Multiple sequence alignment - TraesCS6D01G174500

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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 TraesCS6D01G174500 chr6D 100.000 3904 0 0 1 3904 163934836 163930933 0.000000e+00 7210.0
1 TraesCS6D01G174500 chr6D 86.184 608 83 1 1 608 155837640 155837034 0.000000e+00 656.0
2 TraesCS6D01G174500 chr6D 86.503 163 22 0 679 841 402128316 402128478 3.100000e-41 180.0
3 TraesCS6D01G174500 chr6B 98.073 1661 26 4 1739 3398 309687479 309689134 0.000000e+00 2885.0
4 TraesCS6D01G174500 chr6B 96.616 591 16 2 883 1472 309684869 309685456 0.000000e+00 977.0
5 TraesCS6D01G174500 chr6B 94.061 522 23 2 3384 3904 309690438 309690952 0.000000e+00 785.0
6 TraesCS6D01G174500 chr6B 97.436 195 4 1 1461 1654 309685478 309685672 8.090000e-87 331.0
7 TraesCS6D01G174500 chr6B 97.753 89 2 0 1666 1754 309685939 309686027 1.880000e-33 154.0
8 TraesCS6D01G174500 chr6A 98.503 1536 20 3 1662 3196 258373186 258371653 0.000000e+00 2706.0
9 TraesCS6D01G174500 chr6A 98.230 791 12 1 873 1663 258374088 258373300 0.000000e+00 1382.0
10 TraesCS6D01G174500 chr6A 97.101 690 17 2 3193 3881 258371423 258370736 0.000000e+00 1160.0
11 TraesCS6D01G174500 chr6A 100.000 38 0 0 3867 3904 258370736 258370699 1.950000e-08 71.3
12 TraesCS6D01G174500 chr3D 92.384 604 45 1 2 605 454667922 454668524 0.000000e+00 859.0
13 TraesCS6D01G174500 chr4D 91.989 362 29 0 247 608 507362141 507361780 3.480000e-140 508.0
14 TraesCS6D01G174500 chr4D 91.829 257 21 0 3 259 507372387 507372131 3.710000e-95 359.0
15 TraesCS6D01G174500 chr2A 79.470 604 118 5 5 605 73201998 73201398 1.300000e-114 424.0
16 TraesCS6D01G174500 chr2A 86.747 166 20 2 680 844 100597723 100597887 2.400000e-42 183.0
17 TraesCS6D01G174500 chr2A 86.420 162 22 0 680 841 566852092 566852253 1.110000e-40 178.0
18 TraesCS6D01G174500 chr1D 91.089 303 27 0 302 604 224832152 224832454 1.010000e-110 411.0
19 TraesCS6D01G174500 chr1D 86.688 308 40 1 1 308 224817613 224817919 1.340000e-89 340.0
20 TraesCS6D01G174500 chr5D 80.000 560 101 10 51 605 416078360 416078913 1.690000e-108 403.0
21 TraesCS6D01G174500 chr5D 89.157 166 18 0 679 844 198954906 198955071 1.420000e-49 207.0
22 TraesCS6D01G174500 chr5D 88.079 151 18 0 680 830 27354253 27354403 3.100000e-41 180.0
23 TraesCS6D01G174500 chr2D 77.963 599 126 6 5 600 450256901 450257496 1.710000e-98 370.0
24 TraesCS6D01G174500 chr2D 78.727 550 113 3 57 604 122707877 122708424 7.970000e-97 364.0
25 TraesCS6D01G174500 chr2D 86.335 161 21 1 683 842 524963641 524963801 1.440000e-39 174.0
26 TraesCS6D01G174500 chr1B 89.865 148 14 1 683 830 141294097 141293951 5.150000e-44 189.0
27 TraesCS6D01G174500 chr2B 88.158 152 18 0 679 830 115381524 115381675 8.620000e-42 182.0
28 TraesCS6D01G174500 chr7D 84.091 176 28 0 667 842 76484345 76484520 1.870000e-38 171.0
29 TraesCS6D01G174500 chr5A 70.894 615 154 23 2 605 547606637 547606037 1.910000e-23 121.0


