Multiple sequence alignment - TraesCS1B01G259100

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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 TraesCS1B01G259100 chr1B 100.000 3662 0 0 1 3662 456434805 456431144 0.000000e+00 6763.0
1 TraesCS1B01G259100 chr1B 94.069 843 46 4 2816 3657 90269295 90268456 0.000000e+00 1277.0
2 TraesCS1B01G259100 chr1B 92.335 848 55 5 2816 3657 629943081 629943924 0.000000e+00 1197.0
3 TraesCS1B01G259100 chr1B 96.825 63 1 1 2754 2815 174107900 174107838 1.800000e-18 104.0
4 TraesCS1B01G259100 chr1B 95.161 62 2 1 2755 2815 364117465 364117404 3.010000e-16 97.1
5 TraesCS1B01G259100 chr1B 93.750 64 3 1 2753 2815 585539805 585539742 1.080000e-15 95.3
6 TraesCS1B01G259100 chr1A 95.929 1793 70 3 964 2753 440669802 440668010 0.000000e+00 2904.0
7 TraesCS1B01G259100 chr1A 91.200 250 14 5 964 1206 440673668 440673420 2.110000e-87 333.0
8 TraesCS1B01G259100 chr1A 95.455 66 3 0 835 900 440705339 440705274 5.000000e-19 106.0
9 TraesCS1B01G259100 chr1D 95.984 1718 66 1 964 2678 340983965 340982248 0.000000e+00 2787.0
10 TraesCS1B01G259100 chr1D 89.450 891 67 13 31 900 341022198 341021314 0.000000e+00 1099.0
11 TraesCS1B01G259100 chr1D 92.960 696 31 7 964 1656 341021278 341020598 0.000000e+00 998.0
12 TraesCS1B01G259100 chr1D 91.620 179 15 0 2567 2745 340902057 340901879 7.850000e-62 248.0
13 TraesCS1B01G259100 chr7D 94.836 1743 72 4 1011 2753 364627469 364629193 0.000000e+00 2704.0
14 TraesCS1B01G259100 chr7D 94.464 849 42 5 2814 3657 45126755 45127603 0.000000e+00 1303.0
15 TraesCS1B01G259100 chr7D 89.304 589 54 8 28 615 436862992 436863572 0.000000e+00 730.0
16 TraesCS1B01G259100 chr7D 86.613 620 73 8 3 618 368008061 368008674 0.000000e+00 676.0
17 TraesCS1B01G259100 chr6B 93.042 848 49 6 2815 3657 695268288 695269130 0.000000e+00 1230.0
18 TraesCS1B01G259100 chr6B 92.527 843 60 2 2816 3657 25970346 25971186 0.000000e+00 1205.0
19 TraesCS1B01G259100 chr6B 75.373 1543 300 60 1133 2631 615092506 615091000 0.000000e+00 671.0
20 TraesCS1B01G259100 chr7B 92.417 844 60 3 2815 3657 639678797 639677957 0.000000e+00 1201.0
21 TraesCS1B01G259100 chr7B 95.161 62 2 1 2755 2815 475659716 475659655 3.010000e-16 97.1
22 TraesCS1B01G259100 chr4B 92.335 848 58 6 2815 3657 498924664 498925509 0.000000e+00 1199.0
23 TraesCS1B01G259100 chr4B 87.602 613 70 6 1 612 138606338 138605731 0.000000e+00 706.0
24 TraesCS1B01G259100 chr4B 92.308 65 4 1 2752 2815 64302913 64302977 1.400000e-14 91.6
25 TraesCS1B01G259100 chr4B 92.308 65 4 1 2752 2815 64308742 64308806 1.400000e-14 91.6
26 TraesCS1B01G259100 chrUn 92.521 829 50 10 2838 3657 83965013 83965838 0.000000e+00 1177.0
27 TraesCS1B01G259100 chrUn 93.548 62 3 1 2755 2815 103517773 103517712 1.400000e-14 91.6
28 TraesCS1B01G259100 chr5B 80.408 1567 264 25 1163 2700 376523189 376521637 0.000000e+00 1153.0
29 TraesCS1B01G259100 chr5B 91.647 838 63 6 2821 3657 596913667 596912836 0.000000e+00 1153.0
30 TraesCS1B01G259100 chr5B 86.864 609 74 5 6 612 46157961 46158565 0.000000e+00 676.0
31 TraesCS1B01G259100 chr3D 75.075 1665 344 46 1050 2674 562178436 562180069 0.000000e+00 710.0
32 TraesCS1B01G259100 chr3D 74.422 1599 356 47 1046 2631 338581190 338582748 3.990000e-179 638.0
33 TraesCS1B01G259100 chr4D 88.699 584 61 4 31 614 433822390 433821812 0.000000e+00 708.0
34 TraesCS1B01G259100 chr3B 75.246 1628 326 48 1050 2631 749484905 749486501 0.000000e+00 702.0
