Multiple sequence alignment - TraesCS4D01G245600

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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 TraesCS4D01G245600 chr4D 100.000 2729 0 0 1 2729 414225576 414222848 0.000000e+00 5040.0
1 TraesCS4D01G245600 chr4D 90.363 633 49 10 2 624 102112956 102113586 0.000000e+00 821.0
2 TraesCS4D01G245600 chr4B 93.309 1106 30 10 728 1822 510352892 510351820 0.000000e+00 1592.0
3 TraesCS4D01G245600 chr4B 92.299 922 43 12 1819 2727 510351748 510350842 0.000000e+00 1284.0
4 TraesCS4D01G245600 chr4A 93.670 932 51 5 906 1829 49221109 49222040 0.000000e+00 1387.0
5 TraesCS4D01G245600 chr4A 91.798 317 22 2 1516 1828 49236291 49236607 3.230000e-119 438.0
6 TraesCS4D01G245600 chr4A 93.902 82 5 0 755 836 49214092 49214173 1.030000e-24 124.0
7 TraesCS4D01G245600 chr4A 97.826 46 1 0 825 870 49221057 49221102 2.250000e-11 80.5
8 TraesCS4D01G245600 chr2B 89.490 628 59 6 2 624 181999426 182000051 0.000000e+00 787.0
9 TraesCS4D01G245600 chr2B 89.348 629 61 5 2 624 383343070 383343698 0.000000e+00 785.0
10 TraesCS4D01G245600 chr7D 89.258 633 57 9 1 624 107722793 107723423 0.000000e+00 782.0
11 TraesCS4D01G245600 chr7D 88.517 627 55 13 5 624 535833082 535833698 0.000000e+00 743.0
12 TraesCS4D01G245600 chr6B 89.117 634 52 7 4 624 649828074 649828703 0.000000e+00 773.0
13 TraesCS4D01G245600 chr2D 88.697 637 56 11 2 624 469172048 469171414 0.000000e+00 763.0
14 TraesCS4D01G245600 chr2D 89.831 590 49 8 41 621 20919035 20919622 0.000000e+00 747.0
15 TraesCS4D01G245600 chr3D 87.840 625 70 5 2 621 593766374 593766997 0.000000e+00 728.0


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 TraesCS4D01G245600 chr4D 414222848 414225576 2728 True 5040.00 5040 100.000 1 2729 1 chr4D.!!$R1 2728
1 TraesCS4D01G245600 chr4D 102112956 102113586 630 False 821.00 821 90.363 2 624 1 chr4D.!!$F1 622
2 TraesCS4D01G245600 chr4B 510350842 510352892 2050 True 1438.00 1592 92.804 728 2727 2 chr4B.!!$R1 1999
3 TraesCS4D01G245600 chr4A 49221057 49222040 983 False 733.75 1387 95.748 825 1829 2 chr4A.!!$F3 1004
4 TraesCS4D01G245600 chr2B 181999426 182000051 625 False 787.00 787 89.490 2 624 1 chr2B.!!$F1 622
5 TraesCS4D01G245600 chr2B 383343070 383343698 628 False 785.00 785 89.348 2 624 1 chr2B.!!$F2 622
6 TraesCS4D01G245600 chr7D 107722793 107723423 630 False 782.00 782 89.258 1 624 1 chr7D.!!$F1 623
7 TraesCS4D01G245600 chr7D 535833082 535833698 616 False 743.00 743 88.517 5 624 1 chr7D.!!$F2 619
8 TraesCS4D01G245600 chr6B 649828074 649828703 629 False 773.00 773 89.117 4 624 1 chr6B.!!$F1 620
9 TraesCS4D01G245600 chr2D 469171414 469172048 634 True 763.00 763 88.697 2 624 1 chr2D.!!$R1 622
10 TraesCS4D01G245600 chr2D 20919035 20919622 587 False 747.00 747 89.831 41 621 1 chr2D.!!$F1 580
11 TraesCS4D01G245600 chr3D 593766374 593766997 623 False 728.00 728 87.840 2 621 1 chr3D.!!$F1 619

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
764 808 0.248134 GACGAACGGATCTGGTCTCG 60.248 60.0 17.45 17.04 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2359 0.17691 CCTCTTCTCGAAAGGGCTCC 59.823 60.0 7.27 0.0 0.0 4.7 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
50 59 2.785857 CCAATCCCCCTTCTACTCCATT 59.214 50.000 0.00 0.00 0.00 3.16
152 166 5.721960 TGCTTATCTACCTCTATTCCCCATC 59.278 44.000 0.00 0.00 0.00 3.51
