Multiple sequence alignment - TraesCS5B01G185600

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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 TraesCS5B01G185600 chr5B 100.000 3830 0 0 1 3830 337167109 337163280 0.000000e+00 7073.0
1 TraesCS5B01G185600 chr5B 89.796 931 91 2 1608 2534 337181251 337180321 0.000000e+00 1190.0
2 TraesCS5B01G185600 chr5B 92.775 609 40 3 1 607 337183090 337182484 0.000000e+00 878.0
3 TraesCS5B01G185600 chr5B 85.938 704 89 3 913 1607 337181999 337181297 0.000000e+00 743.0
4 TraesCS5B01G185600 chr5B 94.079 152 9 0 757 908 337182493 337182342 8.270000e-57 231.0
5 TraesCS5B01G185600 chr5B 87.342 158 13 4 603 754 90979630 90979474 1.410000e-39 174.0
6 TraesCS5B01G185600 chr5A 93.430 1522 90 3 1608 3120 402101087 402102607 0.000000e+00 2248.0
7 TraesCS5B01G185600 chr5A 89.312 1338 102 18 2515 3830 402012720 402014038 0.000000e+00 1640.0
8 TraesCS5B01G185600 chr5A 94.842 853 41 2 757 1607 402100190 402101041 0.000000e+00 1328.0
9 TraesCS5B01G185600 chr5A 91.749 909 74 1 1608 2516 402003558 402004465 0.000000e+00 1262.0
10 TraesCS5B01G185600 chr5A 88.210 933 101 8 1608 2534 402095022 402095951 0.000000e+00 1105.0
11 TraesCS5B01G185600 chr5A 87.648 931 95 3 1608 2534 401964247 401965161 0.000000e+00 1064.0
12 TraesCS5B01G185600 chr5A 91.444 748 56 4 757 1504 402002415 402003154 0.000000e+00 1020.0
13 TraesCS5B01G185600 chr5A 94.563 607 31 1 1 607 402099595 402100199 0.000000e+00 937.0
14 TraesCS5B01G185600 chr5A 94.408 608 31 3 1 607 402001819 402002424 0.000000e+00 931.0
15 TraesCS5B01G185600 chr5A 86.147 859 102 8 757 1607 401963352 401964201 0.000000e+00 911.0
16 TraesCS5B01G185600 chr5A 93.081 607 39 2 1 607 401962758 401963361 0.000000e+00 885.0
17 TraesCS5B01G185600 chr5A 92.916 607 41 1 1 607 402093275 402093879 0.000000e+00 881.0
18 TraesCS5B01G185600 chr5A 86.170 658 91 0 950 1607 402094319 402094976 0.000000e+00 712.0
19 TraesCS5B01G185600 chr5A 87.500 608 51 15 3224 3830 402103187 402103770 0.000000e+00 678.0
20 TraesCS5B01G185600 chr5A 93.220 118 8 0 757 874 402093870 402093987 1.410000e-39 174.0
21 TraesCS5B01G185600 chr5A 89.916 119 9 1 641 756 695334684 695334802 2.380000e-32 150.0
22 TraesCS5B01G185600 chr5A 89.916 119 9 1 641 756 695359257 695359375 2.380000e-32 150.0
23 TraesCS5B01G185600 chr5A 89.916 119 9 1 641 756 695412401 695412519 2.380000e-32 150.0
24 TraesCS5B01G185600 chr5D 97.907 621 12 1 1 620 297118485 297117865 0.000000e+00 1074.0
25 TraesCS5B01G185600 chr5D 96.719 640 20 1 968 1607 297117383 297116745 0.000000e+00 1064.0
26 TraesCS5B01G185600 chr5D 84.810 1027 105 32 1530 2534 297122459 297121462 0.000000e+00 985.0
27 TraesCS5B01G185600 chr5D 94.389 606 32 1 2 607 297142968 297142365 0.000000e+00 929.0
28 TraesCS5B01G185600 chr5D 88.070 570 59 4 955 1523 297141728 297141167 0.000000e+00 667.0
29 TraesCS5B01G185600 chr5D 96.774 217 7 0 1608 1824 297116699 297116483 2.810000e-96 363.0
30 TraesCS5B01G185600 chr5D 95.092 163 8 0 744 906 297117868 297117706 1.370000e-64 257.0
31 TraesCS5B01G185600 chr5D 93.077 130 8 1 757 885 297142374 297142245 5.050000e-44 189.0
32 TraesCS5B01G185600 chr7B 79.104 1005 194 10 1671 2675 458453765 458454753 0.000000e+00 678.0
