.0
36 TraesCS3D01G220300 chr2B 83.168 101 16 1 1812 1912 90702668 90702767 1.060000e-14 91.6
37 TraesCS3D01G220300 chr5D 92.481 399 26 2 1988 2384 519644328 519644724 4.020000e-158 568.0
38 TraesCS3D01G220300 chr6D 93.215 339 22 1 1 339 450536542 450536879 5.350000e-137 497.0
39 TraesCS3D01G220300 chrUn 92.593 108 8 0 2674 2781 269813601 269813708 3.710000e-34 156.0
40 TraesCS3D01G220300 chrUn 86.139 101 13 1 1812 1912 27746664 27746565 1.050000e-19 108.0
41 TraesCS3D01G220300 chr6B 85.567 97 14 0 1814 1910 299778652 299778556 4.910000e-18 102.0
42 TraesCS3D01G220300 chr2D 83.168 101 11 6 1815 1912 326251209 326251112 1.370000e-13 87.9
43 TraesCS3D01G220300 chr7B 82.653 98 15 1 1815 1912 635667774 635667679 4.940000e-13 86.1
44 TraesCS3D01G220300 chr7B 81.905 105 13 6 1812 1913 153667064 153667165 1.780000e-12 84.2


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 TraesCS3D01G220300 chr3D 300679849 300682632 2783 True 5142.0 5142 100.0000 1 2784 1 chr3D.!!$R1 2783
1 TraesCS3D01G220300 chr3D 531450005 531450738 733 False 977.0 977 90.7880 1 739 1 chr3D.!!$F4 738
2 TraesCS3D01G220300 chr3D 23089051 23089594 543 False 894.0 894 96.5070 1988 2525 1 chr3D.!!$F2 537
3 TraesCS3D01G220300 chr3D 300582749 300583457 708 False 791.0 791 86.7390 1039 1773 1 chr3D.!!$F3 734
4 TraesCS3D01G220300 chr5A 700670943 700671742 799 False 1330.0 1330 96.7500 1988 2784 1 chr5A.!!$F1 796
5 TraesCS3D01G220300 chr5A 510491055 510491606 551 True 835.0 835 94.0220 1988 2537 1 chr5A.!!$R1 549
6 TraesCS3D01G220300 chr2A 29273411 29274210 799 False 1277.0 1277 95.5000 1986 2784 1 chr2A.!!$F1 798
7 TraesCS3D01G220300 chr2A 166634835 166635625 790 False 1057.0 1057 90.7270 1988 2784 1 chr2A.!!$F2 796
8 TraesCS3D01G220300 chr3A 434786688 434787887 1199 False 1271.0 1271 86.1240 772 1991 1 chr3A.!!$F1 1219
9 TraesCS3D01G220300 chr3A 709502471 709503229 758 False 867.0 867 87.6150 1 743 1 chr3A.!!$F2 742
10 TraesCS3D01G220300 chr3A 709536867 709537624 757 False 837.0 837 86.9390 1 743 1 chr3A.!!$F3 742
11 TraesCS3D01G220300 chr3A 434821875 434822721 846 True 454.0 739 88.0210 772 1647 2 chr3A.!!$R1 875
12 TraesCS3D01G220300 chr4A 65714380 65715137 757 True 1229.0 1229 96.0420 1988 2740 1 chr4A.!!$R1 752
