Multiple sequence alignment - TraesCS4B01G108200

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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 TraesCS4B01G108200 chr4B 100.000 2723 0 0 1 2723 119110544 119107822 0.000000e+00 5029
1 TraesCS4B01G108200 chr4A 98.778 900 8 2 857 1754 496114994 496114096 0.000000e+00 1598
2 TraesCS4B01G108200 chr4A 84.053 972 100 25 1758 2723 448728585 448729507 0.000000e+00 885
3 TraesCS4B01G108200 chr4A 88.854 646 46 15 66 698 496115613 496114981 0.000000e+00 771
4 TraesCS4B01G108200 chr4D 98.667 900 10 1 857 1754 84173847 84172948 0.000000e+00 1594
5 TraesCS4B01G108200 chr4D 87.955 714 51 18 1 698 84174528 84173834 0.000000e+00 809
6 TraesCS4B01G108200 chr4D 80.797 276 29 15 2 254 93088604 93088330 7.690000e-46 195
7 TraesCS4B01G108200 chr4D 91.200 125 9 2 2538 2660 132773708 132773584 4.660000e-38 169
8 TraesCS4B01G108200 chr7D 89.592 932 79 14 1757 2674 46834733 46833806 0.000000e+00 1168
9 TraesCS4B01G108200 chr7D 77.917 240 42 9 2207 2440 351655872 351656106 3.660000e-29 139
10 TraesCS4B01G108200 chr7D 95.588 68 3 0 2205 2272 46834107 46834040 2.870000e-20 110
11 TraesCS4B01G108200 chr5B 82.418 1001 109 37 1757 2723 297975025 297975992 0.000000e+00 811
12 TraesCS4B01G108200 chr5B 96.364 165 5 1 694 858 690679532 690679695 1.240000e-68 270
13 TraesCS4B01G108200 chr5A 83.042 973 88 33 1757 2723 571709448 571708547 0.000000e+00 811
14 TraesCS4B01G108200 chr5A 97.436 156 4 0 699 854 33873152 33872997 1.610000e-67 267
15 TraesCS4B01G108200 chr5A 96.815 157 5 0 698 854 437034024 437033868 2.080000e-66 263
16 TraesCS4B01G108200 chr3D 88.043 644 45 11 1757 2375 569774578 569775214 0.000000e+00 734
17 TraesCS4B01G108200 chr3D 87.605 476 37 1 2248 2723 569775023 569775476 1.440000e-147 532
18 TraesCS4B01G108200 chr3D 82.135 431 62 12 2205 2628 1227110 1226688 3.330000e-94 355
19 TraesCS4B01G108200 chr3D 92.647 136 10 0 2205 2340 1227047 1226912 2.140000e-46 196
20 TraesCS4B01G108200 chr3D 91.579 95 8 0 2248 2342 1227108 1227014 6.120000e-27 132
21 TraesCS4B01G108200 chr1B 96.875 160 5 0 699 858 600259103 600258944 4.470000e-68 268
22 TraesCS4B01G108200 chr2B 97.436 156 4 0 699 854 186376282 186376127 1.610000e-67 267
23 TraesCS4B01G108200 chr3A 97.419 155 4 0 699 853 34441014 34440860 5.780000e-67 265
24 TraesCS4B01G108200 chr3A 94.611 167 6 2 694 857 602890256 602890422 3.480000e-64 255
25 TraesCS4B01G108200 chrUn 96.795 156 5 0 699 854 82169416 82169261 7.480000e-66 261
26 TraesCS4B01G108200 chr2A 95.706 163 6 1 693 854 59936176 59936014 7.480000e-66 261
27 TraesCS4B01G108200 chr2D 92.000 125 8 2 2538 2660 613124834 613124958 1.000000e-39 174
28 TraesCS4B01G108200 chr2D 88.489 139 13 3 2538 2674 613449184 613449047 6.030000e-37 165


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 TraesCS4B01G108200 chr4B 119107822 119110544 2722 True 5029.0 5029 100.000 1 2723 1 chr4B.!!$R1 2722
1 TraesCS4B01G108200 chr4A 496114096 496115613 1517 True 1184.5 1598 93.816 66 1754 2 chr4A.!!$R1 1688
