Multiple sequence alignment - TraesCS5D01G079200

Loading Multiple Alignment...

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 TraesCS5D01G079200 chr5D 100.000 2319 0 0 1 2319 79893861 79896179 0 4283
1 TraesCS5D01G079200 chr5D 92.121 863 65 3 1 861 163999182 164000043 0 1214
2 TraesCS5D01G079200 chr5D 91.194 863 67 9 1 861 308892715 308891860 0 1164
3 TraesCS5D01G079200 chrUn 97.668 1458 33 1 862 2319 189393401 189394857 0 2503
4 TraesCS5D01G079200 chr5A 97.668 1458 33 1 862 2319 300073841 300075297 0 2503
5 TraesCS5D01G079200 chr5A 97.325 1458 36 2 862 2319 16602059 16600605 0 2473
6 TraesCS5D01G079200 chr2A 97.599 1458 34 1 862 2319 618279094 618277638 0 2497
7 TraesCS5D01G079200 chr5B 97.533 1459 34 2 862 2319 679659758 679661215 0 2494
8 TraesCS5D01G079200 chr7B 97.395 1459 36 2 862 2319 743087060 743088517 0 2483
9 TraesCS5D01G079200 chr7D 97.394 1458 37 1 862 2319 626697628 626696172 0 2481
10 TraesCS5D01G079200 chr7D 97.325 1458 38 1 862 2319 203555484 203554028 0 2475
11 TraesCS5D01G079200 chr7D 91.309 863 58 15 2 861 349498240 349499088 0 1162
12 TraesCS5D01G079200 chr6A 97.257 1458 38 2 862 2319 289129493 289130948 0 2470
13 TraesCS5D01G079200 chr1D 93.072 866 53 5 2 863 318898844 318899706 0 1260
14 TraesCS5D01G079200 chr1D 92.005 863 61 7 1 861 195207308 195206452 0 1205
15 TraesCS5D01G079200 chr1D 91.088 864 69 8 1 861 373777308 373776450 0 1162
16 TraesCS5D01G079200 chr1D 91.067 862 69 8 1 861 76526257 76527111 0 1158
17 TraesCS5D01G079200 chr2D 91.638 861 60 9 3 861 259030131 259030981 0 1181
18 TraesCS5D01G079200 chr3D 91.531 862 64 9 1 861 366541351 366540498 0 1179


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 TraesCS5D01G079200 chr5D 79893861 79896179 2318 False 4283 4283 100.000 1 2319 1 chr5D.!!$F1 2318
1 TraesCS5D01G079200 chr5D 163999182 164000043 861 False 1214 1214 92.121 1 861 1 chr5D.!!$F2 860
2 TraesCS5D01G079200 chr5D 308891860 308892715 855 True 1164 1164 91.194 1 861 1 chr5D.!!$R1 860
3 TraesCS5D01G079200 chrUn 189393401 189394857 1456 False 2503 2503 97.668 862 2319 1 chrUn.!!$F1 1457
4 TraesCS5D01G079200 chr5A 300073841 300075297 1456 False 2503 2503 97.668 862 2319 1 chr5A.!!$F1 1457
5 TraesCS5D01G079200 chr5A 16600605 16602059 1454 True 2473 2473 97.325 862 2319 1 chr5A.!!$R1 1457
6 TraesCS5D01G079200 chr2A 618277638 618279094 1456 True 2497 2497 97.599 862 2319 1 chr2A.!!$R1 1457
7 TraesCS5D01G079200 chr5B 679659758 679661215 1457 False 2494 2494 97.533 862 2319 1 chr5B.!!$F1 1457
8 TraesCS5D01G079200 chr7B 743087060 743088517 1457 False 2483 2483 97.395 862 2319 1 chr7B.!!$F1 1457
9 TraesCS5D01G079200 chr7D 626696172 626697628 1456 True 2481 2481 97.394 862 2319 1 chr7D.!!$R2 1457
10 TraesCS5D01G079200 chr7D 203554028 203555484 1456 True 2475 2475 97.325 862 2319 1 chr7D.!!$R1 1457
11 TraesCS5D01G079200 chr7D 349498240 349499088 848 False 1162 1162 91.309 2 861 1 chr7D.!!$F1 859
12 TraesCS5D01G079200 chr6A 289129493 289130948 1455 False 2470 2470 97.257 862 2319 1 chr6A.!!$F1 1457
13 TraesCS5D01G079200 chr1D 318898844 318899706 862 False 1260 1260 93.072 2 863 1 chr1D.!!$F2 861
14 TraesCS5D01G079200 chr1D 195206452 195207308 856 True 1205 1205 92.005 1 861 1 chr1D.!!$R1 860
15 TraesCS5D01G079200 chr1D 373776450 373777308 858 True 1162 1162 91.088 1 861 1 chr1D.!!$R2 860