13 TraesCS3D01G220300 chr1D 307837730 307838465 735 True 1140.0 1140 94.5870 1 739 1 chr1D.!!$R1 738
14 TraesCS3D01G220300 chr1D 426189918 426190660 742 False 992.0 992 90.8850 1 739 1 chr1D.!!$F1 738
15 TraesCS3D01G220300 chr3B 420419149 420420094 945 False 1072.0 1072 87.0550 772 1772 1 chr3B.!!$F1 1000
16 TraesCS3D01G220300 chr3B 420776176 420776882 706 True 784.0 784 86.5670 1039 1773 1 chr3B.!!$R2 734
17 TraesCS3D01G220300 chr6A 546924990 546926608 1618 True 580.5 1050 93.1195 1988 2784 2 chr6A.!!$R1 796
18 TraesCS3D01G220300 chr7D 259362027 259362761 734 True 1046.0 1046 92.2970 1 739 1 chr7D.!!$R1 738
19 TraesCS3D01G220300 chr4D 508246417 508247145 728 False 1003.0 1003 91.6440 19 742 1 chr4D.!!$F3 723
20 TraesCS3D01G220300 chr5B 683085377 683086114 737 True 953.0 953 89.9860 1 739 1 chr5B.!!$R2 738
21 TraesCS3D01G220300 chr4B 384286735 384287409 674 False 725.0 725 86.1560 1 674 1 chr4B.!!$F1 673
22 TraesCS3D01G220300 chr2B 214319619 214320154 535 False 580.0 580 86.9400 1988 2500 1 chr2B.!!$F2 512


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
747 781 0.042581 AAAATTTGGCCCCCTCCGAT 59.957 50.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2417 0.320374 TGAGTGCTTGTACGGAAGGG 59.68 55.0 0.0 0.0 0.0 3.95 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
51 52 1.930817 GCGGCGTTCGATATCATCAGT 60.931 52.381 9.37 0.00 42.43 3.41
61 62 3.324846 CGATATCATCAGTTGGGGAAGGA 59.675 47.826 3.12 0.00 0.00 3.36
62 63 4.019860 CGATATCATCAGTTGGGGAAGGAT 60.020 45.833 3.12 0.00 0.00 3.24
91 92 4.809496 CTCCAGCGGGCAAGGCAT 62.809 66.667 0.00 0.00 0.00 4.40
197 198 2.326428 GCCAGGCCTAACATACTAGGA 58.674 52.381 3.98 0.00 41.02 2.94
225 236 4.721274 AGGTTTACCCGCCCTATAAACTTA 59.279 41.667 6.18 0.00 38.37 2.24
226 237 4.816385 GGTTTACCCGCCCTATAAACTTAC 59.184 45.833 6.18 0.00 38.37 2.34
231 242 4.909695 ACCCGCCCTATAAACTTACCTTAT 59.090 41.667 0.00 0.00 0.00 1.73
329 340 6.714810 ACTATGTGGACAAGTTTGCTATTTGA 59.285 34.615 2.61 0.00 0.00 2.69
609 631 4.329545 GCCACCGTCAGAAGCCCA 62.330 66.667 0.00 0.00 0.00 5.36
637 659 1.751927 CTACGTGACCCTACCGCCT 60.752 63.158 0.00 0.00 0.00 5.52
638 660 1.722636 CTACGTGACCCTACCGCCTC 61.723 65.000 0.00 0.00 0.00 4.70
679 706 7.567590 GCAAAAAGGTCAGATGTCGAATTTTTC 60.568 37.037 0.00 0.00 28.61 2.29