2 TraesCS4B01G108200 chr4A 448728585 448729507 922 False 885.0 885 84.053 1758 2723 1 chr4A.!!$F1 965
3 TraesCS4B01G108200 chr4D 84172948 84174528 1580 True 1201.5 1594 93.311 1 1754 2 chr4D.!!$R3 1753
4 TraesCS4B01G108200 chr7D 46833806 46834733 927 True 639.0 1168 92.590 1757 2674 2 chr7D.!!$R1 917
5 TraesCS4B01G108200 chr5B 297975025 297975992 967 False 811.0 811 82.418 1757 2723 1 chr5B.!!$F1 966
6 TraesCS4B01G108200 chr5A 571708547 571709448 901 True 811.0 811 83.042 1757 2723 1 chr5A.!!$R3 966
7 TraesCS4B01G108200 chr3D 569774578 569775476 898 False 633.0 734 87.824 1757 2723 2 chr3D.!!$F1 966

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
786 802 0.036671 ACCAGAAATTCGTCCCCGAC 60.037 55.0 0.00 0.0 44.13 4.79 F
813 829 0.606673 GAACCCTGGTTGCTGGAGAC 60.607 60.0 6.24 0.0 38.60 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1696 0.610687 GGCTACAGAAGACCAGCACT 59.389 55.0 0.0 0.0 35.69 4.40 R
2123 2156 0.682209 CCCTTGCAGCCAAGCAGTAT 60.682 55.0 0.0 0.0 46.54 2.12 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
63 64 5.452636 GCTTCTAGGGTCCTTCATTGTCTAG 60.453 48.000 0.00 0.00 0.00 2.43
267 275 3.215975 ACGTATCAGTCCCTCTAGCTTC 58.784 50.000 0.00 0.00 0.00 3.86
276 284 1.025812 CCTCTAGCTTCCGACGATGT 58.974 55.000 0.00 0.00 0.00 3.06
352 367 3.004315 CACCACCGCAGTAGAAAATTTGT 59.996 43.478 0.00 0.00 0.00 2.83
391 406 1.075601 AGGGGCTGTTTGGATCAGAA 58.924 50.000 0.00 0.00 35.20 3.02
476 491 0.738389 AAATATTTGGCTCGCCCACG 59.262 50.000 5.33 0.00 45.34 4.94
477 492 1.724582 AATATTTGGCTCGCCCACGC 61.725 55.000 5.33 0.00 45.34 5.34
492 507 3.473647 CGCCCCATCTGCTCTCCA 61.474 66.667 0.00 0.00 0.00 3.86
493 508 2.815945 CGCCCCATCTGCTCTCCAT 61.816 63.158 0.00 0.00 0.00 3.41
551 566 2.286418 CGGCTGAATTGTCCGCTAATTC 60.286 50.000 0.00 0.00 42.22 2.17
555 570 5.065988 GGCTGAATTGTCCGCTAATTCTTTA 59.934 40.000 14.23 0.42 42.31 1.85
568 583 0.742990 TTCTTTAGCGTGCCGATGGG 60.743 55.000 0.00 0.00 0.00 4.00
574 590 4.910585 CGTGCCGATGGGGGTAGC 62.911 72.222 0.00 0.00 35.78 3.58
601 617 4.662961 GGCAGCAACCAAACGGCC 62.663 66.667 0.00 0.00 39.92 6.13
603 619 3.989787 CAGCAACCAAACGGCCCC 61.990 66.667 0.00 0.00 0.00 5.80
632 648 4.079970 TCAGACATCAGAAGGTACTCGTT 58.920 43.478 0.00 0.00 38.49 3.85
642 658 5.696724 CAGAAGGTACTCGTTCACAAATCTT 59.303 40.000 0.00 0.00 38.49 2.40
643 659 5.696724 AGAAGGTACTCGTTCACAAATCTTG 59.303 40.000 0.00 0.00 38.49 3.02
654 670 6.317857 GTTCACAAATCTTGAGGCATACTTC 58.682 40.000 0.00 0.00 0.00 3.01
655 671 5.559770 TCACAAATCTTGAGGCATACTTCA 58.440 37.500 0.00 0.00 0.00 3.02
656 672 6.182627 TCACAAATCTTGAGGCATACTTCAT 58.817 36.000 0.00 0.00 0.00 2.57
658 674 6.750501 CACAAATCTTGAGGCATACTTCATTG 59.249 38.462 0.00 0.00 0.00 2.82
660 676 3.282021 TCTTGAGGCATACTTCATTGGC 58.718 45.455 0.00 0.00 38.60 4.52
661 677 2.804986 TGAGGCATACTTCATTGGCA 57.195 45.000 0.00 0.00 40.61 4.92
662 678 2.646930 TGAGGCATACTTCATTGGCAG 58.353 47.619 0.00 0.00 40.61 4.85
684 700 4.473520 CGCGTTGGAGATGCCCCT 62.474 66.667 0.00 0.00 36.93 4.79