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 TraesCS6D01G174500 chr6D 163930933 163934836 3903 True 7210.000 7210 100.0000 1 3904 1 chr6D.!!$R2 3903
1 TraesCS6D01G174500 chr6D 155837034 155837640 606 True 656.000 656 86.1840 1 608 1 chr6D.!!$R1 607
2 TraesCS6D01G174500 chr6B 309684869 309690952 6083 False 1026.400 2885 96.7878 883 3904 5 chr6B.!!$F1 3021
3 TraesCS6D01G174500 chr6A 258370699 258374088 3389 True 1329.825 2706 98.4585 873 3904 4 chr6A.!!$R1 3031
4 TraesCS6D01G174500 chr3D 454667922 454668524 602 False 859.000 859 92.3840 2 605 1 chr3D.!!$F1 603
5 TraesCS6D01G174500 chr2A 73201398 73201998 600 True 424.000 424 79.4700 5 605 1 chr2A.!!$R1 600
6 TraesCS6D01G174500 chr5D 416078360 416078913 553 False 403.000 403 80.0000 51 605 1 chr5D.!!$F3 554
7 TraesCS6D01G174500 chr2D 450256901 450257496 595 False 370.000 370 77.9630 5 600 1 chr2D.!!$F2 595
8 TraesCS6D01G174500 chr2D 122707877 122708424 547 False 364.000 364 78.7270 57 604 1 chr2D.!!$F1 547

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
297 298 0.037882 CGAGAGTTGAGCTTCAGGCA 60.038 55.000 0.00 0.0 44.79 4.75 F
306 307 0.547075 AGCTTCAGGCATGCAGAGAT 59.453 50.000 21.36 6.9 44.79 2.75 F
439 440 1.202582 CGATCGTGGAGGAAGTGAAGT 59.797 52.381 7.03 0.0 0.00 3.01 F
491 492 1.549170 GTCATGGGTTAGACGTGAGGT 59.451 52.381 0.00 0.0 34.77 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 4035 2.235155 TCCGTAACCATGTGTGCATAGT 59.765 45.455 0.0 0.0 33.30 2.12 R
2763 4531 5.683876 TTTGGAGTTGGGAATGTCAAAAA 57.316 34.783 0.0 0.0 0.00 1.94 R
2846 4614 5.848286 ATTCCTCATATCCACTTATGCCA 57.152 39.130 0.0 0.0 31.02 4.92 R
3028 4796 0.324943 AGGATGGAACCAACCACTCG 59.675 55.000 19.5 0.0 43.03 4.18 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
26 27 2.191400 TGGACAGAGGATTGAGGAAGG 58.809 52.381 0.00 0.00 0.00 3.46
32 33 2.131023 GAGGATTGAGGAAGGGGATGT 58.869 52.381 0.00 0.00 0.00 3.06
108 109 3.554960 GGAATTTCAAACCAGCCAGAACC 60.555 47.826 0.00 0.00 0.00 3.62
176 177 1.999735 CAACGTAGATGGTGCAACGAT 59.000 47.619 12.89 0.00 38.26 3.73
197 198 4.545706 GGTGGGCGATGATGGCGA 62.546 66.667 0.00 0.00 34.76 5.54
242 243 4.263199 CCATGAGGGTGCATATATGAGTGT 60.263 45.833 17.10 0.00 0.00 3.55
297 298 0.037882 CGAGAGTTGAGCTTCAGGCA 60.038 55.000 0.00 0.00 44.79 4.75
306 307 0.547075 AGCTTCAGGCATGCAGAGAT 59.453 50.000 21.36 6.90 44.79 2.75
439 440 1.202582 CGATCGTGGAGGAAGTGAAGT 59.797 52.381 7.03 0.00 0.00 3.01
491 492 1.549170 GTCATGGGTTAGACGTGAGGT 59.451 52.381 0.00 0.00 34.77 3.85
497 498 4.824289 TGGGTTAGACGTGAGGTTAATTC 58.176 43.478 0.00 0.00 0.00 2.17
592 593 8.602328 CAGACTTTATTTTGCATGTTGTTTCAA 58.398 29.630 0.00 0.00 0.00 2.69
605 606 3.433306 TGTTTCAAACGAGATCCCCAT 57.567 42.857 0.00 0.00 0.00 4.00
606 607 3.081061 TGTTTCAAACGAGATCCCCATG 58.919 45.455 0.00 0.00 0.00 3.66
607 608 3.081804 GTTTCAAACGAGATCCCCATGT 58.918 45.455 0.00 0.00 0.00 3.21
608 609 3.433306 TTCAAACGAGATCCCCATGTT 57.567 42.857 0.00 0.00 0.00 2.71
609 610 4.561500 TTCAAACGAGATCCCCATGTTA 57.438 40.909 0.00 0.00 0.00 2.41
