Multiple sequence alignment - TraesCS1D01G266000

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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 TraesCS1D01G266000 chr1D 100.000 2584 0 0 1 2584 361906511 361909094 0.000000e+00 4772.0
1 TraesCS1D01G266000 chr1D 93.481 675 42 2 1 674 109572781 109573454 0.000000e+00 1002.0
2 TraesCS1D01G266000 chr1D 80.000 415 47 21 1332 1737 361802752 361803139 9.110000e-70 274.0
3 TraesCS1D01G266000 chr1D 87.879 231 18 7 992 1217 361802456 361802681 1.970000e-66 263.0
4 TraesCS1D01G266000 chr1B 89.381 1874 110 48 755 2584 484365669 484367497 0.000000e+00 2276.0
5 TraesCS1D01G266000 chr1B 77.657 922 118 59 842 1737 484296973 484297832 5.000000e-132 481.0
6 TraesCS1D01G266000 chr1B 96.629 267 9 0 1333 1599 484147225 484147491 6.560000e-121 444.0
7 TraesCS1D01G266000 chr1B 96.629 267 9 0 1333 1599 484214212 484214478 6.560000e-121 444.0
8 TraesCS1D01G266000 chr1B 91.071 56 4 1 1757 1812 484366641 484366695 9.920000e-10 75.0
9 TraesCS1D01G266000 chr1A 91.618 1026 48 14 762 1767 461356458 461357465 0.000000e+00 1384.0
10 TraesCS1D01G266000 chr1A 90.387 853 53 12 1757 2584 461357409 461358257 0.000000e+00 1094.0
11 TraesCS1D01G266000 chr1A 80.901 466 48 27 775 1217 461337314 461337761 1.920000e-86 329.0
12 TraesCS1D01G266000 chr1A 81.796 401 41 23 1332 1723 461337837 461338214 8.980000e-80 307.0
13 TraesCS1D01G266000 chr1A 83.721 86 14 0 1114 1199 461351352 461351437 5.930000e-12 82.4
14 TraesCS1D01G266000 chr2D 95.407 675 30 1 1 674 364969488 364968814 0.000000e+00 1074.0
15 TraesCS1D01G266000 chr2D 94.214 674 39 0 1 674 513913699 513914372 0.000000e+00 1029.0
16 TraesCS1D01G266000 chr3D 95.259 675 31 1 1 674 283323184 283322510 0.000000e+00 1068.0
17 TraesCS1D01G266000 chr5D 94.675 676 35 1 1 675 521151382 521152057 0.000000e+00 1048.0
18 TraesCS1D01G266000 chr5D 94.170 669 36 3 1 667 395705389 395704722 0.000000e+00 1016.0
19 TraesCS1D01G266000 chr5D 93.195 676 45 1 1 675 558577780 558578455 0.000000e+00 992.0
20 TraesCS1D01G266000 chr4D 94.675 676 33 3 1 674 389485989 389485315 0.000000e+00 1046.0
21 TraesCS1D01G266000 chr4D 93.323 674 45 0 1 674 49296533 49297206 0.000000e+00 996.0


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 TraesCS1D01G266000 chr1D 361906511 361909094 2583 False 4772.0 4772 100.0000 1 2584 1 chr1D.!!$F2 2583
1 TraesCS1D01G266000 chr1D 109572781 109573454 673 False 1002.0 1002 93.4810 1 674 1 chr1D.!!$F1 673
2 TraesCS1D01G266000 chr1D 361802456 361803139 683 False 268.5 274 83.9395 992 1737 2 chr1D.!!$F3 745
3 TraesCS1D01G266000 chr1B 484365669 484367497 1828 False 1175.5 2276 90.2260 755 2584 2 chr1B.!!$F4 1829
4 TraesCS1D01G266000 chr1B 484296973 484297832 859 False 481.0 481 77.6570 842 1737 1 chr1B.!!$F3 895
5 TraesCS1D01G266000 chr1A 461356458 461358257 1799 False 1239.0 1384 91.0025 762 2584 2 chr1A.!!$F3 1822
6 TraesCS1D01G266000 chr1A 461337314 461338214 900 False 318.0 329 81.3485 775 1723 2 chr1A.!!$F2 948
7 TraesCS1D01G266000 chr2D 364968814 364969488 674 True 1074.0 1074 95.4070 1 674 1 chr2D.!!$R1 673
8 TraesCS1D01G266000 chr2D 513913699 513914372 673 False 1029.0 1029 94.2140 1 674 1 chr2D.!!$F1 673
9 TraesCS1D01G266000 chr3D 283322510 283323184 674 True 1068.0 1068 95.2590 1 674 1 chr3D.!!$R1 673
10 TraesCS1D01G266000 chr5D 521151382 521152057 675 False 1048.0 1048 94.6750 1 675 1 chr5D.!!$F1 674