685 701 2.825836 GCGTTGGAGATGCCCCTG 60.826 66.667 0.00 0.00 34.03 4.45
686 702 2.989639 CGTTGGAGATGCCCCTGA 59.010 61.111 0.00 0.00 34.97 3.86
687 703 1.153289 CGTTGGAGATGCCCCTGAG 60.153 63.158 0.00 0.00 34.97 3.35
688 704 1.617018 CGTTGGAGATGCCCCTGAGA 61.617 60.000 0.00 0.00 34.97 3.27
689 705 0.842635 GTTGGAGATGCCCCTGAGAT 59.157 55.000 0.00 0.00 34.97 2.75
690 706 1.135094 TTGGAGATGCCCCTGAGATC 58.865 55.000 0.00 0.00 34.97 2.75
691 707 1.117749 TGGAGATGCCCCTGAGATCG 61.118 60.000 0.00 0.00 34.97 3.69
692 708 1.118356 GGAGATGCCCCTGAGATCGT 61.118 60.000 0.00 0.00 0.00 3.73
693 709 1.621992 GAGATGCCCCTGAGATCGTA 58.378 55.000 0.00 0.00 0.00 3.43
694 710 1.271102 GAGATGCCCCTGAGATCGTAC 59.729 57.143 0.00 0.00 0.00 3.67
695 711 1.133325 AGATGCCCCTGAGATCGTACT 60.133 52.381 0.00 0.00 0.00 2.73
696 712 1.689273 GATGCCCCTGAGATCGTACTT 59.311 52.381 0.00 0.00 0.00 2.24
697 713 1.568504 TGCCCCTGAGATCGTACTTT 58.431 50.000 0.00 0.00 0.00 2.66
698 714 2.742348 TGCCCCTGAGATCGTACTTTA 58.258 47.619 0.00 0.00 0.00 1.85
699 715 3.101437 TGCCCCTGAGATCGTACTTTAA 58.899 45.455 0.00 0.00 0.00 1.52
700 716 3.516300 TGCCCCTGAGATCGTACTTTAAA 59.484 43.478 0.00 0.00 0.00 1.52
701 717 4.020039 TGCCCCTGAGATCGTACTTTAAAA 60.020 41.667 0.00 0.00 0.00 1.52
702 718 4.939439 GCCCCTGAGATCGTACTTTAAAAA 59.061 41.667 0.00 0.00 0.00 1.94
703 719 5.064834 GCCCCTGAGATCGTACTTTAAAAAG 59.935 44.000 0.90 0.90 41.73 2.27
704 720 6.403878 CCCCTGAGATCGTACTTTAAAAAGA 58.596 40.000 9.37 0.00 39.31 2.52
705 721 7.048512 CCCCTGAGATCGTACTTTAAAAAGAT 58.951 38.462 9.37 0.00 39.31 2.40
706 722 7.011482 CCCCTGAGATCGTACTTTAAAAAGATG 59.989 40.741 9.37 0.00 39.31 2.90
707 723 7.764443 CCCTGAGATCGTACTTTAAAAAGATGA 59.236 37.037 9.37 4.48 39.31 2.92
708 724 9.151471 CCTGAGATCGTACTTTAAAAAGATGAA 57.849 33.333 9.37 0.00 39.31 2.57
716 732 9.329913 CGTACTTTAAAAAGATGAAACTCATGG 57.670 33.333 9.37 0.00 37.20 3.66
717 733 9.626045 GTACTTTAAAAAGATGAAACTCATGGG 57.374 33.333 9.37 0.00 37.20 4.00
718 734 7.154656 ACTTTAAAAAGATGAAACTCATGGGC 58.845 34.615 9.37 0.00 37.20 5.36
719 735 6.662865 TTAAAAAGATGAAACTCATGGGCA 57.337 33.333 0.00 0.00 37.20 5.36
720 736 4.525912 AAAAGATGAAACTCATGGGCAC 57.474 40.909 0.00 0.00 37.20 5.01
721 737 3.446442 AAGATGAAACTCATGGGCACT 57.554 42.857 0.00 0.00 37.20 4.40
722 738 4.574674 AAGATGAAACTCATGGGCACTA 57.425 40.909 0.00 0.00 37.20 2.74
723 739 4.148128 AGATGAAACTCATGGGCACTAG 57.852 45.455 0.00 0.00 37.20 2.57
724 740 3.521126 AGATGAAACTCATGGGCACTAGT 59.479 43.478 0.00 0.00 37.20 2.57
725 741 4.716784 AGATGAAACTCATGGGCACTAGTA 59.283 41.667 0.00 0.00 37.20 1.82
726 742 4.202245 TGAAACTCATGGGCACTAGTAC 57.798 45.455 0.00 0.00 0.00 2.73
727 743 3.055385 TGAAACTCATGGGCACTAGTACC 60.055 47.826 3.20 3.20 0.00 3.34
733 749 2.616489 GGGCACTAGTACCCATGGT 58.384 57.895 24.38 1.30 46.22 3.55
734 750 0.916809 GGGCACTAGTACCCATGGTT 59.083 55.000 24.38 0.00 46.22 3.67
735 751 1.283905 GGGCACTAGTACCCATGGTTT 59.716 52.381 24.38 0.00 46.22 3.27
736 752 2.506644 GGGCACTAGTACCCATGGTTTA 59.493 50.000 24.38 0.00 46.22 2.01