33 TraesCS5B01G185600 chr7B 74.797 492 106 7 3342 3817 113566846 113567335 5.020000e-49 206.0
34 TraesCS5B01G185600 chr1D 79.728 883 168 8 1601 2480 117982891 117982017 2.510000e-176 628.0
35 TraesCS5B01G185600 chr3B 81.212 660 121 2 1671 2329 586459196 586459853 2.620000e-146 529.0
36 TraesCS5B01G185600 chr3B 76.610 295 54 5 3486 3766 431125930 431125637 8.570000e-32 148.0
37 TraesCS5B01G185600 chr1A 75.923 623 126 21 1644 2255 115455758 115455149 8.040000e-77 298.0
38 TraesCS5B01G185600 chr2A 75.254 493 102 8 3342 3817 19115226 19115715 2.320000e-52 217.0
39 TraesCS5B01G185600 chr2A 75.000 496 104 8 3342 3820 349739529 349739037 1.080000e-50 211.0
40 TraesCS5B01G185600 chr3A 74.798 496 105 9 3342 3820 738106384 738105892 5.020000e-49 206.0
41 TraesCS5B01G185600 chr3A 85.093 161 12 6 608 762 80223497 80223651 1.840000e-33 154.0
42 TraesCS5B01G185600 chr3A 73.274 449 101 11 2681 3116 575094327 575093885 3.080000e-31 147.0
43 TraesCS5B01G185600 chr7A 74.645 493 105 8 3342 3817 712839069 712839558 2.330000e-47 200.0
44 TraesCS5B01G185600 chr7A 83.333 156 19 3 611 759 6788740 6788895 1.860000e-28 137.0
45 TraesCS5B01G185600 chr7A 76.613 124 27 2 3698 3820 303027167 303027289 2.470000e-07 67.6
46 TraesCS5B01G185600 chrUn 89.916 119 9 1 641 756 405674700 405674818 2.380000e-32 150.0
47 TraesCS5B01G185600 chrUn 91.818 110 6 1 650 756 414267207 414267098 2.380000e-32 150.0
48 TraesCS5B01G185600 chr3D 82.738 168 21 5 604 765 16509467 16509302 3.990000e-30 143.0


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 TraesCS5B01G185600 chr5B 337163280 337167109 3829 True 7073.000000 7073 100.000000 1 3830 1 chr5B.!!$R2 3829
1 TraesCS5B01G185600 chr5B 337180321 337183090 2769 True 760.500000 1190 90.647000 1 2534 4 chr5B.!!$R3 2533
2 TraesCS5B01G185600 chr5A 402012720 402014038 1318 False 1640.000000 1640 89.312000 2515 3830 1 chr5A.!!$F1 1315
3 TraesCS5B01G185600 chr5A 402001819 402004465 2646 False 1071.000000 1262 92.533667 1 2516 3 chr5A.!!$F6 2515
4 TraesCS5B01G185600 chr5A 402093275 402103770 10495 False 1007.875000 2248 91.356375 1 3830 8 chr5A.!!$F7 3829
5 TraesCS5B01G185600 chr5A 401962758 401965161 2403 False 953.333333 1064 88.958667 1 2534 3 chr5A.!!$F5 2533
6 TraesCS5B01G185600 chr5D 297116483 297122459 5976 True 748.600000 1074 94.260400 1 2534 5 chr5D.!!$R1 2533
7 TraesCS5B01G185600 chr5D 297141167 297142968 1801 True 595.000000 929 91.845333 2 1523 3 chr5D.!!$R2 1521
8 TraesCS5B01G185600 chr7B 458453765 458454753 988 False 678.000000 678 79.104000 1671 2675 1 chr7B.!!$F2 1004
9 TraesCS5B01G185600 chr1D 117982017 117982891 874 True 628.000000 628 79.728000 1601 2480 1 chr1D.!!$R1 879
10 TraesCS5B01G185600 chr3B 586459196 586459853 657 False 529.000000 529 81.212000 1671 2329 1 chr3B.!!$F1 658
11 TraesCS5B01G185600 chr1A 115455149 115455758 609 True 298.000000 298 75.923000 1644 2255 1 chr1A.!!$R1 611

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
750 7129 0.322546 AGTGGGGCAAAAGATCCGAC 60.323 55.0 0.00 0.0 0.0 4.79 F
1333 8165 0.389948 ACGCGAAGATGAACTCCACC 60.390 55.0 15.93 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 9472 0.105453 GCCCCTCTAGTGGATCCAGA 60.105 60.0 16.81 8.44 0.0 3.86 R