164 178 2.366972 CCCATCCCCCTCTCCGTT 60.367 66.667 0.00 0.00 0.00 4.44
180 194 2.756207 TCCGTTGTGGATCGAATCTACA 59.244 45.455 9.01 9.01 46.98 2.74
220 237 2.094494 AGTAGTGCATGACGAACAGAGG 60.094 50.000 0.00 0.00 0.00 3.69
333 353 2.831333 CCGATGAGAATTGGGAGAGTG 58.169 52.381 0.00 0.00 0.00 3.51
354 386 1.392534 GGAGAGTGGGGAGAGGGAA 59.607 63.158 0.00 0.00 0.00 3.97
537 573 0.320858 TTAAGGTTCGTGCCATGCGA 60.321 50.000 0.00 0.00 36.51 5.10
625 661 2.733945 GGCAACCAAACACGCCAT 59.266 55.556 0.00 0.00 44.25 4.40
626 662 1.960612 GGCAACCAAACACGCCATA 59.039 52.632 0.00 0.00 44.25 2.74
627 663 0.315568 GGCAACCAAACACGCCATAA 59.684 50.000 0.00 0.00 44.25 1.90
628 664 1.269831 GGCAACCAAACACGCCATAAA 60.270 47.619 0.00 0.00 44.25 1.40
629 665 2.611722 GGCAACCAAACACGCCATAAAT 60.612 45.455 0.00 0.00 44.25 1.40
630 666 2.666022 GCAACCAAACACGCCATAAATC 59.334 45.455 0.00 0.00 0.00 2.17
631 667 3.613910 GCAACCAAACACGCCATAAATCT 60.614 43.478 0.00 0.00 0.00 2.40
632 668 4.380023 GCAACCAAACACGCCATAAATCTA 60.380 41.667 0.00 0.00 0.00 1.98
633 669 5.704888 CAACCAAACACGCCATAAATCTAA 58.295 37.500 0.00 0.00 0.00 2.10
634 670 5.305139 ACCAAACACGCCATAAATCTAAC 57.695 39.130 0.00 0.00 0.00 2.34
635 671 4.142773 ACCAAACACGCCATAAATCTAACG 60.143 41.667 0.00 0.00 0.00 3.18
636 672 4.142773 CCAAACACGCCATAAATCTAACGT 60.143 41.667 0.00 0.00 0.00 3.99
639 675 4.178156 CACGCCATAAATCTAACGTGTC 57.822 45.455 5.27 0.00 44.16 3.67
640 676 3.863424 CACGCCATAAATCTAACGTGTCT 59.137 43.478 5.27 0.00 44.16 3.41
641 677 4.328983 CACGCCATAAATCTAACGTGTCTT 59.671 41.667 5.27 0.00 44.16 3.01
642 678 4.565564 ACGCCATAAATCTAACGTGTCTTC 59.434 41.667 0.00 0.00 31.71 2.87
643 679 4.025979 CGCCATAAATCTAACGTGTCTTCC 60.026 45.833 0.00 0.00 0.00 3.46
644 680 5.116882 GCCATAAATCTAACGTGTCTTCCT 58.883 41.667 0.00 0.00 0.00 3.36
645 681 5.234543 GCCATAAATCTAACGTGTCTTCCTC 59.765 44.000 0.00 0.00 0.00 3.71
646 682 5.753921 CCATAAATCTAACGTGTCTTCCTCC 59.246 44.000 0.00 0.00 0.00 4.30
647 683 6.407074 CCATAAATCTAACGTGTCTTCCTCCT 60.407 42.308 0.00 0.00 0.00 3.69
648 684 4.722361 AATCTAACGTGTCTTCCTCCTC 57.278 45.455 0.00 0.00 0.00 3.71
649 685 3.436577 TCTAACGTGTCTTCCTCCTCT 57.563 47.619 0.00 0.00 0.00 3.69
650 686 3.082548 TCTAACGTGTCTTCCTCCTCTG 58.917 50.000 0.00 0.00 0.00 3.35
651 687 0.318762 AACGTGTCTTCCTCCTCTGC 59.681 55.000 0.00 0.00 0.00 4.26
652 688 0.540830 ACGTGTCTTCCTCCTCTGCT 60.541 55.000 0.00 0.00 0.00 4.24
653 689 0.605589 CGTGTCTTCCTCCTCTGCTT 59.394 55.000 0.00 0.00 0.00 3.91
654 690 1.001406 CGTGTCTTCCTCCTCTGCTTT 59.999 52.381 0.00 0.00 0.00 3.51
655 691 2.421619 GTGTCTTCCTCCTCTGCTTTG 58.578 52.381 0.00 0.00 0.00 2.77
656 692 2.037772 GTGTCTTCCTCCTCTGCTTTGA 59.962 50.000 0.00 0.00 0.00 2.69
657 693 2.301296 TGTCTTCCTCCTCTGCTTTGAG 59.699 50.000 0.00 0.00 0.00 3.02
658 694 2.564947 GTCTTCCTCCTCTGCTTTGAGA 59.435 50.000 4.05 0.00 36.23 3.27
659 695 3.197549 GTCTTCCTCCTCTGCTTTGAGAT 59.802 47.826 4.05 0.00 36.23 2.75
660 696 3.450457 TCTTCCTCCTCTGCTTTGAGATC 59.550 47.826 4.05 0.00 36.23 2.75
661 697 3.113191 TCCTCCTCTGCTTTGAGATCT 57.887 47.619 0.00 0.00 36.23 2.75
662 698 2.765135 TCCTCCTCTGCTTTGAGATCTG 59.235 50.000 0.00 0.00 36.23 2.90
663 699 2.500910 CCTCCTCTGCTTTGAGATCTGT 59.499 50.000 0.00 0.00 36.23 3.41
664 700 3.523547 CTCCTCTGCTTTGAGATCTGTG 58.476 50.000 0.00 0.00 36.23 3.66
