Multiple sequence alignment - TraesCS1D01G154200

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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 TraesCS1D01G154200 chr1D 100.000 3320 0 0 1 3320 215067008 215063689 0.000000e+00 6131.0
1 TraesCS1D01G154200 chr1D 86.667 585 62 11 1 577 293617038 293617614 4.670000e-178 634.0
2 TraesCS1D01G154200 chr1D 90.076 131 1 3 660 790 469813519 469813401 3.430000e-35 159.0
3 TraesCS1D01G154200 chr1D 87.857 140 4 2 660 798 25454375 25454502 5.740000e-33 152.0
4 TraesCS1D01G154200 chr1A 96.834 2274 53 8 786 3057 274110091 274107835 0.000000e+00 3783.0
5 TraesCS1D01G154200 chr1A 96.759 216 6 1 3105 3320 274107834 274107620 3.150000e-95 359.0
6 TraesCS1D01G154200 chr1B 96.770 2074 41 7 792 2857 308383059 308381004 0.000000e+00 3435.0
7 TraesCS1D01G154200 chr1B 88.468 581 54 7 1 577 308383685 308383114 0.000000e+00 689.0
8 TraesCS1D01G154200 chr1B 87.631 574 58 11 1 568 394913460 394914026 0.000000e+00 654.0
9 TraesCS1D01G154200 chr1B 94.413 358 17 2 2963 3320 308380946 308380592 6.260000e-152 547.0
10 TraesCS1D01G154200 chr1B 90.909 66 0 5 643 703 169990004 169990068 2.120000e-12 84.2
11 TraesCS1D01G154200 chrUn 87.370 578 62 6 4 577 223002312 223001742 0.000000e+00 652.0
12 TraesCS1D01G154200 chrUn 85.106 141 9 3 650 790 39802132 39802260 2.080000e-27 134.0
13 TraesCS1D01G154200 chrUn 85.106 141 9 3 650 790 300442908 300443036 2.080000e-27 134.0
14 TraesCS1D01G154200 chr6D 87.219 579 61 10 4 577 243626253 243625683 0.000000e+00 647.0
15 TraesCS1D01G154200 chr6D 88.889 135 11 4 660 793 354222601 354222732 2.650000e-36 163.0
16 TraesCS1D01G154200 chr7D 86.632 576 67 6 4 574 290865581 290865011 2.170000e-176 628.0
17 TraesCS1D01G154200 chr7D 97.802 91 2 0 703 793 461389726 461389636 1.230000e-34 158.0
18 TraesCS1D01G154200 chr7A 86.598 582 63 9 1 577 97579843 97580414 2.170000e-176 628.0
19 TraesCS1D01G154200 chr3D 86.403 581 66 9 1 577 571044444 571043873 1.010000e-174 623.0
20 TraesCS1D01G154200 chr3D 97.778 90 1 1 704 792 65452475 65452564 1.600000e-33 154.0
21 TraesCS1D01G154200 chr7B 86.254 582 66 10 4 578 35636693 35636119 1.310000e-173 619.0
22 TraesCS1D01G154200 chr6B 87.500 144 5 4 659 802 128924768 128924898 1.600000e-33 154.0
23 TraesCS1D01G154200 chr5D 96.739 92 1 2 704 793 543459653 543459744 5.740000e-33 152.0
24 TraesCS1D01G154200 chr4B 85.821 134 18 1 658 791 89394113 89394245 1.240000e-29 141.0
25 TraesCS1D01G154200 chr5B 84.091 132 17 3 662 793 691285745 691285618 1.250000e-24 124.0
26 TraesCS1D01G154200 chr4D 81.176 170 18 5 662 831 5086931 5086776 1.250000e-24 124.0
27 TraesCS1D01G154200 chr4D 83.077 130 10 3 662 791 151935802 151935919 1.260000e-19 108.0
28 TraesCS1D01G154200 chr6A 83.721 129 8 4 662 790 305379974 305379859 3.500000e-20 110.0
29 TraesCS1D01G154200 chr6A 75.333 150 27 9 643 790 26993564 26993705 2.770000e-06 63.9


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 TraesCS1D01G154200 chr1D 215063689 215067008 3319 True 6131 6131 100.0000 1 3320 1 chr1D.!!$R1 3319
1 TraesCS1D01G154200 chr1D 293617038 293617614 576 False 634 634 86.6670 1 577 1 chr1D.!!$F2 576