16 TraesCS5D01G079200 chr1D 76526257 76527111 854 False 1158 1158 91.067 1 861 1 chr1D.!!$F1 860
17 TraesCS5D01G079200 chr2D 259030131 259030981 850 False 1181 1181 91.638 3 861 1 chr2D.!!$F1 858
18 TraesCS5D01G079200 chr3D 366540498 366541351 853 True 1179 1179 91.531 1 861 1 chr3D.!!$R1 860

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
161 162 0.038166 TGGTGGTGGATTGCCTCTTC 59.962 55.0 0.0 0.0 34.31 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1752 0.761187 AGACTGCTCTGAGTTTGCCA 59.239 50.0 6.53 0.0 0.0 4.92 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
22 23 0.981943 AGTTCTTTCCCACCTACCGG 59.018 55.000 0.00 0.00 0.00 5.28
27 28 2.023695 TCTTTCCCACCTACCGGTCTAT 60.024 50.000 12.40 0.00 43.24 1.98
78 79 0.525882 TCGACGAACTCGCAACACAA 60.526 50.000 0.00 0.00 42.62 3.33
89 90 4.036734 ACTCGCAACACAAAAAGACATGAT 59.963 37.500 0.00 0.00 0.00 2.45
161 162 0.038166 TGGTGGTGGATTGCCTCTTC 59.962 55.000 0.00 0.00 34.31 2.87
250 251 1.754380 TTGTGTGGGTGAGGACTCGG 61.754 60.000 0.00 0.00 0.00 4.63
258 259 1.249407 GTGAGGACTCGGTCAGTTCT 58.751 55.000 6.41 0.00 44.79 3.01
259 260 1.614413 GTGAGGACTCGGTCAGTTCTT 59.386 52.381 6.41 0.00 41.71 2.52
265 266 1.550976 ACTCGGTCAGTTCTTGATCCC 59.449 52.381 0.00 0.00 38.29 3.85
268 269 2.168521 TCGGTCAGTTCTTGATCCCATC 59.831 50.000 0.00 0.00 38.29 3.51
372 374 2.095059 CGAGCAATTTGAAAGGGGACAG 60.095 50.000 0.00 0.00 0.00 3.51
406 408 5.063564 GCTATCCTAACAAAAGTGGTCTTCG 59.936 44.000 0.00 0.00 32.90 3.79
458 460 2.300967 GGCTCCATGGTGACCTCCA 61.301 63.158 17.98 0.00 42.01 3.86
465 467 1.064906 CATGGTGACCTCCATCTTGCT 60.065 52.381 2.11 0.00 45.23 3.91
512 514 2.099098 CACCGATATGGAAACCTTTGCC 59.901 50.000 0.00 0.00 42.00 4.52
577 579 0.759346 AGAGGAAACAAGGACGCTGT 59.241 50.000 0.00 0.00 0.00 4.40
617 619 4.873129 CCCGCCTGGTGTCGATCG 62.873 72.222 9.36 9.36 0.00 3.69
618 620 4.129737 CCGCCTGGTGTCGATCGT 62.130 66.667 15.94 0.00 0.00 3.73
619 621 2.579787 CGCCTGGTGTCGATCGTC 60.580 66.667 15.94 10.48 0.00 4.20
620 622 2.571757 GCCTGGTGTCGATCGTCA 59.428 61.111 15.94 13.37 0.00 4.35
621 623 1.141881 GCCTGGTGTCGATCGTCAT 59.858 57.895 17.63 0.00 0.00 3.06
622 624 1.148157 GCCTGGTGTCGATCGTCATG 61.148 60.000 17.63 10.95 0.00 3.07
623 625 0.528466 CCTGGTGTCGATCGTCATGG 60.528 60.000 17.63 15.27 0.00 3.66
624 626 1.148157 CTGGTGTCGATCGTCATGGC 61.148 60.000 17.63 5.72 0.00 4.40
625 627 1.141881 GGTGTCGATCGTCATGGCT 59.858 57.895 17.63 0.00 0.00 4.75
626 628 0.872021 GGTGTCGATCGTCATGGCTC 60.872 60.000 17.63 5.03 0.00 4.70
627 629 0.179137 GTGTCGATCGTCATGGCTCA 60.179 55.000 17.63 2.54 0.00 4.26
628 630 0.179137 TGTCGATCGTCATGGCTCAC 60.179 55.000 15.94 2.87 0.00 3.51
629 631 1.064134 TCGATCGTCATGGCTCACG 59.936 57.895 15.94 0.00 37.36 4.35
630 632 1.226688 CGATCGTCATGGCTCACGT 60.227 57.895 7.03 0.00 37.30 4.49
631 633 1.202973 CGATCGTCATGGCTCACGTC 61.203 60.000 7.03 0.00 37.30 4.34
632 634 0.179137 GATCGTCATGGCTCACGTCA 60.179 55.000 0.00 0.00 37.30 4.35
633 635 0.458543 ATCGTCATGGCTCACGTCAC 60.459 55.000 0.00 0.00 37.30 3.67
634 636 2.436539 CGTCATGGCTCACGTCACG 61.437 63.158 0.00 0.00 0.00 4.35
635 637 2.432456 TCATGGCTCACGTCACGC 60.432 61.111 0.00 0.00 0.00 5.34
637 639 4.050934 ATGGCTCACGTCACGCGA 62.051 61.111 15.93 0.00 44.77 5.87
638 640 3.971453 ATGGCTCACGTCACGCGAG 62.971 63.158 15.93 10.97 44.77 5.03
641 643 4.406173 CTCACGTCACGCGAGCCT 62.406 66.667 15.93 0.00 44.77 4.58
