Multiple sequence alignment - TraesCS1A01G142900

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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 TraesCS1A01G142900 chr1A 100.000 3875 0 0 1 3875 245114482 245118356 0.000000e+00 7156.0
1 TraesCS1A01G142900 chr1A 90.789 532 40 5 3344 3875 541386201 541386723 0.000000e+00 702.0
2 TraesCS1A01G142900 chr1A 90.262 534 43 5 3342 3875 62137634 62138158 0.000000e+00 689.0
3 TraesCS1A01G142900 chr1A 89.888 534 44 6 3343 3875 255231583 255231059 0.000000e+00 678.0
4 TraesCS1A01G142900 chr1D 96.082 2552 74 9 813 3342 196093105 196095652 0.000000e+00 4135.0
5 TraesCS1A01G142900 chr1B 96.889 2379 61 6 818 3186 269221407 269219032 0.000000e+00 3971.0
6 TraesCS1A01G142900 chr1B 90.470 724 66 3 4 725 684411878 684412600 0.000000e+00 952.0
7 TraesCS1A01G142900 chr1B 91.429 105 4 3 3238 3342 269211099 269211000 5.220000e-29 139.0
8 TraesCS1A01G142900 chr1B 100.000 39 0 0 3200 3238 269219003 269218965 5.370000e-09 73.1
9 TraesCS1A01G142900 chr7D 90.847 732 60 5 1 729 158940681 158939954 0.000000e+00 974.0
10 TraesCS1A01G142900 chr7D 90.027 732 65 7 1 729 495281476 495280750 0.000000e+00 941.0
11 TraesCS1A01G142900 chr5D 90.834 731 60 6 1 729 394844716 394845441 0.000000e+00 972.0
12 TraesCS1A01G142900 chr5D 90.710 732 62 6 1 729 437091719 437092447 0.000000e+00 970.0
13 TraesCS1A01G142900 chr5D 91.182 533 39 3 3343 3875 548044294 548043770 0.000000e+00 717.0
14 TraesCS1A01G142900 chr6D 90.110 728 65 5 1 725 387406809 387406086 0.000000e+00 939.0
15 TraesCS1A01G142900 chr6D 89.973 728 70 3 4 729 420203917 420203191 0.000000e+00 937.0
16 TraesCS1A01G142900 chr6D 90.994 533 40 4 3343 3875 144617055 144616531 0.000000e+00 712.0
17 TraesCS1A01G142900 chr6B 89.905 733 57 11 1 729 129449441 129448722 0.000000e+00 928.0
18 TraesCS1A01G142900 chr2A 89.566 738 67 7 1 729 7363489 7362753 0.000000e+00 928.0
19 TraesCS1A01G142900 chr2A 90.299 536 43 5 3340 3875 765576825 765577351 0.000000e+00 693.0
20 TraesCS1A01G142900 chr2A 90.909 495 36 4 3343 3837 442379976 442379491 0.000000e+00 656.0
21 TraesCS1A01G142900 chr2D 90.977 532 38 4 3343 3874 368466747 368466226 0.000000e+00 708.0
22 TraesCS1A01G142900 chr2D 90.619 533 42 3 3343 3875 512504778 512504254 0.000000e+00 701.0
23 TraesCS1A01G142900 chr2D 83.981 412 59 4 3343 3751 6868436 6868843 4.690000e-104 388.0
24 TraesCS1A01G142900 chr5A 90.432 533 43 3 3343 3875 676630622 676631146 0.000000e+00 695.0
25 TraesCS1A01G142900 chr5A 89.869 533 45 5 3343 3875 487615995 487616518 0.000000e+00 676.0
26 TraesCS1A01G142900 chr3D 90.075 534 45 5 3342 3875 4158332 4158857 0.000000e+00 686.0
27 TraesCS1A01G142900 chr7A 88.910 532 54 4 3343 3874 714683139 714683665 0.000000e+00 651.0


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 TraesCS1A01G142900 chr1A 245114482 245118356 3874 False 7156.00 7156 100.0000 1 3875 1 chr1A.!!$F2 3874
1 TraesCS1A01G142900 chr1A 541386201 541386723 522 False 702.00 702 90.7890 3344 3875 1 chr1A.!!$F3 531
2 TraesCS1A01G142900 chr1A 62137634 62138158 524 False 689.00 689 90.2620 3342 3875 1 chr1A.!!$F1 533
3 TraesCS1A01G142900 chr1A 255231059 255231583 524 True 678.00 678 89.8880 3343 3875 1 chr1A.!!$R1 532
4 TraesCS1A01G142900 chr1D 196093105 196095652 2547 False 4135.00 4135 96.0820 813 3342 1 chr1D.!!$F1 2529