11 TraesCS1D01G266000 chr5D 395704722 395705389 667 True 1016.0 1016 94.1700 1 667 1 chr5D.!!$R1 666
12 TraesCS1D01G266000 chr5D 558577780 558578455 675 False 992.0 992 93.1950 1 675 1 chr5D.!!$F2 674
13 TraesCS1D01G266000 chr4D 389485315 389485989 674 True 1046.0 1046 94.6750 1 674 1 chr4D.!!$R1 673
14 TraesCS1D01G266000 chr4D 49296533 49297206 673 False 996.0 996 93.3230 1 674 1 chr4D.!!$F1 673

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
752 755 0.033228 GAGGCAGATCCGATCCACTG 59.967 60.0 4.67 0.0 40.77 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2217 0.10741 ACAACTTCAGGTGGTTCGCA 60.107 50.0 0.0 0.0 0.0 5.1 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
174 175 5.725110 AGAGCGCAATTTAGTAGATGTTG 57.275 39.130 11.47 0.00 0.00 3.33
219 220 3.320541 GGCTAGACATGAGACTAGTGCAT 59.679 47.826 0.00 0.51 40.66 3.96
255 256 4.714632 AGAGGCTAGACATGAGACTAGAC 58.285 47.826 20.93 19.30 45.03 2.59
332 333 1.221840 GCCTCCTCCGCAGATCAAA 59.778 57.895 0.00 0.00 0.00 2.69
373 374 4.323562 GGCACTAATCCAACTTACAGGAGT 60.324 45.833 0.00 0.00 37.34 3.85
429 430 9.020813 GTATTCTTGTGGTTCTTGTTTTCTTTC 57.979 33.333 0.00 0.00 0.00 2.62
481 482 8.257306 GTGATGTATTCCCATGTACCAAAAATT 58.743 33.333 0.00 0.00 0.00 1.82
618 621 0.041090 CCCATTGCCCTACCCAAACT 59.959 55.000 0.00 0.00 0.00 2.66
656 659 3.673484 GACGTCCGTTCGGGGTCA 61.673 66.667 21.55 0.32 36.01 4.02
677 680 3.971702 GGTGGAGCTGGCCTTGGT 61.972 66.667 3.32 1.86 0.00 3.67
678 681 2.360475 GTGGAGCTGGCCTTGGTC 60.360 66.667 16.50 16.50 0.00 4.02
679 682 2.530151 TGGAGCTGGCCTTGGTCT 60.530 61.111 21.40 5.71 33.06 3.85
680 683 2.045536 GGAGCTGGCCTTGGTCTG 60.046 66.667 21.40 0.00 33.06 3.51
681 684 2.045536 GAGCTGGCCTTGGTCTGG 60.046 66.667 17.19 0.00 0.00 3.86
688 691 2.034687 CCTTGGTCTGGCAGGGTG 59.965 66.667 15.73 1.11 0.00 4.61
689 692 2.528818 CCTTGGTCTGGCAGGGTGA 61.529 63.158 15.73 0.00 0.00 4.02
690 693 1.455849 CTTGGTCTGGCAGGGTGAA 59.544 57.895 15.73 2.10 0.00 3.18
691 694 0.038744 CTTGGTCTGGCAGGGTGAAT 59.961 55.000 15.73 0.00 0.00 2.57
692 695 0.038166 TTGGTCTGGCAGGGTGAATC 59.962 55.000 15.73 0.00 0.00 2.52
693 696 1.077429 GGTCTGGCAGGGTGAATCC 60.077 63.158 15.73 2.90 0.00 3.01
694 697 1.566298 GGTCTGGCAGGGTGAATCCT 61.566 60.000 15.73 0.00 37.71 3.24
700 703 3.411517 AGGGTGAATCCTGGGCCG 61.412 66.667 0.00 0.00 35.47 6.13
705 708 4.918201 GAATCCTGGGCCGCCGAG 62.918 72.222 14.28 14.28 0.00 4.63
713 716 2.818274 GGCCGCCGAGTTCGAAAT 60.818 61.111 0.00 0.00 43.02 2.17
714 717 1.519898 GGCCGCCGAGTTCGAAATA 60.520 57.895 0.00 0.00 43.02 1.40
715 718 1.634753 GCCGCCGAGTTCGAAATAC 59.365 57.895 0.00 0.00 43.02 1.89
716 719 0.804933 GCCGCCGAGTTCGAAATACT 60.805 55.000 0.00 0.00 43.02 2.12
717 720 1.534595 GCCGCCGAGTTCGAAATACTA 60.535 52.381 0.00 0.00 43.02 1.82
718 721 2.114825 CCGCCGAGTTCGAAATACTAC 58.885 52.381 0.00 0.00 43.02 2.73
719 722 2.223433 CCGCCGAGTTCGAAATACTACT 60.223 50.000 0.00 0.00 43.02 2.57
720 723 3.432782 CGCCGAGTTCGAAATACTACTT 58.567 45.455 0.00 0.00 43.02 2.24
721 724 3.855950 CGCCGAGTTCGAAATACTACTTT 59.144 43.478 0.00 0.00 43.02 2.66
722 725 4.259292 CGCCGAGTTCGAAATACTACTTTG 60.259 45.833 0.00 0.00 43.02 2.77
723 726 4.624452 GCCGAGTTCGAAATACTACTTTGT 59.376 41.667 0.00 0.00 43.02 2.83
724 727 5.119743 GCCGAGTTCGAAATACTACTTTGTT 59.880 40.000 0.00 0.00 43.02 2.83