665 701 2.902486 TCCTCTGCTTTGAGATCTGTGT 59.098 45.455 0.00 0.00 36.23 3.72
666 702 3.001414 CCTCTGCTTTGAGATCTGTGTG 58.999 50.000 0.00 0.00 36.23 3.82
667 703 3.556633 CCTCTGCTTTGAGATCTGTGTGT 60.557 47.826 0.00 0.00 36.23 3.72
668 704 3.657634 TCTGCTTTGAGATCTGTGTGTC 58.342 45.455 0.00 0.00 0.00 3.67
669 705 3.323115 TCTGCTTTGAGATCTGTGTGTCT 59.677 43.478 0.00 0.00 0.00 3.41
670 706 3.657634 TGCTTTGAGATCTGTGTGTCTC 58.342 45.455 0.00 0.00 40.94 3.36
671 707 3.070015 TGCTTTGAGATCTGTGTGTCTCA 59.930 43.478 0.00 1.23 46.60 3.27
675 711 3.434309 TGAGATCTGTGTGTCTCATCCA 58.566 45.455 0.00 0.00 44.24 3.41
676 712 3.834231 TGAGATCTGTGTGTCTCATCCAA 59.166 43.478 0.00 0.00 44.24 3.53
677 713 4.180057 GAGATCTGTGTGTCTCATCCAAC 58.820 47.826 0.00 0.00 40.41 3.77
678 714 2.438868 TCTGTGTGTCTCATCCAACG 57.561 50.000 0.00 0.00 0.00 4.10
679 715 1.000843 TCTGTGTGTCTCATCCAACGG 59.999 52.381 0.00 0.00 0.00 4.44
680 716 0.602638 TGTGTGTCTCATCCAACGGC 60.603 55.000 0.00 0.00 0.00 5.68
681 717 0.602638 GTGTGTCTCATCCAACGGCA 60.603 55.000 0.00 0.00 0.00 5.69
682 718 0.324614 TGTGTCTCATCCAACGGCAT 59.675 50.000 0.00 0.00 0.00 4.40
683 719 1.009829 GTGTCTCATCCAACGGCATC 58.990 55.000 0.00 0.00 0.00 3.91
684 720 0.460109 TGTCTCATCCAACGGCATCG 60.460 55.000 0.00 0.00 43.02 3.84
695 731 4.794241 GGCATCGTGCGCGTTCAC 62.794 66.667 20.50 7.45 46.21 3.18
705 741 2.778679 GCGTTCACGTGAGATGCC 59.221 61.111 19.11 4.95 42.22 4.40
706 742 2.740714 GCGTTCACGTGAGATGCCC 61.741 63.158 19.11 2.00 42.22 5.36
707 743 1.374125 CGTTCACGTGAGATGCCCA 60.374 57.895 19.11 0.00 34.11 5.36
708 744 1.354337 CGTTCACGTGAGATGCCCAG 61.354 60.000 19.11 1.82 34.11 4.45
709 745 1.375908 TTCACGTGAGATGCCCAGC 60.376 57.895 19.11 0.00 0.00 4.85
710 746 2.046988 CACGTGAGATGCCCAGCA 60.047 61.111 10.90 0.00 44.86 4.41
711 747 2.046892 ACGTGAGATGCCCAGCAC 60.047 61.111 0.00 0.00 43.04 4.40
712 748 3.190849 CGTGAGATGCCCAGCACG 61.191 66.667 0.00 0.00 43.04 5.34
713 749 2.265739 GTGAGATGCCCAGCACGA 59.734 61.111 0.00 0.00 43.04 4.35
714 750 1.375908 GTGAGATGCCCAGCACGAA 60.376 57.895 0.00 0.00 43.04 3.85
715 751 1.078918 TGAGATGCCCAGCACGAAG 60.079 57.895 0.00 0.00 43.04 3.79
716 752 1.219124 GAGATGCCCAGCACGAAGA 59.781 57.895 0.00 0.00 43.04 2.87
717 753 1.078848 AGATGCCCAGCACGAAGAC 60.079 57.895 0.00 0.00 43.04 3.01
718 754 2.434884 ATGCCCAGCACGAAGACG 60.435 61.111 0.00 0.00 43.04 4.18
738 774 2.156917 GTGTTCCCCTACTTTTTCCCG 58.843 52.381 0.00 0.00 0.00 5.14
747 783 1.284715 CTTTTTCCCGTTGGCCGAC 59.715 57.895 13.74 13.74 39.56 4.79
764 808 0.248134 GACGAACGGATCTGGTCTCG 60.248 60.000 17.45 17.04 0.00 4.04
775 819 1.114627 CTGGTCTCGATCCCACATGA 58.885 55.000 0.00 0.00 0.00 3.07
815 859 3.926527 TGTCTTTGATCAGACCGAATTCG 59.073 43.478 20.92 20.92 42.39 3.34
870 914 0.323629 GGGGAACACATCTCGACCAA 59.676 55.000 0.00 0.00 0.00 3.67
871 915 1.065418 GGGGAACACATCTCGACCAAT 60.065 52.381 0.00 0.00 0.00 3.16
873 917 3.370103 GGGGAACACATCTCGACCAATAA 60.370 47.826 0.00 0.00 0.00 1.40
874 918 4.451900 GGGAACACATCTCGACCAATAAT 58.548 43.478 0.00 0.00 0.00 1.28
875 919 4.881850 GGGAACACATCTCGACCAATAATT 59.118 41.667 0.00 0.00 0.00 1.40
876 920 5.007724 GGGAACACATCTCGACCAATAATTC 59.992 44.000 0.00 0.00 0.00 2.17
877 921 5.817816 GGAACACATCTCGACCAATAATTCT 59.182 40.000 0.00 0.00 0.00 2.40
878 922 6.238211 GGAACACATCTCGACCAATAATTCTG 60.238 42.308 0.00 0.00 0.00 3.02