642 644 4.400109 TCACGTCACGCGAGCCTC 62.400 66.667 15.93 0.00 44.77 4.70
662 664 3.373565 GAGGTTTGCCCCGCCTTG 61.374 66.667 0.00 0.00 34.57 3.61
663 665 3.860930 GAGGTTTGCCCCGCCTTGA 62.861 63.158 0.00 0.00 34.57 3.02
664 666 2.679996 GGTTTGCCCCGCCTTGAT 60.680 61.111 0.00 0.00 0.00 2.57
665 667 1.379309 GGTTTGCCCCGCCTTGATA 60.379 57.895 0.00 0.00 0.00 2.15
666 668 0.755327 GGTTTGCCCCGCCTTGATAT 60.755 55.000 0.00 0.00 0.00 1.63
667 669 0.668535 GTTTGCCCCGCCTTGATATC 59.331 55.000 0.00 0.00 0.00 1.63
668 670 0.550914 TTTGCCCCGCCTTGATATCT 59.449 50.000 3.98 0.00 0.00 1.98
669 671 0.108585 TTGCCCCGCCTTGATATCTC 59.891 55.000 3.98 0.00 0.00 2.75
670 672 1.003233 GCCCCGCCTTGATATCTCC 60.003 63.158 3.98 0.00 0.00 3.71
671 673 1.293498 CCCCGCCTTGATATCTCCG 59.707 63.158 3.98 1.70 0.00 4.63
672 674 1.374758 CCCGCCTTGATATCTCCGC 60.375 63.158 3.98 1.72 0.00 5.54
673 675 1.668294 CCGCCTTGATATCTCCGCT 59.332 57.895 3.98 0.00 0.00 5.52
674 676 0.389166 CCGCCTTGATATCTCCGCTC 60.389 60.000 3.98 0.00 0.00 5.03
675 677 0.389166 CGCCTTGATATCTCCGCTCC 60.389 60.000 3.98 0.00 0.00 4.70
676 678 0.972883 GCCTTGATATCTCCGCTCCT 59.027 55.000 3.98 0.00 0.00 3.69
677 679 1.067213 GCCTTGATATCTCCGCTCCTC 60.067 57.143 3.98 0.00 0.00 3.71
678 680 1.201181 CCTTGATATCTCCGCTCCTCG 59.799 57.143 3.98 0.00 38.08 4.63
679 681 1.883275 CTTGATATCTCCGCTCCTCGT 59.117 52.381 3.98 0.00 36.19 4.18
680 682 1.239347 TGATATCTCCGCTCCTCGTG 58.761 55.000 3.98 0.00 36.19 4.35
681 683 1.202770 TGATATCTCCGCTCCTCGTGA 60.203 52.381 3.98 0.00 36.19 4.35
682 684 1.466950 GATATCTCCGCTCCTCGTGAG 59.533 57.143 0.00 1.12 44.47 3.51
689 691 3.073735 CTCCTCGTGAGCCTGCCT 61.074 66.667 0.00 0.00 33.47 4.75
690 692 3.368190 CTCCTCGTGAGCCTGCCTG 62.368 68.421 0.00 0.00 33.47 4.85
691 693 4.463879 CCTCGTGAGCCTGCCTGG 62.464 72.222 0.00 0.00 39.35 4.45
707 709 3.922640 GGCTAGGCCGCTCCTGAG 61.923 72.222 4.61 0.00 46.98 3.35
708 710 3.922640 GCTAGGCCGCTCCTGAGG 61.923 72.222 0.00 0.00 46.98 3.86
709 711 2.123683 CTAGGCCGCTCCTGAGGA 60.124 66.667 0.00 0.00 46.98 3.71
718 720 1.515020 CTCCTGAGGAGGTCTTGCG 59.485 63.158 20.90 0.00 45.43 4.85
719 721 2.125350 CCTGAGGAGGTCTTGCGC 60.125 66.667 0.00 0.00 34.16 6.09
720 722 2.125350 CTGAGGAGGTCTTGCGCC 60.125 66.667 4.18 0.00 0.00 6.53
721 723 3.997064 CTGAGGAGGTCTTGCGCCG 62.997 68.421 4.18 0.00 0.00 6.46
722 724 4.070552 GAGGAGGTCTTGCGCCGT 62.071 66.667 4.18 0.00 0.00 5.68
723 725 3.991536 GAGGAGGTCTTGCGCCGTC 62.992 68.421 4.18 0.00 0.00 4.79
749 751 2.359975 GAGGTTTGGCCCCTCGTG 60.360 66.667 10.40 0.00 39.22 4.35
750 752 2.852075 AGGTTTGGCCCCTCGTGA 60.852 61.111 0.00 0.00 38.26 4.35
751 753 2.359975 GGTTTGGCCCCTCGTGAG 60.360 66.667 0.00 0.00 0.00 3.51
762 764 0.804989 CCTCGTGAGGGTTTGAATGC 59.195 55.000 8.09 0.00 44.87 3.56
763 765 0.804989 CTCGTGAGGGTTTGAATGCC 59.195 55.000 0.00 0.00 0.00 4.40
764 766 0.400213 TCGTGAGGGTTTGAATGCCT 59.600 50.000 0.00 0.00 0.00 4.75
765 767 1.202879 TCGTGAGGGTTTGAATGCCTT 60.203 47.619 0.00 0.00 0.00 4.35
766 768 1.068333 CGTGAGGGTTTGAATGCCTTG 60.068 52.381 0.00 0.00 0.00 3.61
767 769 1.963515 GTGAGGGTTTGAATGCCTTGT 59.036 47.619 0.00 0.00 0.00 3.16
768 770 2.365293 GTGAGGGTTTGAATGCCTTGTT 59.635 45.455 0.00 0.00 0.00 2.83
769 771 2.364970 TGAGGGTTTGAATGCCTTGTTG 59.635 45.455 0.00 0.00 0.00 3.33
770 772 2.627699 GAGGGTTTGAATGCCTTGTTGA 59.372 45.455 0.00 0.00 0.00 3.18