610 611 4.561500 TCAAACGAGATCCCCATGTTAA 57.438 40.909 0.00 0.00 0.00 2.01
611 612 4.513442 TCAAACGAGATCCCCATGTTAAG 58.487 43.478 0.00 0.00 0.00 1.85
612 613 4.019681 TCAAACGAGATCCCCATGTTAAGT 60.020 41.667 0.00 0.00 0.00 2.24
613 614 3.821421 ACGAGATCCCCATGTTAAGTC 57.179 47.619 0.00 0.00 0.00 3.01
614 615 3.104512 ACGAGATCCCCATGTTAAGTCA 58.895 45.455 0.00 0.00 0.00 3.41
615 616 3.133003 ACGAGATCCCCATGTTAAGTCAG 59.867 47.826 0.00 0.00 0.00 3.51
616 617 3.471680 GAGATCCCCATGTTAAGTCAGC 58.528 50.000 0.00 0.00 0.00 4.26
617 618 2.846206 AGATCCCCATGTTAAGTCAGCA 59.154 45.455 0.00 0.00 0.00 4.41
618 619 3.266772 AGATCCCCATGTTAAGTCAGCAA 59.733 43.478 0.00 0.00 0.00 3.91
619 620 2.790433 TCCCCATGTTAAGTCAGCAAC 58.210 47.619 0.00 0.00 0.00 4.17
620 621 2.375174 TCCCCATGTTAAGTCAGCAACT 59.625 45.455 0.00 0.00 41.10 3.16
621 622 2.749621 CCCCATGTTAAGTCAGCAACTC 59.250 50.000 0.00 0.00 37.17 3.01
622 623 3.411446 CCCATGTTAAGTCAGCAACTCA 58.589 45.455 0.00 0.00 37.17 3.41
623 624 3.189287 CCCATGTTAAGTCAGCAACTCAC 59.811 47.826 0.00 0.00 37.17 3.51
624 625 4.067896 CCATGTTAAGTCAGCAACTCACT 58.932 43.478 0.00 0.00 37.17 3.41
625 626 4.516698 CCATGTTAAGTCAGCAACTCACTT 59.483 41.667 0.00 0.00 37.17 3.16
626 627 5.700832 CCATGTTAAGTCAGCAACTCACTTA 59.299 40.000 0.00 0.00 37.17 2.24
627 628 6.128445 CCATGTTAAGTCAGCAACTCACTTAG 60.128 42.308 0.00 0.00 37.17 2.18
628 629 5.914033 TGTTAAGTCAGCAACTCACTTAGT 58.086 37.500 0.00 0.00 41.49 2.24
629 630 7.046292 TGTTAAGTCAGCAACTCACTTAGTA 57.954 36.000 0.00 0.00 37.50 1.82
630 631 7.145985 TGTTAAGTCAGCAACTCACTTAGTAG 58.854 38.462 0.00 0.00 37.50 2.57
631 632 4.181309 AGTCAGCAACTCACTTAGTAGC 57.819 45.455 0.00 0.00 37.50 3.58
632 633 3.829601 AGTCAGCAACTCACTTAGTAGCT 59.170 43.478 0.00 0.00 37.50 3.32
633 634 5.010933 AGTCAGCAACTCACTTAGTAGCTA 58.989 41.667 0.00 0.00 37.50 3.32
634 635 5.124776 AGTCAGCAACTCACTTAGTAGCTAG 59.875 44.000 0.00 0.00 37.50 3.42
635 636 5.124138 GTCAGCAACTCACTTAGTAGCTAGA 59.876 44.000 0.00 0.00 37.50 2.43
636 637 5.710567 TCAGCAACTCACTTAGTAGCTAGAA 59.289 40.000 0.00 0.00 37.50 2.10
637 638 6.208797 TCAGCAACTCACTTAGTAGCTAGAAA 59.791 38.462 0.00 0.00 37.50 2.52
638 639 6.529829 CAGCAACTCACTTAGTAGCTAGAAAG 59.470 42.308 11.68 11.68 37.50 2.62
639 640 5.808030 GCAACTCACTTAGTAGCTAGAAAGG 59.192 44.000 15.84 7.89 37.50 3.11
640 641 5.585820 ACTCACTTAGTAGCTAGAAAGGC 57.414 43.478 15.84 0.00 36.36 4.35
641 642 5.265989 ACTCACTTAGTAGCTAGAAAGGCT 58.734 41.667 15.84 3.03 43.02 4.58
642 643 5.126384 ACTCACTTAGTAGCTAGAAAGGCTG 59.874 44.000 15.84 8.64 40.52 4.85
643 644 5.017490 TCACTTAGTAGCTAGAAAGGCTGT 58.983 41.667 15.84 0.00 40.52 4.40
644 645 5.105716 TCACTTAGTAGCTAGAAAGGCTGTG 60.106 44.000 15.84 8.45 40.52 3.66
645 646 5.017490 ACTTAGTAGCTAGAAAGGCTGTGA 58.983 41.667 15.84 0.00 40.52 3.58
646 647 3.878160 AGTAGCTAGAAAGGCTGTGAC 57.122 47.619 0.00 0.00 40.52 3.67
647 648 3.165875 AGTAGCTAGAAAGGCTGTGACA 58.834 45.455 0.00 0.00 40.52 3.58
648 649 3.578716 AGTAGCTAGAAAGGCTGTGACAA 59.421 43.478 0.00 0.00 40.52 3.18