3312 10936 0.123266 ATTGGAGGAGGGGGAAAGGA 59.877 55.0 0.00 0.00 0.0 3.36 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
338 6714 4.747583 TCCTACCACTAGCCATAGCAATA 58.252 43.478 0.00 0.00 43.56 1.90
417 6793 5.128008 AGCCACATAACCTCTTCTTCTCTAC 59.872 44.000 0.00 0.00 0.00 2.59
620 6999 5.722172 TCCATTCTGGAGAAATTGGATCT 57.278 39.130 7.39 0.00 42.67 2.75
621 7000 6.083487 TCCATTCTGGAGAAATTGGATCTT 57.917 37.500 7.39 0.00 42.67 2.40
622 7001 6.496743 TCCATTCTGGAGAAATTGGATCTTT 58.503 36.000 7.39 0.00 42.67 2.52
624 7003 7.039882 CCATTCTGGAGAAATTGGATCTTTTG 58.960 38.462 3.75 0.00 40.96 2.44
625 7004 5.649782 TCTGGAGAAATTGGATCTTTTGC 57.350 39.130 0.00 0.00 0.00 3.68
626 7005 4.463891 TCTGGAGAAATTGGATCTTTTGCC 59.536 41.667 0.00 0.00 0.00 4.52
627 7006 4.158786 TGGAGAAATTGGATCTTTTGCCA 58.841 39.130 0.00 0.00 0.00 4.92
628 7007 4.221262 TGGAGAAATTGGATCTTTTGCCAG 59.779 41.667 0.00 0.00 35.23 4.85
629 7008 4.221482 GGAGAAATTGGATCTTTTGCCAGT 59.779 41.667 0.00 0.00 35.23 4.00
630 7009 5.279657 GGAGAAATTGGATCTTTTGCCAGTT 60.280 40.000 0.00 0.00 35.89 3.16
631 7010 6.178607 AGAAATTGGATCTTTTGCCAGTTT 57.821 33.333 0.00 0.00 43.84 2.66
632 7011 7.301868 AGAAATTGGATCTTTTGCCAGTTTA 57.698 32.000 0.00 0.00 42.04 2.01
633 7012 7.154656 AGAAATTGGATCTTTTGCCAGTTTAC 58.845 34.615 0.00 0.00 42.04 2.01
634 7013 6.670695 AATTGGATCTTTTGCCAGTTTACT 57.329 33.333 0.00 0.00 35.23 2.24
635 7014 6.670695 ATTGGATCTTTTGCCAGTTTACTT 57.329 33.333 0.00 0.00 35.23 2.24
636 7015 5.705609 TGGATCTTTTGCCAGTTTACTTC 57.294 39.130 0.00 0.00 0.00 3.01
637 7016 5.385198 TGGATCTTTTGCCAGTTTACTTCT 58.615 37.500 0.00 0.00 0.00 2.85
638 7017 5.473504 TGGATCTTTTGCCAGTTTACTTCTC 59.526 40.000 0.00 0.00 0.00 2.87
639 7018 5.106118 GGATCTTTTGCCAGTTTACTTCTCC 60.106 44.000 0.00 0.00 0.00 3.71
640 7019 4.787551 TCTTTTGCCAGTTTACTTCTCCA 58.212 39.130 0.00 0.00 0.00 3.86
641 7020 5.385198 TCTTTTGCCAGTTTACTTCTCCAT 58.615 37.500 0.00 0.00 0.00 3.41
642 7021 5.833131 TCTTTTGCCAGTTTACTTCTCCATT 59.167 36.000 0.00 0.00 0.00 3.16
643 7022 6.323739 TCTTTTGCCAGTTTACTTCTCCATTT 59.676 34.615 0.00 0.00 0.00 2.32
644 7023 5.452078 TTGCCAGTTTACTTCTCCATTTG 57.548 39.130 0.00 0.00 0.00 2.32
645 7024 4.724399 TGCCAGTTTACTTCTCCATTTGA 58.276 39.130 0.00 0.00 0.00 2.69
646 7025 5.324409 TGCCAGTTTACTTCTCCATTTGAT 58.676 37.500 0.00 0.00 0.00 2.57
647 7026 6.480763 TGCCAGTTTACTTCTCCATTTGATA 58.519 36.000 0.00 0.00 0.00 2.15
648 7027 6.945435 TGCCAGTTTACTTCTCCATTTGATAA 59.055 34.615 0.00 0.00 0.00 1.75
649 7028 7.615365 TGCCAGTTTACTTCTCCATTTGATAAT 59.385 33.333 0.00 0.00 0.00 1.28
650 7029 8.470002 GCCAGTTTACTTCTCCATTTGATAATT 58.530 33.333 0.00 0.00 0.00 1.40
653 7032 9.860898 AGTTTACTTCTCCATTTGATAATTTGC 57.139 29.630 0.00 0.00 0.00 3.68
654 7033 9.087424 GTTTACTTCTCCATTTGATAATTTGCC 57.913 33.333 0.00 0.00 0.00 4.52
655 7034 6.225981 ACTTCTCCATTTGATAATTTGCCC 57.774 37.500 0.00 0.00 0.00 5.36
656 7035 5.129320 ACTTCTCCATTTGATAATTTGCCCC 59.871 40.000 0.00 0.00 0.00 5.80
657 7036 3.966665 TCTCCATTTGATAATTTGCCCCC 59.033 43.478 0.00 0.00 0.00 5.40
677 7056 4.767255 GAGAGGCTGCCGTGTGGG 62.767 72.222 13.96 0.00 39.58 4.61