771 773 3.242011 AGGGTTTGAATGCCTTGTTGAT 58.758 40.909 0.00 0.00 0.00 2.57
772 774 3.007182 AGGGTTTGAATGCCTTGTTGATG 59.993 43.478 0.00 0.00 0.00 3.07
773 775 3.006752 GGGTTTGAATGCCTTGTTGATGA 59.993 43.478 0.00 0.00 0.00 2.92
774 776 4.502950 GGGTTTGAATGCCTTGTTGATGAA 60.503 41.667 0.00 0.00 0.00 2.57
775 777 4.687483 GGTTTGAATGCCTTGTTGATGAAG 59.313 41.667 0.00 0.00 0.00 3.02
776 778 5.509501 GGTTTGAATGCCTTGTTGATGAAGA 60.510 40.000 0.00 0.00 0.00 2.87
777 779 5.988310 TTGAATGCCTTGTTGATGAAGAT 57.012 34.783 0.00 0.00 0.00 2.40
778 780 5.319140 TGAATGCCTTGTTGATGAAGATG 57.681 39.130 0.00 0.00 0.00 2.90
779 781 4.158949 TGAATGCCTTGTTGATGAAGATGG 59.841 41.667 0.00 0.00 0.00 3.51
780 782 2.449464 TGCCTTGTTGATGAAGATGGG 58.551 47.619 0.00 0.00 0.00 4.00
781 783 1.135721 GCCTTGTTGATGAAGATGGGC 59.864 52.381 0.00 0.00 0.00 5.36
782 784 1.753073 CCTTGTTGATGAAGATGGGCC 59.247 52.381 0.00 0.00 0.00 5.80
783 785 2.449464 CTTGTTGATGAAGATGGGCCA 58.551 47.619 9.61 9.61 0.00 5.36
784 786 2.832643 TGTTGATGAAGATGGGCCAT 57.167 45.000 21.39 21.39 0.00 4.40
785 787 3.949586 TGTTGATGAAGATGGGCCATA 57.050 42.857 21.26 3.63 0.00 2.74
786 788 3.554934 TGTTGATGAAGATGGGCCATAC 58.445 45.455 21.26 11.88 0.00 2.39
787 789 3.053768 TGTTGATGAAGATGGGCCATACA 60.054 43.478 21.26 19.31 0.00 2.29
788 790 3.497103 TGATGAAGATGGGCCATACAG 57.503 47.619 21.26 0.00 0.00 2.74
789 791 2.107031 TGATGAAGATGGGCCATACAGG 59.893 50.000 21.26 0.00 41.84 4.00
798 800 2.031163 CCATACAGGCCCGCTAGC 59.969 66.667 4.06 4.06 0.00 3.42
799 801 2.807107 CCATACAGGCCCGCTAGCA 61.807 63.158 16.45 0.00 0.00 3.49
800 802 1.146041 CATACAGGCCCGCTAGCAA 59.854 57.895 16.45 0.00 0.00 3.91
801 803 0.463654 CATACAGGCCCGCTAGCAAA 60.464 55.000 16.45 0.00 0.00 3.68
802 804 0.179045 ATACAGGCCCGCTAGCAAAG 60.179 55.000 16.45 3.26 0.00 2.77
810 812 4.166011 GCTAGCAAAGCCACGCCG 62.166 66.667 10.63 0.00 46.25 6.46
811 813 2.742372 CTAGCAAAGCCACGCCGT 60.742 61.111 0.00 0.00 0.00 5.68
812 814 3.027170 CTAGCAAAGCCACGCCGTG 62.027 63.158 10.95 10.95 0.00 4.94
831 833 3.745803 GCTGCAGGCAGGCAAGTC 61.746 66.667 21.63 1.32 44.40 3.01
832 834 2.033757 CTGCAGGCAGGCAAGTCT 59.966 61.111 13.39 0.00 44.40 3.24
833 835 2.281970 TGCAGGCAGGCAAGTCTG 60.282 61.111 7.14 7.14 43.93 3.51
834 836 3.060615 GCAGGCAGGCAAGTCTGG 61.061 66.667 12.46 0.00 41.45 3.86
835 837 2.360852 CAGGCAGGCAAGTCTGGG 60.361 66.667 3.62 0.00 37.58 4.45
836 838 3.655211 AGGCAGGCAAGTCTGGGG 61.655 66.667 3.62 0.00 35.43 4.96
837 839 3.650950 GGCAGGCAAGTCTGGGGA 61.651 66.667 3.62 0.00 35.43 4.81
838 840 2.360475 GCAGGCAAGTCTGGGGAC 60.360 66.667 3.62 0.00 42.41 4.46
850 852 3.572222 GGGGACCCCCGTTCACAA 61.572 66.667 20.38 0.00 46.66 3.33
851 853 2.516909 GGGACCCCCGTTCACAAA 59.483 61.111 0.00 0.00 32.13 2.83
852 854 1.152715 GGGACCCCCGTTCACAAAA 60.153 57.895 0.00 0.00 32.13 2.44
853 855 1.457823 GGGACCCCCGTTCACAAAAC 61.458 60.000 0.00 0.00 32.13 2.43
854 856 1.650363 GACCCCCGTTCACAAAACG 59.350 57.895 3.46 3.46 42.74 3.60
855 857 2.333581 CCCCCGTTCACAAAACGC 59.666 61.111 4.86 0.00 41.85 4.84
856 858 2.333581 CCCCGTTCACAAAACGCC 59.666 61.111 4.86 0.00 41.85 5.68
857 859 2.051703 CCCGTTCACAAAACGCCG 60.052 61.111 4.86 0.00 41.85 6.46
858 860 2.535788 CCCGTTCACAAAACGCCGA 61.536 57.895 4.86 0.00 41.85 5.54
859 861 1.368374 CCGTTCACAAAACGCCGAC 60.368 57.895 4.86 0.00 41.85 4.79