5 TraesCS1A01G142900 chr1B 269218965 269221407 2442 True 2022.05 3971 98.4445 818 3238 2 chr1B.!!$R2 2420
6 TraesCS1A01G142900 chr1B 684411878 684412600 722 False 952.00 952 90.4700 4 725 1 chr1B.!!$F1 721
7 TraesCS1A01G142900 chr7D 158939954 158940681 727 True 974.00 974 90.8470 1 729 1 chr7D.!!$R1 728
8 TraesCS1A01G142900 chr7D 495280750 495281476 726 True 941.00 941 90.0270 1 729 1 chr7D.!!$R2 728
9 TraesCS1A01G142900 chr5D 394844716 394845441 725 False 972.00 972 90.8340 1 729 1 chr5D.!!$F1 728
10 TraesCS1A01G142900 chr5D 437091719 437092447 728 False 970.00 970 90.7100 1 729 1 chr5D.!!$F2 728
11 TraesCS1A01G142900 chr5D 548043770 548044294 524 True 717.00 717 91.1820 3343 3875 1 chr5D.!!$R1 532
12 TraesCS1A01G142900 chr6D 387406086 387406809 723 True 939.00 939 90.1100 1 725 1 chr6D.!!$R2 724
13 TraesCS1A01G142900 chr6D 420203191 420203917 726 True 937.00 937 89.9730 4 729 1 chr6D.!!$R3 725
14 TraesCS1A01G142900 chr6D 144616531 144617055 524 True 712.00 712 90.9940 3343 3875 1 chr6D.!!$R1 532
15 TraesCS1A01G142900 chr6B 129448722 129449441 719 True 928.00 928 89.9050 1 729 1 chr6B.!!$R1 728
16 TraesCS1A01G142900 chr2A 7362753 7363489 736 True 928.00 928 89.5660 1 729 1 chr2A.!!$R1 728
17 TraesCS1A01G142900 chr2A 765576825 765577351 526 False 693.00 693 90.2990 3340 3875 1 chr2A.!!$F1 535
18 TraesCS1A01G142900 chr2D 368466226 368466747 521 True 708.00 708 90.9770 3343 3874 1 chr2D.!!$R1 531
19 TraesCS1A01G142900 chr2D 512504254 512504778 524 True 701.00 701 90.6190 3343 3875 1 chr2D.!!$R2 532
20 TraesCS1A01G142900 chr5A 676630622 676631146 524 False 695.00 695 90.4320 3343 3875 1 chr5A.!!$F2 532
21 TraesCS1A01G142900 chr5A 487615995 487616518 523 False 676.00 676 89.8690 3343 3875 1 chr5A.!!$F1 532
22 TraesCS1A01G142900 chr3D 4158332 4158857 525 False 686.00 686 90.0750 3342 3875 1 chr3D.!!$F1 533
23 TraesCS1A01G142900 chr7A 714683139 714683665 526 False 651.00 651 88.9100 3343 3874 1 chr7A.!!$F1 531

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
790 803 0.109597 AAAATTCAGGAGCGCGCTTG 60.110 50.0 36.87 29.45 0.00 4.01 F
890 904 0.810031 AACTGCACTCACACGGTCAC 60.810 55.0 0.00 0.00 0.00 3.67 F
1410 1431 1.115930 ACACTGACTCCAACTCGGCT 61.116 55.0 0.00 0.00 33.14 5.52 F
2271 2292 0.324943 AAGACATCAAGGTGACCCCG 59.675 55.0 0.00 0.00 38.74 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 1702 0.615331 ACGAGGGAGCATGTGTTGAT 59.385 50.0 0.00 0.00 0.00 2.57 R
2271 2292 1.057636 TGACGTCGCGAAGTTTCATC 58.942 50.0 27.66 15.33 0.00 2.92 R
2832 2853 1.059098 TGACACCATCCTTGCAGTCT 58.941 50.0 0.00 0.00 0.00 3.24 R
3823 3872 0.392729 ACAAACGTGGGAACGGAACA 60.393 50.0 3.09 0.00 37.45 3.18 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
46 47 2.978018 GCGGCACTACAACAAGGGC 61.978 63.158 0.00 0.00 45.60 5.19
66 68 2.486191 GCACTACCTAGCTGATGGCATT 60.486 50.000 0.00 0.00 44.79 3.56
72 74 6.726299 ACTACCTAGCTGATGGCATTTATCTA 59.274 38.462 0.00 0.95 44.79 1.98
94 96 9.911788 ATCTAAGATGGTCTACATTTGTGAAAT 57.088 29.630 0.00 0.00 40.72 2.17
183 185 4.179579 GTCGAGCGGGCATTTGGC 62.180 66.667 0.00 0.00 43.74 4.52
212 214 2.542020 TCTCGATTTGCTGTTGTCCA 57.458 45.000 0.00 0.00 0.00 4.02
217 219 3.067106 CGATTTGCTGTTGTCCAGTACT 58.933 45.455 0.00 0.00 43.55 2.73