725 728 6.347160 GCCGAGTTCGAAATACTACTTTGTTT 60.347 38.462 0.00 0.00 43.02 2.83
726 729 7.225397 CCGAGTTCGAAATACTACTTTGTTTC 58.775 38.462 0.00 0.00 43.02 2.78
727 730 7.115947 CCGAGTTCGAAATACTACTTTGTTTCT 59.884 37.037 0.00 0.00 43.02 2.52
728 731 8.485591 CGAGTTCGAAATACTACTTTGTTTCTT 58.514 33.333 0.00 0.00 43.02 2.52
731 734 9.378597 GTTCGAAATACTACTTTGTTTCTTTCC 57.621 33.333 0.00 0.00 0.00 3.13
732 735 8.091385 TCGAAATACTACTTTGTTTCTTTCCC 57.909 34.615 0.00 0.00 0.00 3.97
733 736 7.013529 CGAAATACTACTTTGTTTCTTTCCCG 58.986 38.462 0.00 0.00 0.00 5.14
734 737 7.095523 CGAAATACTACTTTGTTTCTTTCCCGA 60.096 37.037 0.00 0.00 0.00 5.14
735 738 7.668525 AATACTACTTTGTTTCTTTCCCGAG 57.331 36.000 0.00 0.00 0.00 4.63
736 739 4.386711 ACTACTTTGTTTCTTTCCCGAGG 58.613 43.478 0.00 0.00 0.00 4.63
737 740 1.954382 ACTTTGTTTCTTTCCCGAGGC 59.046 47.619 0.00 0.00 0.00 4.70
738 741 1.953686 CTTTGTTTCTTTCCCGAGGCA 59.046 47.619 0.00 0.00 0.00 4.75
739 742 1.604604 TTGTTTCTTTCCCGAGGCAG 58.395 50.000 0.00 0.00 0.00 4.85
740 743 0.762418 TGTTTCTTTCCCGAGGCAGA 59.238 50.000 0.00 0.00 0.00 4.26
741 744 1.351017 TGTTTCTTTCCCGAGGCAGAT 59.649 47.619 0.00 0.00 0.00 2.90
742 745 2.010497 GTTTCTTTCCCGAGGCAGATC 58.990 52.381 0.00 0.00 0.00 2.75
743 746 0.541863 TTCTTTCCCGAGGCAGATCC 59.458 55.000 0.00 0.00 0.00 3.36
744 747 1.227380 CTTTCCCGAGGCAGATCCG 60.227 63.158 0.00 0.00 40.77 4.18
745 748 1.676678 CTTTCCCGAGGCAGATCCGA 61.677 60.000 0.00 0.00 40.77 4.55
746 749 1.048724 TTTCCCGAGGCAGATCCGAT 61.049 55.000 0.00 0.00 40.77 4.18
747 750 1.464376 TTCCCGAGGCAGATCCGATC 61.464 60.000 0.00 0.00 40.77 3.69
748 751 2.653702 CCGAGGCAGATCCGATCC 59.346 66.667 4.67 0.00 40.77 3.36
749 752 2.203082 CCGAGGCAGATCCGATCCA 61.203 63.158 4.67 0.00 40.77 3.41
750 753 1.006805 CGAGGCAGATCCGATCCAC 60.007 63.158 4.67 0.00 40.77 4.02
751 754 1.459455 CGAGGCAGATCCGATCCACT 61.459 60.000 4.67 1.23 40.77 4.00
752 755 0.033228 GAGGCAGATCCGATCCACTG 59.967 60.000 4.67 0.00 40.77 3.66
753 756 0.397675 AGGCAGATCCGATCCACTGA 60.398 55.000 4.67 0.00 40.77 3.41
766 769 2.928334 TCCACTGATCCCGAGTAGTAC 58.072 52.381 0.00 0.00 0.00 2.73
770 773 2.941720 ACTGATCCCGAGTAGTACGAAC 59.058 50.000 0.00 0.00 0.00 3.95
813 816 1.070821 AATCAGTGTGCACGTGATCG 58.929 50.000 26.26 8.18 43.34 3.69
829 833 2.224402 TGATCGTGTTTGGTGGACATGA 60.224 45.455 0.00 2.09 44.49 3.07
830 834 1.877637 TCGTGTTTGGTGGACATGAG 58.122 50.000 0.00 0.00 37.93 2.90
831 835 1.140052 TCGTGTTTGGTGGACATGAGT 59.860 47.619 0.00 0.00 37.93 3.41
869 880 1.148310 CAATCCACGCCGCCTATAAG 58.852 55.000 0.00 0.00 0.00 1.73
874 887 2.158871 TCCACGCCGCCTATAAGAAAAT 60.159 45.455 0.00 0.00 0.00 1.82
900 913 3.568430 GGAAAACGAGTCCAAGTTTCCAT 59.432 43.478 12.99 0.00 39.36 3.41
901 914 4.320275 GGAAAACGAGTCCAAGTTTCCATC 60.320 45.833 12.99 2.28 39.36 3.51
915 928 2.174685 TCCATCCCAGCTGCTACTAA 57.825 50.000 8.66 0.00 0.00 2.24
932 945 9.330063 CTGCTACTAATCAAACATCTTTATCCA 57.670 33.333 0.00 0.00 0.00 3.41
1011 1039 5.213675 GCCAATCGACGCCTATATATAGAC 58.786 45.833 19.51 8.51 32.05 2.59
1083 1112 3.991051 CCAGACCGACCGCACAGT 61.991 66.667 0.00 0.00 0.00 3.55
1095 1126 1.728971 CCGCACAGTTGAAGTGAGATC 59.271 52.381 7.07 0.00 38.80 2.75
1233 1269 5.526846 GCTCAATCATTTCACCTCTTCCTAG 59.473 44.000 0.00 0.00 0.00 3.02
1250 1293 4.938080 TCCTAGACAAAGCTCGATCATTC 58.062 43.478 0.00 0.00 0.00 2.67