860 862 1.348938 CGTTCACAAAACGCCGACA 59.651 52.632 0.00 0.00 36.82 4.35
912 915 3.511699 TCGACTCACATTTTGATCTCCG 58.488 45.455 0.00 0.00 32.17 4.63
919 922 3.616821 CACATTTTGATCTCCGACGCTTA 59.383 43.478 0.00 0.00 0.00 3.09
920 923 4.271049 CACATTTTGATCTCCGACGCTTAT 59.729 41.667 0.00 0.00 0.00 1.73
937 940 4.686122 CGCTTATTTTCACAGTCCCCCTAT 60.686 45.833 0.00 0.00 0.00 2.57
940 943 4.946160 ATTTTCACAGTCCCCCTATGAA 57.054 40.909 0.00 0.00 0.00 2.57
941 944 4.946160 TTTTCACAGTCCCCCTATGAAT 57.054 40.909 0.00 0.00 0.00 2.57
1018 1021 7.674471 TTCAATATGTTGATTGTACCGAACA 57.326 32.000 5.66 0.00 43.49 3.18
1019 1022 7.302350 TCAATATGTTGATTGTACCGAACAG 57.698 36.000 0.03 0.00 39.36 3.16
1075 1078 2.822764 GTTTGAGGAAGTCACACGTCT 58.177 47.619 0.00 0.00 33.71 4.18
1312 1693 9.282247 CTACACATAAATCAAAGAAGCATTGTC 57.718 33.333 0.00 0.00 0.00 3.18
1327 1708 4.158394 AGCATTGTCGAATAGTGGCATTTT 59.842 37.500 0.00 0.00 0.00 1.82
1371 1752 0.104120 GAAAGGGTTGCCGCAAAACT 59.896 50.000 7.54 6.19 0.00 2.66
1386 1768 2.057137 AAACTGGCAAACTCAGAGCA 57.943 45.000 0.00 0.00 36.22 4.26
1425 1807 0.321387 AGCATAGCGGCATCATCCAG 60.321 55.000 1.45 0.00 35.83 3.86
1428 1810 1.771783 ATAGCGGCATCATCCAGGCA 61.772 55.000 1.45 0.00 0.00 4.75
1588 2112 8.771521 ACTGATTCATCCAATCCAATTTGATA 57.228 30.769 0.00 0.00 40.44 2.15
1686 2210 6.070309 GCTATCTATCCAGATCAGGGTTGAAT 60.070 42.308 5.70 0.00 40.81 2.57
1737 2261 8.225603 ACATAAATCCATTGCGATTAGAAACT 57.774 30.769 0.00 0.00 32.12 2.66
1799 2323 1.512735 AGAATGGGGAGTTAGGGCTC 58.487 55.000 0.00 0.00 34.89 4.70
1866 2390 3.914312 TGCGGACTCACTTCTCTTTTAG 58.086 45.455 0.00 0.00 0.00 1.85
1912 2436 6.828785 AGTTGTCTAATTATGTGGGTGAATCC 59.171 38.462 0.00 0.00 0.00 3.01
1962 2486 3.326297 GGTAGAAGATTGGGCTCTGCTAT 59.674 47.826 0.00 0.00 36.11 2.97
1998 2522 5.148651 ACTAGGAAAGAAGTACGCATTGT 57.851 39.130 0.00 0.00 0.00 2.71
2041 2565 9.386010 CGATCCTAGTTACTAGTAGCTAATCAT 57.614 37.037 23.90 17.34 32.62 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.535833 TAGCGAGCTAGGGCATAGAC 58.464 55.000 10.88 1.48 41.70 2.59
27 28 0.962489 GATCTTAGCGAGCTAGGGCA 59.038 55.000 13.12 0.00 41.70 5.36
89 90 4.443739 CGGTGGCCTGAACCAGTATAAATA 60.444 45.833 11.10 0.00 41.46 1.40
161 162 2.892374 TGTACTGTTCATCATCAGCCG 58.108 47.619 0.00 0.00 35.37 5.52
250 251 2.422093 GGGGATGGGATCAAGAACTGAC 60.422 54.545 0.00 0.00 36.69 3.51
353 354 1.620323 GCTGTCCCCTTTCAAATTGCT 59.380 47.619 0.00 0.00 0.00 3.91
372 374 7.764901 ACTTTTGTTAGGATAGCTTGTACTAGC 59.235 37.037 19.89 19.89 41.53 3.42
390 392 1.676006 CAGGCGAAGACCACTTTTGTT 59.324 47.619 0.00 0.00 31.70 2.83
392 394 0.040067 GCAGGCGAAGACCACTTTTG 60.040 55.000 0.00 0.00 31.70 2.44
417 419 4.025401 CGGCGTCACCACCAAAGC 62.025 66.667 0.00 0.00 39.03 3.51
420 422 3.096633 AAGACGGCGTCACCACCAA 62.097 57.895 37.71 0.00 39.03 3.67
424 426 4.308458 CCCAAGACGGCGTCACCA 62.308 66.667 37.71 0.00 39.03 4.17
447 449 0.325933 CAGCAAGATGGAGGTCACCA 59.674 55.000 0.00 0.00 44.41 4.17
458 460 0.035630 GACCAGCAGGACAGCAAGAT 60.036 55.000 0.35 0.00 38.69 2.40
465 467 1.816863 GACCGAAGACCAGCAGGACA 61.817 60.000 0.35 0.00 38.69 4.02
537 539 2.512515 GTGCTAAGGAGGCAGGCG 60.513 66.667 0.00 0.00 40.54 5.52
603 605 1.141881 ATGACGATCGACACCAGGC 59.858 57.895 24.34 0.00 0.00 4.85
613 615 0.179137 TGACGTGAGCCATGACGATC 60.179 55.000 11.17 6.14 38.94 3.69
614 616 0.458543 GTGACGTGAGCCATGACGAT 60.459 55.000 11.17 0.00 38.94 3.73