263 265 9.152327 AGATCAAATGTAGGAGATCATGACTTA 57.848 33.333 0.00 0.00 39.39 2.24
306 308 0.174389 TCATTGAGAGCGAGCAGGAC 59.826 55.000 0.00 0.00 0.00 3.85
451 453 1.985473 TCAACAACTGCAGCAGGATT 58.015 45.000 26.38 13.90 35.51 3.01
484 486 1.792757 ATGGAGGCTCAAGGGCAACA 61.793 55.000 17.69 2.42 43.56 3.33
512 514 4.445718 GCTCGACGTGTGATGAAATATGAT 59.554 41.667 0.00 0.00 0.00 2.45
513 515 5.050769 GCTCGACGTGTGATGAAATATGATT 60.051 40.000 0.00 0.00 0.00 2.57
662 671 5.694458 CGTGAATATGGACCGATTCATGTTA 59.306 40.000 22.08 3.71 42.43 2.41
668 681 9.958180 AATATGGACCGATTCATGTTAATATCA 57.042 29.630 0.00 0.00 0.00 2.15
671 684 6.183361 TGGACCGATTCATGTTAATATCAGGT 60.183 38.462 0.00 0.00 31.47 4.00
715 728 4.976987 CGAAAAACGGGCACATTTATACT 58.023 39.130 0.00 0.00 38.46 2.12
725 738 6.521162 GGGCACATTTATACTAAAAATGGGG 58.479 40.000 11.53 5.82 44.38 4.96
729 742 6.915843 CACATTTATACTAAAAATGGGGCGAC 59.084 38.462 11.86 0.00 44.80 5.19
742 755 4.803426 GCGACCTGGGCGAGACTG 62.803 72.222 29.22 0.00 0.00 3.51
743 756 4.135153 CGACCTGGGCGAGACTGG 62.135 72.222 19.36 0.00 0.00 4.00
744 757 2.680352 GACCTGGGCGAGACTGGA 60.680 66.667 0.00 0.00 0.00 3.86
745 758 2.681778 ACCTGGGCGAGACTGGAG 60.682 66.667 0.00 0.00 0.00 3.86
746 759 2.363018 CCTGGGCGAGACTGGAGA 60.363 66.667 0.00 0.00 0.00 3.71
747 760 1.760086 CCTGGGCGAGACTGGAGAT 60.760 63.158 0.00 0.00 0.00 2.75
748 761 1.440893 CTGGGCGAGACTGGAGATG 59.559 63.158 0.00 0.00 0.00 2.90
749 762 2.107953 GGGCGAGACTGGAGATGC 59.892 66.667 0.00 0.00 0.00 3.91
750 763 2.430610 GGGCGAGACTGGAGATGCT 61.431 63.158 0.00 0.00 0.00 3.79
751 764 1.067250 GGCGAGACTGGAGATGCTC 59.933 63.158 0.00 0.00 0.00 4.26
752 765 1.391157 GGCGAGACTGGAGATGCTCT 61.391 60.000 0.00 0.00 0.00 4.09
753 766 0.459489 GCGAGACTGGAGATGCTCTT 59.541 55.000 0.00 0.00 0.00 2.85
754 767 1.678627 GCGAGACTGGAGATGCTCTTA 59.321 52.381 0.00 0.00 0.00 2.10
755 768 2.287547 GCGAGACTGGAGATGCTCTTAG 60.288 54.545 0.00 0.00 0.00 2.18
756 769 3.210227 CGAGACTGGAGATGCTCTTAGA 58.790 50.000 0.00 0.00 0.00 2.10
757 770 3.820467 CGAGACTGGAGATGCTCTTAGAT 59.180 47.826 0.00 0.00 0.00 1.98
758 771 5.000591 CGAGACTGGAGATGCTCTTAGATA 58.999 45.833 0.00 0.00 0.00 1.98
759 772 5.106712 CGAGACTGGAGATGCTCTTAGATAC 60.107 48.000 0.00 0.00 0.00 2.24
760 773 5.700183 AGACTGGAGATGCTCTTAGATACA 58.300 41.667 0.00 0.00 0.00 2.29
761 774 5.534654 AGACTGGAGATGCTCTTAGATACAC 59.465 44.000 0.00 0.00 0.00 2.90
762 775 5.454062 ACTGGAGATGCTCTTAGATACACT 58.546 41.667 0.00 0.00 0.00 3.55
763 776 5.301551 ACTGGAGATGCTCTTAGATACACTG 59.698 44.000 0.00 0.00 0.00 3.66
764 777 5.204292 TGGAGATGCTCTTAGATACACTGT 58.796 41.667 0.00 0.00 0.00 3.55
765 778 5.300539 TGGAGATGCTCTTAGATACACTGTC 59.699 44.000 0.00 0.00 0.00 3.51
766 779 5.431420 AGATGCTCTTAGATACACTGTCG 57.569 43.478 0.00 0.00 0.00 4.35
767 780 4.277174 AGATGCTCTTAGATACACTGTCGG 59.723 45.833 0.00 0.00 0.00 4.79
768 781 2.688446 TGCTCTTAGATACACTGTCGGG 59.312 50.000 0.00 0.00 0.00 5.14
769 782 2.034812 GCTCTTAGATACACTGTCGGGG 59.965 54.545 0.00 0.00 0.00 5.73
770 783 3.552875 CTCTTAGATACACTGTCGGGGA 58.447 50.000 0.00 0.00 0.00 4.81
771 784 3.952323 CTCTTAGATACACTGTCGGGGAA 59.048 47.826 0.00 0.00 0.00 3.97
772 785 4.346730 TCTTAGATACACTGTCGGGGAAA 58.653 43.478 0.00 0.00 0.00 3.13
773 786 4.773674 TCTTAGATACACTGTCGGGGAAAA 59.226 41.667 0.00 0.00 0.00 2.29
