Multiple sequence alignment - TraesCS2A01G207800

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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 TraesCS2A01G207800 chr2A 100.000 3460 0 0 1 3460 187949100 187952559 0.000000e+00 6390.0
1 TraesCS2A01G207800 chr2A 85.910 511 51 9 2 495 510822737 510823243 3.060000e-145 525.0
2 TraesCS2A01G207800 chr2D 93.512 2728 91 43 786 3460 176160567 176163261 0.000000e+00 3978.0
3 TraesCS2A01G207800 chr2D 83.771 419 40 13 1 397 524928750 524929162 4.220000e-99 372.0
4 TraesCS2A01G207800 chr2D 95.876 97 4 0 496 592 176160334 176160430 1.290000e-34 158.0
5 TraesCS2A01G207800 chr2B 93.759 2019 62 23 786 2748 233265464 233267474 0.000000e+00 2972.0
6 TraesCS2A01G207800 chr2B 89.053 676 29 20 2819 3460 233267480 233268144 0.000000e+00 797.0
7 TraesCS2A01G207800 chr2B 91.176 102 4 1 496 592 233265285 233265386 2.170000e-27 134.0
8 TraesCS2A01G207800 chr6A 99.194 496 3 1 1 495 73381545 73381050 0.000000e+00 893.0
9 TraesCS2A01G207800 chr6A 98.305 472 5 3 1 470 597331947 597331477 0.000000e+00 824.0
10 TraesCS2A01G207800 chr3A 95.976 497 15 3 1 496 449657488 449656996 0.000000e+00 802.0
11 TraesCS2A01G207800 chr3A 95.181 498 17 6 1 497 522236902 522236411 0.000000e+00 780.0
12 TraesCS2A01G207800 chr3A 94.444 36 0 2 579 614 620772224 620772257 2.000000e-03 54.7
13 TraesCS2A01G207800 chr5A 95.382 498 15 8 2 495 413229942 413229449 0.000000e+00 785.0
14 TraesCS2A01G207800 chr7A 93.548 496 27 4 1 495 40896617 40896126 0.000000e+00 734.0
15 TraesCS2A01G207800 chr7A 86.550 513 41 18 1 493 148504960 148504456 1.090000e-149 540.0
16 TraesCS2A01G207800 chr6D 87.160 514 43 10 1 495 103194570 103195079 2.330000e-156 562.0
17 TraesCS2A01G207800 chr7D 85.965 513 46 12 1 493 147193020 147192514 3.060000e-145 525.0
18 TraesCS2A01G207800 chr7D 85.240 542 42 17 2937 3460 581036187 581035666 1.100000e-144 523.0
19 TraesCS2A01G207800 chr7D 100.000 31 0 0 1225 1255 192057998 192057968 1.340000e-04 58.4
20 TraesCS2A01G207800 chr3D 84.394 487 27 22 2934 3391 604597851 604598317 1.910000e-117 433.0
21 TraesCS2A01G207800 chr3B 100.000 28 0 0 579 606 636455824 636455851 6.000000e-03 52.8


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 TraesCS2A01G207800 chr2A 187949100 187952559 3459 False 6390 6390 100.000000 1 3460 1 chr2A.!!$F1 3459
1 TraesCS2A01G207800 chr2A 510822737 510823243 506 False 525 525 85.910000 2 495 1 chr2A.!!$F2 493
2 TraesCS2A01G207800 chr2D 176160334 176163261 2927 False 2068 3978 94.694000 496 3460 2 chr2D.!!$F2 2964
3 TraesCS2A01G207800 chr2B 233265285 233268144 2859 False 1301 2972 91.329333 496 3460 3 chr2B.!!$F1 2964
4 TraesCS2A01G207800 chr7A 148504456 148504960 504 True 540 540 86.550000 1 493 1 chr7A.!!$R2 492
5 TraesCS2A01G207800 chr6D 103194570 103195079 509 False 562 562 87.160000 1 495 1 chr6D.!!$F1 494
6 TraesCS2A01G207800 chr7D 147192514 147193020 506 True 525 525 85.965000 1 493 1 chr7D.!!$R1 492
7 TraesCS2A01G207800 chr7D 581035666 581036187 521 True 523 523 85.240000 2937 3460 1 chr7D.!!$R3 523

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
845 880 0.181587 TTTCCCACTGGCAACGAGAA 59.818 50.0 0.0 0.0 42.51 2.87 F
2007 2079 0.038892 CGGTGTACTACGTGCCTGTT 60.039 55.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2276 0.033405 CTTCCCCTCCACCGAGTAGA 60.033 60.0 0.0 0.0 33.93 2.59 R
2813 2909 0.890683 AATGCCAGAAAAAGAGCGGG 59.109 50.0 0.0 0.0 0.00 6.13 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
90 97 8.461222 ACAATTCCAGTAAATCACACATGTATG 58.539 33.333 0.00 0.00 0.00 2.39