1328 1377 1.766143 GATTCTGATGCCGTCGGTGC 61.766 60.000 13.94 0.00 34.65 5.01
1331 1381 3.958147 CTGATGCCGTCGGTGCCTT 62.958 63.158 13.94 0.00 0.00 4.35
1736 1795 4.202419 TGGTGCTTGTACTTGTTCACCTAT 60.202 41.667 17.44 0.00 43.10 2.57
1737 1796 4.760204 GGTGCTTGTACTTGTTCACCTATT 59.240 41.667 12.65 0.00 40.42 1.73
1738 1797 5.106673 GGTGCTTGTACTTGTTCACCTATTC 60.107 44.000 12.65 0.00 40.42 1.75
1739 1798 5.701290 GTGCTTGTACTTGTTCACCTATTCT 59.299 40.000 0.00 0.00 0.00 2.40
1740 1799 5.932303 TGCTTGTACTTGTTCACCTATTCTC 59.068 40.000 0.00 0.00 0.00 2.87
1741 1800 5.351740 GCTTGTACTTGTTCACCTATTCTCC 59.648 44.000 0.00 0.00 0.00 3.71
1742 1801 5.068234 TGTACTTGTTCACCTATTCTCCG 57.932 43.478 0.00 0.00 0.00 4.63
1743 1802 4.525487 TGTACTTGTTCACCTATTCTCCGT 59.475 41.667 0.00 0.00 0.00 4.69
1744 1803 4.189639 ACTTGTTCACCTATTCTCCGTC 57.810 45.455 0.00 0.00 0.00 4.79
1745 1804 3.576982 ACTTGTTCACCTATTCTCCGTCA 59.423 43.478 0.00 0.00 0.00 4.35
1746 1805 4.039973 ACTTGTTCACCTATTCTCCGTCAA 59.960 41.667 0.00 0.00 0.00 3.18
1747 1806 4.819105 TGTTCACCTATTCTCCGTCAAT 57.181 40.909 0.00 0.00 0.00 2.57
1748 1807 5.925506 TGTTCACCTATTCTCCGTCAATA 57.074 39.130 0.00 0.00 0.00 1.90
1749 1808 6.288941 TGTTCACCTATTCTCCGTCAATAA 57.711 37.500 0.00 0.00 0.00 1.40
1750 1809 6.703319 TGTTCACCTATTCTCCGTCAATAAA 58.297 36.000 0.00 0.00 0.00 1.40
1751 1810 6.592607 TGTTCACCTATTCTCCGTCAATAAAC 59.407 38.462 0.00 0.00 0.00 2.01
1752 1811 6.288941 TCACCTATTCTCCGTCAATAAACA 57.711 37.500 0.00 0.00 0.00 2.83
1753 1812 6.103997 TCACCTATTCTCCGTCAATAAACAC 58.896 40.000 0.00 0.00 0.00 3.32
1754 1813 5.872617 CACCTATTCTCCGTCAATAAACACA 59.127 40.000 0.00 0.00 0.00 3.72
1755 1814 6.538742 CACCTATTCTCCGTCAATAAACACAT 59.461 38.462 0.00 0.00 0.00 3.21
1756 1815 6.538742 ACCTATTCTCCGTCAATAAACACATG 59.461 38.462 0.00 0.00 0.00 3.21
1757 1816 6.538742 CCTATTCTCCGTCAATAAACACATGT 59.461 38.462 0.00 0.00 0.00 3.21
1758 1817 5.605564 TTCTCCGTCAATAAACACATGTG 57.394 39.130 24.25 24.25 0.00 3.21
1759 1818 4.888917 TCTCCGTCAATAAACACATGTGA 58.111 39.130 31.94 10.65 0.00 3.58
1760 1819 5.487433 TCTCCGTCAATAAACACATGTGAT 58.513 37.500 31.94 18.35 0.00 3.06
1761 1820 5.351189 TCTCCGTCAATAAACACATGTGATG 59.649 40.000 31.94 19.55 0.00 3.07
1762 1821 5.241662 TCCGTCAATAAACACATGTGATGA 58.758 37.500 31.94 21.21 0.00 2.92
1763 1822 5.879777 TCCGTCAATAAACACATGTGATGAT 59.120 36.000 31.94 16.37 0.00 2.45
1764 1823 6.374053 TCCGTCAATAAACACATGTGATGATT 59.626 34.615 31.94 21.25 0.00 2.57
1765 1824 6.469915 CCGTCAATAAACACATGTGATGATTG 59.530 38.462 28.31 28.31 32.74 2.67
1766 1825 7.022979 CGTCAATAAACACATGTGATGATTGT 58.977 34.615 30.63 17.73 32.99 2.71
1767 1826 8.174422 CGTCAATAAACACATGTGATGATTGTA 58.826 33.333 30.63 20.76 32.99 2.41
1768 1827 9.277565 GTCAATAAACACATGTGATGATTGTAC 57.722 33.333 30.63 25.00 32.99 2.90
1769 1828 9.230122 TCAATAAACACATGTGATGATTGTACT 57.770 29.630 30.63 10.62 32.99 2.73
1770 1829 9.844790 CAATAAACACATGTGATGATTGTACTT 57.155 29.630 31.94 8.91 0.00 2.24
1783 1842 5.416083 TGATTGTACTTGTTCACCTATCCG 58.584 41.667 0.00 0.00 0.00 4.18
1812 1871 6.807720 TGAATAAACACATGTGATGATTGTGC 59.192 34.615 31.94 16.39 43.51 4.57
1813 1872 4.859304 AAACACATGTGATGATTGTGCT 57.141 36.364 31.94 2.44 43.51 4.40
1816 1875 3.570975 ACACATGTGATGATTGTGCTTGT 59.429 39.130 31.94 1.18 43.51 3.16
1817 1876 4.761227 ACACATGTGATGATTGTGCTTGTA 59.239 37.500 31.94 0.00 43.51 2.41