686 713 7.307989 GGTCAGATGTCGAATTTTTCTCAAAGA 60.308 37.037 0.00 0.00 0.00 2.52
743 777 1.055849 ACACAAAATTTGGCCCCCTC 58.944 50.000 10.71 0.00 34.12 4.30
744 778 0.324614 CACAAAATTTGGCCCCCTCC 59.675 55.000 10.71 0.00 34.12 4.30
745 779 1.191489 ACAAAATTTGGCCCCCTCCG 61.191 55.000 10.71 0.00 34.12 4.63
746 780 0.902516 CAAAATTTGGCCCCCTCCGA 60.903 55.000 0.00 0.00 0.00 4.55
747 781 0.042581 AAAATTTGGCCCCCTCCGAT 59.957 50.000 0.00 0.00 0.00 4.18
748 782 0.687427 AAATTTGGCCCCCTCCGATG 60.687 55.000 0.00 0.00 0.00 3.84
749 783 2.588029 AATTTGGCCCCCTCCGATGG 62.588 60.000 0.00 0.00 0.00 3.51
752 786 4.506255 GGCCCCCTCCGATGGTTG 62.506 72.222 0.00 0.00 0.00 3.77
753 787 4.506255 GCCCCCTCCGATGGTTGG 62.506 72.222 0.00 0.00 0.00 3.77
754 788 2.690881 CCCCCTCCGATGGTTGGA 60.691 66.667 0.00 0.00 0.00 3.53
755 789 2.305607 CCCCCTCCGATGGTTGGAA 61.306 63.158 0.00 0.00 34.44 3.53
756 790 1.077716 CCCCTCCGATGGTTGGAAC 60.078 63.158 0.00 0.00 34.44 3.62
757 791 1.562672 CCCCTCCGATGGTTGGAACT 61.563 60.000 0.00 0.00 34.44 3.01
758 792 0.328258 CCCTCCGATGGTTGGAACTT 59.672 55.000 0.00 0.00 34.44 2.66
759 793 1.453155 CCTCCGATGGTTGGAACTTG 58.547 55.000 0.00 0.00 34.44 3.16
760 794 1.453155 CTCCGATGGTTGGAACTTGG 58.547 55.000 0.00 0.00 34.44 3.61
761 795 1.003118 CTCCGATGGTTGGAACTTGGA 59.997 52.381 0.00 0.00 34.44 3.53
762 796 1.422024 TCCGATGGTTGGAACTTGGAA 59.578 47.619 0.00 0.00 30.98 3.53
763 797 1.539827 CCGATGGTTGGAACTTGGAAC 59.460 52.381 0.00 0.00 0.00 3.62
764 798 1.539827 CGATGGTTGGAACTTGGAACC 59.460 52.381 0.00 0.00 39.77 3.62
766 800 2.534042 TGGTTGGAACTTGGAACCAA 57.466 45.000 6.12 6.12 44.84 3.67
822 857 1.934589 CGGCATGGAATCGTTACTCA 58.065 50.000 0.00 0.00 0.00 3.41
823 858 1.860950 CGGCATGGAATCGTTACTCAG 59.139 52.381 0.00 0.00 0.00 3.35
824 859 2.481276 CGGCATGGAATCGTTACTCAGA 60.481 50.000 0.00 0.00 0.00 3.27
825 860 3.733337 GGCATGGAATCGTTACTCAGAT 58.267 45.455 0.00 0.00 0.00 2.90
826 861 3.743396 GGCATGGAATCGTTACTCAGATC 59.257 47.826 0.00 0.00 0.00 2.75
828 863 4.447054 GCATGGAATCGTTACTCAGATCAG 59.553 45.833 0.00 0.00 0.00 2.90
836 871 6.132791 TCGTTACTCAGATCAGATTGTACC 57.867 41.667 0.00 0.00 0.00 3.34
909 944 4.037858 AGTTGCCTTACTTATCCGTACG 57.962 45.455 8.69 8.69 0.00 3.67