165 191 3.617540 TGCAATGTTAGTTGACCGTTG 57.382 42.857 0.00 0.00 0.00 4.10
180 206 9.804758 AGTTGACCGTTGAAATTTAACATTTTA 57.195 25.926 1.71 0.00 0.00 1.52
236 264 4.422073 TGCACTCACTAATATTCTGGGG 57.578 45.455 0.00 0.00 0.00 4.96
242 270 7.255277 GCACTCACTAATATTCTGGGGAAAATC 60.255 40.741 0.00 0.00 34.90 2.17
291 319 4.265073 AGATATTGACAGTTCCAGTTGGC 58.735 43.478 0.00 0.00 34.44 4.52
312 341 1.063031 GCTGATGCGGCAAGTTTTTC 58.937 50.000 6.82 0.00 35.55 2.29
367 396 6.263842 ACTTGTCAGAAATCATGTCAACACAT 59.736 34.615 0.00 0.00 44.72 3.21
504 534 3.096852 TGCAATTTCCTCGAGTCCTAGA 58.903 45.455 12.31 0.00 0.00 2.43
506 536 3.119101 GCAATTTCCTCGAGTCCTAGACA 60.119 47.826 12.31 0.00 34.60 3.41
580 615 6.238925 GGGATCAATAATTTTGTCCCTTACCG 60.239 42.308 19.37 0.00 41.63 4.02
581 616 6.238925 GGATCAATAATTTTGTCCCTTACCGG 60.239 42.308 0.00 0.00 0.00 5.28
590 625 3.306379 CCTTACCGGGTCTGGGTC 58.694 66.667 6.32 0.00 38.99 4.46
591 626 1.305887 CCTTACCGGGTCTGGGTCT 60.306 63.158 6.32 0.00 38.99 3.85
604 639 2.294078 GGGTCTGGGTCTGGGTCTG 61.294 68.421 0.00 0.00 0.00 3.51
605 640 2.294078 GGTCTGGGTCTGGGTCTGG 61.294 68.421 0.00 0.00 0.00 3.86
611 646 0.973496 GGGTCTGGGTCTGGACTCTC 60.973 65.000 2.19 0.00 31.68 3.20
630 665 3.894742 GGATCATCCGGAACCCAAA 57.105 52.632 9.01 0.00 32.47 3.28
632 667 1.340600 GGATCATCCGGAACCCAAACA 60.341 52.381 9.01 0.00 32.47 2.83
634 669 1.832883 TCATCCGGAACCCAAACATG 58.167 50.000 9.01 0.00 0.00 3.21
637 672 1.611519 TCCGGAACCCAAACATGTTC 58.388 50.000 12.39 0.00 0.00 3.18
640 675 2.288152 CCGGAACCCAAACATGTTCTTG 60.288 50.000 12.39 7.43 0.00 3.02
643 678 4.119136 GGAACCCAAACATGTTCTTGTTG 58.881 43.478 12.39 5.89 39.68 3.33
646 681 3.384467 ACCCAAACATGTTCTTGTTGGAG 59.616 43.478 22.38 15.94 39.68 3.86
647 682 3.636300 CCCAAACATGTTCTTGTTGGAGA 59.364 43.478 22.38 0.00 39.68 3.71
648 683 4.099266 CCCAAACATGTTCTTGTTGGAGAA 59.901 41.667 22.38 0.00 39.68 2.87
650 685 6.105333 CCAAACATGTTCTTGTTGGAGAAAA 58.895 36.000 17.75 0.00 39.68 2.29
651 686 6.256321 CCAAACATGTTCTTGTTGGAGAAAAG 59.744 38.462 17.75 0.00 39.68 2.27
652 687 4.936891 ACATGTTCTTGTTGGAGAAAAGC 58.063 39.130 0.00 0.00 37.40 3.51
653 688 4.402155 ACATGTTCTTGTTGGAGAAAAGCA 59.598 37.500 0.00 0.00 37.40 3.91
654 689 5.105392 ACATGTTCTTGTTGGAGAAAAGCAA 60.105 36.000 0.00 0.00 37.40 3.91
655 690 4.743493 TGTTCTTGTTGGAGAAAAGCAAC 58.257 39.130 0.00 0.00 37.40 4.17
656 691 4.112634 GTTCTTGTTGGAGAAAAGCAACC 58.887 43.478 0.00 0.00 37.40 3.77
657 692 3.360867 TCTTGTTGGAGAAAAGCAACCA 58.639 40.909 0.00 0.00 0.00 3.67
658 693 3.960102 TCTTGTTGGAGAAAAGCAACCAT 59.040 39.130 0.00 0.00 32.31 3.55
659 694 3.731652 TGTTGGAGAAAAGCAACCATG 57.268 42.857 0.00 0.00 32.31 3.66
660 695 2.364970 TGTTGGAGAAAAGCAACCATGG 59.635 45.455 11.19 11.19 32.31 3.66
662 697 2.956132 TGGAGAAAAGCAACCATGGAA 58.044 42.857 21.47 0.00 0.00 3.53
663 698 3.303938 TGGAGAAAAGCAACCATGGAAA 58.696 40.909 21.47 0.00 0.00 3.13
664 699 3.708631 TGGAGAAAAGCAACCATGGAAAA 59.291 39.130 21.47 0.00 0.00 2.29
665 700 4.202243 TGGAGAAAAGCAACCATGGAAAAG 60.202 41.667 21.47 5.93 0.00 2.27
666 701 4.309933 GAGAAAAGCAACCATGGAAAAGG 58.690 43.478 21.47 3.63 0.00 3.11
667 702 3.711190 AGAAAAGCAACCATGGAAAAGGT 59.289 39.130 21.47 7.54 40.61 3.50
668 703 3.473923 AAAGCAACCATGGAAAAGGTG 57.526 42.857 21.47 7.28 38.37 4.00
669 704 2.380064 AGCAACCATGGAAAAGGTGA 57.620 45.000 21.47 0.00 38.37 4.02
672 707 2.862140 GCAACCATGGAAAAGGTGAACG 60.862 50.000 21.47 0.00 38.37 3.95
674 709 2.504367 ACCATGGAAAAGGTGAACGAG 58.496 47.619 21.47 0.00 36.60 4.18