35 TraesCS1B01G259100 chr5D 88.640 581 57 8 31 608 134665200 134664626 0.000000e+00 699.0
36 TraesCS1B01G259100 chr5D 88.225 586 64 5 28 612 331066616 331067197 0.000000e+00 695.0
37 TraesCS1B01G259100 chr6D 75.105 1663 326 49 1053 2671 100346087 100347705 0.000000e+00 697.0
38 TraesCS1B01G259100 chr6D 87.817 591 67 4 6 596 16571271 16571856 0.000000e+00 688.0
39 TraesCS1B01G259100 chr6D 74.905 1586 302 69 1102 2631 409493445 409491900 1.430000e-178 636.0
40 TraesCS1B01G259100 chr6D 75.385 1235 248 41 1424 2631 410150600 410149395 2.490000e-151 545.0
41 TraesCS1B01G259100 chr2B 88.144 582 65 3 31 612 217522385 217522962 0.000000e+00 689.0
42 TraesCS1B01G259100 chr2B 74.911 1686 330 59 991 2631 549249359 549247722 0.000000e+00 684.0
43 TraesCS1B01G259100 chr2D 74.599 1622 332 55 1062 2631 470240410 470238817 1.110000e-179 640.0
44 TraesCS1B01G259100 chr2D 77.064 218 42 7 1130 1340 608542641 608542857 6.420000e-23 119.0
45 TraesCS1B01G259100 chr6A 76.235 972 185 35 1689 2631 554839912 554838958 1.190000e-129 473.0
46 TraesCS1B01G259100 chr7A 96.774 62 1 1 2755 2815 495545847 495545786 6.470000e-18 102.0
47 TraesCS1B01G259100 chr4A 93.651 63 3 1 2754 2815 624276761 624276699 3.890000e-15 93.5


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 TraesCS1B01G259100 chr1B 456431144 456434805 3661 True 6763.0 6763 100.0000 1 3662 1 chr1B.!!$R4 3661
1 TraesCS1B01G259100 chr1B 90268456 90269295 839 True 1277.0 1277 94.0690 2816 3657 1 chr1B.!!$R1 841
2 TraesCS1B01G259100 chr1B 629943081 629943924 843 False 1197.0 1197 92.3350 2816 3657 1 chr1B.!!$F1 841
3 TraesCS1B01G259100 chr1A 440668010 440673668 5658 True 1618.5 2904 93.5645 964 2753 2 chr1A.!!$R2 1789
4 TraesCS1B01G259100 chr1D 340982248 340983965 1717 True 2787.0 2787 95.9840 964 2678 1 chr1D.!!$R2 1714
5 TraesCS1B01G259100 chr1D 341020598 341022198 1600 True 1048.5 1099 91.2050 31 1656 2 chr1D.!!$R3 1625
6 TraesCS1B01G259100 chr7D 364627469 364629193 1724 False 2704.0 2704 94.8360 1011 2753 1 chr7D.!!$F2 1742
7 TraesCS1B01G259100 chr7D 45126755 45127603 848 False 1303.0 1303 94.4640 2814 3657 1 chr7D.!!$F1 843
8 TraesCS1B01G259100 chr7D 436862992 436863572 580 False 730.0 730 89.3040 28 615 1 chr7D.!!$F4 587
9 TraesCS1B01G259100 chr7D 368008061 368008674 613 False 676.0 676 86.6130 3 618 1 chr7D.!!$F3 615
10 TraesCS1B01G259100 chr6B 695268288 695269130 842 False 1230.0 1230 93.0420 2815 3657 1 chr6B.!!$F2 842
11 TraesCS1B01G259100 chr6B 25970346 25971186 840 False 1205.0 1205 92.5270 2816 3657 1 chr6B.!!$F1 841
12 TraesCS1B01G259100 chr6B 615091000 615092506 1506 True 671.0 671 75.3730 1133 2631 1 chr6B.!!$R1 1498
13 TraesCS1B01G259100 chr7B 639677957 639678797 840 True 1201.0 1201 92.4170 2815 3657 1 chr7B.!!$R2 842
14 TraesCS1B01G259100 chr4B 498924664 498925509 845 False 1199.0 1199 92.3350 2815 3657 1 chr4B.!!$F3 842
15 TraesCS1B01G259100 chr4B 138605731 138606338 607 True 706.0 706 87.6020 1 612 1 chr4B.!!$R1 611
16 TraesCS1B01G259100 chrUn 83965013 83965838 825 False 1177.0 1177 92.5210 2838 3657 1 chrUn.!!$F1 819
17 TraesCS1B01G259100 chr5B 376521637 376523189 1552 True 1153.0 1153 80.4080 1163 2700 1 chr5B.!!$R1 1537
18 TraesCS1B01G259100 chr5B 596912836 596913667 831 True 1153.0 1153 91.6470 2821 3657 1 chr5B.!!$R2 836