2 TraesCS1D01G154200 chr1A 274107620 274110091 2471 True 2071 3783 96.7965 786 3320 2 chr1A.!!$R1 2534
3 TraesCS1D01G154200 chr1B 308380592 308383685 3093 True 1557 3435 93.2170 1 3320 3 chr1B.!!$R1 3319
4 TraesCS1D01G154200 chr1B 394913460 394914026 566 False 654 654 87.6310 1 568 1 chr1B.!!$F2 567
5 TraesCS1D01G154200 chrUn 223001742 223002312 570 True 652 652 87.3700 4 577 1 chrUn.!!$R1 573
6 TraesCS1D01G154200 chr6D 243625683 243626253 570 True 647 647 87.2190 4 577 1 chr6D.!!$R1 573
7 TraesCS1D01G154200 chr7D 290865011 290865581 570 True 628 628 86.6320 4 574 1 chr7D.!!$R1 570
8 TraesCS1D01G154200 chr7A 97579843 97580414 571 False 628 628 86.5980 1 577 1 chr7A.!!$F1 576
9 TraesCS1D01G154200 chr3D 571043873 571044444 571 True 623 623 86.4030 1 577 1 chr3D.!!$R1 576
10 TraesCS1D01G154200 chr7B 35636119 35636693 574 True 619 619 86.2540 4 578 1 chr7B.!!$R1 574

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
680 697 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.00 44.66 2.17 F
786 803 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
788 805 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.0 13.64 0.00 46.06 3.85 F
1509 1527 0.179032 TTGCCATCCACAACGACACT 60.179 50.0 0.00 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1653 0.037326 AGTGCACTGTGATGTACCCG 60.037 55.000 20.97 0.00 35.97 5.28 R
1647 1665 0.743688 CGAGAGCTATGGAGTGCACT 59.256 55.000 21.88 21.88 33.15 4.40 R
1710 1728 1.765597 AAAGGAAGAACCCTCGCCGT 61.766 55.000 0.00 0.00 40.05 5.68 R
2860 2884 1.872952 TGTGCCAACAATTCTCTCGTG 59.127 47.619 0.00 0.00 31.82 4.35 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
124 125 8.676401 AGAGATACTCTAAAGACTTCGGTAAAC 58.324 37.037 0.00 0.00 39.28 2.01
174 176 2.030562 ACTCTTTCACCCGCACGG 59.969 61.111 1.02 1.02 37.81 4.94
206 208 8.364129 TCAATAATGGTTTTTGAAAGCACTTC 57.636 30.769 7.37 0.00 34.31 3.01
258 260 2.494471 TGATCGATGAACGTACTTGGGT 59.506 45.455 0.54 0.00 43.13 4.51
268 270 0.177373 GTACTTGGGTCGGGGATGAC 59.823 60.000 0.00 0.00 38.17 3.06
578 595 2.685380 CTGGAGGCGAGGGGACTT 60.685 66.667 0.00 0.00 44.43 3.01
579 596 2.203938 TGGAGGCGAGGGGACTTT 60.204 61.111 0.00 0.00 44.43 2.66
580 597 1.842381 CTGGAGGCGAGGGGACTTTT 61.842 60.000 0.00 0.00 44.43 2.27
581 598 1.379146 GGAGGCGAGGGGACTTTTT 59.621 57.895 0.00 0.00 44.43 1.94
603 620 3.963476 TTTCTTTTTGAGAGGTGGGGA 57.037 42.857 0.00 0.00 35.37 4.81
604 621 2.951229 TCTTTTTGAGAGGTGGGGAC 57.049 50.000 0.00 0.00 0.00 4.46
622 639 4.452825 GGGACCTAAATTTCTCAGGCTAC 58.547 47.826 5.54 0.00 32.31 3.58
623 640 4.164413 GGGACCTAAATTTCTCAGGCTACT 59.836 45.833 5.54 0.00 32.31 2.57
633 650 1.218047 CAGGCTACTACAAGCGGCA 59.782 57.895 1.45 0.00 43.74 5.69
635 652 0.970937 AGGCTACTACAAGCGGCAGA 60.971 55.000 1.45 0.00 43.74 4.26
642 659 3.211045 ACTACAAGCGGCAGAAGAAAAA 58.789 40.909 1.45 0.00 0.00 1.94
658 675 9.936759 CAGAAGAAAAACCTACTTCTCTTCTAT 57.063 33.333 10.82 0.00 44.46 1.98
666 683 9.631257 AAACCTACTTCTCTTCTATAGTACTCC 57.369 37.037 0.00 0.00 0.00 3.85
667 684 7.748677 ACCTACTTCTCTTCTATAGTACTCCC 58.251 42.308 0.00 0.00 0.00 4.30
668 685 7.573616 ACCTACTTCTCTTCTATAGTACTCCCT 59.426 40.741 0.00 0.00 0.00 4.20