879 923 4.572389 ACACATCTCGACCAATAATTCTGC 59.428 41.667 0.00 0.00 0.00 4.26
880 924 4.571984 CACATCTCGACCAATAATTCTGCA 59.428 41.667 0.00 0.00 0.00 4.41
881 925 4.572389 ACATCTCGACCAATAATTCTGCAC 59.428 41.667 0.00 0.00 0.00 4.57
882 926 4.471904 TCTCGACCAATAATTCTGCACT 57.528 40.909 0.00 0.00 0.00 4.40
883 927 4.832248 TCTCGACCAATAATTCTGCACTT 58.168 39.130 0.00 0.00 0.00 3.16
884 928 5.972935 TCTCGACCAATAATTCTGCACTTA 58.027 37.500 0.00 0.00 0.00 2.24
885 929 5.810587 TCTCGACCAATAATTCTGCACTTAC 59.189 40.000 0.00 0.00 0.00 2.34
886 930 4.565166 TCGACCAATAATTCTGCACTTACG 59.435 41.667 0.00 0.00 0.00 3.18
887 931 4.260212 CGACCAATAATTCTGCACTTACGG 60.260 45.833 0.00 0.00 0.00 4.02
888 932 3.945285 ACCAATAATTCTGCACTTACGGG 59.055 43.478 0.00 0.00 0.00 5.28
889 933 3.315191 CCAATAATTCTGCACTTACGGGG 59.685 47.826 0.00 0.00 0.00 5.73
890 934 2.702592 TAATTCTGCACTTACGGGGG 57.297 50.000 0.00 0.00 0.00 5.40
935 979 2.198304 ATCGGAGCCAGGGTTTCCAC 62.198 60.000 0.00 0.00 34.83 4.02
961 1009 7.201652 CCTCGTATTCAGCGATAGATCAGATAA 60.202 40.741 0.00 0.00 37.74 1.75
1224 1275 0.978146 AGATGACCAAGGACCCCTCG 60.978 60.000 0.00 0.00 30.89 4.63
1492 1543 0.811616 GAATCGAGGCATTGGCGAGT 60.812 55.000 4.38 0.00 42.47 4.18
1497 1548 1.739067 GAGGCATTGGCGAGTTAAGT 58.261 50.000 4.38 0.00 42.47 2.24
1511 1562 4.182339 GAGTTAAGTGTAGGGCTAAGCAC 58.818 47.826 0.00 0.00 0.00 4.40
1692 1746 3.643237 ACTCAATAGGGAGATCACGGAA 58.357 45.455 0.00 0.00 38.30 4.30
1843 1973 2.845363 TTTTTACCACTCCCTCCGTC 57.155 50.000 0.00 0.00 0.00 4.79
1844 1974 2.019807 TTTTACCACTCCCTCCGTCT 57.980 50.000 0.00 0.00 0.00 4.18
1851 1981 2.036475 CCACTCCCTCCGTCTCATAATG 59.964 54.545 0.00 0.00 0.00 1.90
1852 1982 2.695666 CACTCCCTCCGTCTCATAATGT 59.304 50.000 0.00 0.00 0.00 2.71
1853 1983 3.889538 CACTCCCTCCGTCTCATAATGTA 59.110 47.826 0.00 0.00 0.00 2.29
1856 1986 5.163437 ACTCCCTCCGTCTCATAATGTAAAC 60.163 44.000 0.00 0.00 0.00 2.01
1858 1988 5.365605 TCCCTCCGTCTCATAATGTAAACAT 59.634 40.000 0.00 0.00 38.41 2.71
2015 2145 2.554032 ACATCTTTGGTGGCTTTTCTCG 59.446 45.455 0.00 0.00 0.00 4.04
2020 2150 1.593196 TGGTGGCTTTTCTCGAGTTG 58.407 50.000 13.13 2.61 0.00 3.16
2025 2155 2.612212 TGGCTTTTCTCGAGTTGTGTTC 59.388 45.455 13.13 0.00 0.00 3.18
2046 2176 9.260002 GTGTTCATCAAAATTTTGGATGTAGTT 57.740 29.630 26.45 3.76 38.66 2.24
2048 2178 9.260002 GTTCATCAAAATTTTGGATGTAGTTGT 57.740 29.630 26.45 2.58 38.66 3.32
2058 2188 2.354805 GGATGTAGTTGTGACCCCACTC 60.355 54.545 0.00 0.00 43.55 3.51
2069 2199 2.105821 TGACCCCACTCGTTTCAAGAAT 59.894 45.455 0.00 0.00 0.00 2.40
2070 2200 3.146847 GACCCCACTCGTTTCAAGAATT 58.853 45.455 0.00 0.00 0.00 2.17
2099 2229 4.401519 TCCACTACTATTCTCAACGAAGGG 59.598 45.833 0.00 0.00 34.56 3.95
2115 2245 4.142513 ACGAAGGGATAACAACGTAGTCTC 60.143 45.833 0.00 0.00 45.00 3.36
2117 2247 2.098770 AGGGATAACAACGTAGTCTCGC 59.901 50.000 0.00 0.00 45.00 5.03
2122 2252 1.233285 ACAACGTAGTCTCGCCTCGT 61.233 55.000 0.00 0.00 45.00 4.18
2126 2256 1.360194 CGTAGTCTCGCCTCGTGAGT 61.360 60.000 2.41 4.45 40.59 3.41
2170 2300 2.478989 TGGACGAACCGCAACAAAA 58.521 47.368 0.00 0.00 42.61 2.44
2174 2304 3.066342 TGGACGAACCGCAACAAAATAAA 59.934 39.130 0.00 0.00 42.61 1.40
2200 2334 2.293122 TGATGCCAAAACACCTCTTTCG 59.707 45.455 0.00 0.00 0.00 3.46
2218 2352 6.055588 TCTTTCGAATTGTTCCTCTTCTTGT 58.944 36.000 0.00 0.00 0.00 3.16