917 953 7.040478 TGCCTTACTTATCCGTACGTACATATT 60.040 37.037 24.50 9.17 0.00 1.28
930 966 7.417683 CGTACGTACATATTTGAGTTTGTTTCG 59.582 37.037 24.50 0.82 0.00 3.46
931 967 7.181143 ACGTACATATTTGAGTTTGTTTCGT 57.819 32.000 0.00 0.00 31.74 3.85
932 968 8.296799 ACGTACATATTTGAGTTTGTTTCGTA 57.703 30.769 0.00 0.00 33.38 3.43
933 969 8.216453 ACGTACATATTTGAGTTTGTTTCGTAC 58.784 33.333 0.00 0.00 33.38 3.67
934 970 8.430063 CGTACATATTTGAGTTTGTTTCGTACT 58.570 33.333 0.00 0.00 0.00 2.73
937 973 9.485206 ACATATTTGAGTTTGTTTCGTACTAGT 57.515 29.630 0.00 0.00 0.00 2.57
981 1022 5.784578 TTCTTTAAAAGGAAGTTGGCCTC 57.215 39.130 3.32 0.00 33.76 4.70
998 1048 1.801178 CCTCGCTTGGTTCTCTTTGAC 59.199 52.381 0.00 0.00 0.00 3.18
1009 1076 4.025145 GGTTCTCTTTGACCAAACACGTAG 60.025 45.833 0.00 0.00 0.00 3.51
1026 1093 1.971505 TAGGCTTCCATGGCAGGACG 61.972 60.000 13.60 3.00 37.42 4.79
1027 1094 2.268920 GCTTCCATGGCAGGACGA 59.731 61.111 13.60 0.00 37.42 4.20
1035 1102 3.760035 GGCAGGACGAGAGGCGAA 61.760 66.667 0.00 0.00 43.44 4.70
1050 1123 1.860078 CGAACAAGGACGTTGGAGC 59.140 57.895 12.21 0.95 40.90 4.70
1088 1164 2.660802 GGGACGGCGGAGAAAAGA 59.339 61.111 13.24 0.00 0.00 2.52
1121 1197 2.003196 CCAGCGTTTTGGTGTTTGTT 57.997 45.000 0.00 0.00 44.68 2.83
1158 1234 5.049954 TGGCATTAGTTCTCGTTGTTGTTAC 60.050 40.000 0.00 0.00 0.00 2.50
1655 1731 5.042463 TCATCCAACCTTTATATCGGCAA 57.958 39.130 0.00 0.00 0.00 4.52
1691 1767 7.643123 AGTTAGGATTTTATTGTCCTGGATGT 58.357 34.615 0.00 0.00 44.39 3.06
1723 1799 2.798283 TCCTTGTAAGTTTGCGACTTCG 59.202 45.455 8.38 0.00 45.40 3.79
1753 1832 1.070134 TCGCAAACAGCCTCTACAACT 59.930 47.619 0.00 0.00 41.38 3.16
1761 1840 5.746990 ACAGCCTCTACAACTTAGTCATT 57.253 39.130 0.00 0.00 0.00 2.57
1777 1856 8.507249 ACTTAGTCATTAATTTGTTCTGACAGC 58.493 33.333 0.00 0.00 38.90 4.40
1778 1857 6.882610 AGTCATTAATTTGTTCTGACAGCA 57.117 33.333 0.00 0.00 38.90 4.41
1779 1858 7.275888 AGTCATTAATTTGTTCTGACAGCAA 57.724 32.000 0.00 0.00 38.90 3.91
1780 1859 7.365741 AGTCATTAATTTGTTCTGACAGCAAG 58.634 34.615 0.00 0.00 38.90 4.01
1781 1860 7.229306 AGTCATTAATTTGTTCTGACAGCAAGA 59.771 33.333 0.00 0.00 38.90 3.02
1782 1861 7.862372 GTCATTAATTTGTTCTGACAGCAAGAA 59.138 33.333 0.00 0.00 37.04 2.52
1784 1863 8.697067 CATTAATTTGTTCTGACAGCAAGAAAG 58.303 33.333 0.00 0.00 37.04 2.62