669 686 8.098912 CCTACTTCTCTTCTATAGTACTCCCTC 58.901 44.444 0.00 0.00 0.00 4.30
670 687 6.844829 ACTTCTCTTCTATAGTACTCCCTCC 58.155 44.000 0.00 0.00 0.00 4.30
671 688 5.486735 TCTCTTCTATAGTACTCCCTCCG 57.513 47.826 0.00 0.00 0.00 4.63
672 689 4.906664 TCTCTTCTATAGTACTCCCTCCGT 59.093 45.833 0.00 0.00 0.00 4.69
673 690 5.011943 TCTCTTCTATAGTACTCCCTCCGTC 59.988 48.000 0.00 0.00 0.00 4.79
674 691 4.041444 TCTTCTATAGTACTCCCTCCGTCC 59.959 50.000 0.00 0.00 0.00 4.79
675 692 2.301296 TCTATAGTACTCCCTCCGTCCG 59.699 54.545 0.00 0.00 0.00 4.79
676 693 0.110104 ATAGTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
677 694 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
678 695 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
679 696 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
680 697 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
681 698 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
682 699 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
683 700 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
684 701 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
685 702 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
686 703 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
687 704 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
688 705 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
689 706 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
690 707 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
691 708 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
692 709 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
693 710 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
694 711 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
695 712 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
696 713 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
697 714 4.868171 CGGAAATACTTGTCGGAGAAATGA 59.132 41.667 0.00 0.00 39.69 2.57
698 715 5.350365 CGGAAATACTTGTCGGAGAAATGAA 59.650 40.000 0.00 0.00 39.69 2.57
699 716 6.037172 CGGAAATACTTGTCGGAGAAATGAAT 59.963 38.462 0.00 0.00 39.69 2.57
700 717 7.189512 GGAAATACTTGTCGGAGAAATGAATG 58.810 38.462 0.00 0.00 39.69 2.67
701 718 7.148239 GGAAATACTTGTCGGAGAAATGAATGT 60.148 37.037 0.00 0.00 39.69 2.71
702 719 8.786826 AAATACTTGTCGGAGAAATGAATGTA 57.213 30.769 0.00 0.00 39.69 2.29
703 720 8.786826 AATACTTGTCGGAGAAATGAATGTAA 57.213 30.769 0.00 0.00 39.69 2.41
704 721 8.786826 ATACTTGTCGGAGAAATGAATGTAAA 57.213 30.769 0.00 0.00 39.69 2.01
705 722 7.504924 ACTTGTCGGAGAAATGAATGTAAAA 57.495 32.000 0.00 0.00 39.69 1.52
706 723 7.936584 ACTTGTCGGAGAAATGAATGTAAAAA 58.063 30.769 0.00 0.00 39.69 1.94
764 781 8.183104 ACATCTAGATACATTCATTTCTCCGA 57.817 34.615 4.54 0.00 0.00 4.55
765 782 8.085296 ACATCTAGATACATTCATTTCTCCGAC 58.915 37.037 4.54 0.00 0.00 4.79
766 783 7.582667 TCTAGATACATTCATTTCTCCGACA 57.417 36.000 0.00 0.00 0.00 4.35
767 784 8.007405 TCTAGATACATTCATTTCTCCGACAA 57.993 34.615 0.00 0.00 0.00 3.18
768 785 8.138074 TCTAGATACATTCATTTCTCCGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
769 786 6.644347 AGATACATTCATTTCTCCGACAAGT 58.356 36.000 0.00 0.00 0.00 3.16
770 787 7.782049 AGATACATTCATTTCTCCGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