702 7081 2.644887 GCCACTTGCCATTGAGACA 58.355 52.632 0.00 0.00 0.00 3.41
703 7082 0.961019 GCCACTTGCCATTGAGACAA 59.039 50.000 0.00 0.00 0.00 3.18
704 7083 1.547372 GCCACTTGCCATTGAGACAAT 59.453 47.619 0.00 0.00 0.00 2.71
705 7084 2.673043 GCCACTTGCCATTGAGACAATG 60.673 50.000 14.94 14.94 0.00 2.82
707 7086 2.094390 CACTTGCCATTGAGACAATGGG 60.094 50.000 31.20 21.98 45.61 4.00
708 7087 1.479323 CTTGCCATTGAGACAATGGGG 59.521 52.381 31.20 16.55 45.61 4.96
709 7088 0.971959 TGCCATTGAGACAATGGGGC 60.972 55.000 31.20 23.06 45.61 5.80
710 7089 0.971959 GCCATTGAGACAATGGGGCA 60.972 55.000 31.20 0.00 45.61 5.36
711 7090 1.559368 CCATTGAGACAATGGGGCAA 58.441 50.000 26.36 0.00 42.63 4.52
712 7091 1.901159 CCATTGAGACAATGGGGCAAA 59.099 47.619 26.36 0.00 42.63 3.68
713 7092 2.502538 CCATTGAGACAATGGGGCAAAT 59.497 45.455 26.36 0.00 42.63 2.32
714 7093 3.431207 CCATTGAGACAATGGGGCAAATC 60.431 47.826 26.36 0.00 42.63 2.17
715 7094 2.601240 TGAGACAATGGGGCAAATCA 57.399 45.000 0.00 0.00 0.00 2.57
716 7095 3.104519 TGAGACAATGGGGCAAATCAT 57.895 42.857 0.00 0.00 0.00 2.45
717 7096 3.025978 TGAGACAATGGGGCAAATCATC 58.974 45.455 0.00 0.00 0.00 2.92
718 7097 3.025978 GAGACAATGGGGCAAATCATCA 58.974 45.455 0.00 0.00 0.00 3.07
719 7098 3.443052 AGACAATGGGGCAAATCATCAA 58.557 40.909 0.00 0.00 0.00 2.57
720 7099 3.839490 AGACAATGGGGCAAATCATCAAA 59.161 39.130 0.00 0.00 0.00 2.69
721 7100 3.934579 GACAATGGGGCAAATCATCAAAC 59.065 43.478 0.00 0.00 0.00 2.93
722 7101 3.272581 CAATGGGGCAAATCATCAAACC 58.727 45.455 0.00 0.00 0.00 3.27
723 7102 1.274712 TGGGGCAAATCATCAAACCC 58.725 50.000 0.00 0.00 37.20 4.11
725 7104 1.274712 GGGCAAATCATCAAACCCCA 58.725 50.000 0.00 0.00 0.00 4.96
726 7105 1.839354 GGGCAAATCATCAAACCCCAT 59.161 47.619 0.00 0.00 0.00 4.00
727 7106 2.420408 GGGCAAATCATCAAACCCCATG 60.420 50.000 0.00 0.00 0.00 3.66
728 7107 2.236893 GGCAAATCATCAAACCCCATGT 59.763 45.455 0.00 0.00 0.00 3.21
729 7108 3.450457 GGCAAATCATCAAACCCCATGTA 59.550 43.478 0.00 0.00 0.00 2.29
730 7109 4.081198 GGCAAATCATCAAACCCCATGTAA 60.081 41.667 0.00 0.00 0.00 2.41
731 7110 5.486526 GCAAATCATCAAACCCCATGTAAA 58.513 37.500 0.00 0.00 0.00 2.01
732 7111 5.581874 GCAAATCATCAAACCCCATGTAAAG 59.418 40.000 0.00 0.00 0.00 1.85
733 7112 6.700352 CAAATCATCAAACCCCATGTAAAGT 58.300 36.000 0.00 0.00 0.00 2.66
734 7113 5.920193 ATCATCAAACCCCATGTAAAGTG 57.080 39.130 0.00 0.00 0.00 3.16
735 7114 4.085733 TCATCAAACCCCATGTAAAGTGG 58.914 43.478 0.00 0.00 36.47 4.00
743 7122 3.317603 CCATGTAAAGTGGGGCAAAAG 57.682 47.619 0.00 0.00 32.98 2.27
744 7123 2.896685 CCATGTAAAGTGGGGCAAAAGA 59.103 45.455 0.00 0.00 32.98 2.52
745 7124 3.515104 CCATGTAAAGTGGGGCAAAAGAT 59.485 43.478 0.00 0.00 32.98 2.40
746 7125 4.381932 CCATGTAAAGTGGGGCAAAAGATC 60.382 45.833 0.00 0.00 32.98 2.75
747 7126 3.161866 TGTAAAGTGGGGCAAAAGATCC 58.838 45.455 0.00 0.00 0.00 3.36
748 7127 1.256812 AAAGTGGGGCAAAAGATCCG 58.743 50.000 0.00 0.00 0.00 4.18
749 7128 0.404040 AAGTGGGGCAAAAGATCCGA 59.596 50.000 0.00 0.00 0.00 4.55
750 7129 0.322546 AGTGGGGCAAAAGATCCGAC 60.323 55.000 0.00 0.00 0.00 4.79
791 7170 7.041372 GCCATCTGTCTTGTAAGTTTCTACAAA 60.041 37.037 0.00 0.00 40.38 2.83
841 7220 9.929180 TTAATTTAACCATCTAGATCATCTCGG 57.071 33.333 1.03 2.55 0.00 4.63