774 787 5.246656 TCTTAGATACACTGTCGGGGAAAAA 59.753 40.000 0.00 0.00 0.00 1.94
775 788 4.569719 AGATACACTGTCGGGGAAAAAT 57.430 40.909 0.00 0.00 0.00 1.82
776 789 4.918588 AGATACACTGTCGGGGAAAAATT 58.081 39.130 0.00 0.00 0.00 1.82
777 790 4.941873 AGATACACTGTCGGGGAAAAATTC 59.058 41.667 0.00 0.00 0.00 2.17
778 791 2.938838 ACACTGTCGGGGAAAAATTCA 58.061 42.857 0.00 0.00 0.00 2.57
779 792 2.884639 ACACTGTCGGGGAAAAATTCAG 59.115 45.455 0.00 0.00 0.00 3.02
780 793 2.228822 CACTGTCGGGGAAAAATTCAGG 59.771 50.000 0.00 0.00 0.00 3.86
781 794 2.107552 ACTGTCGGGGAAAAATTCAGGA 59.892 45.455 0.00 0.00 0.00 3.86
782 795 2.749621 CTGTCGGGGAAAAATTCAGGAG 59.250 50.000 0.00 0.00 0.00 3.69
783 796 1.472878 GTCGGGGAAAAATTCAGGAGC 59.527 52.381 0.00 0.00 0.00 4.70
784 797 0.451783 CGGGGAAAAATTCAGGAGCG 59.548 55.000 0.00 0.00 0.00 5.03
785 798 0.173481 GGGGAAAAATTCAGGAGCGC 59.827 55.000 0.00 0.00 0.00 5.92
786 799 0.179163 GGGAAAAATTCAGGAGCGCG 60.179 55.000 0.00 0.00 0.00 6.86
787 800 0.798389 GGAAAAATTCAGGAGCGCGC 60.798 55.000 26.66 26.66 0.00 6.86
788 801 0.169009 GAAAAATTCAGGAGCGCGCT 59.831 50.000 37.28 37.28 0.00 5.92
789 802 0.598065 AAAAATTCAGGAGCGCGCTT 59.402 45.000 36.87 18.68 0.00 4.68
790 803 0.109597 AAAATTCAGGAGCGCGCTTG 60.110 50.000 36.87 29.45 0.00 4.01
791 804 2.533391 AAATTCAGGAGCGCGCTTGC 62.533 55.000 36.87 23.37 0.00 4.01
792 805 4.986645 TTCAGGAGCGCGCTTGCA 62.987 61.111 36.87 18.54 39.07 4.08
793 806 4.765449 TCAGGAGCGCGCTTGCAT 62.765 61.111 36.87 18.91 39.07 3.96
794 807 3.807538 CAGGAGCGCGCTTGCATT 61.808 61.111 36.87 12.49 39.07 3.56
795 808 3.058160 AGGAGCGCGCTTGCATTT 61.058 55.556 36.87 11.56 39.07 2.32
796 809 2.126346 GGAGCGCGCTTGCATTTT 60.126 55.556 36.87 10.63 39.07 1.82
797 810 1.734117 GGAGCGCGCTTGCATTTTT 60.734 52.632 36.87 9.72 39.07 1.94
890 904 0.810031 AACTGCACTCACACGGTCAC 60.810 55.000 0.00 0.00 0.00 3.67
901 916 2.179517 CGGTCACACCTCTCTCGC 59.820 66.667 0.00 0.00 35.66 5.03
1218 1233 2.610859 ACCTCCGCCACCTCCAAT 60.611 61.111 0.00 0.00 0.00 3.16
1296 1311 2.600769 AACACCTCCGAGGACGCT 60.601 61.111 21.89 0.22 37.67 5.07
1410 1431 1.115930 ACACTGACTCCAACTCGGCT 61.116 55.000 0.00 0.00 33.14 5.52
2020 2041 1.182667 GAACCACTACATTTGGGGCC 58.817 55.000 0.00 0.00 38.59 5.80
2175 2196 1.938577 CACCTGAAGGAATCTGCATCG 59.061 52.381 2.62 0.00 38.94 3.84
2233 2254 1.556911 AGTGGCACAAGAAGGATCGAT 59.443 47.619 21.41 0.00 44.16 3.59
2241 2262 5.065731 GCACAAGAAGGATCGATTGAAGAAT 59.934 40.000 0.00 0.00 0.00 2.40
2247 2268 7.961351 AGAAGGATCGATTGAAGAATCACTAT 58.039 34.615 0.00 0.00 38.35 2.12
2250 2271 7.607250 AGGATCGATTGAAGAATCACTATACC 58.393 38.462 0.00 0.00 38.35 2.73
2271 2292 0.324943 AAGACATCAAGGTGACCCCG 59.675 55.000 0.00 0.00 38.74 5.73
2283 2304 0.672401 TGACCCCGATGAAACTTCGC 60.672 55.000 0.00 0.00 35.31 4.70
2364 2385 2.279851 CGTGTGTGCGAGGGTGAA 60.280 61.111 0.00 0.00 0.00 3.18
2412 2433 1.531149 CATTTCTTGTGGAAGTCGCGT 59.469 47.619 5.77 0.00 35.16 6.01
2478 2499 1.654105 GATTTCGACTCGATGCACGTT 59.346 47.619 1.07 0.00 43.13 3.99
2736 2757 1.999648 AGGAGCTCAACAATGGCAAA 58.000 45.000 17.19 0.00 0.00 3.68
2831 2852 5.221823 TGGAGACATTCAATGACCTAACACA 60.222 40.000 3.79 0.00 33.40 3.72
2832 2853 5.705441 GGAGACATTCAATGACCTAACACAA 59.295 40.000 3.79 0.00 0.00 3.33
2862 2883 0.657312 ATGGTGTCAATACATGCGCG 59.343 50.000 0.00 0.00 38.08 6.86