771 788 8.424918 AGATACATTCATTTCTCCGACAAGTAT 58.575 33.333 0.00 0.00 0.00 2.12
772 789 8.964476 ATACATTCATTTCTCCGACAAGTATT 57.036 30.769 0.00 0.00 0.00 1.89
773 790 7.687941 ACATTCATTTCTCCGACAAGTATTT 57.312 32.000 0.00 0.00 0.00 1.40
774 791 7.752695 ACATTCATTTCTCCGACAAGTATTTC 58.247 34.615 0.00 0.00 0.00 2.17
775 792 6.737254 TTCATTTCTCCGACAAGTATTTCC 57.263 37.500 0.00 0.00 0.00 3.13
776 793 4.868171 TCATTTCTCCGACAAGTATTTCCG 59.132 41.667 0.00 0.00 0.00 4.30
777 794 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
778 795 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
779 796 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
780 797 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
781 798 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
782 799 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
783 800 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
784 801 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
785 802 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
786 803 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
787 804 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
788 805 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
789 806 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
790 807 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
866 883 1.542915 CAACCAAAGCATCCAGACTGG 59.457 52.381 15.99 15.99 39.43 4.00
867 884 0.610232 ACCAAAGCATCCAGACTGGC 60.610 55.000 17.33 5.33 37.47 4.85
868 885 1.318158 CCAAAGCATCCAGACTGGCC 61.318 60.000 17.33 7.50 37.47 5.36
869 886 1.000396 AAAGCATCCAGACTGGCCC 60.000 57.895 17.33 7.15 37.47 5.80
870 887 1.792757 AAAGCATCCAGACTGGCCCA 61.793 55.000 17.33 0.00 37.47 5.36
871 888 1.792757 AAGCATCCAGACTGGCCCAA 61.793 55.000 17.33 0.00 37.47 4.12
1239 1257 2.131067 CCTCCTTCTCCGCCTCTCC 61.131 68.421 0.00 0.00 0.00 3.71
1326 1344 1.610327 CTCCTCGTCCTCCCTCTCA 59.390 63.158 0.00 0.00 0.00 3.27
1365 1383 3.459063 CCCTTCGACCCGGTCTCC 61.459 72.222 15.70 0.00 0.00 3.71
1506 1524 0.605319 TCCTTGCCATCCACAACGAC 60.605 55.000 0.00 0.00 0.00 4.34
1509 1527 0.179032 TTGCCATCCACAACGACACT 60.179 50.000 0.00 0.00 0.00 3.55
1517 1535 0.874175 CACAACGACACTTCCTCGCA 60.874 55.000 0.00 0.00 34.34 5.10
1620 1638 0.179166 CTCTGCTCTCGTCTGCTCAC 60.179 60.000 0.00 0.00 0.00 3.51
1635 1653 2.951745 CACGTGCTCGCGATCCTC 60.952 66.667 10.36 4.06 41.18 3.71
1647 1665 1.029681 CGATCCTCGGGTACATCACA 58.970 55.000 0.00 0.00 36.00 3.58
1710 1728 4.680237 CGCCACCTGCCTGAACGA 62.680 66.667 0.00 0.00 36.24 3.85
1737 1755 0.536460 GGTTCTTCCTTTCCGGTGCA 60.536 55.000 0.00 0.00 0.00 4.57
2315 2333 1.078356 ATGTGGCAGCTGCTCTCAG 60.078 57.895 35.82 0.00 43.16 3.35
2431 2454 3.199508 ACCTCTTAGTGCTCATTCATGCT 59.800 43.478 0.00 0.00 0.00 3.79
2623 2646 1.067974 GGTTGTTTGGTTCCCTTTCCG 59.932 52.381 0.00 0.00 0.00 4.30
2860 2884 0.690762 TCAGTACCCCAGCTTGTTCC 59.309 55.000 0.00 0.00 0.00 3.62
2862 2886 0.400594 AGTACCCCAGCTTGTTCCAC 59.599 55.000 0.00 0.00 0.00 4.02
2870 2894 2.613977 CCAGCTTGTTCCACGAGAGAAT 60.614 50.000 0.00 0.00 31.05 2.40
2878 2902 1.071542 TCCACGAGAGAATTGTTGGCA 59.928 47.619 0.00 0.00 0.00 4.92