941 7669 2.205462 CCCTCGATCCCCTCCCAT 59.795 66.667 0.00 0.00 0.00 4.00
1260 8092 2.232298 GACTCCCTCTGCCTGGTTCG 62.232 65.000 0.00 0.00 0.00 3.95
1333 8165 0.389948 ACGCGAAGATGAACTCCACC 60.390 55.000 15.93 0.00 0.00 4.61
1344 8176 0.834687 AACTCCACCCCGAGCTACAA 60.835 55.000 0.00 0.00 32.79 2.41
1351 8183 4.430765 CCGAGCTACAACGCCGGT 62.431 66.667 1.90 0.00 38.26 5.28
1499 8332 2.659428 GCTCAATTGGCATAGGTCCTT 58.341 47.619 5.42 0.00 0.00 3.36
1717 8850 1.347707 ACTTCCATTCGGAGTGCTTGA 59.652 47.619 0.00 0.00 44.10 3.02
1889 9024 1.145803 GTTGTGGTTACCGCTGAGAC 58.854 55.000 16.35 6.13 34.70 3.36
1899 9034 2.900273 GCTGAGACCATACGGGCA 59.100 61.111 0.00 0.00 46.60 5.36
2049 9184 1.327303 TCAAGTGCCCCATCAACAAC 58.673 50.000 0.00 0.00 0.00 3.32
2081 9216 0.917533 ATCCAGAAGGCTGATGCTGT 59.082 50.000 0.00 0.00 45.17 4.40
2292 9427 2.987232 GACGGCCTGTCCTTAATCTTT 58.013 47.619 14.46 0.00 42.04 2.52
2337 9472 6.507900 CAAGTGTATCACCTACAAGATCGAT 58.492 40.000 0.00 0.00 41.93 3.59
2349 9484 4.474394 ACAAGATCGATCTGGATCCACTA 58.526 43.478 32.09 1.88 43.07 2.74
2438 9577 0.681733 GACAGCCAGTCTGAGGACAA 59.318 55.000 0.00 0.00 45.72 3.18
2443 9582 0.610687 CCAGTCTGAGGACAACTCCC 59.389 60.000 0.00 0.00 46.01 4.30
2606 9745 0.041833 CTGGAGGAGGAGACCCTGAA 59.958 60.000 0.00 0.00 44.53 3.02
2813 9952 2.671070 CGGAGAAGGTGGCCATGT 59.329 61.111 9.72 0.00 0.00 3.21
2941 10081 0.093026 CGACGTTGCTTCGGATTGTC 59.907 55.000 0.00 0.00 32.66 3.18
2943 10083 1.529438 GACGTTGCTTCGGATTGTCAA 59.471 47.619 0.00 0.00 34.94 3.18
3024 10164 1.227674 GAGGTTAGATGGGGCGCTG 60.228 63.158 7.64 0.00 0.00 5.18
3028 10168 3.697439 TTAGATGGGGCGCTGGCAC 62.697 63.158 7.64 0.00 43.79 5.01
3150 10419 4.489771 CTACCCTTGGGCGCCCTG 62.490 72.222 43.34 33.49 36.94 4.45
3153 10422 4.796495 CCCTTGGGCGCCCTGTAC 62.796 72.222 43.34 19.89 36.94 2.90
3178 10447 3.237741 GGCGCTCAGGGATAGGCT 61.238 66.667 7.64 0.00 0.00 4.58
3212 10481 3.390521 CCCACCGAGCAGCTGGTA 61.391 66.667 20.22 0.00 36.50 3.25
3242 10866 0.461961 GAGCTAGTGTCGGCATTCCT 59.538 55.000 0.00 0.00 0.00 3.36
3315 10939 4.351054 CGGCCAAGCAACCCTCCT 62.351 66.667 2.24 0.00 0.00 3.69
3316 10940 2.118294 GGCCAAGCAACCCTCCTT 59.882 61.111 0.00 0.00 0.00 3.36
3317 10941 1.533994 GGCCAAGCAACCCTCCTTT 60.534 57.895 0.00 0.00 0.00 3.11
3326 10950 2.075278 AACCCTCCTTTCCCCCTCCT 62.075 60.000 0.00 0.00 0.00 3.69
3329 10953 1.082954 CTCCTTTCCCCCTCCTCCA 59.917 63.158 0.00 0.00 0.00 3.86
3336 10960 2.366972 CCCCTCCTCCAATCCCGT 60.367 66.667 0.00 0.00 0.00 5.28
3367 10991 3.400054 GCTAGTTCGGCCCCACCT 61.400 66.667 0.00 0.00 35.61 4.00
3388 11013 2.124411 GAGGGGCCTATTAGTCCAACA 58.876 52.381 0.84 0.00 0.00 3.33
3395 11020 4.332828 GCCTATTAGTCCAACAGTGGTTT 58.667 43.478 0.00 0.00 46.11 3.27
3407 11032 5.047802 CCAACAGTGGTTTCATATGAAGCTT 60.048 40.000 25.52 12.97 40.42 3.74
3416 11041 7.828717 TGGTTTCATATGAAGCTTCTATGTTGA 59.171 33.333 27.10 20.92 35.87 3.18
3470 11095 3.004734 GGCGGCAGCTGATTTATTACATT 59.995 43.478 20.43 0.00 44.37 2.71
3474 11099 5.700832 CGGCAGCTGATTTATTACATTAGGA 59.299 40.000 20.43 0.00 0.00 2.94
3618 11244 2.673523 GCATCCTGCTGGGTGTCT 59.326 61.111 22.43 0.00 46.06 3.41
3623 11249 2.528818 CCTGCTGGGTGTCTGGGAA 61.529 63.158 0.71 0.00 0.00 3.97