2866 2887 2.180204 GTCAATACATGCGCGGCCT 61.180 57.895 8.83 0.00 0.00 5.19
2886 2907 1.140852 TCCGCCTGAATATCTGGTTGG 59.859 52.381 5.37 7.45 37.74 3.77
2951 2972 4.782019 TTTGAACTCACATGTATTGCCC 57.218 40.909 0.00 0.00 0.00 5.36
3123 3146 6.412362 TGTTGCATTTTGGTTATGTTACCT 57.588 33.333 0.00 0.00 39.04 3.08
3124 3147 6.821388 TGTTGCATTTTGGTTATGTTACCTT 58.179 32.000 0.00 0.00 39.04 3.50
3125 3148 6.703607 TGTTGCATTTTGGTTATGTTACCTTG 59.296 34.615 0.00 0.00 39.04 3.61
3183 3206 3.498397 CGCTGTCTTTTACTGTTCCATGT 59.502 43.478 0.00 0.00 0.00 3.21
3186 3209 5.239525 GCTGTCTTTTACTGTTCCATGTCTT 59.760 40.000 0.00 0.00 0.00 3.01
3188 3211 7.639113 TGTCTTTTACTGTTCCATGTCTTTT 57.361 32.000 0.00 0.00 0.00 2.27
3189 3212 7.479980 TGTCTTTTACTGTTCCATGTCTTTTG 58.520 34.615 0.00 0.00 0.00 2.44
3191 3214 6.321181 TCTTTTACTGTTCCATGTCTTTTGCT 59.679 34.615 0.00 0.00 0.00 3.91
3192 3215 3.996150 ACTGTTCCATGTCTTTTGCTG 57.004 42.857 0.00 0.00 0.00 4.41
3193 3216 3.290710 ACTGTTCCATGTCTTTTGCTGT 58.709 40.909 0.00 0.00 0.00 4.40
3194 3217 3.701040 ACTGTTCCATGTCTTTTGCTGTT 59.299 39.130 0.00 0.00 0.00 3.16
3195 3218 4.202050 ACTGTTCCATGTCTTTTGCTGTTC 60.202 41.667 0.00 0.00 0.00 3.18
3196 3219 3.068024 TGTTCCATGTCTTTTGCTGTTCC 59.932 43.478 0.00 0.00 0.00 3.62
3197 3220 3.228188 TCCATGTCTTTTGCTGTTCCT 57.772 42.857 0.00 0.00 0.00 3.36
3198 3221 3.149196 TCCATGTCTTTTGCTGTTCCTC 58.851 45.455 0.00 0.00 0.00 3.71
3241 3279 7.611855 AGATTTGGTTCAGTTTAAGAGTATGGG 59.388 37.037 0.00 0.00 0.00 4.00
3253 3291 0.749649 AGTATGGGAGAGCGCTGAAG 59.250 55.000 18.48 0.00 0.00 3.02
3280 3323 4.775780 ACTACTGCCAGTAACTGAATACCA 59.224 41.667 5.98 0.00 32.44 3.25
3319 3362 1.377333 CCTCTTTGGGGAAGGCGTC 60.377 63.158 0.00 0.00 35.98 5.19
3324 3367 0.177141 TTTGGGGAAGGCGTCTATCG 59.823 55.000 0.00 0.00 43.12 2.92
3327 3370 1.397390 GGGGAAGGCGTCTATCGGAA 61.397 60.000 0.00 0.00 40.26 4.30
3359 3402 6.211384 CCTTTGTTTAGGGATGAAAATGGAGT 59.789 38.462 0.00 0.00 0.00 3.85
3367 3410 3.506067 GGATGAAAATGGAGTGGAAACGT 59.494 43.478 0.00 0.00 0.00 3.99
3402 3445 8.850156 AGGTGCTACCATATTTGTTTTCATATC 58.150 33.333 7.86 0.00 41.95 1.63
3459 3503 6.553255 CGGAAATGAATACGGAAACAAATG 57.447 37.500 0.00 0.00 0.00 2.32
3462 3506 6.034898 GGAAATGAATACGGAAACAAATGCTG 59.965 38.462 0.00 0.00 0.00 4.41
3470 3514 3.611530 CGGAAACAAATGCTGTCGGAAAT 60.612 43.478 0.00 0.00 37.23 2.17
3494 3538 1.355563 CGGAGCGAATACAGAGCGA 59.644 57.895 0.00 0.00 35.78 4.93
3553 3597 4.779993 ACCCCCTTGAATCATAGAGAAC 57.220 45.455 0.00 0.00 0.00 3.01
3721 3770 7.839680 AGTAAAAGTTGGTCCTCAAATGATT 57.160 32.000 0.00 0.00 37.08 2.57
3735 3784 8.267183 TCCTCAAATGATTTAGTCTGCTCATTA 58.733 33.333 0.00 0.00 37.35 1.90
3788 3837 5.435686 ACAAAGCAGTCATGGACCTATAA 57.564 39.130 0.00 0.00 32.18 0.98
3798 3847 6.014499 AGTCATGGACCTATAATAGAAACGGG 60.014 42.308 0.00 0.00 32.18 5.28
3845 3894 0.178533 TCCGTTCCCACGTTTGTTCT 59.821 50.000 0.00 0.00 45.62 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.482156 AATGCCATCAGCTAGGTAGTG 57.518 47.619 0.00 0.00 44.23 2.74
72 74 9.911788 ATAGATTTCACAAATGTAGACCATCTT 57.088 29.630 0.00 0.00 31.23 2.40
94 96 3.632643 TGGCACAGCATTTGAGATAGA 57.367 42.857 0.00 0.00 0.00 1.98
183 185 1.267732 GCAAATCGAGATTGGAGCACG 60.268 52.381 13.66 0.00 0.00 5.34