2936 2960 2.098117 GGCAATGTGTATCTCCAGTTGC 59.902 50.000 0.00 0.00 36.85 4.17
2938 2962 3.064545 GCAATGTGTATCTCCAGTTGCTC 59.935 47.826 0.00 0.00 35.70 4.26
2939 2963 4.256110 CAATGTGTATCTCCAGTTGCTCA 58.744 43.478 0.00 0.00 0.00 4.26
2940 2964 4.767578 ATGTGTATCTCCAGTTGCTCAT 57.232 40.909 0.00 0.00 0.00 2.90
2941 2965 4.558226 TGTGTATCTCCAGTTGCTCATT 57.442 40.909 0.00 0.00 0.00 2.57
2942 2966 5.675684 TGTGTATCTCCAGTTGCTCATTA 57.324 39.130 0.00 0.00 0.00 1.90
2943 2967 6.239217 TGTGTATCTCCAGTTGCTCATTAT 57.761 37.500 0.00 0.00 0.00 1.28
2944 2968 6.653020 TGTGTATCTCCAGTTGCTCATTATT 58.347 36.000 0.00 0.00 0.00 1.40
2946 2970 6.763135 GTGTATCTCCAGTTGCTCATTATTGA 59.237 38.462 0.00 0.00 0.00 2.57
2948 2972 7.828717 TGTATCTCCAGTTGCTCATTATTGAAA 59.171 33.333 0.00 0.00 0.00 2.69
2951 2975 7.541162 TCTCCAGTTGCTCATTATTGAAATTG 58.459 34.615 0.00 0.00 0.00 2.32
2953 2977 7.669427 TCCAGTTGCTCATTATTGAAATTGTT 58.331 30.769 0.00 0.00 0.00 2.83
2954 2978 7.599621 TCCAGTTGCTCATTATTGAAATTGTTG 59.400 33.333 0.00 0.00 0.00 3.33
2955 2979 7.148540 CCAGTTGCTCATTATTGAAATTGTTGG 60.149 37.037 0.00 0.00 0.00 3.77
2956 2980 6.369615 AGTTGCTCATTATTGAAATTGTTGGC 59.630 34.615 0.00 0.00 0.00 4.52
2957 2981 6.040209 TGCTCATTATTGAAATTGTTGGCT 57.960 33.333 0.00 0.00 0.00 4.75
2958 2982 6.101332 TGCTCATTATTGAAATTGTTGGCTC 58.899 36.000 0.00 0.00 0.00 4.70
2959 2983 6.101332 GCTCATTATTGAAATTGTTGGCTCA 58.899 36.000 0.00 0.00 0.00 4.26
2960 2984 6.759827 GCTCATTATTGAAATTGTTGGCTCAT 59.240 34.615 0.00 0.00 0.00 2.90
2961 2985 7.279313 GCTCATTATTGAAATTGTTGGCTCATT 59.721 33.333 0.00 0.00 0.00 2.57
3071 3095 1.726853 CATCCTCCGTGTTTCTGGAC 58.273 55.000 0.00 0.00 0.00 4.02
3074 3098 0.320771 CCTCCGTGTTTCTGGACTGG 60.321 60.000 0.00 0.00 0.00 4.00
3121 3145 2.414481 CACTGCATGTCAACTGCTCTAC 59.586 50.000 0.00 0.00 40.34 2.59
3125 3149 3.264947 GCATGTCAACTGCTCTACATCA 58.735 45.455 0.00 0.00 36.68 3.07
3187 3211 7.112122 TGCTAGTGGATCACTGAAATATGTTT 58.888 34.615 10.46 0.00 45.01 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.785033 AGGTGTTTTCAAGAGATTTCATTGTT 58.215 30.769 0.00 0.00 0.00 2.83
124 125 2.636830 CTCCAGTCCAATTACAGCCTG 58.363 52.381 0.00 0.00 0.00 4.85
206 208 0.447801 CTTTTTGGATGGGCGACTCG 59.552 55.000 0.00 0.00 0.00 4.18
288 291 4.617645 GGTGAAGATATAGTGATTCGACGC 59.382 45.833 0.00 0.00 0.00 5.19
365 368 6.558771 TGAGTTTATGTTGATGTGTCAAGG 57.441 37.500 0.00 0.00 44.58 3.61
375 380 8.812513 ATTTGGATCTGATGAGTTTATGTTGA 57.187 30.769 0.00 0.00 0.00 3.18
490 504 9.653287 ATTTCTATGTTCTTCATCAACGTCTAA 57.347 29.630 0.00 0.00 37.91 2.10
581 598 4.404394 GTCCCCACCTCTCAAAAAGAAAAA 59.596 41.667 0.00 0.00 32.23 1.94
582 599 3.958147 GTCCCCACCTCTCAAAAAGAAAA 59.042 43.478 0.00 0.00 32.23 2.29
583 600 3.562182 GTCCCCACCTCTCAAAAAGAAA 58.438 45.455 0.00 0.00 32.23 2.52
584 601 2.158519 GGTCCCCACCTCTCAAAAAGAA 60.159 50.000 0.00 0.00 40.00 2.52
585 602 1.423921 GGTCCCCACCTCTCAAAAAGA 59.576 52.381 0.00 0.00 40.00 2.52
586 603 1.911057 GGTCCCCACCTCTCAAAAAG 58.089 55.000 0.00 0.00 40.00 2.27
596 613 3.621558 CTGAGAAATTTAGGTCCCCACC 58.378 50.000 0.00 0.00 44.19 4.61
597 614 3.621558 CCTGAGAAATTTAGGTCCCCAC 58.378 50.000 0.00 0.00 0.00 4.61