3650 11276 3.007940 TGTTCTCGGTTGAAGACATGGAT 59.992 43.478 0.00 0.00 0.00 3.41
3668 11298 7.313731 ACATGGATAGAGGGGAATTCTTAGTA 58.686 38.462 5.23 0.00 0.00 1.82
3674 11304 4.908481 AGAGGGGAATTCTTAGTATGTCCC 59.092 45.833 5.23 4.06 43.47 4.46
3679 11309 5.454897 GGGAATTCTTAGTATGTCCCTCACC 60.455 48.000 5.23 0.00 41.37 4.02
3681 11311 3.657398 TCTTAGTATGTCCCTCACCGA 57.343 47.619 0.00 0.00 0.00 4.69
3685 11315 1.755395 TATGTCCCTCACCGACCGG 60.755 63.158 6.94 6.94 42.03 5.28
3737 11376 1.741770 GCTGATCACGGGTGGTCAC 60.742 63.158 10.57 5.10 44.98 3.67
3820 11459 4.510711 GCGGGAGACTTTAACCTTATTAGC 59.489 45.833 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
518 6895 9.315525 CTATAAAAACAGAGGGTAGCTTTACTC 57.684 37.037 0.00 0.00 0.00 2.59
613 6992 5.833131 AGAAGTAAACTGGCAAAAGATCCAA 59.167 36.000 0.00 0.00 30.98 3.53
620 6999 6.097554 TCAAATGGAGAAGTAAACTGGCAAAA 59.902 34.615 0.00 0.00 0.00 2.44
621 7000 5.596361 TCAAATGGAGAAGTAAACTGGCAAA 59.404 36.000 0.00 0.00 0.00 3.68
622 7001 5.136828 TCAAATGGAGAAGTAAACTGGCAA 58.863 37.500 0.00 0.00 0.00 4.52
624 7003 5.904362 ATCAAATGGAGAAGTAAACTGGC 57.096 39.130 0.00 0.00 0.00 4.85
627 7006 9.860898 GCAAATTATCAAATGGAGAAGTAAACT 57.139 29.630 0.00 0.00 28.77 2.66
628 7007 9.087424 GGCAAATTATCAAATGGAGAAGTAAAC 57.913 33.333 0.00 0.00 28.77 2.01
629 7008 8.257306 GGGCAAATTATCAAATGGAGAAGTAAA 58.743 33.333 0.00 0.00 28.77 2.01
630 7009 7.147742 GGGGCAAATTATCAAATGGAGAAGTAA 60.148 37.037 0.00 0.00 28.77 2.24
631 7010 6.323739 GGGGCAAATTATCAAATGGAGAAGTA 59.676 38.462 0.00 0.00 28.77 2.24
632 7011 5.129320 GGGGCAAATTATCAAATGGAGAAGT 59.871 40.000 0.00 0.00 28.77 3.01
633 7012 5.453762 GGGGGCAAATTATCAAATGGAGAAG 60.454 44.000 0.00 0.00 28.77 2.85
634 7013 4.408596 GGGGGCAAATTATCAAATGGAGAA 59.591 41.667 0.00 0.00 0.00 2.87
635 7014 3.966665 GGGGGCAAATTATCAAATGGAGA 59.033 43.478 0.00 0.00 0.00 3.71
636 7015 4.341366 GGGGGCAAATTATCAAATGGAG 57.659 45.455 0.00 0.00 0.00 3.86
660 7039 4.767255 CCCACACGGCAGCCTCTC 62.767 72.222 10.54 0.00 0.00 3.20
684 7063 0.961019 TTGTCTCAATGGCAAGTGGC 59.039 50.000 0.00 0.00 35.04 5.01
685 7064 2.094390 CCATTGTCTCAATGGCAAGTGG 60.094 50.000 22.72 5.42 44.09 4.00
686 7065 2.094390 CCCATTGTCTCAATGGCAAGTG 60.094 50.000 26.59 14.49 44.09 3.16
687 7066 2.173519 CCCATTGTCTCAATGGCAAGT 58.826 47.619 26.59 0.00 44.09 3.16
688 7067 1.479323 CCCCATTGTCTCAATGGCAAG 59.521 52.381 26.59 17.18 44.09 4.01
689 7068 1.559368 CCCCATTGTCTCAATGGCAA 58.441 50.000 26.59 3.61 44.47 4.52
690 7069 0.971959 GCCCCATTGTCTCAATGGCA 60.972 55.000 26.59 0.00 44.47 4.92
691 7070 0.971959 TGCCCCATTGTCTCAATGGC 60.972 55.000 26.59 19.87 44.47 4.40
692 7071 1.559368 TTGCCCCATTGTCTCAATGG 58.441 50.000 25.61 25.61 45.21 3.16
693 7072 3.196039 TGATTTGCCCCATTGTCTCAATG 59.804 43.478 13.47 13.47 0.00 2.82
694 7073 3.443052 TGATTTGCCCCATTGTCTCAAT 58.557 40.909 0.00 0.00 0.00 2.57
695 7074 2.886913 TGATTTGCCCCATTGTCTCAA 58.113 42.857 0.00 0.00 0.00 3.02
696 7075 2.601240 TGATTTGCCCCATTGTCTCA 57.399 45.000 0.00 0.00 0.00 3.27
697 7076 3.025978 TGATGATTTGCCCCATTGTCTC 58.974 45.455 0.00 0.00 0.00 3.36
698 7077 3.104519 TGATGATTTGCCCCATTGTCT 57.895 42.857 0.00 0.00 0.00 3.41