737 753 3.137728 GGGCACTAGTACCCATGGTTTAT 59.862 47.826 24.38 0.00 46.22 1.40
738 754 4.385977 GGGCACTAGTACCCATGGTTTATT 60.386 45.833 24.38 1.05 46.22 1.40
739 755 4.578928 GGCACTAGTACCCATGGTTTATTG 59.421 45.833 11.73 3.53 37.09 1.90
740 756 5.433526 GCACTAGTACCCATGGTTTATTGA 58.566 41.667 11.73 0.00 37.09 2.57
741 757 6.062095 GCACTAGTACCCATGGTTTATTGAT 58.938 40.000 11.73 0.00 37.09 2.57
742 758 7.221450 GCACTAGTACCCATGGTTTATTGATA 58.779 38.462 11.73 0.00 37.09 2.15
743 759 7.883311 GCACTAGTACCCATGGTTTATTGATAT 59.117 37.037 11.73 0.00 37.09 1.63
752 768 9.696917 CCCATGGTTTATTGATATAAAAGAAGC 57.303 33.333 11.73 0.00 37.82 3.86
763 779 8.806429 TGATATAAAAGAAGCATCCTTTGTGA 57.194 30.769 0.00 0.00 34.42 3.58
764 780 8.896744 TGATATAAAAGAAGCATCCTTTGTGAG 58.103 33.333 0.00 0.00 34.42 3.51
765 781 9.113838 GATATAAAAGAAGCATCCTTTGTGAGA 57.886 33.333 0.00 0.00 34.42 3.27
766 782 7.765695 ATAAAAGAAGCATCCTTTGTGAGAA 57.234 32.000 0.00 0.00 34.42 2.87
767 783 6.469782 AAAAGAAGCATCCTTTGTGAGAAA 57.530 33.333 0.00 0.00 34.42 2.52
768 784 5.444663 AAGAAGCATCCTTTGTGAGAAAC 57.555 39.130 0.00 0.00 0.00 2.78
769 785 3.823304 AGAAGCATCCTTTGTGAGAAACC 59.177 43.478 0.00 0.00 0.00 3.27
770 786 3.228188 AGCATCCTTTGTGAGAAACCA 57.772 42.857 0.00 0.00 0.00 3.67
771 787 3.152341 AGCATCCTTTGTGAGAAACCAG 58.848 45.455 0.00 0.00 0.00 4.00
772 788 3.149196 GCATCCTTTGTGAGAAACCAGA 58.851 45.455 0.00 0.00 0.00 3.86
773 789 3.569701 GCATCCTTTGTGAGAAACCAGAA 59.430 43.478 0.00 0.00 0.00 3.02
774 790 4.037923 GCATCCTTTGTGAGAAACCAGAAA 59.962 41.667 0.00 0.00 0.00 2.52
775 791 5.279156 GCATCCTTTGTGAGAAACCAGAAAT 60.279 40.000 0.00 0.00 30.53 2.17
776 792 6.739565 GCATCCTTTGTGAGAAACCAGAAATT 60.740 38.462 0.00 0.00 30.53 1.82
777 793 6.391227 TCCTTTGTGAGAAACCAGAAATTC 57.609 37.500 0.00 0.00 30.53 2.17
778 794 5.008613 TCCTTTGTGAGAAACCAGAAATTCG 59.991 40.000 0.00 0.00 30.53 3.34
779 795 5.221048 CCTTTGTGAGAAACCAGAAATTCGT 60.221 40.000 0.00 0.00 30.53 3.85
780 796 5.418310 TTGTGAGAAACCAGAAATTCGTC 57.582 39.130 0.00 0.00 0.00 4.20
781 797 3.813166 TGTGAGAAACCAGAAATTCGTCC 59.187 43.478 0.00 0.00 0.00 4.79
782 798 3.188667 GTGAGAAACCAGAAATTCGTCCC 59.811 47.826 0.00 0.00 0.00 4.46
783 799 2.747989 GAGAAACCAGAAATTCGTCCCC 59.252 50.000 0.00 0.00 0.00 4.81
784 800 1.467342 GAAACCAGAAATTCGTCCCCG 59.533 52.381 0.00 0.00 0.00 5.73
785 801 0.688487 AACCAGAAATTCGTCCCCGA 59.312 50.000 0.00 0.00 42.41 5.14
786 802 0.036671 ACCAGAAATTCGTCCCCGAC 60.037 55.000 0.00 0.00 44.13 4.79
800 816 4.052229 CGACGTGGCTCGAACCCT 62.052 66.667 16.57 0.00 42.86 4.34
801 817 2.432628 GACGTGGCTCGAACCCTG 60.433 66.667 16.57 0.00 42.86 4.45
802 818 3.934391 GACGTGGCTCGAACCCTGG 62.934 68.421 16.57 0.00 42.86 4.45
803 819 4.003788 CGTGGCTCGAACCCTGGT 62.004 66.667 2.21 0.00 42.86 4.00
804 820 2.430367 GTGGCTCGAACCCTGGTT 59.570 61.111 1.61 0.07 41.54 3.67
805 821 1.966451 GTGGCTCGAACCCTGGTTG 60.966 63.158 6.24 0.00 38.60 3.77
806 822 3.056328 GGCTCGAACCCTGGTTGC 61.056 66.667 6.24 3.86 38.60 4.17