212 214 2.823154 GACCAAGTCTGAGCAGAGTACT 59.177 50.000 8.17 0.00 40.04 2.73
217 219 1.328279 TTCGACCAAGTCTGAGCAGA 58.672 50.000 0.00 0.00 34.56 4.26
248 250 6.550938 TGACACAATAAGTCATGATCTCCT 57.449 37.500 0.00 0.00 40.80 3.69
484 486 0.452184 CATCACACGTCGAGCTAGGT 59.548 55.000 0.00 0.00 0.00 3.08
619 624 0.802494 GTGGTTCGGCGTGAATTCAT 59.198 50.000 12.12 0.00 39.21 2.57
662 671 6.687081 TTCGGCGAAAAATAACCTGATATT 57.313 33.333 21.53 0.00 0.00 1.28
668 681 3.057806 CCACTTTCGGCGAAAAATAACCT 60.058 43.478 31.70 9.02 30.84 3.50
671 684 2.351932 GCCCACTTTCGGCGAAAAATAA 60.352 45.455 31.70 13.13 36.47 1.40
712 725 2.356330 CCAGGTCGCCCCATTTTTAGTA 60.356 50.000 0.00 0.00 34.66 1.82
715 728 0.323908 CCCAGGTCGCCCCATTTTTA 60.324 55.000 0.00 0.00 34.66 1.52
725 738 4.803426 CAGTCTCGCCCAGGTCGC 62.803 72.222 0.00 0.00 0.00 5.19
729 742 1.760086 ATCTCCAGTCTCGCCCAGG 60.760 63.158 0.00 0.00 0.00 4.45
730 743 1.440893 CATCTCCAGTCTCGCCCAG 59.559 63.158 0.00 0.00 0.00 4.45
731 744 2.725312 GCATCTCCAGTCTCGCCCA 61.725 63.158 0.00 0.00 0.00 5.36
732 745 2.107953 GCATCTCCAGTCTCGCCC 59.892 66.667 0.00 0.00 0.00 6.13
733 746 1.067250 GAGCATCTCCAGTCTCGCC 59.933 63.158 0.00 0.00 0.00 5.54
734 747 4.728058 GAGCATCTCCAGTCTCGC 57.272 61.111 0.00 0.00 0.00 5.03
745 758 4.541779 CCGACAGTGTATCTAAGAGCATC 58.458 47.826 0.00 0.00 0.00 3.91
746 759 3.319405 CCCGACAGTGTATCTAAGAGCAT 59.681 47.826 0.00 0.00 0.00 3.79
747 760 2.688446 CCCGACAGTGTATCTAAGAGCA 59.312 50.000 0.00 0.00 0.00 4.26
748 761 2.034812 CCCCGACAGTGTATCTAAGAGC 59.965 54.545 0.00 0.00 0.00 4.09
749 762 3.552875 TCCCCGACAGTGTATCTAAGAG 58.447 50.000 0.00 0.00 0.00 2.85
750 763 3.657398 TCCCCGACAGTGTATCTAAGA 57.343 47.619 0.00 0.00 0.00 2.10
751 764 4.730949 TTTCCCCGACAGTGTATCTAAG 57.269 45.455 0.00 0.00 0.00 2.18
752 765 5.486735 TTTTTCCCCGACAGTGTATCTAA 57.513 39.130 0.00 0.00 0.00 2.10
753 766 5.687166 ATTTTTCCCCGACAGTGTATCTA 57.313 39.130 0.00 0.00 0.00 1.98
754 767 4.569719 ATTTTTCCCCGACAGTGTATCT 57.430 40.909 0.00 0.00 0.00 1.98
755 768 4.698304 TGAATTTTTCCCCGACAGTGTATC 59.302 41.667 0.00 0.00 0.00 2.24
756 769 4.658063 TGAATTTTTCCCCGACAGTGTAT 58.342 39.130 0.00 0.00 0.00 2.29
757 770 4.069304 CTGAATTTTTCCCCGACAGTGTA 58.931 43.478 0.00 0.00 0.00 2.90
758 771 2.884639 CTGAATTTTTCCCCGACAGTGT 59.115 45.455 0.00 0.00 0.00 3.55
759 772 2.228822 CCTGAATTTTTCCCCGACAGTG 59.771 50.000 0.00 0.00 0.00 3.66
760 773 2.107552 TCCTGAATTTTTCCCCGACAGT 59.892 45.455 0.00 0.00 0.00 3.55
761 774 2.749621 CTCCTGAATTTTTCCCCGACAG 59.250 50.000 0.00 0.00 0.00 3.51
762 775 2.790433 CTCCTGAATTTTTCCCCGACA 58.210 47.619 0.00 0.00 0.00 4.35
763 776 1.472878 GCTCCTGAATTTTTCCCCGAC 59.527 52.381 0.00 0.00 0.00 4.79
764 777 1.834188 GCTCCTGAATTTTTCCCCGA 58.166 50.000 0.00 0.00 0.00 5.14
765 778 0.451783 CGCTCCTGAATTTTTCCCCG 59.548 55.000 0.00 0.00 0.00 5.73
766 779 0.173481 GCGCTCCTGAATTTTTCCCC 59.827 55.000 0.00 0.00 0.00 4.81
767 780 0.179163 CGCGCTCCTGAATTTTTCCC 60.179 55.000 5.56 0.00 0.00 3.97
768 781 0.798389 GCGCGCTCCTGAATTTTTCC 60.798 55.000 26.67 0.00 0.00 3.13
769 782 0.169009 AGCGCGCTCCTGAATTTTTC 59.831 50.000 31.32 0.00 0.00 2.29
770 783 0.598065 AAGCGCGCTCCTGAATTTTT 59.402 45.000 36.57 12.02 0.00 1.94
771 784 0.109597 CAAGCGCGCTCCTGAATTTT 60.110 50.000 36.57 12.91 0.00 1.82