649 650 3.492102 AGCTAGAAAGGCTGTGACAAA 57.508 42.857 0.00 0.00 38.73 2.83
650 651 4.026356 AGCTAGAAAGGCTGTGACAAAT 57.974 40.909 0.00 0.00 38.73 2.32
651 652 5.165961 AGCTAGAAAGGCTGTGACAAATA 57.834 39.130 0.00 0.00 38.73 1.40
652 653 5.560724 AGCTAGAAAGGCTGTGACAAATAA 58.439 37.500 0.00 0.00 38.73 1.40
653 654 6.003950 AGCTAGAAAGGCTGTGACAAATAAA 58.996 36.000 0.00 0.00 38.73 1.40
654 655 6.660949 AGCTAGAAAGGCTGTGACAAATAAAT 59.339 34.615 0.00 0.00 38.73 1.40
655 656 7.177392 AGCTAGAAAGGCTGTGACAAATAAATT 59.823 33.333 0.00 0.00 38.73 1.82
656 657 7.814587 GCTAGAAAGGCTGTGACAAATAAATTT 59.185 33.333 0.00 0.00 0.00 1.82
657 658 9.696917 CTAGAAAGGCTGTGACAAATAAATTTT 57.303 29.630 0.00 0.00 0.00 1.82
658 659 8.962884 AGAAAGGCTGTGACAAATAAATTTTT 57.037 26.923 0.00 0.00 0.00 1.94
694 695 4.586306 AAAATGTATTCCCTCCGTTCCT 57.414 40.909 0.00 0.00 0.00 3.36
695 696 5.703730 AAAATGTATTCCCTCCGTTCCTA 57.296 39.130 0.00 0.00 0.00 2.94
696 697 5.703730 AAATGTATTCCCTCCGTTCCTAA 57.296 39.130 0.00 0.00 0.00 2.69
697 698 5.703730 AATGTATTCCCTCCGTTCCTAAA 57.296 39.130 0.00 0.00 0.00 1.85
698 699 5.906772 ATGTATTCCCTCCGTTCCTAAAT 57.093 39.130 0.00 0.00 0.00 1.40
699 700 7.383156 AATGTATTCCCTCCGTTCCTAAATA 57.617 36.000 0.00 0.00 0.00 1.40
700 701 7.569599 ATGTATTCCCTCCGTTCCTAAATAT 57.430 36.000 0.00 0.00 0.00 1.28
701 702 8.674925 ATGTATTCCCTCCGTTCCTAAATATA 57.325 34.615 0.00 0.00 0.00 0.86
702 703 8.495160 TGTATTCCCTCCGTTCCTAAATATAA 57.505 34.615 0.00 0.00 0.00 0.98
703 704 8.591072 TGTATTCCCTCCGTTCCTAAATATAAG 58.409 37.037 0.00 0.00 0.00 1.73
704 705 7.867160 ATTCCCTCCGTTCCTAAATATAAGA 57.133 36.000 0.00 0.00 0.00 2.10
705 706 6.661304 TCCCTCCGTTCCTAAATATAAGAC 57.339 41.667 0.00 0.00 0.00 3.01
706 707 5.541484 TCCCTCCGTTCCTAAATATAAGACC 59.459 44.000 0.00 0.00 0.00 3.85
707 708 5.543020 CCCTCCGTTCCTAAATATAAGACCT 59.457 44.000 0.00 0.00 0.00 3.85
708 709 6.042897 CCCTCCGTTCCTAAATATAAGACCTT 59.957 42.308 0.00 0.00 0.00 3.50
709 710 7.419865 CCCTCCGTTCCTAAATATAAGACCTTT 60.420 40.741 0.00 0.00 0.00 3.11
710 711 7.991460 CCTCCGTTCCTAAATATAAGACCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
759 760 8.764524 ACAGAGTGAAATTAGTGAATCTACAC 57.235 34.615 0.00 0.00 40.60 2.90
802 803 7.210718 ACATTCGTATGTAATCCATAGTCGA 57.789 36.000 5.81 0.00 43.12 4.20
803 804 7.654568 ACATTCGTATGTAATCCATAGTCGAA 58.345 34.615 5.81 8.98 43.09 3.71
804 805 8.304596 ACATTCGTATGTAATCCATAGTCGAAT 58.695 33.333 5.81 11.56 45.92 3.34
805 806 8.799091 CATTCGTATGTAATCCATAGTCGAATC 58.201 37.037 13.24 0.00 43.98 2.52
806 807 7.683437 TCGTATGTAATCCATAGTCGAATCT 57.317 36.000 0.00 0.00 36.71 2.40
807 808 8.107399 TCGTATGTAATCCATAGTCGAATCTT 57.893 34.615 0.00 0.00 36.71 2.40
808 809 8.573885 TCGTATGTAATCCATAGTCGAATCTTT 58.426 33.333 0.00 0.00 36.71 2.52
809 810 9.836076 CGTATGTAATCCATAGTCGAATCTTTA 57.164 33.333 0.00 0.00 36.71 1.85
817 818 9.892130 ATCCATAGTCGAATCTTTAAAAAGTCT 57.108 29.630 0.00 0.00 37.31 3.24