2225 2359 1.876156 GTTCCTCTTCTTGTGGCAGTG 59.124 52.381 0.00 0.00 0.00 3.66
2237 2371 2.347490 GCAGTGGAGCCCTTTCGA 59.653 61.111 0.00 0.00 0.00 3.71
2254 2388 0.249238 CGAGAAGAGGCCTGATTCGG 60.249 60.000 12.00 8.38 0.00 4.30
2255 2389 1.115467 GAGAAGAGGCCTGATTCGGA 58.885 55.000 12.00 0.00 0.00 4.55
2256 2390 0.827368 AGAAGAGGCCTGATTCGGAC 59.173 55.000 12.00 0.00 0.00 4.79
2257 2391 0.537188 GAAGAGGCCTGATTCGGACA 59.463 55.000 12.00 0.00 33.12 4.02
2258 2392 0.250513 AAGAGGCCTGATTCGGACAC 59.749 55.000 12.00 0.00 33.12 3.67
2259 2393 1.519455 GAGGCCTGATTCGGACACG 60.519 63.158 12.00 0.00 42.74 4.49
2260 2394 2.511600 GGCCTGATTCGGACACGG 60.512 66.667 0.00 0.00 41.39 4.94
2261 2395 3.195698 GCCTGATTCGGACACGGC 61.196 66.667 0.00 0.00 41.39 5.68
2262 2396 2.579201 CCTGATTCGGACACGGCT 59.421 61.111 0.00 0.00 41.39 5.52
2295 2429 5.743117 CTCCAGAAGATCAAAGAAGTCCAT 58.257 41.667 0.00 0.00 0.00 3.41
2307 2441 4.679373 AGAAGTCCATGCGATGAACTAT 57.321 40.909 0.00 0.00 0.00 2.12
2368 2502 9.829507 TTTCTTTTGTCATCATTTTGTAATGGT 57.170 25.926 0.00 0.00 41.23 3.55
2530 2670 8.761575 TTTTCACATAAATTCATTCAAGAGGC 57.238 30.769 0.00 0.00 0.00 4.70
2569 2709 3.059597 CCACACATTCGAACACTCTGAAC 60.060 47.826 0.00 0.00 0.00 3.18
2599 2739 6.697019 CCATGTCCAAAAACTTTTACACAGAG 59.303 38.462 0.00 0.00 29.64 3.35
2712 2853 1.852626 AACAAGGCCTAGGCTGGGT 60.853 57.895 32.18 23.01 38.81 4.51
2727 2868 1.452833 GGGTGCCTGCTTCATCCTC 60.453 63.158 0.00 0.00 32.04 3.71
2728 2869 1.606531 GGTGCCTGCTTCATCCTCT 59.393 57.895 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 59 5.080337 AGATCGGAATAGAGGTAGATGCAA 58.920 41.667 0.00 0.00 0.00 4.08
119 128 4.164988 AGAGGTAGATAAGCATGGCAGTTT 59.835 41.667 0.00 0.00 0.00 2.66
152 166 2.606519 TCCACAACGGAGAGGGGG 60.607 66.667 0.00 0.00 39.64 5.40
164 178 1.407618 CCGGTGTAGATTCGATCCACA 59.592 52.381 0.00 0.00 0.00 4.17
180 194 0.945265 TTTTTCGCGTTCGATCCGGT 60.945 50.000 5.77 0.00 45.04 5.28
316 335 1.849039 CCCCACTCTCCCAATTCTCAT 59.151 52.381 0.00 0.00 0.00 2.90
322 342 0.327000 CTCTCCCCCACTCTCCCAAT 60.327 60.000 0.00 0.00 0.00 3.16
333 353 2.041405 CTCTCCCCACTCTCCCCC 60.041 72.222 0.00 0.00 0.00 5.40
537 573 1.523758 CCTGCTTTTACTGTTCGGCT 58.476 50.000 0.00 0.00 0.00 5.52
624 660 6.608002 AGAGGAGGAAGACACGTTAGATTTAT 59.392 38.462 0.00 0.00 0.00 1.40
625 661 5.950549 AGAGGAGGAAGACACGTTAGATTTA 59.049 40.000 0.00 0.00 0.00 1.40
626 662 4.773149 AGAGGAGGAAGACACGTTAGATTT 59.227 41.667 0.00 0.00 0.00 2.17
627 663 4.158764 CAGAGGAGGAAGACACGTTAGATT 59.841 45.833 0.00 0.00 0.00 2.40
628 664 3.697045 CAGAGGAGGAAGACACGTTAGAT 59.303 47.826 0.00 0.00 0.00 1.98
629 665 3.082548 CAGAGGAGGAAGACACGTTAGA 58.917 50.000 0.00 0.00 0.00 2.10
630 666 2.416162 GCAGAGGAGGAAGACACGTTAG 60.416 54.545 0.00 0.00 0.00 2.34
631 667 1.544691 GCAGAGGAGGAAGACACGTTA 59.455 52.381 0.00 0.00 0.00 3.18
632 668 0.318762 GCAGAGGAGGAAGACACGTT 59.681 55.000 0.00 0.00 0.00 3.99
633 669 0.540830 AGCAGAGGAGGAAGACACGT 60.541 55.000 0.00 0.00 0.00 4.49
634 670 0.605589 AAGCAGAGGAGGAAGACACG 59.394 55.000 0.00 0.00 0.00 4.49
635 671 2.037772 TCAAAGCAGAGGAGGAAGACAC 59.962 50.000 0.00 0.00 0.00 3.67
636 672 2.301296 CTCAAAGCAGAGGAGGAAGACA 59.699 50.000 0.00 0.00 31.94 3.41
637 673 2.564947 TCTCAAAGCAGAGGAGGAAGAC 59.435 50.000 1.73 0.00 36.30 3.01
638 674 2.894731 TCTCAAAGCAGAGGAGGAAGA 58.105 47.619 1.73 0.00 36.30 2.87