699 7078 3.891422 TTGATGATTTGCCCCATTGTC 57.109 42.857 0.00 0.00 0.00 3.18
700 7079 3.307621 GGTTTGATGATTTGCCCCATTGT 60.308 43.478 0.00 0.00 0.00 2.71
701 7080 3.272581 GGTTTGATGATTTGCCCCATTG 58.727 45.455 0.00 0.00 0.00 2.82
702 7081 2.239402 GGGTTTGATGATTTGCCCCATT 59.761 45.455 0.00 0.00 0.00 3.16
703 7082 1.839354 GGGTTTGATGATTTGCCCCAT 59.161 47.619 0.00 0.00 0.00 4.00
704 7083 1.274712 GGGTTTGATGATTTGCCCCA 58.725 50.000 0.00 0.00 0.00 4.96
706 7085 1.274712 TGGGGTTTGATGATTTGCCC 58.725 50.000 0.00 0.00 35.52 5.36
707 7086 2.236893 ACATGGGGTTTGATGATTTGCC 59.763 45.455 0.00 0.00 0.00 4.52
708 7087 3.615224 ACATGGGGTTTGATGATTTGC 57.385 42.857 0.00 0.00 0.00 3.68
709 7088 6.591062 CACTTTACATGGGGTTTGATGATTTG 59.409 38.462 0.00 0.00 0.00 2.32
710 7089 6.295802 CCACTTTACATGGGGTTTGATGATTT 60.296 38.462 0.00 0.00 33.18 2.17
711 7090 5.187576 CCACTTTACATGGGGTTTGATGATT 59.812 40.000 0.00 0.00 33.18 2.57
712 7091 4.711355 CCACTTTACATGGGGTTTGATGAT 59.289 41.667 0.00 0.00 33.18 2.45
713 7092 4.085733 CCACTTTACATGGGGTTTGATGA 58.914 43.478 0.00 0.00 33.18 2.92
714 7093 4.454728 CCACTTTACATGGGGTTTGATG 57.545 45.455 0.00 0.00 33.18 3.07
723 7102 2.896685 TCTTTTGCCCCACTTTACATGG 59.103 45.455 0.00 0.00 36.94 3.66
724 7103 4.381932 GGATCTTTTGCCCCACTTTACATG 60.382 45.833 0.00 0.00 0.00 3.21
725 7104 3.769300 GGATCTTTTGCCCCACTTTACAT 59.231 43.478 0.00 0.00 0.00 2.29
726 7105 3.161866 GGATCTTTTGCCCCACTTTACA 58.838 45.455 0.00 0.00 0.00 2.41
727 7106 2.163613 CGGATCTTTTGCCCCACTTTAC 59.836 50.000 0.00 0.00 0.00 2.01
728 7107 2.040545 TCGGATCTTTTGCCCCACTTTA 59.959 45.455 0.00 0.00 0.00 1.85
729 7108 1.203001 TCGGATCTTTTGCCCCACTTT 60.203 47.619 0.00 0.00 0.00 2.66
730 7109 0.404040 TCGGATCTTTTGCCCCACTT 59.596 50.000 0.00 0.00 0.00 3.16
731 7110 0.322546 GTCGGATCTTTTGCCCCACT 60.323 55.000 0.00 0.00 0.00 4.00
732 7111 1.313091 GGTCGGATCTTTTGCCCCAC 61.313 60.000 0.00 0.00 0.00 4.61
733 7112 1.001393 GGTCGGATCTTTTGCCCCA 60.001 57.895 0.00 0.00 0.00 4.96
734 7113 1.753078 GGGTCGGATCTTTTGCCCC 60.753 63.158 0.00 0.00 0.00 5.80
735 7114 1.753078 GGGGTCGGATCTTTTGCCC 60.753 63.158 0.00 0.00 35.52 5.36
736 7115 1.753078 GGGGGTCGGATCTTTTGCC 60.753 63.158 0.00 0.00 0.00 4.52
737 7116 3.920031 GGGGGTCGGATCTTTTGC 58.080 61.111 0.00 0.00 0.00 3.68
791 7170 8.721133 AAGAAACTTTGGGGTGAGTAATATTT 57.279 30.769 0.00 0.00 0.00 1.40
841 7220 1.804748 CCAAACCTAGCGAAGTTGGTC 59.195 52.381 0.00 0.00 31.64 4.02
1239 8071 2.681778 CCAGGCAGAGGGAGTCGT 60.682 66.667 0.00 0.00 0.00 4.34
1344 8176 2.633509 GGAGTACACAGACCGGCGT 61.634 63.158 6.01 0.00 0.00 5.68
1351 8183 0.395311 CTAGGGGCGGAGTACACAGA 60.395 60.000 0.00 0.00 0.00 3.41
1889 9024 1.227380 GACAGCTCTGCCCGTATGG 60.227 63.158 0.00 0.00 37.09 2.74
1899 9034 2.915349 CCAATGTATGCTGACAGCTCT 58.085 47.619 26.94 16.79 42.97 4.09
2049 9184 4.515944 GCCTTCTGGATTGAGATCATGAAG 59.484 45.833 0.00 10.73 39.78 3.02
2104 9239 1.210204 ATGAGCATCCACACCTGGGT 61.210 55.000 0.00 0.00 38.25 4.51
2152 9287 2.097825 GATGGCCTTGAGAATGTGCTT 58.902 47.619 3.32 0.00 0.00 3.91
2292 9427 2.500229 CCCTTGTTCTTGCCGAAGTAA 58.500 47.619 0.00 0.00 30.85 2.24
2337 9472 0.105453 GCCCCTCTAGTGGATCCAGA 60.105 60.000 16.81 8.44 0.00 3.86