615 617 1.080772 GTGACGTGAGCCATGACGA 60.081 57.895 11.17 0.00 38.94 4.20
616 618 2.436539 CGTGACGTGAGCCATGACG 61.437 63.158 0.00 0.00 41.41 4.35
617 619 2.730672 GCGTGACGTGAGCCATGAC 61.731 63.158 6.91 0.00 0.00 3.06
618 620 2.432456 GCGTGACGTGAGCCATGA 60.432 61.111 6.91 0.00 0.00 3.07
619 621 3.842126 CGCGTGACGTGAGCCATG 61.842 66.667 14.00 0.00 39.94 3.66
620 622 4.050934 TCGCGTGACGTGAGCCAT 62.051 61.111 17.99 0.00 41.48 4.40
625 627 4.400109 GAGGCTCGCGTGACGTGA 62.400 66.667 20.57 20.57 44.12 4.35
645 647 3.373565 CAAGGCGGGGCAAACCTC 61.374 66.667 0.00 0.00 40.03 3.85
646 648 1.858739 TATCAAGGCGGGGCAAACCT 61.859 55.000 0.00 0.00 40.03 3.50
647 649 0.755327 ATATCAAGGCGGGGCAAACC 60.755 55.000 0.00 0.00 39.11 3.27
648 650 0.668535 GATATCAAGGCGGGGCAAAC 59.331 55.000 0.00 0.00 0.00 2.93
649 651 0.550914 AGATATCAAGGCGGGGCAAA 59.449 50.000 5.32 0.00 0.00 3.68
650 652 0.108585 GAGATATCAAGGCGGGGCAA 59.891 55.000 5.32 0.00 0.00 4.52
651 653 1.754745 GAGATATCAAGGCGGGGCA 59.245 57.895 5.32 0.00 0.00 5.36
652 654 1.003233 GGAGATATCAAGGCGGGGC 60.003 63.158 5.32 0.00 0.00 5.80
653 655 1.293498 CGGAGATATCAAGGCGGGG 59.707 63.158 5.32 0.00 0.00 5.73
654 656 1.374758 GCGGAGATATCAAGGCGGG 60.375 63.158 5.32 0.00 0.00 6.13
655 657 0.389166 GAGCGGAGATATCAAGGCGG 60.389 60.000 5.32 0.00 0.00 6.13
656 658 0.389166 GGAGCGGAGATATCAAGGCG 60.389 60.000 5.32 0.00 0.00 5.52
657 659 0.972883 AGGAGCGGAGATATCAAGGC 59.027 55.000 5.32 4.74 0.00 4.35
658 660 1.201181 CGAGGAGCGGAGATATCAAGG 59.799 57.143 5.32 0.00 36.03 3.61
659 661 1.883275 ACGAGGAGCGGAGATATCAAG 59.117 52.381 5.32 0.00 46.49 3.02
660 662 1.609072 CACGAGGAGCGGAGATATCAA 59.391 52.381 5.32 0.00 46.49 2.57
661 663 1.202770 TCACGAGGAGCGGAGATATCA 60.203 52.381 5.32 0.00 46.49 2.15
662 664 1.466950 CTCACGAGGAGCGGAGATATC 59.533 57.143 0.00 0.00 46.49 1.63
663 665 1.529226 CTCACGAGGAGCGGAGATAT 58.471 55.000 0.00 0.00 46.49 1.63
664 666 3.008141 CTCACGAGGAGCGGAGATA 57.992 57.895 0.00 0.00 46.49 1.98
665 667 3.834726 CTCACGAGGAGCGGAGAT 58.165 61.111 0.00 0.00 46.49 2.75
672 674 3.073735 AGGCAGGCTCACGAGGAG 61.074 66.667 0.00 0.00 46.93 3.69
673 675 3.385384 CAGGCAGGCTCACGAGGA 61.385 66.667 0.00 0.00 0.00 3.71
674 676 4.463879 CCAGGCAGGCTCACGAGG 62.464 72.222 0.00 0.00 0.00 4.63
699 701 2.570582 CGCAAGACCTCCTCAGGAGC 62.571 65.000 16.33 2.35 44.63 4.70
700 702 1.515020 CGCAAGACCTCCTCAGGAG 59.485 63.158 14.68 14.68 45.26 3.69
701 703 2.650116 GCGCAAGACCTCCTCAGGA 61.650 63.158 0.30 0.00 41.10 3.86
702 704 2.125350 GCGCAAGACCTCCTCAGG 60.125 66.667 0.30 0.00 41.87 3.86
703 705 2.125350 GGCGCAAGACCTCCTCAG 60.125 66.667 10.83 0.00 42.36 3.35
733 735 2.852075 TCACGAGGGGCCAAACCT 60.852 61.111 4.39 0.55 42.18 3.50
734 736 2.359975 CTCACGAGGGGCCAAACC 60.360 66.667 4.39 0.00 37.93 3.27
735 737 2.359975 CCTCACGAGGGGCCAAAC 60.360 66.667 4.39 0.00 44.87 2.93
744 746 0.804989 GGCATTCAAACCCTCACGAG 59.195 55.000 0.00 0.00 0.00 4.18
745 747 0.400213 AGGCATTCAAACCCTCACGA 59.600 50.000 0.00 0.00 0.00 4.35
746 748 1.068333 CAAGGCATTCAAACCCTCACG 60.068 52.381 0.00 0.00 0.00 4.35
747 749 1.963515 ACAAGGCATTCAAACCCTCAC 59.036 47.619 0.00 0.00 0.00 3.51
748 750 2.364970 CAACAAGGCATTCAAACCCTCA 59.635 45.455 0.00 0.00 0.00 3.86
749 751 2.627699 TCAACAAGGCATTCAAACCCTC 59.372 45.455 0.00 0.00 0.00 4.30
750 752 2.676748 TCAACAAGGCATTCAAACCCT 58.323 42.857 0.00 0.00 0.00 4.34