1803 1900 5.814705 AGAAAGCTAATTCTGGTTCATCTCG 59.185 40.000 0.00 0.00 38.22 4.04
1824 1921 1.343176 GGGCTGGTTAGTACTCCCTCT 60.343 57.143 0.00 0.00 0.00 3.69
1827 1924 3.827876 GGCTGGTTAGTACTCCCTCTATC 59.172 52.174 0.00 0.00 0.00 2.08
1828 1925 3.827876 GCTGGTTAGTACTCCCTCTATCC 59.172 52.174 0.00 0.00 0.00 2.59
1829 1926 4.409187 CTGGTTAGTACTCCCTCTATCCC 58.591 52.174 0.00 0.00 0.00 3.85
1830 1927 3.795545 TGGTTAGTACTCCCTCTATCCCA 59.204 47.826 0.00 0.00 0.00 4.37
1836 1933 8.931568 GTTAGTACTCCCTCTATCCCAAAATAA 58.068 37.037 0.00 0.00 0.00 1.40
1837 1934 7.619512 AGTACTCCCTCTATCCCAAAATAAG 57.380 40.000 0.00 0.00 0.00 1.73
1838 1935 7.140304 AGTACTCCCTCTATCCCAAAATAAGT 58.860 38.462 0.00 0.00 0.00 2.24
1840 1937 5.731678 ACTCCCTCTATCCCAAAATAAGTGT 59.268 40.000 0.00 0.00 0.00 3.55
1841 1938 6.126739 ACTCCCTCTATCCCAAAATAAGTGTC 60.127 42.308 0.00 0.00 0.00 3.67
1842 1939 5.970640 TCCCTCTATCCCAAAATAAGTGTCT 59.029 40.000 0.00 0.00 0.00 3.41
1843 1940 6.099845 TCCCTCTATCCCAAAATAAGTGTCTC 59.900 42.308 0.00 0.00 0.00 3.36
1844 1941 6.126768 CCCTCTATCCCAAAATAAGTGTCTCA 60.127 42.308 0.00 0.00 0.00 3.27
1845 1942 7.338710 CCTCTATCCCAAAATAAGTGTCTCAA 58.661 38.462 0.00 0.00 0.00 3.02
1846 1943 7.829211 CCTCTATCCCAAAATAAGTGTCTCAAA 59.171 37.037 0.00 0.00 0.00 2.69
1847 1944 9.401058 CTCTATCCCAAAATAAGTGTCTCAAAT 57.599 33.333 0.00 0.00 0.00 2.32
1848 1945 9.753674 TCTATCCCAAAATAAGTGTCTCAAATT 57.246 29.630 0.00 0.00 0.00 1.82
1981 2078 5.120830 ACATTTGTGCGTATCTGAAGAGTTC 59.879 40.000 0.00 0.00 0.00 3.01
1991 2088 7.630924 CGTATCTGAAGAGTTCAAGTGTTTTT 58.369 34.615 0.00 0.00 39.58 1.94
2113 2210 1.291132 GCCTCCTACACGAGCAAATC 58.709 55.000 0.00 0.00 0.00 2.17
2191 2289 4.866508 TCACGAAGAGACATAAGGTGTT 57.133 40.909 0.00 0.00 42.36 3.32
2198 2296 8.095169 ACGAAGAGACATAAGGTGTTTAATCTT 58.905 33.333 0.00 0.00 42.36 2.40
2319 2417 3.575630 TCTCTGTATTGTGAACGACAGC 58.424 45.455 0.00 0.00 39.33 4.40
2326 2424 2.027625 GTGAACGACAGCCCTTCCG 61.028 63.158 0.00 0.00 0.00 4.30
2442 2540 0.835971 TACCAGAACCTGCTGAGCCA 60.836 55.000 0.23 0.00 38.14 4.75
2563 2706 6.639686 GGCAGCAAAATTATCACATGATACAG 59.360 38.462 0.00 0.00 36.81 2.74
2594 2738 6.200878 TCCCTTACTTGTTTCAGAGGAAAT 57.799 37.500 0.00 0.00 44.32 2.17
2675 2820 3.876236 GGGCGGGGGCGGTTTATA 61.876 66.667 0.00 0.00 0.00 0.98