675 710 1.812571 CCATGGAAAAGGTGAACGAGG 59.187 52.381 5.56 0.00 0.00 4.63
676 711 2.552155 CCATGGAAAAGGTGAACGAGGA 60.552 50.000 5.56 0.00 0.00 3.71
677 712 3.347216 CATGGAAAAGGTGAACGAGGAT 58.653 45.455 0.00 0.00 0.00 3.24
678 713 4.513442 CATGGAAAAGGTGAACGAGGATA 58.487 43.478 0.00 0.00 0.00 2.59
680 715 3.325425 TGGAAAAGGTGAACGAGGATACA 59.675 43.478 0.00 0.00 41.41 2.29
681 716 4.019681 TGGAAAAGGTGAACGAGGATACAT 60.020 41.667 0.00 0.00 41.41 2.29
682 717 4.941873 GGAAAAGGTGAACGAGGATACATT 59.058 41.667 0.00 0.00 41.41 2.71
683 718 5.064834 GGAAAAGGTGAACGAGGATACATTC 59.935 44.000 0.00 0.00 41.41 2.67
684 719 5.422214 AAAGGTGAACGAGGATACATTCT 57.578 39.130 0.00 0.00 41.41 2.40
691 726 3.972950 CGAGGATACATTCTCGTGTCT 57.027 47.619 11.10 0.00 45.27 3.41
692 727 4.294416 CGAGGATACATTCTCGTGTCTT 57.706 45.455 11.10 0.00 45.27 3.01
694 729 4.438880 CGAGGATACATTCTCGTGTCTTGT 60.439 45.833 11.10 0.00 45.27 3.16
696 731 3.307242 GGATACATTCTCGTGTCTTGTGC 59.693 47.826 0.00 0.00 33.62 4.57
697 732 1.139989 ACATTCTCGTGTCTTGTGCG 58.860 50.000 0.00 0.00 0.00 5.34
698 733 1.139989 CATTCTCGTGTCTTGTGCGT 58.860 50.000 0.00 0.00 0.00 5.24
701 736 1.205657 TCTCGTGTCTTGTGCGTTTC 58.794 50.000 0.00 0.00 0.00 2.78
702 737 1.202371 TCTCGTGTCTTGTGCGTTTCT 60.202 47.619 0.00 0.00 0.00 2.52
703 738 2.033675 TCTCGTGTCTTGTGCGTTTCTA 59.966 45.455 0.00 0.00 0.00 2.10
706 741 3.183574 TCGTGTCTTGTGCGTTTCTATTG 59.816 43.478 0.00 0.00 0.00 1.90
707 742 3.664276 CGTGTCTTGTGCGTTTCTATTGG 60.664 47.826 0.00 0.00 0.00 3.16
708 743 2.225491 TGTCTTGTGCGTTTCTATTGGC 59.775 45.455 0.00 0.00 0.00 4.52
709 744 1.463056 TCTTGTGCGTTTCTATTGGCG 59.537 47.619 0.00 0.00 0.00 5.69
710 745 1.463056 CTTGTGCGTTTCTATTGGCGA 59.537 47.619 0.00 0.00 0.00 5.54
711 746 1.514003 TGTGCGTTTCTATTGGCGAA 58.486 45.000 0.00 0.00 0.00 4.70
712 747 1.874231 TGTGCGTTTCTATTGGCGAAA 59.126 42.857 0.00 0.00 0.00 3.46
720 755 6.300879 GTTTCTATTGGCGAAACGATTTTC 57.699 37.500 0.00 0.00 40.31 2.29
721 756 4.609691 TCTATTGGCGAAACGATTTTCC 57.390 40.909 0.00 0.00 38.35 3.13
722 757 4.258543 TCTATTGGCGAAACGATTTTCCT 58.741 39.130 0.00 0.00 38.35 3.36
723 758 3.934457 ATTGGCGAAACGATTTTCCTT 57.066 38.095 0.00 0.00 38.35 3.36
724 759 2.981400 TGGCGAAACGATTTTCCTTC 57.019 45.000 0.00 0.00 38.35 3.46
725 760 1.195900 TGGCGAAACGATTTTCCTTCG 59.804 47.619 0.00 0.00 42.66 3.79
735 770 3.362986 CGATTTTCCTTCGTGTCACACTG 60.363 47.826 6.33 0.00 31.34 3.66
736 771 1.295792 TTTCCTTCGTGTCACACTGC 58.704 50.000 6.33 0.00 31.34 4.40
737 772 0.531974 TTCCTTCGTGTCACACTGCC 60.532 55.000 6.33 0.00 31.34 4.85
738 773 1.069765 CCTTCGTGTCACACTGCCT 59.930 57.895 6.33 0.00 31.34 4.75
739 774 0.532862 CCTTCGTGTCACACTGCCTT 60.533 55.000 6.33 0.00 31.34 4.35
740 775 1.270094 CCTTCGTGTCACACTGCCTTA 60.270 52.381 6.33 0.00 31.34 2.69
741 776 2.612972 CCTTCGTGTCACACTGCCTTAT 60.613 50.000 6.33 0.00 31.34 1.73
742 777 2.078849 TCGTGTCACACTGCCTTATG 57.921 50.000 6.33 0.00 31.34 1.90
743 778 1.078709 CGTGTCACACTGCCTTATGG 58.921 55.000 6.33 0.00 31.34 2.74
744 779 1.337728 CGTGTCACACTGCCTTATGGA 60.338 52.381 6.33 0.00 31.07 3.41
745 780 2.778299 GTGTCACACTGCCTTATGGAA 58.222 47.619 0.00 0.00 34.57 3.53
746 781 3.347216 GTGTCACACTGCCTTATGGAAT 58.653 45.455 0.00 0.00 34.57 3.01
747 782 3.375299 GTGTCACACTGCCTTATGGAATC 59.625 47.826 0.00 0.00 34.57 2.52
748 783 2.609459 GTCACACTGCCTTATGGAATCG 59.391 50.000 0.00 0.00 34.57 3.34
749 784 1.331756 CACACTGCCTTATGGAATCGC 59.668 52.381 0.00 0.00 34.57 4.58
750 785 1.210478 ACACTGCCTTATGGAATCGCT 59.790 47.619 0.00 0.00 34.57 4.93