807 823 2.032681 GCTCGAACCCTGGTTGCT 59.967 61.111 6.24 0.00 38.60 3.91
808 824 2.328099 GCTCGAACCCTGGTTGCTG 61.328 63.158 6.24 0.00 38.60 4.41
809 825 1.672356 CTCGAACCCTGGTTGCTGG 60.672 63.158 6.24 0.00 38.60 4.85
810 826 2.111999 CTCGAACCCTGGTTGCTGGA 62.112 60.000 6.24 0.00 38.60 3.86
811 827 1.672356 CGAACCCTGGTTGCTGGAG 60.672 63.158 6.24 0.00 38.60 3.86
812 828 1.761174 GAACCCTGGTTGCTGGAGA 59.239 57.895 6.24 0.00 38.60 3.71
813 829 0.606673 GAACCCTGGTTGCTGGAGAC 60.607 60.000 6.24 0.00 38.60 3.36
814 830 2.046892 CCCTGGTTGCTGGAGACG 60.047 66.667 0.00 0.00 0.00 4.18
815 831 2.743928 CCTGGTTGCTGGAGACGC 60.744 66.667 0.00 0.00 0.00 5.19
816 832 2.743928 CTGGTTGCTGGAGACGCC 60.744 66.667 0.00 0.00 37.10 5.68
817 833 3.535629 CTGGTTGCTGGAGACGCCA 62.536 63.158 0.00 0.00 46.96 5.69
818 834 3.050275 GGTTGCTGGAGACGCCAC 61.050 66.667 0.00 0.00 43.33 5.01
819 835 2.031163 GTTGCTGGAGACGCCACT 59.969 61.111 0.00 0.00 43.33 4.00
820 836 2.031012 TTGCTGGAGACGCCACTG 59.969 61.111 0.00 0.00 43.33 3.66
821 837 4.687215 TGCTGGAGACGCCACTGC 62.687 66.667 0.00 0.00 43.33 4.40
835 851 4.711949 CTGCGCTCCCTTGCCACT 62.712 66.667 9.73 0.00 0.00 4.00
836 852 3.315142 CTGCGCTCCCTTGCCACTA 62.315 63.158 9.73 0.00 0.00 2.74
837 853 2.512515 GCGCTCCCTTGCCACTAG 60.513 66.667 0.00 0.00 0.00 2.57
838 854 2.187946 CGCTCCCTTGCCACTAGG 59.812 66.667 0.00 0.00 38.23 3.02
1317 1333 4.388499 TCCTTCAGGTTCGGCGGC 62.388 66.667 7.21 0.00 36.34 6.53
1754 1772 8.367660 TCTTAGAGCTATGGGTGGATAATTAG 57.632 38.462 0.00 0.00 0.00 1.73
1755 1773 5.428184 AGAGCTATGGGTGGATAATTAGC 57.572 43.478 0.00 0.00 0.00 3.09
1795 1814 3.127533 GCTGATTTCCACGCCGCT 61.128 61.111 0.00 0.00 0.00 5.52
1819 1839 2.970324 GCCTGGAACGCACGACAA 60.970 61.111 0.00 0.00 0.00 3.18
1902 1926 2.204151 CCCACTCCTTCCCACCCT 60.204 66.667 0.00 0.00 0.00 4.34
1917 1949 1.358759 CCCTTTGTTGTCACGCACC 59.641 57.895 0.00 0.00 0.00 5.01
2213 2246 1.550524 TCGGAGCTACAGTGCTTCAAT 59.449 47.619 0.00 0.00 44.17 2.57
2235 2268 2.046988 CATCCGTGGTGCTGCTCA 60.047 61.111 0.00 0.00 0.00 4.26
2394 2468 2.028876 CTTCAATGCAGCATCCATGGA 58.971 47.619 18.88 18.88 0.00 3.41
2444 2518 2.191375 CATCCATGGTGCTCGGCT 59.809 61.111 12.58 0.00 0.00 5.52
2449 2523 3.790437 ATGGTGCTCGGCTGGAGG 61.790 66.667 7.31 0.00 43.36 4.30
2516 2594 0.944386 GGAGTTGCAACGAAGCTTCA 59.056 50.000 25.47 3.89 34.99 3.02
2523 2601 1.714794 CAACGAAGCTTCATCGGAGT 58.285 50.000 25.47 11.48 44.32 3.85
2632 2710 0.895100 GGTTGCAATGGAGCTCACCA 60.895 55.000 17.19 6.29 44.41 4.17
2693 2772 4.451652 GGCGCTGCGTTGAAGCTC 62.452 66.667 24.04 3.64 38.57 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 262 0.183014 ATCGTCGGAAGCTAGAGGGA 59.817 55.000 0.00 0.00 0.00 4.20
267 275 3.560902 ACATAGCTATGACATCGTCGG 57.439 47.619 34.86 9.43 37.15 4.79
352 367 0.040058 ACATGCCTCAAAGCCATGGA 59.960 50.000 18.40 0.00 0.00 3.41
372 387 1.075601 TTCTGATCCAAACAGCCCCT 58.924 50.000 0.00 0.00 35.61 4.79
474 489 3.474570 GGAGAGCAGATGGGGCGT 61.475 66.667 0.00 0.00 36.08 5.68