2759 3743 5.988561 GCTCAATATCAGGAAGAGGTTGTAG 59.011 44.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.001745 TGATGATATCGAACGCCGCG 61.002 55.000 12.14 12.14 38.37 6.46
31 32 0.710567 CTGATGATATCGAACGCCGC 59.289 55.000 0.00 0.00 38.37 6.53
51 52 2.679342 CGCCTCCATCCTTCCCCAA 61.679 63.158 0.00 0.00 0.00 4.12
91 92 1.227823 CGTTCAAGCACTCCCACCA 60.228 57.895 0.00 0.00 0.00 4.17
193 194 0.031817 CGGGTAAACCTCCCCTCCTA 60.032 60.000 0.00 0.00 41.78 2.94
197 198 3.013327 GGCGGGTAAACCTCCCCT 61.013 66.667 0.00 0.00 41.78 4.79
225 236 2.552315 CGGTGCAACAAGTTCATAAGGT 59.448 45.455 0.98 0.00 39.98 3.50
226 237 2.552315 ACGGTGCAACAAGTTCATAAGG 59.448 45.455 0.98 0.00 39.98 2.69
231 242 1.542030 ACAAACGGTGCAACAAGTTCA 59.458 42.857 0.98 0.00 38.05 3.18
621 643 3.066814 GAGGCGGTAGGGTCACGT 61.067 66.667 0.00 0.00 0.00 4.49
679 706 2.998316 GGGATCTGACCCTCTTTGAG 57.002 55.000 7.74 0.00 45.90 3.02
743 777 1.539827 GTTCCAAGTTCCAACCATCGG 59.460 52.381 0.00 0.00 0.00 4.18
744 778 1.539827 GGTTCCAAGTTCCAACCATCG 59.460 52.381 7.39 0.00 39.61 3.84
745 779 2.593026 TGGTTCCAAGTTCCAACCATC 58.407 47.619 10.10 0.00 43.77 3.51
746 780 2.765689 TGGTTCCAAGTTCCAACCAT 57.234 45.000 10.10 0.00 43.77 3.55
747 781 2.383855 CTTGGTTCCAAGTTCCAACCA 58.616 47.619 19.86 10.10 46.33 3.67
758 792 9.967451 TGTCTATAATAATTCAACTTGGTTCCA 57.033 29.630 0.00 0.00 0.00 3.53
769 803 9.647918 ACTCAGGAGTCTGTCTATAATAATTCA 57.352 33.333 0.00 0.00 41.59 2.57
798 832 1.656818 AACGATTCCATGCCGCCTTG 61.657 55.000 0.00 0.00 0.00 3.61
799 833 0.107410 TAACGATTCCATGCCGCCTT 60.107 50.000 0.00 0.00 0.00 4.35
822 857 6.299805 TGCAAACTAGGTACAATCTGATCT 57.700 37.500 0.00 0.00 0.00 2.75
823 858 6.074088 CGATGCAAACTAGGTACAATCTGATC 60.074 42.308 0.00 0.00 0.00 2.92
824 859 5.755375 CGATGCAAACTAGGTACAATCTGAT 59.245 40.000 0.00 0.00 0.00 2.90
825 860 5.109210 CGATGCAAACTAGGTACAATCTGA 58.891 41.667 0.00 0.00 0.00 3.27
826 861 4.870426 ACGATGCAAACTAGGTACAATCTG 59.130 41.667 0.00 0.00 0.00 2.90
828 863 4.868171 TCACGATGCAAACTAGGTACAATC 59.132 41.667 0.00 0.00 0.00 2.67
953 989 9.332502 GGCCAACTTCCTTTTAAAGAAAAATAA 57.667 29.630 6.24 0.00 36.49 1.40
954 990 8.710239 AGGCCAACTTCCTTTTAAAGAAAAATA 58.290 29.630 5.01 0.00 36.49 1.40