818 819 9.720769 TCCATAGTCGAATCTTTAAAAAGTCTT 57.279 29.630 0.00 0.00 37.31 3.01
846 847 6.576662 TTAGGAATAGAAGGAGTATGAGCG 57.423 41.667 0.00 0.00 0.00 5.03
847 848 4.475345 AGGAATAGAAGGAGTATGAGCGT 58.525 43.478 0.00 0.00 0.00 5.07
848 849 4.279671 AGGAATAGAAGGAGTATGAGCGTG 59.720 45.833 0.00 0.00 0.00 5.34
849 850 4.038162 GGAATAGAAGGAGTATGAGCGTGT 59.962 45.833 0.00 0.00 0.00 4.49
850 851 2.949451 AGAAGGAGTATGAGCGTGTG 57.051 50.000 0.00 0.00 0.00 3.82
851 852 2.447443 AGAAGGAGTATGAGCGTGTGA 58.553 47.619 0.00 0.00 0.00 3.58
852 853 2.425312 AGAAGGAGTATGAGCGTGTGAG 59.575 50.000 0.00 0.00 0.00 3.51
853 854 1.840737 AGGAGTATGAGCGTGTGAGT 58.159 50.000 0.00 0.00 0.00 3.41
854 855 3.000684 AGGAGTATGAGCGTGTGAGTA 57.999 47.619 0.00 0.00 0.00 2.59
855 856 3.353557 AGGAGTATGAGCGTGTGAGTAA 58.646 45.455 0.00 0.00 0.00 2.24
856 857 3.762288 AGGAGTATGAGCGTGTGAGTAAA 59.238 43.478 0.00 0.00 0.00 2.01
857 858 4.219944 AGGAGTATGAGCGTGTGAGTAAAA 59.780 41.667 0.00 0.00 0.00 1.52
858 859 4.563184 GGAGTATGAGCGTGTGAGTAAAAG 59.437 45.833 0.00 0.00 0.00 2.27
859 860 5.386958 AGTATGAGCGTGTGAGTAAAAGA 57.613 39.130 0.00 0.00 0.00 2.52
860 861 5.779922 AGTATGAGCGTGTGAGTAAAAGAA 58.220 37.500 0.00 0.00 0.00 2.52
861 862 6.220930 AGTATGAGCGTGTGAGTAAAAGAAA 58.779 36.000 0.00 0.00 0.00 2.52
862 863 6.704493 AGTATGAGCGTGTGAGTAAAAGAAAA 59.296 34.615 0.00 0.00 0.00 2.29
863 864 5.804692 TGAGCGTGTGAGTAAAAGAAAAA 57.195 34.783 0.00 0.00 0.00 1.94
864 865 5.806286 TGAGCGTGTGAGTAAAAGAAAAAG 58.194 37.500 0.00 0.00 0.00 2.27
865 866 5.583061 TGAGCGTGTGAGTAAAAGAAAAAGA 59.417 36.000 0.00 0.00 0.00 2.52
866 867 6.092944 TGAGCGTGTGAGTAAAAGAAAAAGAA 59.907 34.615 0.00 0.00 0.00 2.52
867 868 6.848451 AGCGTGTGAGTAAAAGAAAAAGAAA 58.152 32.000 0.00 0.00 0.00 2.52
868 869 7.309920 AGCGTGTGAGTAAAAGAAAAAGAAAA 58.690 30.769 0.00 0.00 0.00 2.29
869 870 7.810759 AGCGTGTGAGTAAAAGAAAAAGAAAAA 59.189 29.630 0.00 0.00 0.00 1.94
870 871 8.592155 GCGTGTGAGTAAAAGAAAAAGAAAAAT 58.408 29.630 0.00 0.00 0.00 1.82
1083 1085 2.604686 TTCCTCCCTGCGAGCACT 60.605 61.111 0.00 0.00 37.27 4.40
1384 1386 6.252015 CGTTAGCTGCTGTTTCGTAAATAGTA 59.748 38.462 13.43 0.00 32.81 1.82
1392 1394 6.420008 GCTGTTTCGTAAATAGTATCCGTGAT 59.580 38.462 0.00 0.00 32.81 3.06
1776 3543 2.113807 TCTCACTAGGATGTGCATGCT 58.886 47.619 20.33 10.82 42.33 3.79
2267 4035 2.028203 TCGCTCATTGGTCTTGATGTGA 60.028 45.455 0.00 0.00 0.00 3.58
2846 4614 7.280205 CAGCCAAATACGAGGTTAAGAATTACT 59.720 37.037 0.00 0.00 0.00 2.24
3028 4796 0.726827 TCGAAATGCTGCCATTCGTC 59.273 50.000 25.58 9.88 40.69 4.20
3060 4828 5.047660 TGGTTCCATCCTTTTGTTTATTCCG 60.048 40.000 0.00 0.00 0.00 4.30
3301 5302 6.183360 TGGTTGTGGTTTTGCAGAAATCTTAT 60.183 34.615 0.00 0.00 0.00 1.73
3460 6780 0.532573 TCTCTCAGGGTAAAGCTGCG 59.467 55.000 0.00 0.00 0.00 5.18
3520 6840 4.518211 AGCCACTTCACTGAAGAGAAAATG 59.482 41.667 23.08 10.78 41.71 2.32
3632 6952 7.463961 AGTCCGAGAGTAATTAGAAACTTCA 57.536 36.000 0.00 0.00 0.00 3.02
3658 6978 2.125512 CCGACCTGCTGTAGTGGC 60.126 66.667 0.00 0.00 0.00 5.01