19 TraesCS1B01G259100 chr5B 46157961 46158565 604 False 676.0 676 86.8640 6 612 1 chr5B.!!$F1 606
20 TraesCS1B01G259100 chr3D 562178436 562180069 1633 False 710.0 710 75.0750 1050 2674 1 chr3D.!!$F2 1624
21 TraesCS1B01G259100 chr3D 338581190 338582748 1558 False 638.0 638 74.4220 1046 2631 1 chr3D.!!$F1 1585
22 TraesCS1B01G259100 chr4D 433821812 433822390 578 True 708.0 708 88.6990 31 614 1 chr4D.!!$R1 583
23 TraesCS1B01G259100 chr3B 749484905 749486501 1596 False 702.0 702 75.2460 1050 2631 1 chr3B.!!$F1 1581
24 TraesCS1B01G259100 chr5D 134664626 134665200 574 True 699.0 699 88.6400 31 608 1 chr5D.!!$R1 577
25 TraesCS1B01G259100 chr5D 331066616 331067197 581 False 695.0 695 88.2250 28 612 1 chr5D.!!$F1 584
26 TraesCS1B01G259100 chr6D 100346087 100347705 1618 False 697.0 697 75.1050 1053 2671 1 chr6D.!!$F2 1618
27 TraesCS1B01G259100 chr6D 16571271 16571856 585 False 688.0 688 87.8170 6 596 1 chr6D.!!$F1 590
28 TraesCS1B01G259100 chr6D 409491900 409493445 1545 True 636.0 636 74.9050 1102 2631 1 chr6D.!!$R1 1529
29 TraesCS1B01G259100 chr6D 410149395 410150600 1205 True 545.0 545 75.3850 1424 2631 1 chr6D.!!$R2 1207
30 TraesCS1B01G259100 chr2B 217522385 217522962 577 False 689.0 689 88.1440 31 612 1 chr2B.!!$F1 581
31 TraesCS1B01G259100 chr2B 549247722 549249359 1637 True 684.0 684 74.9110 991 2631 1 chr2B.!!$R1 1640
32 TraesCS1B01G259100 chr2D 470238817 470240410 1593 True 640.0 640 74.5990 1062 2631 1 chr2D.!!$R1 1569
33 TraesCS1B01G259100 chr6A 554838958 554839912 954 True 473.0 473 76.2350 1689 2631 1 chr6A.!!$R1 942

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
902 931 0.036199 TTGGGGCTGCATCAATTTGC 60.036 50.0 0.5 0.0 43.07 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2810 6931 0.248784 GCGTTATCGGCGTCCTAGTT 60.249 55.0 6.85 0.0 37.56 2.24 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
29 30 8.031864 GCTATGCTAATCTGCACTCTTCTAATA 58.968 37.037 0.00 0.00 46.33 0.98
49 50 9.190317 TCTAATACTTCAAGATGCTAGTCTTCA 57.810 33.333 0.00 0.00 36.33 3.02
125 127 7.906736 AGATATAGCCCCATTCCTTTGATACTA 59.093 37.037 0.00 0.00 0.00 1.82
166 168 7.268586 AGATTTGATGTAAGTCTTGCGAGTAT 58.731 34.615 0.00 0.00 32.01 2.12
174 176 7.324935 TGTAAGTCTTGCGAGTATTTTGGATA 58.675 34.615 0.00 0.00 0.00 2.59
192 194 3.864003 GGATAAGTACTCACGGTTGCTTC 59.136 47.826 0.00 0.00 0.00 3.86
197 199 0.246635 ACTCACGGTTGCTTCGCTAT 59.753 50.000 0.00 0.00 0.00 2.97
235 238 2.102420 ACCCGATTGTTGCGATCAGATA 59.898 45.455 0.00 0.00 0.00 1.98
251 254 1.133009 AGATAACGGATCCCAGGAGCT 60.133 52.381 6.06 0.00 34.80 4.09
253 256 2.464796 TAACGGATCCCAGGAGCTAA 57.535 50.000 6.06 0.00 0.00 3.09
257 260 1.879796 CGGATCCCAGGAGCTAAATGC 60.880 57.143 6.06 0.00 43.29 3.56
258 261 1.546548 GGATCCCAGGAGCTAAATGCC 60.547 57.143 0.00 0.00 44.23 4.40
276 281 1.080974 CACACCACCGACGACTACC 60.081 63.158 0.00 0.00 0.00 3.18
278 283 1.108727 ACACCACCGACGACTACCAA 61.109 55.000 0.00 0.00 0.00 3.67
399 404 4.714632 TGTTTGTGCTAGCCTTCTTAAGT 58.285 39.130 13.29 0.00 0.00 2.24
427 434 8.526147 GGACTTGTTTACCTTATGTCTGTACTA 58.474 37.037 0.00 0.00 0.00 1.82
497 518 4.762251 CCCCTGGCTTGTAATATAAAGCTC 59.238 45.833 14.07 7.78 46.42 4.09
533 554 3.792401 TGTGTCTAGAGTTGTGTTGTGG 58.208 45.455 0.00 0.00 0.00 4.17
539 560 6.094061 GTCTAGAGTTGTGTTGTGGTATCTC 58.906 44.000 0.00 0.00 0.00 2.75
640 663 9.099454 CTCCTAACAAATAGAAAGGTACATGTC 57.901 37.037 0.00 0.00 33.04 3.06