955 991 7.573710 AGGCCAACTTCCTTTTAAAGAAAAAT 58.426 30.769 5.01 0.00 36.49 1.82
956 992 6.953101 AGGCCAACTTCCTTTTAAAGAAAAA 58.047 32.000 5.01 0.00 34.16 1.94
957 993 6.553953 AGGCCAACTTCCTTTTAAAGAAAA 57.446 33.333 5.01 0.00 33.48 2.29
958 994 5.221165 CGAGGCCAACTTCCTTTTAAAGAAA 60.221 40.000 5.01 0.00 33.24 2.52
959 995 4.277423 CGAGGCCAACTTCCTTTTAAAGAA 59.723 41.667 5.01 0.00 33.24 2.52
960 996 3.818773 CGAGGCCAACTTCCTTTTAAAGA 59.181 43.478 5.01 0.00 33.24 2.52
961 997 3.611766 GCGAGGCCAACTTCCTTTTAAAG 60.612 47.826 5.01 0.00 33.24 1.85
974 1010 1.302511 GAGAACCAAGCGAGGCCAA 60.303 57.895 5.01 0.00 0.00 4.52
976 1017 0.606673 AAAGAGAACCAAGCGAGGCC 60.607 55.000 0.00 0.00 0.00 5.19
981 1022 1.593196 TGGTCAAAGAGAACCAAGCG 58.407 50.000 0.00 0.00 30.86 4.68
998 1048 1.468520 CATGGAAGCCTACGTGTTTGG 59.531 52.381 0.00 0.00 0.00 3.28
1009 1076 2.825836 CGTCCTGCCATGGAAGCC 60.826 66.667 18.40 6.75 37.93 4.35
1026 1093 0.319641 AACGTCCTTGTTCGCCTCTC 60.320 55.000 0.00 0.00 0.00 3.20
1027 1094 0.600255 CAACGTCCTTGTTCGCCTCT 60.600 55.000 0.00 0.00 0.00 3.69
1035 1102 2.030562 CCGCTCCAACGTCCTTGT 59.969 61.111 0.00 0.00 0.00 3.16
1121 1197 2.227494 AATGCCAGCCCCACTGCATA 62.227 55.000 0.00 0.00 45.78 3.14
1158 1234 1.524621 CCCAAGGCTATCGCACTGG 60.525 63.158 0.00 2.73 38.48 4.00
1412 1488 3.173240 GACGCTCAACTCCGACGC 61.173 66.667 0.00 0.00 0.00 5.19
1444 1520 3.123620 CGAGGCAAGAGCACCTGC 61.124 66.667 0.00 0.00 44.61 4.85
1691 1767 3.950397 ACTTACAAGGAATGCCGATGAA 58.050 40.909 5.63 0.00 39.96 2.57
1723 1799 2.478539 GGCTGTTTGCGATCAGAATTCC 60.479 50.000 15.07 3.94 44.05 3.01
1753 1832 8.389779 TGCTGTCAGAACAAATTAATGACTAA 57.610 30.769 3.32 0.00 40.67 2.24
1761 1840 6.039717 AGCTTTCTTGCTGTCAGAACAAATTA 59.960 34.615 3.32 0.00 42.33 1.40
1773 1852 4.401925 ACCAGAATTAGCTTTCTTGCTGT 58.598 39.130 0.00 0.00 43.87 4.40
1774 1853 5.048504 TGAACCAGAATTAGCTTTCTTGCTG 60.049 40.000 0.00 0.00 43.87 4.41
1775 1854 5.072741 TGAACCAGAATTAGCTTTCTTGCT 58.927 37.500 0.00 0.00 46.11 3.91
1776 1855 5.376854 TGAACCAGAATTAGCTTTCTTGC 57.623 39.130 0.00 0.00 33.69 4.01
1777 1856 7.388460 AGATGAACCAGAATTAGCTTTCTTG 57.612 36.000 0.00 0.00 33.69 3.02
1778 1857 6.314896 CGAGATGAACCAGAATTAGCTTTCTT 59.685 38.462 0.00 0.00 33.69 2.52