1818 1877 5.090757 CACATGTGATGATTGTGCTTGTAC 58.909 41.667 21.64 0.00 34.89 2.90
1819 1878 5.005740 ACATGTGATGATTGTGCTTGTACT 58.994 37.500 0.00 0.00 0.00 2.73
1822 1881 5.308014 TGTGATGATTGTGCTTGTACTCTT 58.692 37.500 0.00 0.00 0.00 2.85
1823 1882 5.179929 TGTGATGATTGTGCTTGTACTCTTG 59.820 40.000 0.00 0.00 0.00 3.02
1824 1883 5.180117 GTGATGATTGTGCTTGTACTCTTGT 59.820 40.000 0.00 0.00 0.00 3.16
1825 1884 5.409520 TGATGATTGTGCTTGTACTCTTGTC 59.590 40.000 0.00 0.00 0.00 3.18
1826 1885 4.960938 TGATTGTGCTTGTACTCTTGTCT 58.039 39.130 0.00 0.00 0.00 3.41
1827 1886 4.751600 TGATTGTGCTTGTACTCTTGTCTG 59.248 41.667 0.00 0.00 0.00 3.51
1828 1887 3.819564 TGTGCTTGTACTCTTGTCTGT 57.180 42.857 0.00 0.00 0.00 3.41
1829 1888 4.137116 TGTGCTTGTACTCTTGTCTGTT 57.863 40.909 0.00 0.00 0.00 3.16
1830 1889 5.270893 TGTGCTTGTACTCTTGTCTGTTA 57.729 39.130 0.00 0.00 0.00 2.41
1831 1890 5.853936 TGTGCTTGTACTCTTGTCTGTTAT 58.146 37.500 0.00 0.00 0.00 1.89
1832 1891 5.696270 TGTGCTTGTACTCTTGTCTGTTATG 59.304 40.000 0.00 0.00 0.00 1.90
1833 1892 5.696724 GTGCTTGTACTCTTGTCTGTTATGT 59.303 40.000 0.00 0.00 0.00 2.29
1834 1893 6.202954 GTGCTTGTACTCTTGTCTGTTATGTT 59.797 38.462 0.00 0.00 0.00 2.71
1835 1894 6.765989 TGCTTGTACTCTTGTCTGTTATGTTT 59.234 34.615 0.00 0.00 0.00 2.83
1896 1995 3.202829 ACCTTTCTACTTTCGGCACAA 57.797 42.857 0.00 0.00 0.00 3.33
1947 2057 1.745489 ATCTTTCGGCGGCAAGTCC 60.745 57.895 10.53 0.00 0.00 3.85
1992 2108 2.906897 CGTGGTGGCTGCCAAGTT 60.907 61.111 25.23 0.00 40.68 2.66
2101 2217 6.112058 TGGCTAAAAATTGAACTTGCTGTTT 58.888 32.000 0.00 0.00 39.30 2.83
2113 2229 1.008538 GCTGTTTGCGAACCACCTG 60.009 57.895 14.35 1.27 34.80 4.00
2284 2401 4.872691 ACTTCAGCATCACATAGTACTTGC 59.127 41.667 0.00 3.47 0.00 4.01
2319 2436 2.396590 AAACATACGAACCGGCTGAT 57.603 45.000 0.00 0.00 0.00 2.90
2411 2528 8.778358 AGTTCTGAAAAATAAGACAGACATCAC 58.222 33.333 0.00 0.00 38.77 3.06
2434 2551 9.283768 TCACTGTGATGTATACTTCATGTTTTT 57.716 29.630 20.64 4.42 33.49 1.94
2497 2615 4.702392 GTGTAGCTCACATCAAAACTTCG 58.298 43.478 10.30 0.00 45.51 3.79
2510 2628 5.568482 TCAAAACTTCGTCATGAACACTTG 58.432 37.500 0.00 0.00 31.87 3.16
2572 2700 5.806654 ACATGCAACAAGAAATTAACCCT 57.193 34.783 0.00 0.00 0.00 4.34
2575 2703 7.906327 ACATGCAACAAGAAATTAACCCTAAT 58.094 30.769 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 4.442706 TCTATGCTAGCTAAAAGTGCACC 58.557 43.478 17.23 0.00 36.44 5.01
219 220 6.154534 TGTCTAGCCTCTAATCTAGCAACAAA 59.845 38.462 0.00 0.00 33.94 2.83
332 333 3.018856 TGCCTTCTCGATGCATTCATTT 58.981 40.909 0.00 0.00 31.96 2.32
429 430 9.382244 CCAAATTTTGACTAGAAAAGTAAGACG 57.618 33.333 10.72 0.00 39.07 4.18
504 506 3.057876 TCCGCGTACATTTTTCTTTGCAT 60.058 39.130 4.92 0.00 0.00 3.96
580 583 1.592400 GTCGTGTCCGGACCGTTTT 60.592 57.895 31.11 0.00 33.95 2.43
618 621 2.139917 CGTTTTGTCCGGATTCTGTCA 58.860 47.619 7.81 0.00 0.00 3.58
675 678 1.077429 GGATTCACCCTGCCAGACC 60.077 63.158 0.00 0.00 0.00 3.85
676 679 0.393537 CAGGATTCACCCTGCCAGAC 60.394 60.000 0.00 0.00 46.16 3.51
677 680 1.993653 CAGGATTCACCCTGCCAGA 59.006 57.895 0.00 0.00 46.16 3.86
678 681 4.651867 CAGGATTCACCCTGCCAG 57.348 61.111 0.00 0.00 46.16 4.85
683 686 3.411517 CGGCCCAGGATTCACCCT 61.412 66.667 0.00 0.00 40.05 4.34
688 691 4.918201 CTCGGCGGCCCAGGATTC 62.918 72.222 14.55 0.00 0.00 2.52
695 698 2.911332 TATTTCGAACTCGGCGGCCC 62.911 60.000 14.55 0.00 40.29 5.80