476 491 1.228184 CATGGAGAGCAGATGGGGC 60.228 63.158 0.00 0.00 0.00 5.80
477 492 0.549950 AACATGGAGAGCAGATGGGG 59.450 55.000 0.00 0.00 0.00 4.96
492 507 8.970020 TCAATATTTTGGCTACAGAATCAACAT 58.030 29.630 0.00 0.00 33.85 2.71
493 508 8.243426 GTCAATATTTTGGCTACAGAATCAACA 58.757 33.333 0.00 0.00 34.53 3.33
583 599 4.999939 GCCGTTTGGTTGCTGCCG 63.000 66.667 0.00 0.00 37.67 5.69
601 617 3.251479 TCTGATGTCTGAAATCACGGG 57.749 47.619 6.42 0.00 30.94 5.28
603 619 4.248859 ACCTTCTGATGTCTGAAATCACG 58.751 43.478 6.42 4.18 34.24 4.35
632 648 5.559770 TGAAGTATGCCTCAAGATTTGTGA 58.440 37.500 0.00 0.00 0.00 3.58
642 658 2.646930 CTGCCAATGAAGTATGCCTCA 58.353 47.619 0.00 0.00 0.00 3.86
643 659 1.952296 CCTGCCAATGAAGTATGCCTC 59.048 52.381 0.00 0.00 0.00 4.70
655 671 4.344865 AACGCGGACCCTGCCAAT 62.345 61.111 12.47 0.00 0.00 3.16
660 676 3.019003 ATCTCCAACGCGGACCCTG 62.019 63.158 12.47 0.00 39.64 4.45
661 677 2.683933 ATCTCCAACGCGGACCCT 60.684 61.111 12.47 0.00 39.64 4.34
662 678 2.511600 CATCTCCAACGCGGACCC 60.512 66.667 12.47 0.00 39.64 4.46
690 706 9.329913 CCATGAGTTTCATCTTTTTAAAGTACG 57.670 33.333 0.00 0.00 34.28 3.67
691 707 9.626045 CCCATGAGTTTCATCTTTTTAAAGTAC 57.374 33.333 0.00 0.00 34.28 2.73
692 708 8.303876 GCCCATGAGTTTCATCTTTTTAAAGTA 58.696 33.333 0.00 0.00 34.28 2.24
693 709 7.154656 GCCCATGAGTTTCATCTTTTTAAAGT 58.845 34.615 0.00 0.00 34.28 2.66
694 710 7.116805 GTGCCCATGAGTTTCATCTTTTTAAAG 59.883 37.037 0.00 0.00 34.28 1.85
695 711 6.928492 GTGCCCATGAGTTTCATCTTTTTAAA 59.072 34.615 0.00 0.00 34.28 1.52
696 712 6.267471 AGTGCCCATGAGTTTCATCTTTTTAA 59.733 34.615 0.00 0.00 34.28 1.52
697 713 5.774690 AGTGCCCATGAGTTTCATCTTTTTA 59.225 36.000 0.00 0.00 34.28 1.52
698 714 4.590222 AGTGCCCATGAGTTTCATCTTTTT 59.410 37.500 0.00 0.00 34.28 1.94
699 715 4.154942 AGTGCCCATGAGTTTCATCTTTT 58.845 39.130 0.00 0.00 34.28 2.27
700 716 3.771216 AGTGCCCATGAGTTTCATCTTT 58.229 40.909 0.00 0.00 34.28 2.52
701 717 3.446442 AGTGCCCATGAGTTTCATCTT 57.554 42.857 0.00 0.00 34.28 2.40
702 718 3.521126 ACTAGTGCCCATGAGTTTCATCT 59.479 43.478 0.00 0.00 34.28 2.90
703 719 3.878778 ACTAGTGCCCATGAGTTTCATC 58.121 45.455 0.00 0.00 34.28 2.92
704 720 4.384208 GGTACTAGTGCCCATGAGTTTCAT 60.384 45.833 18.61 0.00 37.65 2.57
705 721 3.055385 GGTACTAGTGCCCATGAGTTTCA 60.055 47.826 18.61 0.00 0.00 2.69
706 722 3.532542 GGTACTAGTGCCCATGAGTTTC 58.467 50.000 18.61 0.00 0.00 2.78
707 723 3.629142 GGTACTAGTGCCCATGAGTTT 57.371 47.619 18.61 0.00 0.00 2.66
716 732 2.801077 AAACCATGGGTACTAGTGCC 57.199 50.000 20.88 20.88 33.12 5.01
717 733 5.433526 TCAATAAACCATGGGTACTAGTGC 58.566 41.667 18.09 3.50 33.12 4.40
726 742 9.696917 GCTTCTTTTATATCAATAAACCATGGG 57.303 33.333 18.09 0.00 37.30 4.00
737 753 9.241919 TCACAAAGGATGCTTCTTTTATATCAA 57.758 29.630 9.01 0.00 32.72 2.57
738 754 8.806429 TCACAAAGGATGCTTCTTTTATATCA 57.194 30.769 9.01 0.00 32.72 2.15
739 755 9.113838 TCTCACAAAGGATGCTTCTTTTATATC 57.886 33.333 9.01 0.00 32.72 1.63
740 756 9.466497 TTCTCACAAAGGATGCTTCTTTTATAT 57.534 29.630 9.01 0.00 32.72 0.86