1779 1858 5.814705 CGAGATGAACCAGAATTAGCTTTCT 59.185 40.000 0.00 0.00 36.38 2.52
1780 1859 5.007136 CCGAGATGAACCAGAATTAGCTTTC 59.993 44.000 0.00 0.00 0.00 2.62
1781 1860 4.878397 CCGAGATGAACCAGAATTAGCTTT 59.122 41.667 0.00 0.00 0.00 3.51
1782 1861 4.446371 CCGAGATGAACCAGAATTAGCTT 58.554 43.478 0.00 0.00 0.00 3.74
1784 1863 3.134458 CCCGAGATGAACCAGAATTAGC 58.866 50.000 0.00 0.00 0.00 3.09
1803 1900 0.326332 AGGGAGTACTAACCAGCCCC 60.326 60.000 16.13 11.20 34.21 5.80
1883 1980 8.852671 TCCCTCCATTCCAAAATAAATGTATT 57.147 30.769 0.00 0.00 32.20 1.89
1884 1981 8.067488 ACTCCCTCCATTCCAAAATAAATGTAT 58.933 33.333 0.00 0.00 32.20 2.29
1886 1983 6.263754 ACTCCCTCCATTCCAAAATAAATGT 58.736 36.000 0.00 0.00 32.20 2.71
1887 1984 6.796785 ACTCCCTCCATTCCAAAATAAATG 57.203 37.500 0.00 0.00 33.57 2.32
1888 1985 6.839134 GGTACTCCCTCCATTCCAAAATAAAT 59.161 38.462 0.00 0.00 0.00 1.40
1893 1990 3.265489 AGGTACTCCCTCCATTCCAAAA 58.735 45.455 0.00 0.00 40.71 2.44
1894 1991 2.929301 AGGTACTCCCTCCATTCCAAA 58.071 47.619 0.00 0.00 40.71 3.28
1895 1992 2.661176 AGGTACTCCCTCCATTCCAA 57.339 50.000 0.00 0.00 40.71 3.53
1896 1993 2.661176 AAGGTACTCCCTCCATTCCA 57.339 50.000 0.00 0.00 45.47 3.53
1897 1994 4.317530 AAAAAGGTACTCCCTCCATTCC 57.682 45.455 0.00 0.00 45.47 3.01
1923 2020 1.593196 TGCAAGACACGGGAGAAAAG 58.407 50.000 0.00 0.00 0.00 2.27
2032 2129 4.244425 TGGAGCTAGCTACGATTGATTC 57.756 45.455 22.04 3.67 0.00 2.52
2113 2210 8.839310 AATAAAGTTAGTGATAGCATAGCCAG 57.161 34.615 0.00 0.00 0.00 4.85
2191 2289 9.608617 CTACTCGTCGCTTATTATGAAGATTAA 57.391 33.333 0.00 0.00 0.00 1.40
2198 2296 4.084171 CGGTCTACTCGTCGCTTATTATGA 60.084 45.833 0.00 0.00 0.00 2.15
2309 2407 1.180456 TACGGAAGGGCTGTCGTTCA 61.180 55.000 15.51 0.00 40.81 3.18
2319 2417 0.320374 TGAGTGCTTGTACGGAAGGG 59.680 55.000 0.00 0.00 0.00 3.95
2442 2540 3.008375 CGGATGGGTCTTATGGTGATGAT 59.992 47.826 0.00 0.00 0.00 2.45
2563 2706 6.016276 TCTGAAACAAGTAAGGGAAAATCAGC 60.016 38.462 0.00 0.00 32.65 4.26
2594 2738 3.448093 TCATTGGCATTAAGGTGGACA 57.552 42.857 0.00 0.00 0.00 4.02
2675 2820 1.619827 TCCGTAACGAGGTGGTTCATT 59.380 47.619 0.00 0.00 0.00 2.57
2759 3743 4.439289 GGAAAGAATGGTTGCTACATGCTC 60.439 45.833 0.00 0.00 43.37 4.26



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

AutoCloner maintained by Alex Coulton.