641 664 8.044908 TCCTAACAAATAGAAAGGTACATGTCC 58.955 37.037 0.00 3.73 33.04 4.02
642 665 8.047310 CCTAACAAATAGAAAGGTACATGTCCT 58.953 37.037 0.00 6.31 33.41 3.85
675 704 7.542130 GGACAATCACAAGTACATCAAATTTCC 59.458 37.037 0.00 0.00 0.00 3.13
687 716 3.658709 TCAAATTTCCGTGGATTTTGCC 58.341 40.909 15.03 0.00 32.47 4.52
702 731 6.825721 TGGATTTTGCCACAAGTTACAAAAAT 59.174 30.769 11.74 0.00 43.07 1.82
708 737 7.283625 TGCCACAAGTTACAAAAATGTATCT 57.716 32.000 0.00 0.00 0.00 1.98
790 819 2.349438 CGTGTGTGTGCAGTAATTCCAC 60.349 50.000 0.00 0.00 0.00 4.02
871 900 4.735662 TCGTGGGAACAAAATAAGAACG 57.264 40.909 0.00 0.00 46.06 3.95
900 929 3.613030 GAATTTGGGGCTGCATCAATTT 58.387 40.909 0.50 7.81 0.00 1.82
901 930 2.476126 TTTGGGGCTGCATCAATTTG 57.524 45.000 0.50 0.00 0.00 2.32
902 931 0.036199 TTGGGGCTGCATCAATTTGC 60.036 50.000 0.50 0.00 43.07 3.68
903 932 1.153309 GGGGCTGCATCAATTTGCC 60.153 57.895 0.50 2.37 42.06 4.52
904 933 4.526770 GGCTGCATCAATTTGCCC 57.473 55.556 0.50 0.00 42.06 5.36
905 934 1.597989 GGCTGCATCAATTTGCCCA 59.402 52.632 0.50 0.00 42.06 5.36
906 935 0.179468 GGCTGCATCAATTTGCCCAT 59.821 50.000 0.50 0.00 42.06 4.00
908 937 1.295792 CTGCATCAATTTGCCCATGC 58.704 50.000 12.31 12.31 42.06 4.06
909 938 0.107606 TGCATCAATTTGCCCATGCC 60.108 50.000 15.13 3.21 40.86 4.40
910 939 0.816421 GCATCAATTTGCCCATGCCC 60.816 55.000 9.33 0.00 36.44 5.36
912 941 0.620990 ATCAATTTGCCCATGCCCCA 60.621 50.000 0.00 0.00 36.33 4.96
914 943 1.080722 AATTTGCCCATGCCCCAGA 59.919 52.632 0.00 0.00 36.33 3.86
915 944 0.547229 AATTTGCCCATGCCCCAGAA 60.547 50.000 0.00 0.00 36.33 3.02
917 946 1.193462 TTTGCCCATGCCCCAGAAAG 61.193 55.000 0.00 0.00 36.33 2.62
918 947 2.037847 GCCCATGCCCCAGAAAGT 59.962 61.111 0.00 0.00 0.00 2.66
919 948 2.054453 GCCCATGCCCCAGAAAGTC 61.054 63.158 0.00 0.00 0.00 3.01
920 949 1.750399 CCCATGCCCCAGAAAGTCG 60.750 63.158 0.00 0.00 0.00 4.18
921 950 1.002134 CCATGCCCCAGAAAGTCGT 60.002 57.895 0.00 0.00 0.00 4.34
922 951 1.026718 CCATGCCCCAGAAAGTCGTC 61.027 60.000 0.00 0.00 0.00 4.20
923 952 1.079127 ATGCCCCAGAAAGTCGTCG 60.079 57.895 0.00 0.00 0.00 5.12
924 953 2.434359 GCCCCAGAAAGTCGTCGG 60.434 66.667 0.00 0.00 0.00 4.79
925 954 2.264794 CCCCAGAAAGTCGTCGGG 59.735 66.667 0.00 0.00 36.59 5.14
926 955 2.434359 CCCAGAAAGTCGTCGGGC 60.434 66.667 0.00 0.00 32.04 6.13
927 956 2.434359 CCAGAAAGTCGTCGGGCC 60.434 66.667 0.00 0.00 0.00 5.80
929 958 1.079127 CAGAAAGTCGTCGGGCCAT 60.079 57.895 4.39 0.00 0.00 4.40
930 959 0.673644 CAGAAAGTCGTCGGGCCATT 60.674 55.000 4.39 0.00 0.00 3.16
931 960 0.673644 AGAAAGTCGTCGGGCCATTG 60.674 55.000 4.39 0.00 0.00 2.82
932 961 2.253414 GAAAGTCGTCGGGCCATTGC 62.253 60.000 4.39 0.00 0.00 3.56
934 963 3.499737 GTCGTCGGGCCATTGCTG 61.500 66.667 4.39 0.00 37.74 4.41
942 971 2.999063 GCCATTGCTGCCCCTGTT 60.999 61.111 0.00 0.00 33.53 3.16
943 972 2.586293 GCCATTGCTGCCCCTGTTT 61.586 57.895 0.00 0.00 33.53 2.83
944 973 2.060370 CCATTGCTGCCCCTGTTTT 58.940 52.632 0.00 0.00 0.00 2.43
945 974 0.320946 CCATTGCTGCCCCTGTTTTG 60.321 55.000 0.00 0.00 0.00 2.44
946 975 0.393820 CATTGCTGCCCCTGTTTTGT 59.606 50.000 0.00 0.00 0.00 2.83
947 976 1.130777 ATTGCTGCCCCTGTTTTGTT 58.869 45.000 0.00 0.00 0.00 2.83
948 977 0.463620 TTGCTGCCCCTGTTTTGTTC 59.536 50.000 0.00 0.00 0.00 3.18
949 978 1.007387 GCTGCCCCTGTTTTGTTCG 60.007 57.895 0.00 0.00 0.00 3.95
950 979 1.007387 CTGCCCCTGTTTTGTTCGC 60.007 57.895 0.00 0.00 0.00 4.70