598 615 2.025321 GCCTGAGAAATTTAGGTCCCCA 60.025 50.000 7.22 0.00 34.06 4.96
599 616 2.242452 AGCCTGAGAAATTTAGGTCCCC 59.758 50.000 7.22 0.00 34.06 4.81
600 617 3.653835 AGCCTGAGAAATTTAGGTCCC 57.346 47.619 7.22 0.00 34.06 4.46
601 618 5.360649 AGTAGCCTGAGAAATTTAGGTCC 57.639 43.478 7.22 0.00 34.06 4.46
602 619 6.875076 TGTAGTAGCCTGAGAAATTTAGGTC 58.125 40.000 7.22 1.21 34.06 3.85
603 620 6.869206 TGTAGTAGCCTGAGAAATTTAGGT 57.131 37.500 7.22 0.00 34.06 3.08
604 621 6.258947 GCTTGTAGTAGCCTGAGAAATTTAGG 59.741 42.308 1.64 1.64 35.06 2.69
615 632 0.807667 CTGCCGCTTGTAGTAGCCTG 60.808 60.000 0.00 0.00 37.90 4.85
618 635 1.135083 TCTTCTGCCGCTTGTAGTAGC 60.135 52.381 0.00 0.00 37.80 3.58
622 639 3.555518 GTTTTTCTTCTGCCGCTTGTAG 58.444 45.455 0.00 0.00 0.00 2.74
623 640 2.292292 GGTTTTTCTTCTGCCGCTTGTA 59.708 45.455 0.00 0.00 0.00 2.41
642 659 7.573616 AGGGAGTACTATAGAAGAGAAGTAGGT 59.426 40.741 6.78 0.00 0.00 3.08
658 675 0.982852 TCCGGACGGAGGGAGTACTA 60.983 60.000 9.76 0.00 39.76 1.82
659 676 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
660 677 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
661 678 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
662 679 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
663 680 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
664 681 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
665 682 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
666 683 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
667 684 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
668 685 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
669 686 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
670 687 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
671 688 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
672 689 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
673 690 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
674 691 4.868171 TCATTTCTCCGACAAGTATTTCCG 59.132 41.667 0.00 0.00 0.00 4.30
675 692 6.737254 TTCATTTCTCCGACAAGTATTTCC 57.263 37.500 0.00 0.00 0.00 3.13
676 693 7.752695 ACATTCATTTCTCCGACAAGTATTTC 58.247 34.615 0.00 0.00 0.00 2.17
677 694 7.687941 ACATTCATTTCTCCGACAAGTATTT 57.312 32.000 0.00 0.00 0.00 1.40
678 695 8.786826 TTACATTCATTTCTCCGACAAGTATT 57.213 30.769 0.00 0.00 0.00 1.89
679 696 8.786826 TTTACATTCATTTCTCCGACAAGTAT 57.213 30.769 0.00 0.00 0.00 2.12
680 697 8.610248 TTTTACATTCATTTCTCCGACAAGTA 57.390 30.769 0.00 0.00 0.00 2.24
681 698 7.504924 TTTTACATTCATTTCTCCGACAAGT 57.495 32.000 0.00 0.00 0.00 3.16
738 755 9.297037 TCGGAGAAATGAATGTATCTAGATGTA 57.703 33.333 15.79 4.44 0.00 2.29
739 756 8.085296 GTCGGAGAAATGAATGTATCTAGATGT 58.915 37.037 15.79 0.00 39.69 3.06
740 757 8.084684 TGTCGGAGAAATGAATGTATCTAGATG 58.915 37.037 15.79 0.00 39.69 2.90
741 758 8.183104 TGTCGGAGAAATGAATGTATCTAGAT 57.817 34.615 10.73 10.73 39.69 1.98
742 759 7.582667 TGTCGGAGAAATGAATGTATCTAGA 57.417 36.000 0.00 0.00 39.69 2.43
743 760 7.923344 ACTTGTCGGAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 39.69 2.43
744 761 7.782049 ACTTGTCGGAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 39.69 1.98