3738 7058 1.607628 CGACGGACCCTTCACCTATAG 59.392 57.143 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.038159 CCTCCTCGCGATTACATCCC 60.038 60.000 10.36 0.00 0.00 3.85
32 33 1.030457 GAAGACCCTCCTCGCGATTA 58.970 55.000 10.36 0.00 0.00 1.75
90 91 1.028905 CGGTTCTGGCTGGTTTGAAA 58.971 50.000 0.00 0.00 0.00 2.69
108 109 3.031736 TCTCCATTTCTCCCTAACCTCG 58.968 50.000 0.00 0.00 0.00 4.63
176 177 2.745308 CCATCATCGCCCACCCTCA 61.745 63.158 0.00 0.00 0.00 3.86
197 198 2.747177 TCCGGAATATCACTCCAGTGT 58.253 47.619 0.00 0.00 45.76 3.55
242 243 2.655090 TGGGAGAAAGTGACATGCAA 57.345 45.000 0.00 0.00 0.00 4.08
272 273 2.794820 AAGCTCAACTCTCGCTGGGC 62.795 60.000 0.00 0.00 39.47 5.36
306 307 2.438254 CCCGCCATAACAGCTGCA 60.438 61.111 15.27 1.58 0.00 4.41
392 393 1.446366 GGCGATAAGTCCCTGTCCC 59.554 63.158 0.00 0.00 0.00 4.46
398 399 2.280186 CCAGCGGCGATAAGTCCC 60.280 66.667 12.98 0.00 0.00 4.46
439 440 1.142531 CTCGTGATGCCAGCAGCTA 59.857 57.895 9.54 0.00 44.23 3.32
491 492 5.812642 GCTACTAAGTGAGCTGCTGAATTAA 59.187 40.000 7.01 0.00 35.73 1.40
522 523 5.277058 CGAATCTAGCTTATTTGTCACAGCC 60.277 44.000 0.00 0.00 32.25 4.85
592 593 3.517901 TGACTTAACATGGGGATCTCGTT 59.482 43.478 0.00 0.00 0.00 3.85
605 606 5.914033 ACTAAGTGAGTTGCTGACTTAACA 58.086 37.500 8.91 0.00 39.04 2.41
606 607 7.569677 CTACTAAGTGAGTTGCTGACTTAAC 57.430 40.000 8.91 0.00 39.04 2.01
616 617 5.808030 GCCTTTCTAGCTACTAAGTGAGTTG 59.192 44.000 0.00 0.00 39.81 3.16
617 618 5.717654 AGCCTTTCTAGCTACTAAGTGAGTT 59.282 40.000 0.00 0.00 39.29 3.01
618 619 5.126384 CAGCCTTTCTAGCTACTAAGTGAGT 59.874 44.000 0.00 0.00 38.95 3.41
619 620 5.126384 ACAGCCTTTCTAGCTACTAAGTGAG 59.874 44.000 0.00 0.00 38.95 3.51
620 621 5.017490 ACAGCCTTTCTAGCTACTAAGTGA 58.983 41.667 0.00 0.00 38.95 3.41
621 622 5.105716 TCACAGCCTTTCTAGCTACTAAGTG 60.106 44.000 0.00 0.00 38.95 3.16
622 623 5.017490 TCACAGCCTTTCTAGCTACTAAGT 58.983 41.667 0.00 0.00 38.95 2.24
623 624 5.105716 TGTCACAGCCTTTCTAGCTACTAAG 60.106 44.000 0.00 0.00 38.95 2.18
624 625 4.770531 TGTCACAGCCTTTCTAGCTACTAA 59.229 41.667 0.00 0.00 38.95 2.24
625 626 4.341487 TGTCACAGCCTTTCTAGCTACTA 58.659 43.478 0.00 0.00 38.95 1.82
626 627 3.165875 TGTCACAGCCTTTCTAGCTACT 58.834 45.455 0.00 0.00 38.95 2.57
627 628 3.594603 TGTCACAGCCTTTCTAGCTAC 57.405 47.619 0.00 0.00 38.95 3.58
628 629 4.617253 TTTGTCACAGCCTTTCTAGCTA 57.383 40.909 0.00 0.00 38.95 3.32
629 630 3.492102 TTTGTCACAGCCTTTCTAGCT 57.508 42.857 0.00 0.00 42.70 3.32
630 631 5.880054 TTATTTGTCACAGCCTTTCTAGC 57.120 39.130 0.00 0.00 0.00 3.42
631 632 9.696917 AAAATTTATTTGTCACAGCCTTTCTAG 57.303 29.630 0.00 0.00 0.00 2.43
633 634 8.962884 AAAAATTTATTTGTCACAGCCTTTCT 57.037 26.923 0.00 0.00 0.00 2.52
672 673 4.930696 AGGAACGGAGGGAATACATTTTT 58.069 39.130 0.00 0.00 0.00 1.94
673 674 4.586306 AGGAACGGAGGGAATACATTTT 57.414 40.909 0.00 0.00 0.00 1.82
674 675 5.703730 TTAGGAACGGAGGGAATACATTT 57.296 39.130 0.00 0.00 0.00 2.32
675 676 5.703730 TTTAGGAACGGAGGGAATACATT 57.296 39.130 0.00 0.00 0.00 2.71