951 980 1.454847 TGCCCCTGTTTTGTTCGCT 60.455 52.632 0.00 0.00 0.00 4.93
952 981 1.040339 TGCCCCTGTTTTGTTCGCTT 61.040 50.000 0.00 0.00 0.00 4.68
953 982 0.597377 GCCCCTGTTTTGTTCGCTTG 60.597 55.000 0.00 0.00 0.00 4.01
954 983 1.028905 CCCCTGTTTTGTTCGCTTGA 58.971 50.000 0.00 0.00 0.00 3.02
955 984 1.407258 CCCCTGTTTTGTTCGCTTGAA 59.593 47.619 0.00 0.00 0.00 2.69
956 985 2.159170 CCCCTGTTTTGTTCGCTTGAAA 60.159 45.455 0.00 0.00 32.31 2.69
957 986 3.115554 CCCTGTTTTGTTCGCTTGAAAG 58.884 45.455 0.00 0.00 32.31 2.62
995 1024 2.093973 TCAAGAATCGGAGAGGTTCAGC 60.094 50.000 0.00 0.00 42.37 4.26
1206 5139 2.748798 CGATCTCCTCCTTTCGGTCCTA 60.749 54.545 0.00 0.00 0.00 2.94
1416 5395 2.194056 CGGGAGCTCATGCCCAAT 59.806 61.111 17.19 0.00 44.94 3.16
2508 6603 1.528129 TGCGCCATGTCACAATGTTA 58.472 45.000 4.18 0.00 0.00 2.41
2532 6630 2.331893 CGGGCATGCTCGGAACAAA 61.332 57.895 32.24 0.00 36.08 2.83
2729 6850 9.604626 GCACATGCTTCTTTGTAATCTATATTC 57.395 33.333 0.00 0.00 38.21 1.75
2730 6851 9.803130 CACATGCTTCTTTGTAATCTATATTCG 57.197 33.333 0.00 0.00 0.00 3.34
2763 6884 8.826765 TGGAATTTATAATCTCATACTCCCTCC 58.173 37.037 0.00 0.00 0.00 4.30
2764 6885 7.982354 GGAATTTATAATCTCATACTCCCTCCG 59.018 40.741 0.00 0.00 0.00 4.63
2765 6886 8.437274 AATTTATAATCTCATACTCCCTCCGT 57.563 34.615 0.00 0.00 0.00 4.69
2766 6887 7.463961 TTTATAATCTCATACTCCCTCCGTC 57.536 40.000 0.00 0.00 0.00 4.79
2767 6888 3.314307 AATCTCATACTCCCTCCGTCA 57.686 47.619 0.00 0.00 0.00 4.35
2768 6889 2.350057 TCTCATACTCCCTCCGTCAG 57.650 55.000 0.00 0.00 0.00 3.51
2769 6890 1.133761 TCTCATACTCCCTCCGTCAGG 60.134 57.143 0.00 0.00 43.01 3.86
2782 6903 4.386867 TCCGTCAGGAAATACTGTCATC 57.613 45.455 0.00 0.00 45.12 2.92
2783 6904 3.767131 TCCGTCAGGAAATACTGTCATCA 59.233 43.478 0.00 0.00 45.12 3.07
2784 6905 4.221924 TCCGTCAGGAAATACTGTCATCAA 59.778 41.667 0.00 0.00 45.12 2.57
2785 6906 4.935205 CCGTCAGGAAATACTGTCATCAAA 59.065 41.667 0.00 0.00 41.02 2.69
2786 6907 5.411361 CCGTCAGGAAATACTGTCATCAAAA 59.589 40.000 0.00 0.00 41.02 2.44
2787 6908 6.094048 CCGTCAGGAAATACTGTCATCAAAAT 59.906 38.462 0.00 0.00 41.02 1.82
2788 6909 6.963242 CGTCAGGAAATACTGTCATCAAAATG 59.037 38.462 0.00 0.00 39.48 2.32
2789 6910 7.253422 GTCAGGAAATACTGTCATCAAAATGG 58.747 38.462 0.00 0.00 39.48 3.16
2790 6911 7.121168 GTCAGGAAATACTGTCATCAAAATGGA 59.879 37.037 0.00 0.00 39.48 3.41
2791 6912 7.835682 TCAGGAAATACTGTCATCAAAATGGAT 59.164 33.333 0.00 0.00 39.48 3.41
2792 6913 7.919091 CAGGAAATACTGTCATCAAAATGGATG 59.081 37.037 0.00 0.00 44.78 3.51
2807 6928 9.690913 TCAAAATGGATGAAAAGAGATGTATCT 57.309 29.630 0.00 0.00 40.50 1.98
2869 6993 2.807247 GGTCTGCCCACACAGTTTT 58.193 52.632 0.00 0.00 38.84 2.43
2968 7102 1.919816 TCCCTCTCACATGCCTGCA 60.920 57.895 0.00 0.00 0.00 4.41
3035 7169 2.186903 CTTATGGTCCCGCACGCT 59.813 61.111 0.00 0.00 0.00 5.07
3099 7233 4.463539 TGGACCATCTTCCATGTTCATTTG 59.536 41.667 0.00 0.00 41.00 2.32
3242 7377 5.308759 ACTTTAGGAGTTGCCACCTACTAAA 59.691 40.000 6.52 6.52 41.08 1.85
3259 7394 5.153950 ACTAAAACTAGGCAGTTGAGAGG 57.846 43.478 13.71 4.51 44.41 3.69
3333 7472 1.270041 TGTCATCTGCTTACGTGCACA 60.270 47.619 18.64 0.00 38.12 4.57
3346 7486 1.960763 TGCACACTAGGCAGTTGCG 60.961 57.895 0.00 0.00 43.26 4.85
3445 7585 2.621055 GTGTACCCTGCAAAACACATGA 59.379 45.455 0.00 0.00 41.43 3.07
3446 7586 3.067461 GTGTACCCTGCAAAACACATGAA 59.933 43.478 0.00 0.00 41.43 2.57