639 675 3.451902 AGATCTCAAAGCAGAGGAGGAAG 59.548 47.826 0.00 0.00 36.30 3.46
640 676 3.197333 CAGATCTCAAAGCAGAGGAGGAA 59.803 47.826 0.00 0.00 36.30 3.36
641 677 2.765135 CAGATCTCAAAGCAGAGGAGGA 59.235 50.000 0.00 0.00 36.30 3.71
642 678 2.500910 ACAGATCTCAAAGCAGAGGAGG 59.499 50.000 0.00 0.00 36.30 4.30
643 679 3.055963 ACACAGATCTCAAAGCAGAGGAG 60.056 47.826 0.00 0.00 36.30 3.69
644 680 2.902486 ACACAGATCTCAAAGCAGAGGA 59.098 45.455 0.00 0.00 36.30 3.71
645 681 3.001414 CACACAGATCTCAAAGCAGAGG 58.999 50.000 0.00 0.00 36.30 3.69
646 682 3.661944 ACACACAGATCTCAAAGCAGAG 58.338 45.455 0.00 0.00 36.97 3.35
647 683 3.323115 AGACACACAGATCTCAAAGCAGA 59.677 43.478 0.00 0.00 0.00 4.26
648 684 3.661944 AGACACACAGATCTCAAAGCAG 58.338 45.455 0.00 0.00 0.00 4.24
649 685 3.070015 TGAGACACACAGATCTCAAAGCA 59.930 43.478 1.52 0.00 46.47 3.91
650 686 3.657634 TGAGACACACAGATCTCAAAGC 58.342 45.455 1.52 0.00 46.47 3.51
655 691 4.180057 GTTGGATGAGACACACAGATCTC 58.820 47.826 0.00 0.00 41.54 2.75
656 692 3.367806 CGTTGGATGAGACACACAGATCT 60.368 47.826 0.00 0.00 0.00 2.75
657 693 2.926200 CGTTGGATGAGACACACAGATC 59.074 50.000 0.00 0.00 0.00 2.75
658 694 2.354103 CCGTTGGATGAGACACACAGAT 60.354 50.000 0.00 0.00 0.00 2.90
659 695 1.000843 CCGTTGGATGAGACACACAGA 59.999 52.381 0.00 0.00 0.00 3.41
660 696 1.432514 CCGTTGGATGAGACACACAG 58.567 55.000 0.00 0.00 0.00 3.66
661 697 0.602638 GCCGTTGGATGAGACACACA 60.603 55.000 0.00 0.00 0.00 3.72
662 698 0.602638 TGCCGTTGGATGAGACACAC 60.603 55.000 0.00 0.00 0.00 3.82
663 699 0.324614 ATGCCGTTGGATGAGACACA 59.675 50.000 0.00 0.00 0.00 3.72
664 700 1.009829 GATGCCGTTGGATGAGACAC 58.990 55.000 0.00 0.00 0.00 3.67
665 701 0.460109 CGATGCCGTTGGATGAGACA 60.460 55.000 0.00 0.00 0.00 3.41
666 702 2.301505 CGATGCCGTTGGATGAGAC 58.698 57.895 0.00 0.00 0.00 3.36
667 703 4.833811 CGATGCCGTTGGATGAGA 57.166 55.556 0.00 0.00 0.00 3.27
678 714 4.794241 GTGAACGCGCACGATGCC 62.794 66.667 5.73 0.00 41.12 4.40
684 720 2.372690 ATCTCACGTGAACGCGCAC 61.373 57.895 20.49 6.38 44.43 5.34
685 721 2.049526 ATCTCACGTGAACGCGCA 60.050 55.556 20.49 0.00 44.43 6.09
686 722 2.391821 CATCTCACGTGAACGCGC 59.608 61.111 20.49 0.00 44.43 6.86
687 723 2.391821 GCATCTCACGTGAACGCG 59.608 61.111 20.49 3.53 44.43 6.01
688 724 2.740714 GGGCATCTCACGTGAACGC 61.741 63.158 20.49 20.06 44.43 4.84
689 725 1.354337 CTGGGCATCTCACGTGAACG 61.354 60.000 20.49 9.16 46.33 3.95
690 726 1.639298 GCTGGGCATCTCACGTGAAC 61.639 60.000 20.49 9.16 0.00 3.18
691 727 1.375908 GCTGGGCATCTCACGTGAA 60.376 57.895 20.49 11.00 0.00 3.18
692 728 2.265739 GCTGGGCATCTCACGTGA 59.734 61.111 18.88 18.88 0.00 4.35
693 729 2.046988 TGCTGGGCATCTCACGTG 60.047 61.111 9.94 9.94 31.71 4.49
694 730 2.046892 GTGCTGGGCATCTCACGT 60.047 61.111 0.00 0.00 41.91 4.49
695 731 3.190849 CGTGCTGGGCATCTCACG 61.191 66.667 6.45 6.45 44.62 4.35
696 732 1.364626 CTTCGTGCTGGGCATCTCAC 61.365 60.000 0.00 0.00 41.91 3.51
697 733 1.078918 CTTCGTGCTGGGCATCTCA 60.079 57.895 0.00 0.00 41.91 3.27
698 734 1.086634 GTCTTCGTGCTGGGCATCTC 61.087 60.000 0.00 0.00 41.91 2.75
699 735 1.078848 GTCTTCGTGCTGGGCATCT 60.079 57.895 0.00 0.00 41.91 2.90
700 736 2.456119 CGTCTTCGTGCTGGGCATC 61.456 63.158 0.00 0.00 41.91 3.91
701 737 2.434884 CGTCTTCGTGCTGGGCAT 60.435 61.111 0.00 0.00 41.91 4.40
711 747 0.886563 AGTAGGGGAACACGTCTTCG 59.113 55.000 0.00 0.00 43.34 3.79