772 785 1.503542 CAAGCGCGCTCCTGAATTT 59.496 52.632 36.57 13.79 0.00 1.82
773 786 3.044059 GCAAGCGCGCTCCTGAATT 62.044 57.895 36.57 14.68 0.00 2.17
774 787 3.503363 GCAAGCGCGCTCCTGAAT 61.503 61.111 36.57 15.57 0.00 2.57
775 788 4.986645 TGCAAGCGCGCTCCTGAA 62.987 61.111 36.57 22.59 42.97 3.02
776 789 4.765449 ATGCAAGCGCGCTCCTGA 62.765 61.111 36.57 18.93 42.97 3.86
777 790 2.807631 AAAATGCAAGCGCGCTCCTG 62.808 55.000 36.57 29.89 42.97 3.86
778 791 2.146073 AAAAATGCAAGCGCGCTCCT 62.146 50.000 36.57 18.28 42.97 3.69
779 792 1.734117 AAAAATGCAAGCGCGCTCC 60.734 52.632 36.57 27.35 42.97 4.70
780 793 3.846754 AAAAATGCAAGCGCGCTC 58.153 50.000 36.57 23.67 42.97 5.03
799 812 9.667107 TCTTTGTCGGATTTCATTTTATAGAGT 57.333 29.630 0.00 0.00 0.00 3.24
800 813 9.922305 GTCTTTGTCGGATTTCATTTTATAGAG 57.078 33.333 0.00 0.00 0.00 2.43
801 814 9.443323 TGTCTTTGTCGGATTTCATTTTATAGA 57.557 29.630 0.00 0.00 0.00 1.98
804 817 8.739039 TGATGTCTTTGTCGGATTTCATTTTAT 58.261 29.630 0.00 0.00 0.00 1.40
805 818 8.105097 TGATGTCTTTGTCGGATTTCATTTTA 57.895 30.769 0.00 0.00 0.00 1.52
806 819 6.980593 TGATGTCTTTGTCGGATTTCATTTT 58.019 32.000 0.00 0.00 0.00 1.82
807 820 6.573664 TGATGTCTTTGTCGGATTTCATTT 57.426 33.333 0.00 0.00 0.00 2.32
808 821 6.207417 AGTTGATGTCTTTGTCGGATTTCATT 59.793 34.615 0.00 0.00 0.00 2.57
809 822 5.707298 AGTTGATGTCTTTGTCGGATTTCAT 59.293 36.000 0.00 0.00 0.00 2.57
810 823 5.063204 AGTTGATGTCTTTGTCGGATTTCA 58.937 37.500 0.00 0.00 0.00 2.69
811 824 5.613358 AGTTGATGTCTTTGTCGGATTTC 57.387 39.130 0.00 0.00 0.00 2.17
890 904 2.282147 CTGAGCTGGCGAGAGAGGTG 62.282 65.000 0.00 0.00 0.00 4.00
901 916 2.183811 CAGGACGAGCTGAGCTGG 59.816 66.667 13.71 14.51 39.88 4.85
937 952 2.706071 GAGGGGGAGGGATCTGGT 59.294 66.667 0.00 0.00 0.00 4.00
1083 1098 2.769602 AGAGCCCGAATAGGAGGTTA 57.230 50.000 0.00 0.00 45.00 2.85
1173 1188 2.224159 GGTGAGCTGGTGGGAGGAA 61.224 63.158 0.00 0.00 0.00 3.36
1218 1233 2.602267 TCGGCGAGGAAGGTGGAA 60.602 61.111 4.99 0.00 0.00 3.53
1274 1289 1.609501 TCCTCGGAGGTGTTGGAGG 60.610 63.158 22.88 0.00 45.93 4.30
1282 1297 3.063084 GTGAGCGTCCTCGGAGGT 61.063 66.667 22.88 4.16 41.13 3.85
1296 1311 3.986006 GGTCCGACAGTGGCGTGA 61.986 66.667 18.86 11.54 0.00 4.35
1395 1410 2.343758 GCAGCCGAGTTGGAGTCA 59.656 61.111 0.00 0.00 42.00 3.41
1681 1702 0.615331 ACGAGGGAGCATGTGTTGAT 59.385 50.000 0.00 0.00 0.00 2.57
1755 1776 3.752339 CCCTTCTTGCCCTTGCGC 61.752 66.667 0.00 0.00 41.78 6.09
2020 2041 1.195448 CTCACCTAGCGCACACAAAAG 59.805 52.381 11.47 0.00 0.00 2.27
2175 2196 3.380004 AGAACTGACTCTGATCGATCACC 59.620 47.826 23.99 13.25 32.50 4.02
2233 2254 7.165460 TGTCTTCGGTATAGTGATTCTTCAA 57.835 36.000 0.00 0.00 32.48 2.69
2241 2262 4.954202 ACCTTGATGTCTTCGGTATAGTGA 59.046 41.667 0.00 0.00 0.00 3.41
2247 2268 2.232941 GGTCACCTTGATGTCTTCGGTA 59.767 50.000 0.00 0.00 0.00 4.02
2250 2271 1.676014 GGGGTCACCTTGATGTCTTCG 60.676 57.143 0.00 0.00 36.80 3.79
2271 2292 1.057636 TGACGTCGCGAAGTTTCATC 58.942 50.000 27.66 15.33 0.00 2.92
2283 2304 2.050351 AGCGTGTCCTTGACGTCG 60.050 61.111 11.62 0.00 39.08 5.12
2364 2385 1.463674 GTTTGATCATGGCCTCCGTT 58.536 50.000 3.32 0.00 0.00 4.44
2412 2433 2.234661 AGACACAATCTCCATCAAGCGA 59.765 45.455 0.00 0.00 28.16 4.93
2478 2499 1.270907 GGGCTTTCTCTCCTCTCACA 58.729 55.000 0.00 0.00 0.00 3.58
2736 2757 1.477685 AACCATCGAACTCCACCGGT 61.478 55.000 0.00 0.00 0.00 5.28