2606 9745 0.533755 GCGAACATCCAGCCTAGCAT 60.534 55.000 0.00 0.00 0.00 3.79
2701 9840 3.468140 GAGGGTACAGGCCGGGTC 61.468 72.222 8.08 0.00 0.00 4.46
2772 9911 3.708544 TAGGAACCCAACCGCCCG 61.709 66.667 0.00 0.00 0.00 6.13
2925 10065 2.679355 TTTGACAATCCGAAGCAACG 57.321 45.000 0.00 0.00 0.00 4.10
2941 10081 5.801947 CCTTCTCGCCTTGAAATACAATTTG 59.198 40.000 0.00 0.00 37.88 2.32
2943 10083 4.399303 CCCTTCTCGCCTTGAAATACAATT 59.601 41.667 0.00 0.00 37.88 2.32
3033 10173 2.125952 TGCTCAGCACGATCACGG 60.126 61.111 0.00 0.00 44.46 4.94
3034 10174 2.163390 CCTGCTCAGCACGATCACG 61.163 63.158 0.00 0.00 45.75 4.35
3038 10178 3.790437 CCCCCTGCTCAGCACGAT 61.790 66.667 0.00 0.00 33.79 3.73
3150 10419 2.187163 GAGCGCCCTTCCCTGTAC 59.813 66.667 2.29 0.00 0.00 2.90
3153 10422 4.479993 CCTGAGCGCCCTTCCCTG 62.480 72.222 2.29 0.00 0.00 4.45
3212 10481 3.760035 CTAGCTCCACGCACCGGT 61.760 66.667 0.00 0.00 42.61 5.28
3219 10488 2.202623 GCCGACACTAGCTCCACG 60.203 66.667 0.00 0.00 0.00 4.94
3309 10933 1.694525 GAGGAGGGGGAAAGGAGGG 60.695 68.421 0.00 0.00 0.00 4.30
3310 10934 1.694525 GGAGGAGGGGGAAAGGAGG 60.695 68.421 0.00 0.00 0.00 4.30
3311 10935 0.550147 TTGGAGGAGGGGGAAAGGAG 60.550 60.000 0.00 0.00 0.00 3.69
3312 10936 0.123266 ATTGGAGGAGGGGGAAAGGA 59.877 55.000 0.00 0.00 0.00 3.36
3313 10937 0.553333 GATTGGAGGAGGGGGAAAGG 59.447 60.000 0.00 0.00 0.00 3.11
3314 10938 0.553333 GGATTGGAGGAGGGGGAAAG 59.447 60.000 0.00 0.00 0.00 2.62
3315 10939 0.924226 GGGATTGGAGGAGGGGGAAA 60.924 60.000 0.00 0.00 0.00 3.13
3316 10940 1.308746 GGGATTGGAGGAGGGGGAA 60.309 63.158 0.00 0.00 0.00 3.97
3317 10941 2.376842 GGGATTGGAGGAGGGGGA 59.623 66.667 0.00 0.00 0.00 4.81
3326 10950 1.451207 CGCCATTCACGGGATTGGA 60.451 57.895 28.42 0.00 43.95 3.53
3367 10991 2.124411 GTTGGACTAATAGGCCCCTCA 58.876 52.381 10.14 0.00 45.26 3.86
3388 11013 7.341805 ACATAGAAGCTTCATATGAAACCACT 58.658 34.615 31.14 16.37 33.07 4.00
3395 11020 8.791327 TGTTTCAACATAGAAGCTTCATATGA 57.209 30.769 31.14 23.16 33.17 2.15
3416 11041 1.082117 CCTCGAAGCCGCGTATGTTT 61.082 55.000 4.92 0.00 35.37 2.83
3456 11081 9.717942 CTCCTCCTTCCTAATGTAATAAATCAG 57.282 37.037 0.00 0.00 0.00 2.90
3470 11095 7.676043 CCTACAATATCAATCTCCTCCTTCCTA 59.324 40.741 0.00 0.00 0.00 2.94
3474 11099 7.698163 AACCTACAATATCAATCTCCTCCTT 57.302 36.000 0.00 0.00 0.00 3.36
3485 11110 5.428253 GTCTCCTGCAAACCTACAATATCA 58.572 41.667 0.00 0.00 0.00 2.15
3517 11142 3.324246 TCCTGGATGGAGAAGTCCC 57.676 57.895 0.00 0.00 43.15 4.46
3546 11172 0.736053 GCAAACAAGTGTCGGGACAA 59.264 50.000 2.58 0.00 43.77 3.18
3583 11209 1.719063 GCCCCCAGATAGCCCAATCA 61.719 60.000 0.00 0.00 0.00 2.57
3618 11244 1.938585 ACCGAGAACAGATCTTCCCA 58.061 50.000 0.00 0.00 38.96 4.37
3623 11249 3.574396 TGTCTTCAACCGAGAACAGATCT 59.426 43.478 0.00 0.00 42.61 2.75
3650 11276 6.082707 GGGACATACTAAGAATTCCCCTCTA 58.917 44.000 0.65 0.00 37.33 2.43
3668 11298 3.075005 CCGGTCGGTGAGGGACAT 61.075 66.667 0.55 0.00 36.12 3.06
3679 11309 4.065281 AGGTTCCTTCGCCGGTCG 62.065 66.667 1.90 7.73 40.15 4.79
3681 11311 4.016706 CCAGGTTCCTTCGCCGGT 62.017 66.667 1.90 0.00 0.00 5.28
3685 11315 0.036388 TGATCACCAGGTTCCTTCGC 60.036 55.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.