676 677 5.906772 ATTTAGGAACGGAGGGAATACAT 57.093 39.130 0.00 0.00 0.00 2.29
677 678 8.495160 TTATATTTAGGAACGGAGGGAATACA 57.505 34.615 0.00 0.00 0.00 2.29
678 679 8.810041 TCTTATATTTAGGAACGGAGGGAATAC 58.190 37.037 0.00 0.00 0.00 1.89
679 680 8.810041 GTCTTATATTTAGGAACGGAGGGAATA 58.190 37.037 0.00 0.00 0.00 1.75
680 681 7.256583 GGTCTTATATTTAGGAACGGAGGGAAT 60.257 40.741 0.00 0.00 0.00 3.01
681 682 6.042437 GGTCTTATATTTAGGAACGGAGGGAA 59.958 42.308 0.00 0.00 0.00 3.97
682 683 5.541484 GGTCTTATATTTAGGAACGGAGGGA 59.459 44.000 0.00 0.00 0.00 4.20
683 684 5.543020 AGGTCTTATATTTAGGAACGGAGGG 59.457 44.000 0.00 0.00 0.00 4.30
684 685 6.667558 AGGTCTTATATTTAGGAACGGAGG 57.332 41.667 0.00 0.00 0.00 4.30
685 686 8.959705 AAAAGGTCTTATATTTAGGAACGGAG 57.040 34.615 0.00 0.00 0.00 4.63
733 734 9.856488 GTGTAGATTCACTAATTTCACTCTGTA 57.144 33.333 0.00 0.00 35.68 2.74
734 735 8.589338 AGTGTAGATTCACTAATTTCACTCTGT 58.411 33.333 0.00 0.00 45.31 3.41
735 736 8.994429 AGTGTAGATTCACTAATTTCACTCTG 57.006 34.615 0.00 0.00 45.31 3.35
776 777 8.953313 TCGACTATGGATTACATACGAATGTAT 58.047 33.333 0.00 0.00 45.67 2.29
777 778 8.326680 TCGACTATGGATTACATACGAATGTA 57.673 34.615 0.00 0.00 44.66 2.29
781 782 8.107399 AGATTCGACTATGGATTACATACGAA 57.893 34.615 13.58 13.58 45.89 3.85
782 783 7.683437 AGATTCGACTATGGATTACATACGA 57.317 36.000 0.00 0.00 41.03 3.43
783 784 8.744008 AAAGATTCGACTATGGATTACATACG 57.256 34.615 0.00 0.00 41.03 3.06
791 792 9.892130 AGACTTTTTAAAGATTCGACTATGGAT 57.108 29.630 9.09 0.00 39.31 3.41
792 793 9.720769 AAGACTTTTTAAAGATTCGACTATGGA 57.279 29.630 9.09 0.00 39.31 3.41
820 821 8.740906 CGCTCATACTCCTTCTATTCCTAAATA 58.259 37.037 0.00 0.00 0.00 1.40
821 822 7.233757 ACGCTCATACTCCTTCTATTCCTAAAT 59.766 37.037 0.00 0.00 0.00 1.40
822 823 6.550108 ACGCTCATACTCCTTCTATTCCTAAA 59.450 38.462 0.00 0.00 0.00 1.85
823 824 6.016192 CACGCTCATACTCCTTCTATTCCTAA 60.016 42.308 0.00 0.00 0.00 2.69
824 825 5.473846 CACGCTCATACTCCTTCTATTCCTA 59.526 44.000 0.00 0.00 0.00 2.94
825 826 4.279671 CACGCTCATACTCCTTCTATTCCT 59.720 45.833 0.00 0.00 0.00 3.36
826 827 4.038162 ACACGCTCATACTCCTTCTATTCC 59.962 45.833 0.00 0.00 0.00 3.01
827 828 4.979197 CACACGCTCATACTCCTTCTATTC 59.021 45.833 0.00 0.00 0.00 1.75
828 829 4.645136 TCACACGCTCATACTCCTTCTATT 59.355 41.667 0.00 0.00 0.00 1.73
829 830 4.207955 TCACACGCTCATACTCCTTCTAT 58.792 43.478 0.00 0.00 0.00 1.98
830 831 3.617284 TCACACGCTCATACTCCTTCTA 58.383 45.455 0.00 0.00 0.00 2.10
831 832 2.425312 CTCACACGCTCATACTCCTTCT 59.575 50.000 0.00 0.00 0.00 2.85
832 833 2.164624 ACTCACACGCTCATACTCCTTC 59.835 50.000 0.00 0.00 0.00 3.46
833 834 2.171840 ACTCACACGCTCATACTCCTT 58.828 47.619 0.00 0.00 0.00 3.36
834 835 1.840737 ACTCACACGCTCATACTCCT 58.159 50.000 0.00 0.00 0.00 3.69
835 836 3.777465 TTACTCACACGCTCATACTCC 57.223 47.619 0.00 0.00 0.00 3.85
836 837 5.399858 TCTTTTACTCACACGCTCATACTC 58.600 41.667 0.00 0.00 0.00 2.59
837 838 5.386958 TCTTTTACTCACACGCTCATACT 57.613 39.130 0.00 0.00 0.00 2.12