745 762 6.644347 ACTTGTCGGAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 39.69 1.98
746 763 6.910536 ACTTGTCGGAGAAATGAATGTATC 57.089 37.500 0.00 0.00 39.69 2.24
747 764 8.964476 AATACTTGTCGGAGAAATGAATGTAT 57.036 30.769 0.00 0.00 39.69 2.29
748 765 8.786826 AAATACTTGTCGGAGAAATGAATGTA 57.213 30.769 0.00 0.00 39.69 2.29
749 766 7.148239 GGAAATACTTGTCGGAGAAATGAATGT 60.148 37.037 0.00 0.00 39.69 2.71
750 767 7.189512 GGAAATACTTGTCGGAGAAATGAATG 58.810 38.462 0.00 0.00 39.69 2.67
751 768 6.037172 CGGAAATACTTGTCGGAGAAATGAAT 59.963 38.462 0.00 0.00 39.69 2.57
752 769 5.350365 CGGAAATACTTGTCGGAGAAATGAA 59.650 40.000 0.00 0.00 39.69 2.57
753 770 4.868171 CGGAAATACTTGTCGGAGAAATGA 59.132 41.667 0.00 0.00 39.69 2.57
754 771 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
755 772 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
756 773 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
757 774 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
758 775 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
759 776 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
760 777 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
761 778 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
762 779 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
763 780 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
764 781 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
765 782 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
766 783 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
767 784 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
768 785 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
769 786 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
770 787 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
771 788 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
772 789 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
773 790 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
774 791 0.817229 GTAGTACTCCCTCCGTCCGG 60.817 65.000 0.00 0.00 0.00 5.14
775 792 0.107508 TGTAGTACTCCCTCCGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
776 793 1.955080 CATGTAGTACTCCCTCCGTCC 59.045 57.143 0.00 0.00 0.00 4.79
777 794 1.955080 CCATGTAGTACTCCCTCCGTC 59.045 57.143 0.00 0.00 0.00 4.79
778 795 1.567649 TCCATGTAGTACTCCCTCCGT 59.432 52.381 0.00 0.00 0.00 4.69
779 796 2.359981 TCCATGTAGTACTCCCTCCG 57.640 55.000 0.00 0.00 0.00 4.63
780 797 4.287552 TCTTTCCATGTAGTACTCCCTCC 58.712 47.826 0.00 0.00 0.00 4.30
781 798 5.934402 TTCTTTCCATGTAGTACTCCCTC 57.066 43.478 0.00 0.00 0.00 4.30
782 799 6.674419 AGATTTCTTTCCATGTAGTACTCCCT 59.326 38.462 0.00 0.00 0.00 4.20
783 800 6.890293 AGATTTCTTTCCATGTAGTACTCCC 58.110 40.000 0.00 0.00 0.00 4.30
784 801 7.787028 AGAGATTTCTTTCCATGTAGTACTCC 58.213 38.462 0.00 0.00 0.00 3.85
787 804 9.315525 GGTTAGAGATTTCTTTCCATGTAGTAC 57.684 37.037 0.00 0.00 34.79 2.73
788 805 8.483758 GGGTTAGAGATTTCTTTCCATGTAGTA 58.516 37.037 0.00 0.00 34.79 1.82
789 806 7.037586 TGGGTTAGAGATTTCTTTCCATGTAGT 60.038 37.037 0.00 0.00 34.79 2.73
790 807 7.338710 TGGGTTAGAGATTTCTTTCCATGTAG 58.661 38.462 0.00 0.00 34.79 2.74