751 786 1.869767 CACTGCCTTATGGAATCGCTC 59.130 52.381 0.00 0.00 34.57 5.03
752 787 1.765314 ACTGCCTTATGGAATCGCTCT 59.235 47.619 0.00 0.00 34.57 4.09
753 788 2.141517 CTGCCTTATGGAATCGCTCTG 58.858 52.381 0.00 0.00 34.57 3.35
754 789 1.202687 TGCCTTATGGAATCGCTCTGG 60.203 52.381 0.00 0.00 34.57 3.86
755 790 1.070758 GCCTTATGGAATCGCTCTGGA 59.929 52.381 0.00 0.00 34.57 3.86
756 791 2.485479 GCCTTATGGAATCGCTCTGGAA 60.485 50.000 0.00 0.00 34.57 3.53
757 792 3.808728 CCTTATGGAATCGCTCTGGAAA 58.191 45.455 0.00 0.00 34.57 3.13
758 793 4.199310 CCTTATGGAATCGCTCTGGAAAA 58.801 43.478 0.00 0.00 34.57 2.29
759 794 4.823989 CCTTATGGAATCGCTCTGGAAAAT 59.176 41.667 0.00 0.00 34.57 1.82
760 795 5.997746 CCTTATGGAATCGCTCTGGAAAATA 59.002 40.000 0.00 0.00 34.57 1.40
761 796 6.656693 CCTTATGGAATCGCTCTGGAAAATAT 59.343 38.462 0.00 0.00 34.57 1.28
762 797 7.824289 CCTTATGGAATCGCTCTGGAAAATATA 59.176 37.037 0.00 0.00 34.57 0.86
763 798 9.388506 CTTATGGAATCGCTCTGGAAAATATAT 57.611 33.333 0.00 0.00 0.00 0.86
766 801 9.911788 ATGGAATCGCTCTGGAAAATATATATT 57.088 29.630 1.91 1.91 0.00 1.28
767 802 9.739276 TGGAATCGCTCTGGAAAATATATATTT 57.261 29.630 13.85 13.85 37.49 1.40
822 857 6.221659 AGCACAGTAGGAAAGTTGTAAGTAC 58.778 40.000 0.00 0.00 0.00 2.73
823 858 6.041751 AGCACAGTAGGAAAGTTGTAAGTACT 59.958 38.462 0.00 0.00 0.00 2.73
831 866 6.940867 AGGAAAGTTGTAAGTACTGATTTCCC 59.059 38.462 15.37 3.12 39.50 3.97
840 875 1.620822 ACTGATTTCCCACTGGCAAC 58.379 50.000 0.00 0.00 0.00 4.17
843 878 0.804989 GATTTCCCACTGGCAACGAG 59.195 55.000 0.00 0.00 42.51 4.18
845 880 0.181587 TTTCCCACTGGCAACGAGAA 59.818 50.000 0.00 0.00 42.51 2.87
862 897 5.057149 ACGAGAATCACCATTTACCATAGC 58.943 41.667 0.00 0.00 33.17 2.97
867 902 9.120538 GAGAATCACCATTTACCATAGCTTAAA 57.879 33.333 0.00 0.00 33.17 1.52
911 950 5.422331 TGTAGTAGAGGACAGGAAAGGAATG 59.578 44.000 0.00 0.00 0.00 2.67
914 953 3.525862 AGAGGACAGGAAAGGAATGACT 58.474 45.455 0.00 0.00 0.00 3.41
916 955 2.087646 GGACAGGAAAGGAATGACTGC 58.912 52.381 0.00 0.00 32.60 4.40
919 958 2.290577 ACAGGAAAGGAATGACTGCTCC 60.291 50.000 0.00 0.00 32.60 4.70
942 981 3.366374 GGTTTGGATCACAGCTAGCAAAC 60.366 47.826 18.83 14.82 0.00 2.93
953 992 3.622060 TAGCAAACGGGCCCAGCTC 62.622 63.158 25.70 10.06 36.80 4.09
1725 1797 0.389948 GGTTCGTCGACCAGCTCAAT 60.390 55.000 10.58 0.00 39.57 2.57
2007 2079 0.038892 CGGTGTACTACGTGCCTGTT 60.039 55.000 0.00 0.00 0.00 3.16
2296 2387 3.818787 CGCATGGGCTGTTCCTGC 61.819 66.667 0.00 0.00 38.10 4.85
2305 2396 2.251600 CTGTTCCTGCAGCTGGTTC 58.748 57.895 17.12 11.96 0.00 3.62
2400 2491 5.010820 GGGTTACTCTTGGTAGCTGTATAGG 59.989 48.000 0.00 0.00 33.12 2.57
2507 2598 9.032624 AGTACATTTGGTGTGATTAGTACTAGT 57.967 33.333 0.00 0.00 42.24 2.57
2510 2601 7.980099 ACATTTGGTGTGATTAGTACTAGTAGC 59.020 37.037 1.87 0.00 40.28 3.58
2511 2602 7.470935 TTTGGTGTGATTAGTACTAGTAGCA 57.529 36.000 1.87 0.00 0.00 3.49
2512 2603 6.694877 TGGTGTGATTAGTACTAGTAGCAG 57.305 41.667 1.87 0.00 0.00 4.24
2513 2604 5.593095 TGGTGTGATTAGTACTAGTAGCAGG 59.407 44.000 1.87 0.00 0.00 4.85
2629 2725 2.786777 TGATGCTGGATGTATCATGGC 58.213 47.619 0.00 0.00 41.66 4.40
2688 2784 5.925397 TGCGAATGTTTGCATATTTGTTCTT 59.075 32.000 3.58 0.00 42.41 2.52
2774 2870 3.034635 TGCTTTTGGTAACCCACATTGT 58.965 40.909 0.00 0.00 41.67 2.71
2813 2909 6.554334 TTTACACTTGCTGTTTATCCTGAC 57.446 37.500 0.00 0.00 33.91 3.51
2815 2911 2.749621 CACTTGCTGTTTATCCTGACCC 59.250 50.000 0.00 0.00 0.00 4.46
2824 2920 3.713826 TTATCCTGACCCGCTCTTTTT 57.286 42.857 0.00 0.00 0.00 1.94