696 699 1.519898 TATTTCGAACTCGGCGGCC 60.520 57.895 9.54 9.54 40.29 6.13
697 700 0.804933 AGTATTTCGAACTCGGCGGC 60.805 55.000 7.21 0.00 40.29 6.53
698 701 2.114825 GTAGTATTTCGAACTCGGCGG 58.885 52.381 7.21 0.00 40.29 6.13
699 702 3.062323 AGTAGTATTTCGAACTCGGCG 57.938 47.619 0.00 0.00 40.29 6.46
700 703 4.624452 ACAAAGTAGTATTTCGAACTCGGC 59.376 41.667 0.00 0.00 40.29 5.54
701 704 6.701432 AACAAAGTAGTATTTCGAACTCGG 57.299 37.500 0.00 0.00 40.29 4.63
702 705 8.004585 AGAAACAAAGTAGTATTTCGAACTCG 57.995 34.615 0.00 0.00 36.41 4.18
705 708 9.378597 GGAAAGAAACAAAGTAGTATTTCGAAC 57.621 33.333 0.00 0.00 36.41 3.95
706 709 8.562052 GGGAAAGAAACAAAGTAGTATTTCGAA 58.438 33.333 0.00 0.00 36.41 3.71
707 710 7.095523 CGGGAAAGAAACAAAGTAGTATTTCGA 60.096 37.037 0.00 0.00 36.41 3.71
708 711 7.013529 CGGGAAAGAAACAAAGTAGTATTTCG 58.986 38.462 0.00 0.00 36.41 3.46
709 712 8.091385 TCGGGAAAGAAACAAAGTAGTATTTC 57.909 34.615 0.00 0.00 0.00 2.17
710 713 7.174426 CCTCGGGAAAGAAACAAAGTAGTATTT 59.826 37.037 0.00 0.00 0.00 1.40
711 714 6.653740 CCTCGGGAAAGAAACAAAGTAGTATT 59.346 38.462 0.00 0.00 0.00 1.89
712 715 6.171213 CCTCGGGAAAGAAACAAAGTAGTAT 58.829 40.000 0.00 0.00 0.00 2.12
713 716 5.544650 CCTCGGGAAAGAAACAAAGTAGTA 58.455 41.667 0.00 0.00 0.00 1.82
714 717 4.386711 CCTCGGGAAAGAAACAAAGTAGT 58.613 43.478 0.00 0.00 0.00 2.73
715 718 3.188667 GCCTCGGGAAAGAAACAAAGTAG 59.811 47.826 0.00 0.00 0.00 2.57
716 719 3.143728 GCCTCGGGAAAGAAACAAAGTA 58.856 45.455 0.00 0.00 0.00 2.24
717 720 1.954382 GCCTCGGGAAAGAAACAAAGT 59.046 47.619 0.00 0.00 0.00 2.66
718 721 1.953686 TGCCTCGGGAAAGAAACAAAG 59.046 47.619 0.00 0.00 0.00 2.77
719 722 1.953686 CTGCCTCGGGAAAGAAACAAA 59.046 47.619 0.00 0.00 0.00 2.83
720 723 1.142060 TCTGCCTCGGGAAAGAAACAA 59.858 47.619 0.00 0.00 0.00 2.83
721 724 0.762418 TCTGCCTCGGGAAAGAAACA 59.238 50.000 0.00 0.00 0.00 2.83
722 725 2.010497 GATCTGCCTCGGGAAAGAAAC 58.990 52.381 0.00 0.00 0.00 2.78
723 726 1.065418 GGATCTGCCTCGGGAAAGAAA 60.065 52.381 0.00 0.00 0.00 2.52
724 727 0.541863 GGATCTGCCTCGGGAAAGAA 59.458 55.000 0.00 0.00 0.00 2.52
725 728 1.676678 CGGATCTGCCTCGGGAAAGA 61.677 60.000 0.00 0.00 0.00 2.52
726 729 1.227380 CGGATCTGCCTCGGGAAAG 60.227 63.158 0.00 0.00 0.00 2.62
727 730 1.048724 ATCGGATCTGCCTCGGGAAA 61.049 55.000 0.00 0.00 0.00 3.13
728 731 1.457643 ATCGGATCTGCCTCGGGAA 60.458 57.895 0.00 0.00 0.00 3.97
729 732 1.903890 GATCGGATCTGCCTCGGGA 60.904 63.158 10.73 0.00 0.00 5.14
730 733 2.653702 GATCGGATCTGCCTCGGG 59.346 66.667 10.73 0.00 0.00 5.14
731 734 2.203082 TGGATCGGATCTGCCTCGG 61.203 63.158 16.96 0.00 0.00 4.63
732 735 1.006805 GTGGATCGGATCTGCCTCG 60.007 63.158 16.96 0.00 0.00 4.63
733 736 0.033228 CAGTGGATCGGATCTGCCTC 59.967 60.000 16.96 3.49 0.00 4.70
734 737 0.397675 TCAGTGGATCGGATCTGCCT 60.398 55.000 16.96 8.05 0.00 4.75
735 738 0.683973 ATCAGTGGATCGGATCTGCC 59.316 55.000 16.96 2.79 0.00 4.85
736 739 2.077413 GATCAGTGGATCGGATCTGC 57.923 55.000 16.96 10.26 41.94 4.26
745 748 2.757894 ACTACTCGGGATCAGTGGAT 57.242 50.000 0.00 0.00 36.13 3.41
746 749 2.744166 CGTACTACTCGGGATCAGTGGA 60.744 54.545 0.00 0.00 0.00 4.02
747 750 1.602851 CGTACTACTCGGGATCAGTGG 59.397 57.143 0.00 0.00 0.00 4.00
748 751 2.558378 TCGTACTACTCGGGATCAGTG 58.442 52.381 0.00 0.00 0.00 3.66
749 752 2.941720 GTTCGTACTACTCGGGATCAGT 59.058 50.000 0.00 0.00 0.00 3.41