3585 7726 4.760047 GCGTGTGGGCGAGATGGT 62.760 66.667 0.00 0.00 0.00 3.55
3608 7749 3.166434 CCCACACACCAGCCCTTA 58.834 61.111 0.00 0.00 0.00 2.69
3657 7799 0.250727 ACTGCTAAACGCCCACACAT 60.251 50.000 0.00 0.00 38.05 3.21
3658 7800 0.881118 CTGCTAAACGCCCACACATT 59.119 50.000 0.00 0.00 38.05 2.71
3659 7801 0.595588 TGCTAAACGCCCACACATTG 59.404 50.000 0.00 0.00 38.05 2.82
3660 7802 0.109319 GCTAAACGCCCACACATTGG 60.109 55.000 0.00 0.00 46.47 3.16
3661 7803 0.109319 CTAAACGCCCACACATTGGC 60.109 55.000 0.00 0.00 45.37 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.271511 CCTATTGAAGACTAGCATCTTGAAGT 58.728 38.462 0.56 0.00 39.08 3.01
49 50 5.534070 AGAGAAGGGAAAGTCTAGCCTATT 58.466 41.667 0.00 0.00 0.00 1.73
59 60 2.057922 TGCCAGAAGAGAAGGGAAAGT 58.942 47.619 0.00 0.00 0.00 2.66
95 97 5.930209 AAGGAATGGGGCTATATCTTTGA 57.070 39.130 0.00 0.00 0.00 2.69
136 138 7.386573 TCGCAAGACTTACATCAAATCTAAACA 59.613 33.333 0.00 0.00 45.01 2.83
166 168 4.453136 GCAACCGTGAGTACTTATCCAAAA 59.547 41.667 0.00 0.00 0.00 2.44
174 176 1.779569 CGAAGCAACCGTGAGTACTT 58.220 50.000 0.00 0.00 0.00 2.24
192 194 0.551396 AGGGGAAAAAGGGGATAGCG 59.449 55.000 0.00 0.00 0.00 4.26
197 199 2.505987 GGGTATAGGGGAAAAAGGGGA 58.494 52.381 0.00 0.00 0.00 4.81
235 238 1.580059 TTTAGCTCCTGGGATCCGTT 58.420 50.000 5.45 0.00 0.00 4.44
251 254 0.951525 CGTCGGTGGTGTGGCATTTA 60.952 55.000 0.00 0.00 0.00 1.40
253 256 2.668212 CGTCGGTGGTGTGGCATT 60.668 61.111 0.00 0.00 0.00 3.56
257 260 1.080974 GTAGTCGTCGGTGGTGTGG 60.081 63.158 0.00 0.00 0.00 4.17
258 261 1.080974 GGTAGTCGTCGGTGGTGTG 60.081 63.158 0.00 0.00 0.00 3.82
315 320 3.066900 CCTCCTAACTACTCATGGTCGTG 59.933 52.174 0.00 0.00 0.00 4.35
323 328 1.644337 TGGGAGCCTCCTAACTACTCA 59.356 52.381 11.29 0.00 36.57 3.41
359 364 6.021074 CACAAACATCAACAACGATCGAAAAA 60.021 34.615 24.34 2.09 0.00 1.94
399 404 5.011329 ACAGACATAAGGTAAACAAGTCCGA 59.989 40.000 0.00 0.00 0.00 4.55
465 486 3.239627 AAGCCAGGGGTCTCGAGGA 62.240 63.158 13.56 0.00 0.00 3.71
497 518 9.355215 ACTCTAGACACAAATTAAAGTCATACG 57.645 33.333 0.00 0.00 33.56 3.06
533 554 0.535553 AGAGACTCGCGGGGAGATAC 60.536 60.000 26.41 16.48 46.23 2.24
539 560 1.388065 AAGATCAGAGACTCGCGGGG 61.388 60.000 12.42 4.49 0.00 5.73
586 607 3.301794 TGCCCAGACTTAATCATGCAT 57.698 42.857 0.00 0.00 0.00 3.96
601 622 1.555075 GTTAGGAGAGTGTGATGCCCA 59.445 52.381 0.00 0.00 0.00 5.36
640 663 2.566833 TGTGATTGTCCCAGTCAAGG 57.433 50.000 0.00 0.00 32.25 3.61
641 664 3.480470 ACTTGTGATTGTCCCAGTCAAG 58.520 45.455 0.00 0.00 32.25 3.02
642 665 3.576078 ACTTGTGATTGTCCCAGTCAA 57.424 42.857 0.00 0.00 32.25 3.18
656 685 5.049060 TCCACGGAAATTTGATGTACTTGTG 60.049 40.000 0.00 0.00 0.00 3.33
687 716 9.760660 GAGCTAGATACATTTTTGTAACTTGTG 57.239 33.333 0.00 0.00 31.39 3.33
727 756 3.191371 GCTGTCATGTTCAGGTTTAAGGG 59.809 47.826 17.26 0.00 33.98 3.95
733 762 2.346766 TGTGCTGTCATGTTCAGGTT 57.653 45.000 17.26 0.00 33.98 3.50
871 900 3.460868 CCCCAAATTCCCTGCCGC 61.461 66.667 0.00 0.00 0.00 6.53
900 929 2.037687 CTTTCTGGGGCATGGGCA 59.962 61.111 0.00 0.00 43.71 5.36
901 930 2.037847 ACTTTCTGGGGCATGGGC 59.962 61.111 0.00 0.00 40.13 5.36
902 931 1.750399 CGACTTTCTGGGGCATGGG 60.750 63.158 0.00 0.00 0.00 4.00
903 932 1.002134 ACGACTTTCTGGGGCATGG 60.002 57.895 0.00 0.00 0.00 3.66
904 933 1.361668 CGACGACTTTCTGGGGCATG 61.362 60.000 0.00 0.00 0.00 4.06
905 934 1.079127 CGACGACTTTCTGGGGCAT 60.079 57.895 0.00 0.00 0.00 4.40