2902 2998 7.818997 TTCTCTACTTATTAGAATGGCTCGA 57.181 36.000 0.00 0.00 36.32 4.04
2928 3032 6.424883 TCTTCGAGTAGAACTAGGGAGAAAT 58.575 40.000 0.00 0.00 34.66 2.17
2969 3073 4.516698 TGACTTGATTCAAGAGGAAAGTGC 59.483 41.667 28.60 9.48 43.42 4.40
3042 3147 4.764172 AGAGACAGTGGCTTGTATCATTC 58.236 43.478 0.00 0.00 40.76 2.67
3051 3156 4.210331 GGCTTGTATCATTCCCAGAACAT 58.790 43.478 0.00 0.00 0.00 2.71
3097 3211 2.296190 ACAATGCTGCAGATATGCCATG 59.704 45.455 20.43 8.35 0.00 3.66
3101 3215 1.467734 GCTGCAGATATGCCATGCTAC 59.532 52.381 20.43 0.00 40.62 3.58
3156 3286 5.511386 AGATTCAGGTTCAGGTTTGATCT 57.489 39.130 0.00 0.00 32.27 2.75
3183 3313 7.321746 GCTATAGAAAAAGAGTCGTCTACATCG 59.678 40.741 3.21 0.00 30.45 3.84
3184 3314 5.373981 AGAAAAAGAGTCGTCTACATCGT 57.626 39.130 0.00 0.00 30.45 3.73
3185 3315 6.492007 AGAAAAAGAGTCGTCTACATCGTA 57.508 37.500 0.00 0.00 30.45 3.43
3186 3316 6.544622 AGAAAAAGAGTCGTCTACATCGTAG 58.455 40.000 0.00 0.00 30.45 3.51
3190 3320 4.367450 AGAGTCGTCTACATCGTAGGTAC 58.633 47.826 1.53 0.00 0.00 3.34
3221 3351 4.517285 TCAGAGCCCTCAAAATGTGATAC 58.483 43.478 0.00 0.00 35.07 2.24
3222 3352 4.225942 TCAGAGCCCTCAAAATGTGATACT 59.774 41.667 0.00 0.00 35.07 2.12
3223 3353 5.425217 TCAGAGCCCTCAAAATGTGATACTA 59.575 40.000 0.00 0.00 35.07 1.82
3224 3354 5.525378 CAGAGCCCTCAAAATGTGATACTAC 59.475 44.000 0.00 0.00 35.07 2.73
3225 3355 5.426833 AGAGCCCTCAAAATGTGATACTACT 59.573 40.000 0.00 0.00 35.07 2.57
3226 3356 6.611642 AGAGCCCTCAAAATGTGATACTACTA 59.388 38.462 0.00 0.00 35.07 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 227 6.713903 AGTGAGTGCATCTATGATTTATTGGG 59.286 38.462 0.00 0.00 0.00 4.12
213 241 4.999950 CCCCAGAATATTAGTGAGTGCATC 59.000 45.833 0.00 0.00 0.00 3.91
236 264 4.813027 TGCTTCAATTGAGCTGGATTTTC 58.187 39.130 22.12 3.12 0.00 2.29
242 270 3.928727 TCTTTGCTTCAATTGAGCTGG 57.071 42.857 22.12 15.01 0.00 4.85
291 319 0.038892 AAAACTTGCCGCATCAGCAG 60.039 50.000 0.00 0.00 42.17 4.24
312 341 1.155889 TGTAAGTGCATCACGGCAAG 58.844 50.000 0.00 0.00 46.93 4.01
319 348 3.146066 GGTCCAGTTTGTAAGTGCATCA 58.854 45.455 0.00 0.00 0.00 3.07
321 350 2.158534 TGGGTCCAGTTTGTAAGTGCAT 60.159 45.455 0.00 0.00 0.00 3.96
390 419 4.707448 ACATATTGGGGTAATTCGTTGCAA 59.293 37.500 0.00 0.00 0.00 4.08
504 534 0.252197 GCCCTAGGGAAACGACATGT 59.748 55.000 33.21 0.00 37.50 3.21
506 536 0.831307 GAGCCCTAGGGAAACGACAT 59.169 55.000 33.21 5.49 37.50 3.06
580 615 2.122954 AGACCCAGACCCAGACCC 59.877 66.667 0.00 0.00 0.00 4.46
581 616 2.294078 CCAGACCCAGACCCAGACC 61.294 68.421 0.00 0.00 0.00 3.85
582 617 2.294078 CCCAGACCCAGACCCAGAC 61.294 68.421 0.00 0.00 0.00 3.51
583 618 2.122729 CCCAGACCCAGACCCAGA 59.877 66.667 0.00 0.00 0.00 3.86
584 619 2.203998 ACCCAGACCCAGACCCAG 60.204 66.667 0.00 0.00 0.00 4.45
585 620 2.203938 GACCCAGACCCAGACCCA 60.204 66.667 0.00 0.00 0.00 4.51
586 621 2.122954 AGACCCAGACCCAGACCC 59.877 66.667 0.00 0.00 0.00 4.46
587 622 2.294078 CCAGACCCAGACCCAGACC 61.294 68.421 0.00 0.00 0.00 3.85
588 623 1.229209 TCCAGACCCAGACCCAGAC 60.229 63.158 0.00 0.00 0.00 3.51
589 624 1.229209 GTCCAGACCCAGACCCAGA 60.229 63.158 0.00 0.00 0.00 3.86
590 625 1.229336 AGTCCAGACCCAGACCCAG 60.229 63.158 0.00 0.00 33.29 4.45
591 626 1.229209 GAGTCCAGACCCAGACCCA 60.229 63.158 0.00 0.00 33.29 4.51
622 657 4.119136 CCAACAAGAACATGTTTGGGTTC 58.881 43.478 13.36 0.00 41.44 3.62
623 658 3.772025 TCCAACAAGAACATGTTTGGGTT 59.228 39.130 20.83 17.09 41.44 4.11
626 661 4.916983 TCTCCAACAAGAACATGTTTGG 57.083 40.909 13.36 15.45 41.44 3.28
629 664 5.105392 TGCTTTTCTCCAACAAGAACATGTT 60.105 36.000 11.78 11.78 44.08 2.71