750 753 2.941064 TGTTCGTACTACTCGGGATCAG 59.059 50.000 0.00 0.00 0.00 2.90
751 754 2.679837 GTGTTCGTACTACTCGGGATCA 59.320 50.000 0.00 0.00 0.00 2.92
752 755 2.679837 TGTGTTCGTACTACTCGGGATC 59.320 50.000 0.00 0.00 0.00 3.36
753 756 2.715046 TGTGTTCGTACTACTCGGGAT 58.285 47.619 0.00 0.00 0.00 3.85
766 769 2.923655 ACGACAGCAGATATTGTGTTCG 59.076 45.455 0.00 0.00 0.00 3.95
770 773 1.328680 GCCACGACAGCAGATATTGTG 59.671 52.381 0.00 0.00 0.00 3.33
813 816 1.608590 CCACTCATGTCCACCAAACAC 59.391 52.381 0.00 0.00 0.00 3.32
814 817 1.214175 ACCACTCATGTCCACCAAACA 59.786 47.619 0.00 0.00 0.00 2.83
820 824 0.108585 ACACCACCACTCATGTCCAC 59.891 55.000 0.00 0.00 0.00 4.02
829 833 0.843309 TTGACATGGACACCACCACT 59.157 50.000 0.00 0.00 43.03 4.00
830 834 1.336755 GTTTGACATGGACACCACCAC 59.663 52.381 0.00 0.00 43.03 4.16
831 835 1.064389 TGTTTGACATGGACACCACCA 60.064 47.619 0.00 0.00 44.41 4.17
869 880 2.161012 GGACTCGTTTTCCCGGATTTTC 59.839 50.000 0.73 0.00 0.00 2.29
874 887 0.034337 CTTGGACTCGTTTTCCCGGA 59.966 55.000 0.73 0.00 31.33 5.14
900 913 3.263170 TGTTTGATTAGTAGCAGCTGGGA 59.737 43.478 17.12 0.00 0.00 4.37
901 914 3.609853 TGTTTGATTAGTAGCAGCTGGG 58.390 45.455 17.12 0.00 0.00 4.45
915 928 6.256053 AGTTGGGTGGATAAAGATGTTTGAT 58.744 36.000 0.00 0.00 0.00 2.57
932 945 3.772572 GCCCATTATTTGGTTAGTTGGGT 59.227 43.478 6.92 0.00 44.83 4.51
953 966 1.419143 GATGCTGCGATCGCTATGC 59.581 57.895 37.01 33.34 42.51 3.14
1011 1039 2.467826 GGCTAAAGCTGCGAGCAGG 61.468 63.158 24.25 10.00 45.56 4.85
1083 1112 3.515630 CTTAGCGCAGATCTCACTTCAA 58.484 45.455 11.47 0.00 0.00 2.69
1095 1126 1.293924 CTGATGAACCCTTAGCGCAG 58.706 55.000 11.47 0.00 0.00 5.18
1233 1269 2.029728 CACGGAATGATCGAGCTTTGTC 59.970 50.000 6.53 0.00 0.00 3.18
1250 1293 3.083349 TCCCTCTGGGCATCACGG 61.083 66.667 0.00 0.00 43.94 4.94
1275 1319 6.347270 TCACTTATAAGACGAGACGAGAAG 57.653 41.667 19.38 0.00 0.00 2.85
1736 1795 5.301555 TCACATGTGTTTATTGACGGAGAA 58.698 37.500 24.63 0.00 0.00 2.87
1737 1796 4.888917 TCACATGTGTTTATTGACGGAGA 58.111 39.130 24.63 0.00 0.00 3.71
1738 1797 5.351189 TCATCACATGTGTTTATTGACGGAG 59.649 40.000 24.63 2.03 0.00 4.63
1739 1798 5.241662 TCATCACATGTGTTTATTGACGGA 58.758 37.500 24.63 5.61 0.00 4.69
1740 1799 5.544136 TCATCACATGTGTTTATTGACGG 57.456 39.130 24.63 3.38 0.00 4.79
1741 1800 7.022979 ACAATCATCACATGTGTTTATTGACG 58.977 34.615 31.61 20.73 33.05 4.35
1742 1801 9.277565 GTACAATCATCACATGTGTTTATTGAC 57.722 33.333 31.61 24.30 33.05 3.18
1743 1802 9.230122 AGTACAATCATCACATGTGTTTATTGA 57.770 29.630 31.61 23.65 33.05 2.57
1744 1803 9.844790 AAGTACAATCATCACATGTGTTTATTG 57.155 29.630 27.16 27.16 33.94 1.90
1745 1804 9.844790 CAAGTACAATCATCACATGTGTTTATT 57.155 29.630 24.63 16.22 0.00 1.40
1746 1805 9.013229 ACAAGTACAATCATCACATGTGTTTAT 57.987 29.630 24.63 11.28 0.00 1.40
1747 1806 8.389779 ACAAGTACAATCATCACATGTGTTTA 57.610 30.769 24.63 9.37 0.00 2.01
1748 1807 7.275888 ACAAGTACAATCATCACATGTGTTT 57.724 32.000 24.63 11.50 0.00 2.83
1749 1808 6.882610 ACAAGTACAATCATCACATGTGTT 57.117 33.333 24.63 14.55 0.00 3.32
1750 1809 6.486320 TGAACAAGTACAATCATCACATGTGT 59.514 34.615 24.63 10.13 0.00 3.72
1751 1810 6.798476 GTGAACAAGTACAATCATCACATGTG 59.202 38.462 20.18 20.18 36.58 3.21
1752 1811 6.072508 GGTGAACAAGTACAATCATCACATGT 60.073 38.462 15.76 0.00 37.91 3.21
1753 1812 6.149973 AGGTGAACAAGTACAATCATCACATG 59.850 38.462 15.76 0.00 37.91 3.21
