Multiple sequence alignment - TraesCS4A01G208300

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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 TraesCS4A01G208300 chr4A 100.000 2926 0 0 1 2926 501259011 501261936 0.000000e+00 5404.0
1 TraesCS4A01G208300 chr4A 92.676 669 40 9 1 665 624150143 624150806 0.000000e+00 955.0
2 TraesCS4A01G208300 chr4A 90.526 665 51 9 3 664 733583289 733583944 0.000000e+00 869.0
3 TraesCS4A01G208300 chr4A 83.333 72 12 0 1790 1861 55653186 55653115 1.880000e-07 67.6
4 TraesCS4A01G208300 chr5B 91.865 2102 165 5 827 2926 27448508 27446411 0.000000e+00 2929.0
5 TraesCS4A01G208300 chr2D 93.677 854 52 2 1921 2774 10159053 10158202 0.000000e+00 1277.0
6 TraesCS4A01G208300 chr2D 95.159 723 33 2 828 1549 10160263 10159542 0.000000e+00 1140.0
7 TraesCS4A01G208300 chr2D 95.455 220 10 0 1617 1836 10159545 10159326 4.640000e-93 351.0
8 TraesCS4A01G208300 chr2D 98.148 54 1 0 2873 2926 10158207 10158154 8.630000e-16 95.3
9 TraesCS4A01G208300 chr3D 93.083 665 38 7 3 665 576154943 576154285 0.000000e+00 966.0
10 TraesCS4A01G208300 chr3D 91.071 672 51 9 3 669 412658146 412658813 0.000000e+00 900.0
11 TraesCS4A01G208300 chr1D 93.072 664 41 5 3 665 407041069 407041728 0.000000e+00 966.0
12 TraesCS4A01G208300 chr2A 91.604 667 47 7 1 665 509953320 509953979 0.000000e+00 913.0
13 TraesCS4A01G208300 chr2A 90.732 669 53 8 3 665 551515245 551515910 0.000000e+00 883.0
14 TraesCS4A01G208300 chr6B 91.141 666 51 7 4 665 711433284 711432623 0.000000e+00 896.0
15 TraesCS4A01G208300 chr7D 90.841 666 53 7 3 665 247066098 247065438 0.000000e+00 885.0
16 TraesCS4A01G208300 chr4D 97.674 43 1 0 750 792 88476550 88476592 1.120000e-09 75.0


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 TraesCS4A01G208300 chr4A 501259011 501261936 2925 False 5404.000 5404 100.00000 1 2926 1 chr4A.!!$F1 2925
1 TraesCS4A01G208300 chr4A 624150143 624150806 663 False 955.000 955 92.67600 1 665 1 chr4A.!!$F2 664
2 TraesCS4A01G208300 chr4A 733583289 733583944 655 False 869.000 869 90.52600 3 664 1 chr4A.!!$F3 661
3 TraesCS4A01G208300 chr5B 27446411 27448508 2097 True 2929.000 2929 91.86500 827 2926 1 chr5B.!!$R1 2099
4 TraesCS4A01G208300 chr2D 10158154 10160263 2109 True 715.825 1277 95.60975 828 2926 4 chr2D.!!$R1 2098
5 TraesCS4A01G208300 chr3D 576154285 576154943 658 True 966.000 966 93.08300 3 665 1 chr3D.!!$R1 662
6 TraesCS4A01G208300 chr3D 412658146 412658813 667 False 900.000 900 91.07100 3 669 1 chr3D.!!$F1 666
7 TraesCS4A01G208300 chr1D 407041069 407041728 659 False 966.000 966 93.07200 3 665 1 chr1D.!!$F1 662
8 TraesCS4A01G208300 chr2A 509953320 509953979 659 False 913.000 913 91.60400 1 665 1 chr2A.!!$F1 664
9 TraesCS4A01G208300 chr2A 551515245 551515910 665 False 883.000 883 90.73200 3 665 1 chr2A.!!$F2 662
10 TraesCS4A01G208300 chr6B 711432623 711433284 661 True 896.000 896 91.14100 4 665 1 chr6B.!!$R1 661
11 TraesCS4A01G208300 chr7D 247065438 247066098 660 True 885.000 885 90.84100 3 665 1 chr7D.!!$R1 662