741 757 8.862325 TTCTCACAAAGGATGCTTCTTTTATA 57.138 30.769 9.01 0.00 32.72 0.98
742 758 7.765695 TTCTCACAAAGGATGCTTCTTTTAT 57.234 32.000 9.01 0.00 32.72 1.40
743 759 7.425606 GTTTCTCACAAAGGATGCTTCTTTTA 58.574 34.615 9.01 0.00 32.72 1.52
744 760 6.276091 GTTTCTCACAAAGGATGCTTCTTTT 58.724 36.000 0.00 4.13 32.72 2.27
745 761 5.221322 GGTTTCTCACAAAGGATGCTTCTTT 60.221 40.000 0.00 0.00 35.09 2.52
746 762 4.279420 GGTTTCTCACAAAGGATGCTTCTT 59.721 41.667 0.00 0.00 0.00 2.52
747 763 3.823304 GGTTTCTCACAAAGGATGCTTCT 59.177 43.478 0.00 0.00 0.00 2.85
748 764 3.569701 TGGTTTCTCACAAAGGATGCTTC 59.430 43.478 0.00 0.00 0.00 3.86
749 765 3.565307 TGGTTTCTCACAAAGGATGCTT 58.435 40.909 0.00 0.00 0.00 3.91
750 766 3.152341 CTGGTTTCTCACAAAGGATGCT 58.848 45.455 0.00 0.00 0.00 3.79
751 767 3.149196 TCTGGTTTCTCACAAAGGATGC 58.851 45.455 0.00 0.00 0.00 3.91
752 768 5.772825 TTTCTGGTTTCTCACAAAGGATG 57.227 39.130 0.00 0.00 0.00 3.51
753 769 6.294176 CGAATTTCTGGTTTCTCACAAAGGAT 60.294 38.462 0.00 0.00 0.00 3.24
754 770 5.008613 CGAATTTCTGGTTTCTCACAAAGGA 59.991 40.000 0.00 0.00 0.00 3.36
755 771 5.215160 CGAATTTCTGGTTTCTCACAAAGG 58.785 41.667 0.00 0.00 0.00 3.11
756 772 5.821204 ACGAATTTCTGGTTTCTCACAAAG 58.179 37.500 0.00 0.00 0.00 2.77
757 773 5.220970 GGACGAATTTCTGGTTTCTCACAAA 60.221 40.000 0.00 0.00 0.00 2.83
758 774 4.274950 GGACGAATTTCTGGTTTCTCACAA 59.725 41.667 0.00 0.00 0.00 3.33
759 775 3.813166 GGACGAATTTCTGGTTTCTCACA 59.187 43.478 0.00 0.00 0.00 3.58
760 776 3.188667 GGGACGAATTTCTGGTTTCTCAC 59.811 47.826 0.00 0.00 0.00 3.51
761 777 3.408634 GGGACGAATTTCTGGTTTCTCA 58.591 45.455 0.00 0.00 0.00 3.27
762 778 2.747989 GGGGACGAATTTCTGGTTTCTC 59.252 50.000 0.00 0.00 0.00 2.87
763 779 2.791655 GGGGACGAATTTCTGGTTTCT 58.208 47.619 0.00 0.00 0.00 2.52
783 799 4.052229 AGGGTTCGAGCCACGTCG 62.052 66.667 20.67 0.00 43.13 5.12
784 800 2.432628 CAGGGTTCGAGCCACGTC 60.433 66.667 20.67 2.28 43.13 4.34
785 801 4.003788 CCAGGGTTCGAGCCACGT 62.004 66.667 20.67 0.71 43.13 4.49
786 802 3.530910 AACCAGGGTTCGAGCCACG 62.531 63.158 20.67 9.76 38.48 4.94
787 803 1.966451 CAACCAGGGTTCGAGCCAC 60.966 63.158 20.67 9.47 38.48 5.01
788 804 2.429930 CAACCAGGGTTCGAGCCA 59.570 61.111 20.67 0.00 38.48 4.75
789 805 3.056328 GCAACCAGGGTTCGAGCC 61.056 66.667 10.28 10.28 36.00 4.70
790 806 2.032681 AGCAACCAGGGTTCGAGC 59.967 61.111 0.00 2.37 36.00 5.03
791 807 1.672356 CCAGCAACCAGGGTTCGAG 60.672 63.158 0.00 0.00 36.00 4.04
792 808 2.111999 CTCCAGCAACCAGGGTTCGA 62.112 60.000 0.00 0.00 36.00 3.71
793 809 1.672356 CTCCAGCAACCAGGGTTCG 60.672 63.158 0.00 0.00 36.00 3.95
794 810 0.606673 GTCTCCAGCAACCAGGGTTC 60.607 60.000 0.00 0.00 36.00 3.62
795 811 1.456287 GTCTCCAGCAACCAGGGTT 59.544 57.895 0.00 0.00 39.13 4.11
796 812 2.883828 CGTCTCCAGCAACCAGGGT 61.884 63.158 0.00 0.00 0.00 4.34
797 813 2.046892 CGTCTCCAGCAACCAGGG 60.047 66.667 0.00 0.00 0.00 4.45
798 814 2.743928 GCGTCTCCAGCAACCAGG 60.744 66.667 0.00 0.00 34.19 4.45
799 815 2.743928 GGCGTCTCCAGCAACCAG 60.744 66.667 0.00 0.00 36.08 4.00
800 816 3.555324 TGGCGTCTCCAGCAACCA 61.555 61.111 0.00 0.00 40.72 3.67