630 665 4.402155 TGCTTTTCTCCAACAAGAACATGT 59.598 37.500 0.00 0.00 35.06 3.21
632 667 5.351458 GTTGCTTTTCTCCAACAAGAACAT 58.649 37.500 0.00 0.00 40.66 2.71
634 669 4.112634 GGTTGCTTTTCTCCAACAAGAAC 58.887 43.478 5.95 0.00 42.26 3.01
637 672 3.799281 TGGTTGCTTTTCTCCAACAAG 57.201 42.857 5.95 0.00 42.26 3.16
640 675 2.627699 TCCATGGTTGCTTTTCTCCAAC 59.372 45.455 12.58 0.00 40.34 3.77
643 678 4.309933 CTTTTCCATGGTTGCTTTTCTCC 58.690 43.478 12.58 0.00 0.00 3.71
646 681 3.809279 CACCTTTTCCATGGTTGCTTTTC 59.191 43.478 12.58 0.00 33.75 2.29
647 682 3.454082 TCACCTTTTCCATGGTTGCTTTT 59.546 39.130 12.58 0.00 33.75 2.27
648 683 3.037549 TCACCTTTTCCATGGTTGCTTT 58.962 40.909 12.58 0.00 33.75 3.51
650 685 2.365293 GTTCACCTTTTCCATGGTTGCT 59.635 45.455 12.58 0.00 33.75 3.91
651 686 2.754472 GTTCACCTTTTCCATGGTTGC 58.246 47.619 12.58 0.00 33.75 4.17
652 687 2.621055 TCGTTCACCTTTTCCATGGTTG 59.379 45.455 12.58 0.51 33.75 3.77
653 688 2.884639 CTCGTTCACCTTTTCCATGGTT 59.115 45.455 12.58 0.00 33.75 3.67
654 689 2.504367 CTCGTTCACCTTTTCCATGGT 58.496 47.619 12.58 0.00 36.96 3.55
655 690 1.812571 CCTCGTTCACCTTTTCCATGG 59.187 52.381 4.97 4.97 0.00 3.66
656 691 2.778299 TCCTCGTTCACCTTTTCCATG 58.222 47.619 0.00 0.00 0.00 3.66
657 692 3.721087 ATCCTCGTTCACCTTTTCCAT 57.279 42.857 0.00 0.00 0.00 3.41
658 693 3.325425 TGTATCCTCGTTCACCTTTTCCA 59.675 43.478 0.00 0.00 0.00 3.53
659 694 3.934068 TGTATCCTCGTTCACCTTTTCC 58.066 45.455 0.00 0.00 0.00 3.13
660 695 5.875359 AGAATGTATCCTCGTTCACCTTTTC 59.125 40.000 0.00 0.00 36.24 2.29
662 697 5.420409 GAGAATGTATCCTCGTTCACCTTT 58.580 41.667 0.00 0.00 36.24 3.11
663 698 4.440250 CGAGAATGTATCCTCGTTCACCTT 60.440 45.833 0.00 0.00 44.99 3.50
664 699 3.066900 CGAGAATGTATCCTCGTTCACCT 59.933 47.826 0.00 0.00 44.99 4.00
665 700 3.372954 CGAGAATGTATCCTCGTTCACC 58.627 50.000 0.00 0.00 44.99 4.02
672 707 4.800993 CACAAGACACGAGAATGTATCCTC 59.199 45.833 0.00 0.00 31.24 3.71
674 709 3.307242 GCACAAGACACGAGAATGTATCC 59.693 47.826 0.00 0.00 31.24 2.59
675 710 3.000674 CGCACAAGACACGAGAATGTATC 60.001 47.826 0.00 0.00 31.24 2.24
676 711 2.923655 CGCACAAGACACGAGAATGTAT 59.076 45.455 0.00 0.00 31.24 2.29
677 712 2.287970 ACGCACAAGACACGAGAATGTA 60.288 45.455 0.00 0.00 31.24 2.29
678 713 1.139989 CGCACAAGACACGAGAATGT 58.860 50.000 0.00 0.00 34.78 2.71
680 715 1.865865 AACGCACAAGACACGAGAAT 58.134 45.000 0.00 0.00 0.00 2.40
681 716 1.591158 GAAACGCACAAGACACGAGAA 59.409 47.619 0.00 0.00 0.00 2.87
682 717 1.202371 AGAAACGCACAAGACACGAGA 60.202 47.619 0.00 0.00 0.00 4.04
683 718 1.209128 AGAAACGCACAAGACACGAG 58.791 50.000 0.00 0.00 0.00 4.18
684 719 2.495409 TAGAAACGCACAAGACACGA 57.505 45.000 0.00 0.00 0.00 4.35
687 722 2.225491 GCCAATAGAAACGCACAAGACA 59.775 45.455 0.00 0.00 0.00 3.41
688 723 2.724839 CGCCAATAGAAACGCACAAGAC 60.725 50.000 0.00 0.00 0.00 3.01
689 724 1.463056 CGCCAATAGAAACGCACAAGA 59.537 47.619 0.00 0.00 0.00 3.02
690 725 1.463056 TCGCCAATAGAAACGCACAAG 59.537 47.619 0.00 0.00 0.00 3.16
691 726 1.514003 TCGCCAATAGAAACGCACAA 58.486 45.000 0.00 0.00 0.00 3.33
692 727 1.514003 TTCGCCAATAGAAACGCACA 58.486 45.000 0.00 0.00 0.00 4.57
694 729 2.604969 GTTTCGCCAATAGAAACGCA 57.395 45.000 6.14 0.00 44.99 5.24
698 733 5.182380 AGGAAAATCGTTTCGCCAATAGAAA 59.818 36.000 0.00 0.00 43.56 2.52
701 736 4.616181 AGGAAAATCGTTTCGCCAATAG 57.384 40.909 0.00 0.00 43.56 1.73
702 737 4.436317 CGAAGGAAAATCGTTTCGCCAATA 60.436 41.667 0.00 0.00 43.56 1.90
703 738 3.669557 CGAAGGAAAATCGTTTCGCCAAT 60.670 43.478 0.00 0.00 43.56 3.16