2831 2852 1.421268 TGACACCATCCTTGCAGTCTT 59.579 47.619 0.00 0.00 0.00 3.01
2832 2853 1.059098 TGACACCATCCTTGCAGTCT 58.941 50.000 0.00 0.00 0.00 3.24
2866 2887 1.140852 CCAACCAGATATTCAGGCGGA 59.859 52.381 0.00 0.00 0.00 5.54
2869 2890 2.736670 ACCCAACCAGATATTCAGGC 57.263 50.000 0.00 0.00 0.00 4.85
2886 2907 2.165437 CTGAGACTCAGCTCACCTTACC 59.835 54.545 19.25 0.00 39.84 2.85
3123 3146 6.183360 ACAACAGAGATACAATGCAACAACAA 60.183 34.615 0.00 0.00 0.00 2.83
3124 3147 5.299028 ACAACAGAGATACAATGCAACAACA 59.701 36.000 0.00 0.00 0.00 3.33
3125 3148 5.762045 ACAACAGAGATACAATGCAACAAC 58.238 37.500 0.00 0.00 0.00 3.32
3183 3206 5.888161 AGAAAAGAAGAGGAACAGCAAAAGA 59.112 36.000 0.00 0.00 0.00 2.52
3186 3209 6.601613 TGTAAGAAAAGAAGAGGAACAGCAAA 59.398 34.615 0.00 0.00 0.00 3.68
3188 3211 5.680619 TGTAAGAAAAGAAGAGGAACAGCA 58.319 37.500 0.00 0.00 0.00 4.41
3189 3212 6.809630 ATGTAAGAAAAGAAGAGGAACAGC 57.190 37.500 0.00 0.00 0.00 4.40
3191 3214 8.210946 TCTCAATGTAAGAAAAGAAGAGGAACA 58.789 33.333 0.00 0.00 0.00 3.18
3192 3215 8.608844 TCTCAATGTAAGAAAAGAAGAGGAAC 57.391 34.615 0.00 0.00 0.00 3.62
3193 3216 9.799106 AATCTCAATGTAAGAAAAGAAGAGGAA 57.201 29.630 0.00 0.00 0.00 3.36
3194 3217 9.799106 AAATCTCAATGTAAGAAAAGAAGAGGA 57.201 29.630 0.00 0.00 0.00 3.71
3195 3218 9.837525 CAAATCTCAATGTAAGAAAAGAAGAGG 57.162 33.333 0.00 0.00 0.00 3.69
3196 3219 9.837525 CCAAATCTCAATGTAAGAAAAGAAGAG 57.162 33.333 0.00 0.00 0.00 2.85
3197 3220 9.354673 ACCAAATCTCAATGTAAGAAAAGAAGA 57.645 29.630 0.00 0.00 0.00 2.87
3198 3221 9.971922 AACCAAATCTCAATGTAAGAAAAGAAG 57.028 29.630 0.00 0.00 0.00 2.85
3241 3279 4.286910 CAGTAGTAATCTTCAGCGCTCTC 58.713 47.826 7.13 0.00 0.00 3.20
3253 3291 7.652507 GGTATTCAGTTACTGGCAGTAGTAATC 59.347 40.741 25.00 14.74 43.00 1.75
3307 3350 2.131709 CCGATAGACGCCTTCCCCA 61.132 63.158 0.00 0.00 41.07 4.96
3319 3362 9.640963 CCTAAACAAAGGTATCTATTCCGATAG 57.359 37.037 0.00 0.00 33.51 2.08
3324 3367 8.437575 TCATCCCTAAACAAAGGTATCTATTCC 58.562 37.037 0.00 0.00 34.56 3.01
3359 3402 2.030007 CACCTAGTTCCGTACGTTTCCA 60.030 50.000 15.21 0.00 0.00 3.53
3367 3410 2.512692 TGGTAGCACCTAGTTCCGTA 57.487 50.000 6.83 0.00 39.58 4.02
3402 3445 1.780860 CGTTTCCGCTTCTGCAAAAAG 59.219 47.619 4.50 4.50 39.64 2.27
3459 3503 1.135199 TCCGTGTCTATTTCCGACAGC 60.135 52.381 0.00 0.00 41.62 4.40
3462 3506 1.557651 GCTCCGTGTCTATTTCCGAC 58.442 55.000 0.00 0.00 0.00 4.79
3470 3514 2.612672 CTCTGTATTCGCTCCGTGTCTA 59.387 50.000 0.00 0.00 0.00 2.59
3494 3538 4.561105 ACACACCATTTTGTTTTCGTGTT 58.439 34.783 0.00 0.00 32.74 3.32
3672 3721 4.687948 CCACACACATTCTCAACTAGACAG 59.312 45.833 0.00 0.00 32.51 3.51
3721 3770 7.064966 CACACAATGACATAATGAGCAGACTAA 59.935 37.037 5.98 0.00 0.00 2.24
3735 3784 4.734398 ACCAAACAACACACAATGACAT 57.266 36.364 0.00 0.00 0.00 3.06
3781 3830 7.383156 TGGAATTCCCGTTTCTATTATAGGT 57.617 36.000 21.90 0.00 37.93 3.08
3788 3837 6.426937 CGTGAATATGGAATTCCCGTTTCTAT 59.573 38.462 21.90 9.03 37.93 1.98
3823 3872 0.392729 ACAAACGTGGGAACGGAACA 60.393 50.000 3.09 0.00 37.45 3.18
3832 3881 2.536761 TCCAGTAGAACAAACGTGGG 57.463 50.000 0.00 0.00 0.00 4.61
3845 3894 2.903798 ACGAAACGGTGTTTTCCAGTA 58.096 42.857 0.00 0.00 32.67 2.74


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

AutoCloner maintained by Alex Coulton.