906 935 2.342279 CGACGACTTTCTGGGGCA 59.658 61.111 0.00 0.00 0.00 5.36
908 937 2.264794 CCCGACGACTTTCTGGGG 59.735 66.667 0.00 0.00 36.16 4.96
909 938 2.434359 GCCCGACGACTTTCTGGG 60.434 66.667 0.00 0.00 43.02 4.45
910 939 2.434359 GGCCCGACGACTTTCTGG 60.434 66.667 0.00 0.00 0.00 3.86
912 941 0.673644 CAATGGCCCGACGACTTTCT 60.674 55.000 0.00 0.00 0.00 2.52
914 943 2.332654 GCAATGGCCCGACGACTTT 61.333 57.895 0.00 0.00 0.00 2.66
915 944 2.746277 GCAATGGCCCGACGACTT 60.746 61.111 0.00 0.00 0.00 3.01
917 946 3.499737 CAGCAATGGCCCGACGAC 61.500 66.667 0.00 0.00 42.56 4.34
925 954 2.115734 AAAACAGGGGCAGCAATGGC 62.116 55.000 0.00 0.00 41.61 4.40
926 955 0.320946 CAAAACAGGGGCAGCAATGG 60.321 55.000 0.00 0.00 0.00 3.16
927 956 0.393820 ACAAAACAGGGGCAGCAATG 59.606 50.000 0.00 0.00 0.00 2.82
929 958 0.463620 GAACAAAACAGGGGCAGCAA 59.536 50.000 0.00 0.00 0.00 3.91
930 959 1.733402 CGAACAAAACAGGGGCAGCA 61.733 55.000 0.00 0.00 0.00 4.41
931 960 1.007387 CGAACAAAACAGGGGCAGC 60.007 57.895 0.00 0.00 0.00 5.25
932 961 1.007387 GCGAACAAAACAGGGGCAG 60.007 57.895 0.00 0.00 0.00 4.85
934 963 0.597377 CAAGCGAACAAAACAGGGGC 60.597 55.000 0.00 0.00 0.00 5.80
935 964 1.028905 TCAAGCGAACAAAACAGGGG 58.971 50.000 0.00 0.00 0.00 4.79
936 965 2.861462 TTCAAGCGAACAAAACAGGG 57.139 45.000 0.00 0.00 0.00 4.45
937 966 2.535574 GCTTTCAAGCGAACAAAACAGG 59.464 45.455 0.00 0.00 42.88 4.00
938 967 3.823716 GCTTTCAAGCGAACAAAACAG 57.176 42.857 0.00 0.00 42.88 3.16
950 979 4.932200 ACAGAGACGGATTTAGCTTTCAAG 59.068 41.667 0.00 0.00 0.00 3.02
951 980 4.894784 ACAGAGACGGATTTAGCTTTCAA 58.105 39.130 0.00 0.00 0.00 2.69
952 981 4.537135 ACAGAGACGGATTTAGCTTTCA 57.463 40.909 0.00 0.00 0.00 2.69
953 982 4.929808 TGAACAGAGACGGATTTAGCTTTC 59.070 41.667 0.00 0.00 0.00 2.62
954 983 4.894784 TGAACAGAGACGGATTTAGCTTT 58.105 39.130 0.00 0.00 0.00 3.51
955 984 4.537135 TGAACAGAGACGGATTTAGCTT 57.463 40.909 0.00 0.00 0.00 3.74
956 985 4.220821 TCTTGAACAGAGACGGATTTAGCT 59.779 41.667 0.00 0.00 0.00 3.32
957 986 4.495422 TCTTGAACAGAGACGGATTTAGC 58.505 43.478 0.00 0.00 0.00 3.09
958 987 6.020281 CGATTCTTGAACAGAGACGGATTTAG 60.020 42.308 0.00 0.00 31.12 1.85
959 988 5.805486 CGATTCTTGAACAGAGACGGATTTA 59.195 40.000 0.00 0.00 31.12 1.40
960 989 4.627467 CGATTCTTGAACAGAGACGGATTT 59.373 41.667 0.00 0.00 31.12 2.17
961 990 4.177026 CGATTCTTGAACAGAGACGGATT 58.823 43.478 0.00 0.00 31.12 3.01
962 991 3.429547 CCGATTCTTGAACAGAGACGGAT 60.430 47.826 0.00 0.00 46.23 4.18
1416 5395 1.133598 CGGTGCTCGTACCTTGTGATA 59.866 52.381 2.77 0.00 38.62 2.15
2311 6385 0.836400 ATGTGGACGTGGAGGGTCTT 60.836 55.000 0.00 0.00 34.82 3.01
2508 6603 2.436646 CGAGCATGCCCGTTCCTT 60.437 61.111 14.08 0.00 0.00 3.36
2532 6630 4.270153 TCCCAGTCCCAGTGCCCT 62.270 66.667 0.00 0.00 0.00 5.19
2745 6866 4.999310 TGACGGAGGGAGTATGAGATTAT 58.001 43.478 0.00 0.00 0.00 1.28
2753 6874 2.544844 TTTCCTGACGGAGGGAGTAT 57.455 50.000 3.12 0.00 43.06 2.12
2754 6875 2.544844 ATTTCCTGACGGAGGGAGTA 57.455 50.000 3.12 0.00 43.06 2.59
2755 6876 2.108970 GTATTTCCTGACGGAGGGAGT 58.891 52.381 3.12 0.00 43.06 3.85
2756 6877 2.101582 CAGTATTTCCTGACGGAGGGAG 59.898 54.545 3.12 0.00 43.06 4.30
2757 6878 2.108168 CAGTATTTCCTGACGGAGGGA 58.892 52.381 3.12 0.00 43.06 4.20
2758 6879 1.831736 ACAGTATTTCCTGACGGAGGG 59.168 52.381 3.12 0.00 43.06 4.30
2759 6880 2.496070 TGACAGTATTTCCTGACGGAGG 59.504 50.000 0.00 0.00 44.45 4.30