818 834 3.315142 TAGTGGCAAGGGAGCGCAG 62.315 63.158 11.47 0.00 34.64 5.18
819 835 3.315142 CTAGTGGCAAGGGAGCGCA 62.315 63.158 11.47 0.00 34.64 6.09
820 836 2.512515 CTAGTGGCAAGGGAGCGC 60.513 66.667 0.00 0.00 34.64 5.92
821 837 2.187946 CCTAGTGGCAAGGGAGCG 59.812 66.667 0.00 0.00 34.64 5.03
838 854 2.159028 CCCAGAAGAACTAGGCTGTAGC 60.159 54.545 0.00 0.00 41.14 3.58
839 855 3.366396 TCCCAGAAGAACTAGGCTGTAG 58.634 50.000 0.00 0.00 0.00 2.74
840 856 3.468071 TCCCAGAAGAACTAGGCTGTA 57.532 47.619 0.00 0.00 0.00 2.74
841 857 2.327325 TCCCAGAAGAACTAGGCTGT 57.673 50.000 0.00 0.00 0.00 4.40
842 858 2.223923 CGATCCCAGAAGAACTAGGCTG 60.224 54.545 0.00 0.00 0.00 4.85
843 859 2.035632 CGATCCCAGAAGAACTAGGCT 58.964 52.381 0.00 0.00 0.00 4.58
844 860 1.757699 ACGATCCCAGAAGAACTAGGC 59.242 52.381 0.00 0.00 0.00 3.93
845 861 4.208746 AGTACGATCCCAGAAGAACTAGG 58.791 47.826 0.00 0.00 0.00 3.02
846 862 5.838531 AAGTACGATCCCAGAAGAACTAG 57.161 43.478 0.00 0.00 0.00 2.57
847 863 5.163683 CGAAAGTACGATCCCAGAAGAACTA 60.164 44.000 0.00 0.00 35.09 2.24
848 864 4.380655 CGAAAGTACGATCCCAGAAGAACT 60.381 45.833 0.00 0.00 35.09 3.01
849 865 3.858238 CGAAAGTACGATCCCAGAAGAAC 59.142 47.826 0.00 0.00 35.09 3.01
850 866 3.508793 ACGAAAGTACGATCCCAGAAGAA 59.491 43.478 0.00 0.00 46.88 2.52
851 867 3.087031 ACGAAAGTACGATCCCAGAAGA 58.913 45.455 0.00 0.00 46.88 2.87
852 868 3.505464 ACGAAAGTACGATCCCAGAAG 57.495 47.619 0.00 0.00 46.88 2.85
1680 1696 0.610687 GGCTACAGAAGACCAGCACT 59.389 55.000 0.00 0.00 35.69 4.40
1754 1772 4.201419 CGGCTTAATTTAAACGTTTTCCGC 60.201 41.667 20.19 11.65 41.42 5.54
1755 1773 4.321480 CCGGCTTAATTTAAACGTTTTCCG 59.679 41.667 20.19 16.42 44.03 4.30
1795 1814 2.975799 GCGTTCCAGGCGGTTTGA 60.976 61.111 0.00 0.00 0.00 2.69
1859 1880 1.997669 GTGTGGACACGGAGAAGATC 58.002 55.000 0.00 0.00 37.10 2.75
1902 1926 1.433053 CTCCGGTGCGTGACAACAAA 61.433 55.000 0.00 0.00 34.73 2.83
1917 1949 2.176273 CGCCATGCCTCTTTCTCCG 61.176 63.158 0.00 0.00 0.00 4.63
2067 2099 1.548719 TGTGCTGTATTGTAGCTCCGT 59.451 47.619 0.00 0.00 41.66 4.69
2123 2156 0.682209 CCCTTGCAGCCAAGCAGTAT 60.682 55.000 0.00 0.00 46.54 2.12
2196 2229 2.079158 TGCATTGAAGCACTGTAGCTC 58.921 47.619 0.00 0.00 45.89 4.09
2201 2234 2.723231 TGCTGCATTGAAGCACTGT 58.277 47.368 15.62 0.00 45.50 3.55
2235 2268 3.509137 TTGAAGCTTCGTCGCCGGT 62.509 57.895 21.11 0.00 33.95 5.28
2342 2416 2.125912 CGTTGCAGCTCTACCGCT 60.126 61.111 0.00 0.00 41.90 5.52
2366 2440 1.961378 CTGCATTGAAGCACCAGCA 59.039 52.632 0.00 0.00 45.49 4.41
2368 2442 1.961378 TGCTGCATTGAAGCACCAG 59.039 52.632 15.62 0.00 45.50 4.00
2444 2518 2.159819 GAAGCTCGACTGCACCTCCA 62.160 60.000 0.00 0.00 34.99 3.86
2480 2554 4.379243 CGGCCGAGCTCCAACACT 62.379 66.667 24.07 0.00 0.00 3.55
2516 2594 4.636249 GATAAAGCTCCAATGACTCCGAT 58.364 43.478 0.00 0.00 0.00 4.18
2523 2601 1.476833 GCCCCGATAAAGCTCCAATGA 60.477 52.381 0.00 0.00 0.00 2.57
2632 2710 4.385405 GCAGCACTGACGGCCTCT 62.385 66.667 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.