712 748 3.397849 AAAGTAGGGGAACACGTCTTC 57.602 47.619 0.00 0.00 0.00 2.87
713 749 3.851458 AAAAGTAGGGGAACACGTCTT 57.149 42.857 0.00 0.00 0.00 3.01
714 750 3.495629 GGAAAAAGTAGGGGAACACGTCT 60.496 47.826 0.00 0.00 0.00 4.18
715 751 2.810274 GGAAAAAGTAGGGGAACACGTC 59.190 50.000 0.00 0.00 0.00 4.34
716 752 2.487805 GGGAAAAAGTAGGGGAACACGT 60.488 50.000 0.00 0.00 0.00 4.49
717 753 2.156917 GGGAAAAAGTAGGGGAACACG 58.843 52.381 0.00 0.00 0.00 4.49
718 754 2.156917 CGGGAAAAAGTAGGGGAACAC 58.843 52.381 0.00 0.00 0.00 3.32
719 755 1.776063 ACGGGAAAAAGTAGGGGAACA 59.224 47.619 0.00 0.00 0.00 3.18
720 756 2.555325 CAACGGGAAAAAGTAGGGGAAC 59.445 50.000 0.00 0.00 0.00 3.62
721 757 2.489437 CCAACGGGAAAAAGTAGGGGAA 60.489 50.000 0.00 0.00 35.59 3.97
722 758 1.074244 CCAACGGGAAAAAGTAGGGGA 59.926 52.381 0.00 0.00 35.59 4.81
723 759 1.541379 CCAACGGGAAAAAGTAGGGG 58.459 55.000 0.00 0.00 35.59 4.79
724 760 0.885879 GCCAACGGGAAAAAGTAGGG 59.114 55.000 0.00 0.00 35.59 3.53
725 761 0.885879 GGCCAACGGGAAAAAGTAGG 59.114 55.000 0.00 0.00 35.59 3.18
726 762 0.519961 CGGCCAACGGGAAAAAGTAG 59.480 55.000 2.24 0.00 39.42 2.57
747 783 0.663688 ATCGAGACCAGATCCGTTCG 59.336 55.000 0.00 0.00 0.00 3.95
753 789 1.403814 TGTGGGATCGAGACCAGATC 58.596 55.000 10.81 1.55 42.68 2.75
764 808 2.744202 GTGCCGAATATCATGTGGGATC 59.256 50.000 0.00 0.00 0.00 3.36
815 859 2.095718 GTGTTGGGCGAAGAACAGATTC 60.096 50.000 0.00 0.00 32.81 2.52
870 914 3.208747 CCCCCGTAAGTGCAGAATTAT 57.791 47.619 0.00 0.00 0.00 1.28
871 915 2.702592 CCCCCGTAAGTGCAGAATTA 57.297 50.000 0.00 0.00 0.00 1.40
887 931 1.978580 CCCTCCGATATATATGCCCCC 59.021 57.143 0.00 0.00 0.00 5.40
888 932 1.348036 GCCCTCCGATATATATGCCCC 59.652 57.143 0.00 0.00 0.00 5.80
889 933 1.348036 GGCCCTCCGATATATATGCCC 59.652 57.143 0.00 0.00 0.00 5.36
890 934 2.047061 TGGCCCTCCGATATATATGCC 58.953 52.381 0.00 10.98 38.13 4.40
891 935 5.683876 ATATGGCCCTCCGATATATATGC 57.316 43.478 0.00 0.00 34.14 3.14
893 937 9.521841 CGATATATATGGCCCTCCGATATATAT 57.478 37.037 21.50 21.50 39.97 0.86
894 938 7.942894 CCGATATATATGGCCCTCCGATATATA 59.057 40.741 16.39 16.39 37.00 0.86
895 939 6.778069 CCGATATATATGGCCCTCCGATATAT 59.222 42.308 13.98 13.98 38.20 0.86
896 940 6.069264 TCCGATATATATGGCCCTCCGATATA 60.069 42.308 0.00 0.86 33.69 0.86
897 941 4.956700 CCGATATATATGGCCCTCCGATAT 59.043 45.833 0.00 0.00 34.14 1.63
898 942 4.043686 TCCGATATATATGGCCCTCCGATA 59.956 45.833 0.00 0.00 34.14 2.92
899 943 3.165875 CCGATATATATGGCCCTCCGAT 58.834 50.000 0.00 0.00 34.14 4.18
900 944 2.176148 TCCGATATATATGGCCCTCCGA 59.824 50.000 0.00 0.00 34.14 4.55
901 945 2.558795 CTCCGATATATATGGCCCTCCG 59.441 54.545 0.00 0.00 34.14 4.63
902 946 2.300437 GCTCCGATATATATGGCCCTCC 59.700 54.545 0.00 0.00 0.00 4.30
935 979 4.393371 TCTGATCTATCGCTGAATACGAGG 59.607 45.833 0.00 0.00 43.74 4.63
996 1047 3.567797 GCCGAGAGCGCCATTGTC 61.568 66.667 2.29 0.00 35.83 3.18
1071 1122 2.254350 GCTTTGCCGGTTCCGAAC 59.746 61.111 13.08 2.37 0.00 3.95
1072 1123 2.981350 GGCTTTGCCGGTTCCGAA 60.981 61.111 13.08 0.00 39.62 4.30
1102 1153 1.402194 GCTGACGACCTTCAGAGTCTG 60.402 57.143 14.36 14.36 45.19 3.51
1103 1154 0.885196 GCTGACGACCTTCAGAGTCT 59.115 55.000 7.57 0.00 45.19 3.24
1209 1260 3.316573 CTGCGAGGGGTCCTTGGTC 62.317 68.421 3.62 0.00 35.62 4.02
1224 1275 1.369625 AGTAACATACGCCTTGCTGC 58.630 50.000 0.00 0.00 0.00 5.25