706 741 1.878373 CGAAGGAAAATCGTTTCGCC 58.122 50.000 0.00 0.00 43.56 5.54
714 749 3.607078 GCAGTGTGACACGAAGGAAAATC 60.607 47.826 10.41 0.00 39.64 2.17
715 750 2.290641 GCAGTGTGACACGAAGGAAAAT 59.709 45.455 10.41 0.00 39.64 1.82
716 751 1.668751 GCAGTGTGACACGAAGGAAAA 59.331 47.619 10.41 0.00 39.64 2.29
717 752 1.295792 GCAGTGTGACACGAAGGAAA 58.704 50.000 10.41 0.00 39.64 3.13
718 753 0.531974 GGCAGTGTGACACGAAGGAA 60.532 55.000 10.41 0.00 39.64 3.36
719 754 1.069090 GGCAGTGTGACACGAAGGA 59.931 57.895 10.41 0.00 39.64 3.36
720 755 0.532862 AAGGCAGTGTGACACGAAGG 60.533 55.000 10.41 2.94 39.64 3.46
721 756 2.148916 TAAGGCAGTGTGACACGAAG 57.851 50.000 10.41 5.83 39.64 3.79
722 757 2.412870 CATAAGGCAGTGTGACACGAA 58.587 47.619 10.41 0.00 39.64 3.85
723 758 1.337728 CCATAAGGCAGTGTGACACGA 60.338 52.381 10.41 0.00 39.64 4.35
724 759 1.078709 CCATAAGGCAGTGTGACACG 58.921 55.000 10.41 6.63 39.64 4.49
725 760 2.472695 TCCATAAGGCAGTGTGACAC 57.527 50.000 7.83 7.83 33.74 3.67
726 761 3.609853 GATTCCATAAGGCAGTGTGACA 58.390 45.455 0.00 0.00 33.74 3.58
727 762 2.609459 CGATTCCATAAGGCAGTGTGAC 59.391 50.000 0.00 0.00 33.74 3.67
728 763 2.905075 CGATTCCATAAGGCAGTGTGA 58.095 47.619 0.00 0.00 33.74 3.58
729 764 1.331756 GCGATTCCATAAGGCAGTGTG 59.668 52.381 0.00 0.00 33.74 3.82
731 766 1.869767 GAGCGATTCCATAAGGCAGTG 59.130 52.381 0.00 0.00 33.74 3.66
732 767 1.765314 AGAGCGATTCCATAAGGCAGT 59.235 47.619 0.00 0.00 33.74 4.40
735 770 1.070758 TCCAGAGCGATTCCATAAGGC 59.929 52.381 0.00 0.00 33.74 4.35
736 771 3.475566 TTCCAGAGCGATTCCATAAGG 57.524 47.619 0.00 0.00 0.00 2.69
737 772 7.678947 ATATTTTCCAGAGCGATTCCATAAG 57.321 36.000 0.00 0.00 0.00 1.73
740 775 9.911788 AATATATATTTTCCAGAGCGATTCCAT 57.088 29.630 1.91 0.00 0.00 3.41
741 776 9.739276 AAATATATATTTTCCAGAGCGATTCCA 57.261 29.630 13.85 0.00 32.28 3.53
796 831 5.758784 ACTTACAACTTTCCTACTGTGCTTC 59.241 40.000 0.00 0.00 0.00 3.86
797 832 5.681639 ACTTACAACTTTCCTACTGTGCTT 58.318 37.500 0.00 0.00 0.00 3.91
798 833 5.291905 ACTTACAACTTTCCTACTGTGCT 57.708 39.130 0.00 0.00 0.00 4.40
799 834 6.145696 CAGTACTTACAACTTTCCTACTGTGC 59.854 42.308 0.00 0.00 0.00 4.57
800 835 7.431249 TCAGTACTTACAACTTTCCTACTGTG 58.569 38.462 0.00 0.00 34.03 3.66
801 836 7.592885 TCAGTACTTACAACTTTCCTACTGT 57.407 36.000 0.00 0.00 34.03 3.55
802 837 9.490379 AAATCAGTACTTACAACTTTCCTACTG 57.510 33.333 0.00 0.00 33.76 2.74
804 839 8.933807 GGAAATCAGTACTTACAACTTTCCTAC 58.066 37.037 10.63 0.00 36.79 3.18
805 840 8.098912 GGGAAATCAGTACTTACAACTTTCCTA 58.901 37.037 14.92 0.00 38.13 2.94
822 857 0.523072 CGTTGCCAGTGGGAAATCAG 59.477 55.000 18.72 6.38 34.18 2.90
823 858 0.109532 TCGTTGCCAGTGGGAAATCA 59.890 50.000 18.72 1.80 34.18 2.57
831 866 0.798776 GGTGATTCTCGTTGCCAGTG 59.201 55.000 0.00 0.00 0.00 3.66
840 875 5.300752 AGCTATGGTAAATGGTGATTCTCG 58.699 41.667 0.00 0.00 0.00 4.04
876 911 7.661847 CCTGTCCTCTACTACAACTTTTGAAAT 59.338 37.037 0.00 0.00 0.00 2.17
879 914 5.836898 TCCTGTCCTCTACTACAACTTTTGA 59.163 40.000 0.00 0.00 0.00 2.69
880 915 6.097915 TCCTGTCCTCTACTACAACTTTTG 57.902 41.667 0.00 0.00 0.00 2.44
894 929 3.604582 CAGTCATTCCTTTCCTGTCCTC 58.395 50.000 0.00 0.00 0.00 3.71
895 930 2.290577 GCAGTCATTCCTTTCCTGTCCT 60.291 50.000 0.00 0.00 0.00 3.85
897 932 3.006247 GAGCAGTCATTCCTTTCCTGTC 58.994 50.000 0.00 0.00 0.00 3.51
899 934 2.363683 GGAGCAGTCATTCCTTTCCTG 58.636 52.381 0.00 0.00 0.00 3.86
919 958 1.009829 GCTAGCTGTGATCCAAACCG 58.990 55.000 7.70 0.00 0.00 4.44
1047 1089 1.148273 GCGAGGTGGCATTGGGATA 59.852 57.895 0.00 0.00 0.00 2.59
1214 1262 3.648982 CGTTGCCGTTGCTGCTGA 61.649 61.111 0.00 0.00 38.71 4.26