751 753 3.006752 TCATCAACAAGGCATTCAAACCC 59.993 43.478 0.00 0.00 0.00 4.11
752 754 4.255833 TCATCAACAAGGCATTCAAACC 57.744 40.909 0.00 0.00 0.00 3.27
753 755 5.531634 TCTTCATCAACAAGGCATTCAAAC 58.468 37.500 0.00 0.00 0.00 2.93
754 756 5.787953 TCTTCATCAACAAGGCATTCAAA 57.212 34.783 0.00 0.00 0.00 2.69
755 757 5.336929 CCATCTTCATCAACAAGGCATTCAA 60.337 40.000 0.00 0.00 0.00 2.69
756 758 4.158949 CCATCTTCATCAACAAGGCATTCA 59.841 41.667 0.00 0.00 0.00 2.57
757 759 4.441079 CCCATCTTCATCAACAAGGCATTC 60.441 45.833 0.00 0.00 0.00 2.67
758 760 3.449737 CCCATCTTCATCAACAAGGCATT 59.550 43.478 0.00 0.00 0.00 3.56
759 761 3.028850 CCCATCTTCATCAACAAGGCAT 58.971 45.455 0.00 0.00 0.00 4.40
760 762 2.449464 CCCATCTTCATCAACAAGGCA 58.551 47.619 0.00 0.00 0.00 4.75
761 763 1.135721 GCCCATCTTCATCAACAAGGC 59.864 52.381 0.00 0.00 0.00 4.35
762 764 1.753073 GGCCCATCTTCATCAACAAGG 59.247 52.381 0.00 0.00 0.00 3.61
763 765 2.449464 TGGCCCATCTTCATCAACAAG 58.551 47.619 0.00 0.00 0.00 3.16
764 766 2.601240 TGGCCCATCTTCATCAACAA 57.399 45.000 0.00 0.00 0.00 2.83
765 767 2.832643 ATGGCCCATCTTCATCAACA 57.167 45.000 0.00 0.00 0.00 3.33
766 768 3.554934 TGTATGGCCCATCTTCATCAAC 58.445 45.455 0.00 0.00 0.00 3.18
767 769 3.435457 CCTGTATGGCCCATCTTCATCAA 60.435 47.826 0.00 0.00 0.00 2.57
768 770 2.107031 CCTGTATGGCCCATCTTCATCA 59.893 50.000 0.00 0.00 0.00 3.07
769 771 2.787994 CCTGTATGGCCCATCTTCATC 58.212 52.381 0.00 0.00 0.00 2.92
770 772 2.965671 CCTGTATGGCCCATCTTCAT 57.034 50.000 0.00 0.00 0.00 2.57
781 783 2.031163 GCTAGCGGGCCTGTATGG 59.969 66.667 14.55 5.67 39.35 2.74
782 784 0.463654 TTTGCTAGCGGGCCTGTATG 60.464 55.000 14.55 4.47 0.00 2.39
783 785 0.179045 CTTTGCTAGCGGGCCTGTAT 60.179 55.000 14.55 4.96 0.00 2.29
784 786 1.220749 CTTTGCTAGCGGGCCTGTA 59.779 57.895 14.55 3.62 0.00 2.74
785 787 2.045926 CTTTGCTAGCGGGCCTGT 60.046 61.111 14.55 2.47 0.00 4.00
786 788 3.512516 GCTTTGCTAGCGGGCCTG 61.513 66.667 7.41 7.41 40.71 4.85
794 796 2.742372 ACGGCGTGGCTTTGCTAG 60.742 61.111 13.76 0.00 0.00 3.42
795 797 3.047280 CACGGCGTGGCTTTGCTA 61.047 61.111 31.19 0.00 0.00 3.49
814 816 3.745803 GACTTGCCTGCCTGCAGC 61.746 66.667 13.63 9.62 43.21 5.25
815 817 2.033757 AGACTTGCCTGCCTGCAG 59.966 61.111 12.17 12.17 43.21 4.41
816 818 2.281970 CAGACTTGCCTGCCTGCA 60.282 61.111 0.00 0.00 40.07 4.41
817 819 3.060615 CCAGACTTGCCTGCCTGC 61.061 66.667 0.00 0.00 32.97 4.85
818 820 2.360852 CCCAGACTTGCCTGCCTG 60.361 66.667 0.00 0.00 32.97 4.85
819 821 3.655211 CCCCAGACTTGCCTGCCT 61.655 66.667 0.00 0.00 32.97 4.75
820 822 3.650950 TCCCCAGACTTGCCTGCC 61.651 66.667 0.00 0.00 32.97 4.85
821 823 2.360475 GTCCCCAGACTTGCCTGC 60.360 66.667 0.00 0.00 40.10 4.85
822 824 2.352805 GGTCCCCAGACTTGCCTG 59.647 66.667 0.00 0.00 43.05 4.85
823 825 2.936032 GGGTCCCCAGACTTGCCT 60.936 66.667 0.00 0.00 43.05 4.75
824 826 4.048470 GGGGTCCCCAGACTTGCC 62.048 72.222 23.53 0.00 44.65 4.52
834 836 1.152715 TTTTGTGAACGGGGGTCCC 60.153 57.895 0.00 0.00 41.09 4.46
835 837 1.788067 CGTTTTGTGAACGGGGGTCC 61.788 60.000 3.56 0.00 39.73 4.46
836 838 1.650363 CGTTTTGTGAACGGGGGTC 59.350 57.895 3.56 0.00 39.73 4.46
837 839 2.483197 GCGTTTTGTGAACGGGGGT 61.483 57.895 12.45 0.00 43.25 4.95
838 840 2.333581 GCGTTTTGTGAACGGGGG 59.666 61.111 12.45 0.00 43.25 5.40
839 841 2.333581 GGCGTTTTGTGAACGGGG 59.666 61.111 12.45 0.00 43.25 5.73