1754 1813 6.240894 AGGTGAACAAGTACAATCATCACAT 58.759 36.000 15.76 9.37 37.91 3.21
1755 1814 5.620206 AGGTGAACAAGTACAATCATCACA 58.380 37.500 15.76 0.00 37.91 3.58
1756 1815 7.011482 GGATAGGTGAACAAGTACAATCATCAC 59.989 40.741 0.00 3.20 36.01 3.06
1757 1816 7.047891 GGATAGGTGAACAAGTACAATCATCA 58.952 38.462 0.00 0.00 0.00 3.07
1758 1817 6.201044 CGGATAGGTGAACAAGTACAATCATC 59.799 42.308 0.00 0.00 0.00 2.92
1759 1818 6.049149 CGGATAGGTGAACAAGTACAATCAT 58.951 40.000 0.00 0.00 0.00 2.45
1760 1819 5.416083 CGGATAGGTGAACAAGTACAATCA 58.584 41.667 0.00 0.00 0.00 2.57
1761 1820 4.270325 GCGGATAGGTGAACAAGTACAATC 59.730 45.833 0.00 0.00 0.00 2.67
1762 1821 4.189231 GCGGATAGGTGAACAAGTACAAT 58.811 43.478 0.00 0.00 0.00 2.71
1763 1822 3.592059 GCGGATAGGTGAACAAGTACAA 58.408 45.455 0.00 0.00 0.00 2.41
1764 1823 2.093869 GGCGGATAGGTGAACAAGTACA 60.094 50.000 0.00 0.00 0.00 2.90
1765 1824 2.547826 GGCGGATAGGTGAACAAGTAC 58.452 52.381 0.00 0.00 0.00 2.73
1766 1825 1.135527 CGGCGGATAGGTGAACAAGTA 59.864 52.381 0.00 0.00 0.00 2.24
1767 1826 0.108329 CGGCGGATAGGTGAACAAGT 60.108 55.000 0.00 0.00 0.00 3.16
1768 1827 0.108329 ACGGCGGATAGGTGAACAAG 60.108 55.000 13.24 0.00 0.00 3.16
1769 1828 0.390603 CACGGCGGATAGGTGAACAA 60.391 55.000 13.24 0.00 33.58 2.83
1770 1829 1.216977 CACGGCGGATAGGTGAACA 59.783 57.895 13.24 0.00 33.58 3.18
1783 1842 3.822594 TCACATGTGTTTATTCACGGC 57.177 42.857 24.63 0.00 40.74 5.68
1812 1871 8.826710 TGAAAACATAACAGACAAGAGTACAAG 58.173 33.333 0.00 0.00 0.00 3.16
1813 1872 8.609176 GTGAAAACATAACAGACAAGAGTACAA 58.391 33.333 0.00 0.00 0.00 2.41
1816 1875 6.982141 ACGTGAAAACATAACAGACAAGAGTA 59.018 34.615 0.00 0.00 0.00 2.59
1817 1876 5.815740 ACGTGAAAACATAACAGACAAGAGT 59.184 36.000 0.00 0.00 0.00 3.24
1818 1877 6.201044 AGACGTGAAAACATAACAGACAAGAG 59.799 38.462 0.00 0.00 0.00 2.85
1819 1878 6.046593 AGACGTGAAAACATAACAGACAAGA 58.953 36.000 0.00 0.00 0.00 3.02
1822 1881 5.353111 TGAGACGTGAAAACATAACAGACA 58.647 37.500 0.00 0.00 0.00 3.41
1823 1882 5.900339 TGAGACGTGAAAACATAACAGAC 57.100 39.130 0.00 0.00 0.00 3.51
1824 1883 6.307077 CGTATGAGACGTGAAAACATAACAGA 59.693 38.462 0.00 0.00 46.86 3.41
1825 1884 6.458503 CGTATGAGACGTGAAAACATAACAG 58.541 40.000 0.00 0.00 46.86 3.16
1826 1885 6.384178 CGTATGAGACGTGAAAACATAACA 57.616 37.500 0.00 0.00 46.86 2.41
1896 1995 2.159198 AGTACGTCGGACAGTTGTTTGT 60.159 45.455 10.88 0.00 0.00 2.83
1947 2057 0.971386 AAGGCAGCCATGAAAGTTGG 59.029 50.000 15.80 0.00 37.31 3.77
2073 2189 7.092716 CAGCAAGTTCAATTTTTAGCCATACT 58.907 34.615 0.00 0.00 0.00 2.12
2088 2204 1.202245 GGTTCGCAAACAGCAAGTTCA 60.202 47.619 0.00 0.00 46.13 3.18
2101 2217 0.107410 ACAACTTCAGGTGGTTCGCA 60.107 50.000 0.00 0.00 0.00 5.10
2144 2260 5.819901 AGGCGAAAGGAAGAAGATAATTGAG 59.180 40.000 0.00 0.00 0.00 3.02
2156 2272 3.273434 TCATGATCAAGGCGAAAGGAAG 58.727 45.455 0.00 0.00 0.00 3.46
2219 2335 3.004752 AGCCTGGTTATGCTTTCGAAT 57.995 42.857 0.00 0.00 32.94 3.34
2300 2417 2.396590 ATCAGCCGGTTCGTATGTTT 57.603 45.000 1.90 0.00 0.00 2.83
2386 2503 8.778358 AGTGATGTCTGTCTTATTTTTCAGAAC 58.222 33.333 0.00 0.00 38.40 3.01
2497 2615 5.581605 ACATGTTTGTCAAGTGTTCATGAC 58.418 37.500 0.00 0.00 44.84 3.06
2510 2628 6.202954 GGGATGCATACTAGTACATGTTTGTC 59.797 42.308 9.27 0.35 37.28 3.18


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

AutoCloner maintained by Alex Coulton.