1292 1364 4.678499 TGCACATGAGGCGCACGA 62.678 61.111 10.83 0.00 0.00 4.35
1968 2040 4.418328 TGCCCCATGTACGGTGGC 62.418 66.667 10.75 9.43 40.73 5.01
1982 2054 2.202703 CGTAGTACACCGGCTGCC 60.203 66.667 9.11 9.11 0.00 4.85
2096 2168 0.606944 CGAGTAGAGATCTCCCGGGG 60.607 65.000 23.50 12.05 0.00 5.73
2204 2276 0.033405 CTTCCCCTCCACCGAGTAGA 60.033 60.000 0.00 0.00 33.93 2.59
2305 2396 7.043258 GCTCAGATATAAGCGATCATCAGAATG 60.043 40.741 0.00 0.00 37.54 2.67
2400 2491 1.341156 CCATCCTCCACCTCCCTCAC 61.341 65.000 0.00 0.00 0.00 3.51
2507 2598 4.098155 TCCCACATTACAGTAACCTGCTA 58.902 43.478 0.00 0.00 42.81 3.49
2509 2600 3.343941 TCCCACATTACAGTAACCTGC 57.656 47.619 0.00 0.00 42.81 4.85
2510 2601 4.640201 CCAATCCCACATTACAGTAACCTG 59.360 45.833 0.00 0.00 44.68 4.00
2511 2602 4.538490 TCCAATCCCACATTACAGTAACCT 59.462 41.667 0.00 0.00 0.00 3.50
2512 2603 4.850680 TCCAATCCCACATTACAGTAACC 58.149 43.478 0.00 0.00 0.00 2.85
2513 2604 6.601613 TGAATCCAATCCCACATTACAGTAAC 59.398 38.462 0.00 0.00 0.00 2.50
2629 2725 9.653516 AGAGTAGATATATAGGACATTCATGGG 57.346 37.037 0.00 0.00 0.00 4.00
2688 2784 7.518161 CGAATTCAGTACATTAAGCTTTCACA 58.482 34.615 3.20 0.00 0.00 3.58
2792 2888 4.564821 GGGTCAGGATAAACAGCAAGTGTA 60.565 45.833 0.00 0.00 39.03 2.90
2793 2889 3.412386 GGTCAGGATAAACAGCAAGTGT 58.588 45.455 0.00 0.00 43.24 3.55
2794 2890 2.749621 GGGTCAGGATAAACAGCAAGTG 59.250 50.000 0.00 0.00 0.00 3.16
2795 2891 2.615493 CGGGTCAGGATAAACAGCAAGT 60.615 50.000 0.00 0.00 0.00 3.16
2796 2892 2.009774 CGGGTCAGGATAAACAGCAAG 58.990 52.381 0.00 0.00 0.00 4.01
2798 2894 0.392461 GCGGGTCAGGATAAACAGCA 60.392 55.000 0.00 0.00 0.00 4.41
2799 2895 0.107654 AGCGGGTCAGGATAAACAGC 60.108 55.000 0.00 0.00 0.00 4.40
2800 2896 1.482593 AGAGCGGGTCAGGATAAACAG 59.517 52.381 10.15 0.00 0.00 3.16
2813 2909 0.890683 AATGCCAGAAAAAGAGCGGG 59.109 50.000 0.00 0.00 0.00 6.13
2815 2911 4.159377 TGTTAATGCCAGAAAAAGAGCG 57.841 40.909 0.00 0.00 0.00 5.03
2851 2947 6.241882 TCCGGATATGTTCAAATTAGTCCA 57.758 37.500 0.00 0.00 0.00 4.02
2855 2951 9.224267 AGAATCATCCGGATATGTTCAAATTAG 57.776 33.333 25.24 9.71 34.28 1.73
2856 2952 9.219603 GAGAATCATCCGGATATGTTCAAATTA 57.780 33.333 25.24 1.39 34.28 1.40
2862 2958 7.164230 AGTAGAGAATCATCCGGATATGTTC 57.836 40.000 18.63 19.50 37.82 3.18
2902 2998 6.003859 TCTCCCTAGTTCTACTCGAAGATT 57.996 41.667 0.00 0.00 33.89 2.40
2928 3032 9.739276 ATCAAGTCAACAATGGAACTCTAATTA 57.261 29.630 0.00 0.00 0.00 1.40
2934 3038 6.317789 TGAATCAAGTCAACAATGGAACTC 57.682 37.500 0.00 0.00 0.00 3.01
2969 3073 2.760374 AGCTTCTCTGTTCAGAAACGG 58.240 47.619 4.09 0.00 42.21 4.44
3042 3147 2.101415 TGCAGAGTCGATATGTTCTGGG 59.899 50.000 12.50 0.00 37.97 4.45
3051 3156 1.123077 AGGGCAATGCAGAGTCGATA 58.877 50.000 7.79 0.00 0.00 2.92
3097 3211 7.713073 AGCAATCTGAATAGTTAAAGAGGTAGC 59.287 37.037 0.00 0.00 0.00 3.58
3101 3215 9.995003 AGATAGCAATCTGAATAGTTAAAGAGG 57.005 33.333 0.00 0.00 41.08 3.69
3156 3286 7.387119 TGTAGACGACTCTTTTTCTATAGCA 57.613 36.000 0.00 0.00 0.00 3.49
3183 3313 4.278919 GGCTCTGAATCTGGTAGTACCTAC 59.721 50.000 20.07 7.62 39.58 3.18
3184 3314 4.471548 GGCTCTGAATCTGGTAGTACCTA 58.528 47.826 20.07 8.94 39.58 3.08
3185 3315 3.301274 GGCTCTGAATCTGGTAGTACCT 58.699 50.000 20.07 0.00 39.58 3.08
3186 3316 2.365941 GGGCTCTGAATCTGGTAGTACC 59.634 54.545 12.80 12.80 39.22 3.34
3190 3320 2.392662 TGAGGGCTCTGAATCTGGTAG 58.607 52.381 0.00 0.00 0.00 3.18
3244 3374 8.008513 TGTATACAGTCTATGGAAGGAGAAAC 57.991 38.462 0.08 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.