2760 6881 3.868757 TGACAGTATTTCCTGACGGAG 57.131 47.619 0.00 0.00 41.25 4.63
2761 6882 3.767131 TGATGACAGTATTTCCTGACGGA 59.233 43.478 0.00 0.00 37.60 4.69
2762 6883 4.123497 TGATGACAGTATTTCCTGACGG 57.877 45.455 0.00 0.00 36.30 4.79
2763 6884 6.480524 TTTTGATGACAGTATTTCCTGACG 57.519 37.500 0.00 0.00 36.30 4.35
2764 6885 7.121168 TCCATTTTGATGACAGTATTTCCTGAC 59.879 37.037 0.00 0.00 36.30 3.51
2765 6886 7.174413 TCCATTTTGATGACAGTATTTCCTGA 58.826 34.615 0.00 0.00 36.30 3.86
2766 6887 7.395190 TCCATTTTGATGACAGTATTTCCTG 57.605 36.000 0.00 0.00 38.45 3.86
2767 6888 7.835682 TCATCCATTTTGATGACAGTATTTCCT 59.164 33.333 0.00 0.00 44.65 3.36
2768 6889 7.999679 TCATCCATTTTGATGACAGTATTTCC 58.000 34.615 0.00 0.00 44.65 3.13
2781 6902 9.690913 AGATACATCTCTTTTCATCCATTTTGA 57.309 29.630 0.00 0.00 29.30 2.69
2793 6914 9.804758 CGTCCTAGTTTTAGATACATCTCTTTT 57.195 33.333 0.00 0.00 38.32 2.27
2794 6915 7.921745 GCGTCCTAGTTTTAGATACATCTCTTT 59.078 37.037 0.00 0.00 38.32 2.52
2795 6916 7.427214 GCGTCCTAGTTTTAGATACATCTCTT 58.573 38.462 0.00 0.00 38.32 2.85
2796 6917 6.016108 GGCGTCCTAGTTTTAGATACATCTCT 60.016 42.308 0.00 0.00 38.32 3.10
2797 6918 6.151004 GGCGTCCTAGTTTTAGATACATCTC 58.849 44.000 0.00 0.00 38.32 2.75
2798 6919 5.278364 CGGCGTCCTAGTTTTAGATACATCT 60.278 44.000 0.00 0.00 40.86 2.90
2799 6920 4.916249 CGGCGTCCTAGTTTTAGATACATC 59.084 45.833 0.00 0.00 0.00 3.06
2800 6921 4.581824 TCGGCGTCCTAGTTTTAGATACAT 59.418 41.667 6.85 0.00 0.00 2.29
2801 6922 3.947196 TCGGCGTCCTAGTTTTAGATACA 59.053 43.478 6.85 0.00 0.00 2.29
2802 6923 4.558538 TCGGCGTCCTAGTTTTAGATAC 57.441 45.455 6.85 0.00 0.00 2.24
2803 6924 6.566564 CGTTATCGGCGTCCTAGTTTTAGATA 60.567 42.308 6.85 0.00 0.00 1.98
2804 6925 5.527033 GTTATCGGCGTCCTAGTTTTAGAT 58.473 41.667 6.85 0.00 0.00 1.98
2805 6926 4.496341 CGTTATCGGCGTCCTAGTTTTAGA 60.496 45.833 6.85 0.00 0.00 2.10
2806 6927 3.727723 CGTTATCGGCGTCCTAGTTTTAG 59.272 47.826 6.85 0.00 0.00 1.85
2807 6928 3.694734 CGTTATCGGCGTCCTAGTTTTA 58.305 45.455 6.85 0.00 0.00 1.52
2808 6929 2.533266 CGTTATCGGCGTCCTAGTTTT 58.467 47.619 6.85 0.00 0.00 2.43
2809 6930 1.800286 GCGTTATCGGCGTCCTAGTTT 60.800 52.381 6.85 0.00 37.56 2.66
2810 6931 0.248784 GCGTTATCGGCGTCCTAGTT 60.249 55.000 6.85 0.00 37.56 2.24
2811 6932 1.099879 AGCGTTATCGGCGTCCTAGT 61.100 55.000 6.85 0.00 37.56 2.57
2812 6933 0.385723 GAGCGTTATCGGCGTCCTAG 60.386 60.000 6.85 0.00 37.56 3.02
2869 6993 4.943705 GGCTGATCCTCTTAAACATCACAA 59.056 41.667 0.00 0.00 0.00 3.33
2942 7076 2.680352 GTGAGAGGGACCGCCAGA 60.680 66.667 0.00 0.00 35.15 3.86
2945 7079 2.187946 CATGTGAGAGGGACCGCC 59.812 66.667 0.00 0.00 0.00 6.13
2968 7102 3.317993 GGCGTTATCTATTTTGCCCACAT 59.682 43.478 0.00 0.00 36.51 3.21
3082 7216 7.170965 ACTACAGTCAAATGAACATGGAAGAT 58.829 34.615 0.00 0.00 0.00 2.40
3099 7233 0.721718 GCGACATGGCAACTACAGTC 59.278 55.000 0.00 0.00 37.61 3.51
3333 7472 1.134788 GGTACATCGCAACTGCCTAGT 60.135 52.381 0.00 0.00 39.32 2.57
3445 7585 5.838531 TTTTACCCGAACATGTCAGTTTT 57.161 34.783 0.00 0.00 0.00 2.43
3446 7586 5.838531 TTTTTACCCGAACATGTCAGTTT 57.161 34.783 0.00 0.00 0.00 2.66
3505 7646 1.979855 TGCAGTGTACATGGCAACTT 58.020 45.000 18.49 0.00 32.54 2.66
3585 7726 0.897863 GGCTGGTGTGTGGGCATTTA 60.898 55.000 0.00 0.00 0.00 1.40
3608 7749 2.548057 ACGTCAATTTTCACTCACGCAT 59.452 40.909 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.