1492 1543 2.564062 ACGTGCTTAGCCCTACACTTAA 59.436 45.455 0.29 0.00 0.00 1.85
1497 1548 0.037697 CACACGTGCTTAGCCCTACA 60.038 55.000 17.22 0.00 0.00 2.74
1511 1562 4.838152 CCGGCTGGGGATCACACG 62.838 72.222 2.57 0.00 0.00 4.49
1692 1746 0.323816 TCCTGATCGTCCTGAGCACT 60.324 55.000 0.00 0.00 38.27 4.40
1864 1994 5.190677 CAATTAATAACCACTCCCTCCGTT 58.809 41.667 0.00 0.00 0.00 4.44
1865 1995 4.777463 CAATTAATAACCACTCCCTCCGT 58.223 43.478 0.00 0.00 0.00 4.69
1936 2066 8.763984 AGGTACGAGGAGAATTCTAAGATTAA 57.236 34.615 8.25 0.00 0.00 1.40
1939 2069 6.431852 GCTAGGTACGAGGAGAATTCTAAGAT 59.568 42.308 8.25 0.00 0.00 2.40
1949 2079 1.525535 GCCGCTAGGTACGAGGAGA 60.526 63.158 0.00 0.00 40.50 3.71
1998 2128 2.222027 ACTCGAGAAAAGCCACCAAAG 58.778 47.619 21.68 0.00 0.00 2.77
2003 2133 1.940613 ACACAACTCGAGAAAAGCCAC 59.059 47.619 21.68 0.00 0.00 5.01
2015 2145 7.769272 TCCAAAATTTTGATGAACACAACTC 57.231 32.000 28.44 0.00 40.55 3.01
2020 2150 8.816640 ACTACATCCAAAATTTTGATGAACAC 57.183 30.769 29.59 0.00 40.55 3.32
2025 2155 8.702438 GTCACAACTACATCCAAAATTTTGATG 58.298 33.333 28.44 26.59 40.55 3.07
2046 2176 0.542333 TTGAAACGAGTGGGGTCACA 59.458 50.000 0.00 0.00 45.91 3.58
2048 2178 1.124780 TCTTGAAACGAGTGGGGTCA 58.875 50.000 0.00 0.00 0.00 4.02
2082 2212 6.540438 TGTTATCCCTTCGTTGAGAATAGT 57.460 37.500 0.00 0.00 38.34 2.12
2099 2229 3.361414 GAGGCGAGACTACGTTGTTATC 58.639 50.000 3.70 5.31 35.59 1.75
2115 2245 1.438710 CGCAAAAACTCACGAGGCG 60.439 57.895 0.00 0.00 36.93 5.52
2117 2247 1.082104 GCCGCAAAAACTCACGAGG 60.082 57.895 0.00 0.00 0.00 4.63
2122 2252 1.664873 CCATGGCCGCAAAAACTCA 59.335 52.632 0.00 0.00 0.00 3.41
2126 2256 1.375652 CATGCCATGGCCGCAAAAA 60.376 52.632 33.44 13.93 40.22 1.94
2174 2304 5.294734 AGAGGTGTTTTGGCATCAATTTT 57.705 34.783 0.00 0.00 32.28 1.82
2178 2308 3.243367 CGAAAGAGGTGTTTTGGCATCAA 60.243 43.478 0.00 0.00 0.00 2.57
2179 2309 2.293122 CGAAAGAGGTGTTTTGGCATCA 59.707 45.455 0.00 0.00 0.00 3.07
2180 2310 2.552315 TCGAAAGAGGTGTTTTGGCATC 59.448 45.455 0.00 0.00 34.84 3.91
2183 2313 3.643159 ATTCGAAAGAGGTGTTTTGGC 57.357 42.857 0.00 0.00 43.69 4.52
2200 2334 3.569701 TGCCACAAGAAGAGGAACAATTC 59.430 43.478 0.00 0.00 0.00 2.17
2225 2359 0.176910 CCTCTTCTCGAAAGGGCTCC 59.823 60.000 7.27 0.00 0.00 4.70
2237 2371 0.827368 GTCCGAATCAGGCCTCTTCT 59.173 55.000 18.15 0.00 0.00 2.85
2254 2388 1.661112 GAGCATAACTTCAGCCGTGTC 59.339 52.381 0.00 0.00 0.00 3.67
2255 2389 1.676014 GGAGCATAACTTCAGCCGTGT 60.676 52.381 0.00 0.00 0.00 4.49
2256 2390 1.009829 GGAGCATAACTTCAGCCGTG 58.990 55.000 0.00 0.00 0.00 4.94
2257 2391 0.613260 TGGAGCATAACTTCAGCCGT 59.387 50.000 0.00 0.00 27.45 5.68
2258 2392 1.293924 CTGGAGCATAACTTCAGCCG 58.706 55.000 0.00 0.00 45.19 5.52
2262 2396 5.682234 TGATCTTCTGGAGCATAACTTCA 57.318 39.130 0.00 0.00 35.23 3.02
2295 2429 5.929697 GAATTGATCCATAGTTCATCGCA 57.070 39.130 0.00 0.00 0.00 5.10
2368 2502 7.246171 ACAAGAGAGCAGATCCTTAGTTTAA 57.754 36.000 0.00 0.00 0.00 1.52
2508 2648 7.465353 TTGCCTCTTGAATGAATTTATGTGA 57.535 32.000 0.00 0.00 0.00 3.58
2526 2666 4.048504 GGTGTGTGTTGTATTTTTGCCTC 58.951 43.478 0.00 0.00 0.00 4.70
2530 2670 5.164233 TGTGTGGTGTGTGTTGTATTTTTG 58.836 37.500 0.00 0.00 0.00 2.44
2569 2709 3.817709 AAGTTTTTGGACATGGGTGTG 57.182 42.857 0.00 0.00 39.09 3.82


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

AutoCloner maintained by Alex Coulton.