838 839 6.462073 TTTCTTTTACTCACACGCTCATAC 57.538 37.500 0.00 0.00 0.00 2.39
839 840 7.439955 TCTTTTTCTTTTACTCACACGCTCATA 59.560 33.333 0.00 0.00 0.00 2.15
840 841 6.260050 TCTTTTTCTTTTACTCACACGCTCAT 59.740 34.615 0.00 0.00 0.00 2.90
841 842 5.583061 TCTTTTTCTTTTACTCACACGCTCA 59.417 36.000 0.00 0.00 0.00 4.26
842 843 6.044512 TCTTTTTCTTTTACTCACACGCTC 57.955 37.500 0.00 0.00 0.00 5.03
843 844 6.431198 TTCTTTTTCTTTTACTCACACGCT 57.569 33.333 0.00 0.00 0.00 5.07
844 845 7.500807 TTTTCTTTTTCTTTTACTCACACGC 57.499 32.000 0.00 0.00 0.00 5.34
852 853 9.811655 GCTGGCATATTTTTCTTTTTCTTTTAC 57.188 29.630 0.00 0.00 0.00 2.01
853 854 8.998377 GGCTGGCATATTTTTCTTTTTCTTTTA 58.002 29.630 0.00 0.00 0.00 1.52
854 855 7.307930 CGGCTGGCATATTTTTCTTTTTCTTTT 60.308 33.333 1.08 0.00 0.00 2.27
855 856 6.147656 CGGCTGGCATATTTTTCTTTTTCTTT 59.852 34.615 1.08 0.00 0.00 2.52
856 857 5.639082 CGGCTGGCATATTTTTCTTTTTCTT 59.361 36.000 1.08 0.00 0.00 2.52
857 858 5.170748 CGGCTGGCATATTTTTCTTTTTCT 58.829 37.500 1.08 0.00 0.00 2.52
858 859 4.929211 ACGGCTGGCATATTTTTCTTTTTC 59.071 37.500 1.08 0.00 0.00 2.29
859 860 4.893608 ACGGCTGGCATATTTTTCTTTTT 58.106 34.783 1.08 0.00 0.00 1.94
860 861 4.535526 ACGGCTGGCATATTTTTCTTTT 57.464 36.364 1.08 0.00 0.00 2.27
861 862 4.244862 CAACGGCTGGCATATTTTTCTTT 58.755 39.130 1.08 0.00 0.00 2.52
862 863 3.368323 CCAACGGCTGGCATATTTTTCTT 60.368 43.478 1.08 0.00 38.76 2.52
863 864 2.166254 CCAACGGCTGGCATATTTTTCT 59.834 45.455 1.08 0.00 38.76 2.52
864 865 2.539476 CCAACGGCTGGCATATTTTTC 58.461 47.619 1.08 0.00 38.76 2.29
865 866 2.671130 CCAACGGCTGGCATATTTTT 57.329 45.000 1.08 0.00 38.76 1.94
1360 1362 6.404712 ACTATTTACGAAACAGCAGCTAAC 57.595 37.500 0.00 0.00 0.00 2.34
1384 1386 6.038271 GCTCAAGTGGTATTTAAATCACGGAT 59.962 38.462 3.39 0.00 35.50 4.18
1776 3543 6.707440 TCCAATTTTCTTTCTAACACTGCA 57.293 33.333 0.00 0.00 0.00 4.41
2267 4035 2.235155 TCCGTAACCATGTGTGCATAGT 59.765 45.455 0.00 0.00 33.30 2.12
2763 4531 5.683876 TTTGGAGTTGGGAATGTCAAAAA 57.316 34.783 0.00 0.00 0.00 1.94
2846 4614 5.848286 ATTCCTCATATCCACTTATGCCA 57.152 39.130 0.00 0.00 31.02 4.92
3028 4796 0.324943 AGGATGGAACCAACCACTCG 59.675 55.000 19.50 0.00 43.03 4.18
3060 4828 1.000938 CAAAGGAACACAAGAGCTGGC 60.001 52.381 0.00 0.00 0.00 4.85
3301 5302 7.279615 TGTCTTTCTCATGGACTTAAAAGTGA 58.720 34.615 0.00 0.00 39.88 3.41
3460 6780 4.099419 ACTTGTGACCAAATCCAGTTTTCC 59.901 41.667 0.00 0.00 0.00 3.13
3520 6840 5.023551 GTCTGCATTTAGACAGTCAACAC 57.976 43.478 2.66 0.00 45.03 3.32
3584 6904 3.056035 GTGGCTTTAGGTAGTGTGCTAGT 60.056 47.826 0.00 0.00 0.00 2.57
3632 6952 2.031163 GCAGGTCGGAGCAGTGTT 59.969 61.111 10.15 0.00 0.00 3.32
3658 6978 2.158957 ACTATAGCAATGTCCCCGTGTG 60.159 50.000 0.00 0.00 0.00 3.82
3664 6984 4.377897 GTGTACCACTATAGCAATGTCCC 58.622 47.826 0.00 0.00 0.00 4.46
3738 7058 0.459078 GTGGGTCCCGTAAGAGTAGC 59.541 60.000 2.65 0.00 43.02 3.58


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

AutoCloner maintained by Alex Coulton.