867 884 2.999063 CTTGGGCTTGGGCTTGGG 60.999 66.667 0.00 0.00 38.73 4.12
868 885 3.698820 GCTTGGGCTTGGGCTTGG 61.699 66.667 0.00 0.00 38.73 3.61
869 886 2.786512 TAGGCTTGGGCTTGGGCTTG 62.787 60.000 0.00 0.00 39.70 4.01
870 887 2.505364 CTAGGCTTGGGCTTGGGCTT 62.505 60.000 0.00 0.00 39.70 4.35
871 888 2.941025 TAGGCTTGGGCTTGGGCT 60.941 61.111 0.00 0.00 39.70 5.19
1506 1524 1.018226 CAGGCTTCTGCGAGGAAGTG 61.018 60.000 15.60 6.78 43.13 3.16
1635 1653 0.037326 AGTGCACTGTGATGTACCCG 60.037 55.000 20.97 0.00 35.97 5.28
1647 1665 0.743688 CGAGAGCTATGGAGTGCACT 59.256 55.000 21.88 21.88 33.15 4.40
1710 1728 1.765597 AAAGGAAGAACCCTCGCCGT 61.766 55.000 0.00 0.00 40.05 5.68
1737 1755 2.507944 CTCCTAGCGCCCATTGCT 59.492 61.111 2.29 0.00 46.29 3.91
2511 2534 3.244887 TGTCAAGTTCTCTCTCCCTCA 57.755 47.619 0.00 0.00 0.00 3.86
2623 2646 3.555966 CATCTTACCTCCCATGGAAACC 58.444 50.000 15.22 0.00 0.00 3.27
2836 2860 3.658725 ACAAGCTGGGGTACTGATAGAT 58.341 45.455 0.00 0.00 0.00 1.98
2837 2861 3.116096 ACAAGCTGGGGTACTGATAGA 57.884 47.619 0.00 0.00 0.00 1.98
2860 2884 1.872952 TGTGCCAACAATTCTCTCGTG 59.127 47.619 0.00 0.00 31.82 4.35
2862 2886 3.837213 AATGTGCCAACAATTCTCTCG 57.163 42.857 0.00 0.00 40.46 4.04
2870 2894 9.941325 ATAAGAATTTCAATAATGTGCCAACAA 57.059 25.926 0.00 0.00 40.46 2.83
2936 2960 8.712285 AATGAGCCAACAATTTCAATAATGAG 57.288 30.769 0.00 0.00 36.78 2.90
2942 2966 9.504708 TTTGAATAATGAGCCAACAATTTCAAT 57.495 25.926 0.00 0.00 32.20 2.57
2943 2967 8.772705 GTTTGAATAATGAGCCAACAATTTCAA 58.227 29.630 0.00 0.00 31.24 2.69
2944 2968 7.930325 TGTTTGAATAATGAGCCAACAATTTCA 59.070 29.630 0.00 0.00 0.00 2.69
2946 2970 7.714377 TGTGTTTGAATAATGAGCCAACAATTT 59.286 29.630 0.00 0.00 0.00 1.82
2948 2972 6.757237 TGTGTTTGAATAATGAGCCAACAAT 58.243 32.000 0.00 0.00 0.00 2.71
2951 2975 6.624423 AGATGTGTTTGAATAATGAGCCAAC 58.376 36.000 0.00 0.00 0.00 3.77
2953 2977 5.357878 GGAGATGTGTTTGAATAATGAGCCA 59.642 40.000 0.00 0.00 0.00 4.75
2954 2978 5.357878 TGGAGATGTGTTTGAATAATGAGCC 59.642 40.000 0.00 0.00 0.00 4.70
2955 2979 6.441093 TGGAGATGTGTTTGAATAATGAGC 57.559 37.500 0.00 0.00 0.00 4.26
2956 2980 6.094464 TGCTGGAGATGTGTTTGAATAATGAG 59.906 38.462 0.00 0.00 0.00 2.90
2957 2981 5.945191 TGCTGGAGATGTGTTTGAATAATGA 59.055 36.000 0.00 0.00 0.00 2.57
2958 2982 6.032094 GTGCTGGAGATGTGTTTGAATAATG 58.968 40.000 0.00 0.00 0.00 1.90
2959 2983 5.948162 AGTGCTGGAGATGTGTTTGAATAAT 59.052 36.000 0.00 0.00 0.00 1.28
2960 2984 5.316167 AGTGCTGGAGATGTGTTTGAATAA 58.684 37.500 0.00 0.00 0.00 1.40
2961 2985 4.910195 AGTGCTGGAGATGTGTTTGAATA 58.090 39.130 0.00 0.00 0.00 1.75
3071 3095 5.589050 GGGTTACTAATAAGAAACTGGCCAG 59.411 44.000 31.60 31.60 0.00 4.85
3074 3098 6.765036 GGTAGGGTTACTAATAAGAAACTGGC 59.235 42.308 0.00 0.00 32.37 4.85
3121 3145 6.453003 GCGTAATATTCGACTGCATAGTGATG 60.453 42.308 10.26 0.00 37.25 3.07
3125 3149 5.122512 AGCGTAATATTCGACTGCATAGT 57.877 39.130 10.26 0.00 40.66 2.12
3187 3211 6.998074 ACCAATCAATGAACTGTAAGAACTCA 59.002 34.615 0.00 0.00 37.43 3.41
3278 3302 9.678260 AAGTCAGCTTTATCTTCTGAACATATT 57.322 29.630 0.00 0.00 38.42 1.28


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

AutoCloner maintained by Alex Coulton.