840 842 2.051703 CGGCGTTTTGTGAACGGG 60.052 61.111 12.45 0.00 43.25 5.28
841 843 1.368374 GTCGGCGTTTTGTGAACGG 60.368 57.895 6.85 0.00 43.25 4.44
842 844 0.041663 ATGTCGGCGTTTTGTGAACG 60.042 50.000 6.85 6.92 45.56 3.95
843 845 2.113910 AATGTCGGCGTTTTGTGAAC 57.886 45.000 6.85 0.00 0.00 3.18
844 846 2.541999 GGAAATGTCGGCGTTTTGTGAA 60.542 45.455 8.88 0.00 34.27 3.18
845 847 1.002251 GGAAATGTCGGCGTTTTGTGA 60.002 47.619 8.88 0.00 34.27 3.58
846 848 1.001815 AGGAAATGTCGGCGTTTTGTG 60.002 47.619 8.88 0.00 34.27 3.33
847 849 1.001815 CAGGAAATGTCGGCGTTTTGT 60.002 47.619 8.88 0.00 34.27 2.83
848 850 1.685302 CAGGAAATGTCGGCGTTTTG 58.315 50.000 8.88 0.17 34.27 2.44
849 851 0.039527 GCAGGAAATGTCGGCGTTTT 60.040 50.000 8.88 5.86 34.27 2.43
850 852 0.889186 AGCAGGAAATGTCGGCGTTT 60.889 50.000 6.98 6.98 36.61 3.60
851 853 0.889186 AAGCAGGAAATGTCGGCGTT 60.889 50.000 6.85 0.00 31.88 4.84
852 854 1.298859 GAAGCAGGAAATGTCGGCGT 61.299 55.000 6.85 0.00 31.88 5.68
853 855 1.425428 GAAGCAGGAAATGTCGGCG 59.575 57.895 0.00 0.00 31.88 6.46
854 856 1.657751 GGGAAGCAGGAAATGTCGGC 61.658 60.000 0.00 0.00 0.00 5.54
855 857 1.032114 GGGGAAGCAGGAAATGTCGG 61.032 60.000 0.00 0.00 0.00 4.79
856 858 0.035056 AGGGGAAGCAGGAAATGTCG 60.035 55.000 0.00 0.00 0.00 4.35
857 859 2.222227 AAGGGGAAGCAGGAAATGTC 57.778 50.000 0.00 0.00 0.00 3.06
858 860 2.702270 AAAGGGGAAGCAGGAAATGT 57.298 45.000 0.00 0.00 0.00 2.71
859 861 4.322725 GGTAAAAAGGGGAAGCAGGAAATG 60.323 45.833 0.00 0.00 0.00 2.32
860 862 3.838317 GGTAAAAAGGGGAAGCAGGAAAT 59.162 43.478 0.00 0.00 0.00 2.17
912 915 2.418976 GGGGACTGTGAAAATAAGCGTC 59.581 50.000 0.00 0.00 0.00 5.19
937 940 3.855255 TCATTGATTCCGGGCTATTCA 57.145 42.857 0.00 0.00 0.00 2.57
940 943 2.711009 TCCTTCATTGATTCCGGGCTAT 59.289 45.455 0.00 0.00 0.00 2.97
941 944 2.104792 CTCCTTCATTGATTCCGGGCTA 59.895 50.000 0.00 0.00 0.00 3.93
1018 1021 4.487714 TTCGTGATAAGGCAAATCCTCT 57.512 40.909 0.00 0.00 46.94 3.69
1019 1022 4.496507 GCTTTCGTGATAAGGCAAATCCTC 60.497 45.833 0.00 0.00 46.94 3.71
1312 1693 5.231991 GCCATTAACAAAATGCCACTATTCG 59.768 40.000 0.00 0.00 0.00 3.34
1327 1708 9.290988 TCACTAAGAACATTTTAGCCATTAACA 57.709 29.630 0.00 0.00 32.58 2.41
1371 1752 0.761187 AGACTGCTCTGAGTTTGCCA 59.239 50.000 6.53 0.00 0.00 4.92
1386 1768 4.774726 TGCTCCTATTCACTTTCAGAGACT 59.225 41.667 0.00 0.00 0.00 3.24
1425 1807 0.868406 CTGAGGAGACGTGTTTTGCC 59.132 55.000 0.00 0.00 0.00 4.52
1428 1810 3.458189 CTTGACTGAGGAGACGTGTTTT 58.542 45.455 0.00 0.00 0.00 2.43
1686 2210 1.614996 TGGCTTTTCCATTCGCTTCA 58.385 45.000 0.00 0.00 40.72 3.02
1737 2261 1.960471 GCCCTGGCTGTAGAGTCACTA 60.960 57.143 0.00 0.00 38.26 2.74
1799 2323 1.980052 TGGCTACAGAGGAAACCGG 59.020 57.895 0.00 0.00 0.00 5.28
1866 2390 7.342026 ACAACTTGGATAATAAAAGTCATCCCC 59.658 37.037 0.00 0.00 36.85 4.81
1896 2420 5.708736 TGTACTGGATTCACCCACATAAT 57.291 39.130 0.00 0.00 38.00 1.28
1900 2424 2.439880 TGTTGTACTGGATTCACCCACA 59.560 45.455 0.00 0.00 38.00 4.17
1912 2436 4.302455 CTCTGACCTGACTTGTTGTACTG 58.698 47.826 0.00 0.00 0.00 2.74
1962 2486 2.820178 TCCTAGTTGAGTGGATCTGCA 58.180 47.619 0.00 0.00 0.00 4.41
1998 2522 3.807622 GGATCGTTCAAACAGTCAGTCAA 59.192 43.478 0.00 0.00 0.00 3.18
2041 2565 1.982395 CGGCCACCCTACTCTGACA 60.982 63.158 2.24 0.00 0.00 3.58
2083 2607 4.884164 AGTAGAGTCTGTGCTTTGCTTTTT 59.116 37.500 1.86 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.