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
675 697 0.032217 CCCCAACAGGTATTGCCCAT 60.032 55.0 0.00 0.00 38.26 4.00 F
703 725 0.178992 CCCTCCAGCAGTGTTTGGAA 60.179 55.0 16.17 4.72 42.61 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1889 0.327591 CTCCAGCTTCCTTCCTTGCT 59.672 55.0 0.0 0.0 36.04 3.91 R
1948 2160 0.687757 AGGCTATCGCTCCCACTTCA 60.688 55.0 0.0 0.0 36.09 3.02 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
318 331 2.959201 CCCCCTCCACCATAATCCA 58.041 57.895 0.00 0.00 0.00 3.41
345 361 4.673441 GATCATATCGTAGCGGTGCTTAT 58.327 43.478 0.00 0.00 40.44 1.73
422 439 0.178958 ACTCTCCCTCAACACTCGGT 60.179 55.000 0.00 0.00 0.00 4.69
536 557 1.466192 CGTACGACTACATCAACCGCA 60.466 52.381 10.44 0.00 0.00 5.69
665 687 3.622166 ATTAGTACGTTCCCCAACAGG 57.378 47.619 0.00 0.00 32.14 4.00
666 688 2.014010 TAGTACGTTCCCCAACAGGT 57.986 50.000 0.00 0.00 32.14 4.00
667 689 2.014010 AGTACGTTCCCCAACAGGTA 57.986 50.000 0.00 0.00 32.14 3.08
668 690 2.543635 AGTACGTTCCCCAACAGGTAT 58.456 47.619 0.00 0.00 32.14 2.73
669 691 2.908351 AGTACGTTCCCCAACAGGTATT 59.092 45.455 0.00 0.00 32.14 1.89
670 692 2.194201 ACGTTCCCCAACAGGTATTG 57.806 50.000 0.00 0.00 32.14 1.90
671 693 0.808755 CGTTCCCCAACAGGTATTGC 59.191 55.000 0.00 0.00 32.14 3.56
672 694 1.182667 GTTCCCCAACAGGTATTGCC 58.817 55.000 0.00 0.00 32.14 4.52
673 695 0.040499 TTCCCCAACAGGTATTGCCC 59.960 55.000 0.00 0.00 38.26 5.36
674 696 1.143329 TCCCCAACAGGTATTGCCCA 61.143 55.000 0.00 0.00 38.26 5.36
675 697 0.032217 CCCCAACAGGTATTGCCCAT 60.032 55.000 0.00 0.00 38.26 4.00
676 698 1.113788 CCCAACAGGTATTGCCCATG 58.886 55.000 0.00 0.00 38.26 3.66
677 699 1.341877 CCCAACAGGTATTGCCCATGA 60.342 52.381 0.00 0.00 38.26 3.07
678 700 2.669781 CCAACAGGTATTGCCCATGAT 58.330 47.619 0.00 0.00 38.26 2.45
679 701 3.033184 CCAACAGGTATTGCCCATGATT 58.967 45.455 0.00 0.00 38.26 2.57
680 702 3.451902 CCAACAGGTATTGCCCATGATTT 59.548 43.478 0.00 0.00 38.26 2.17
681 703 4.080975 CCAACAGGTATTGCCCATGATTTT 60.081 41.667 0.00 0.00 38.26 1.82
682 704 4.741321 ACAGGTATTGCCCATGATTTTG 57.259 40.909 0.00 0.00 38.26 2.44
683 705 4.352009 ACAGGTATTGCCCATGATTTTGA 58.648 39.130 0.00 0.00 38.26 2.69
684 706 4.160252 ACAGGTATTGCCCATGATTTTGAC 59.840 41.667 0.00 0.00 38.26 3.18
685 707 3.706086 AGGTATTGCCCATGATTTTGACC 59.294 43.478 0.00 0.00 38.26 4.02
686 708 3.181466 GGTATTGCCCATGATTTTGACCC 60.181 47.826 0.00 0.00 0.00 4.46
687 709 2.323999 TTGCCCATGATTTTGACCCT 57.676 45.000 0.00 0.00 0.00 4.34
688 710 1.851304 TGCCCATGATTTTGACCCTC 58.149 50.000 0.00 0.00 0.00 4.30
689 711 1.114627 GCCCATGATTTTGACCCTCC 58.885 55.000 0.00 0.00 0.00 4.30
690 712 1.619432 GCCCATGATTTTGACCCTCCA 60.619 52.381 0.00 0.00 0.00 3.86
691 713 2.381911 CCCATGATTTTGACCCTCCAG 58.618 52.381 0.00 0.00 0.00 3.86
692 714 1.753073 CCATGATTTTGACCCTCCAGC 59.247 52.381 0.00 0.00 0.00 4.85
693 715 2.449464 CATGATTTTGACCCTCCAGCA 58.551 47.619 0.00 0.00 0.00 4.41
694 716 2.205022 TGATTTTGACCCTCCAGCAG 57.795 50.000 0.00 0.00 0.00 4.24
695 717 1.425066 TGATTTTGACCCTCCAGCAGT 59.575 47.619 0.00 0.00 0.00 4.40
696 718 1.815003 GATTTTGACCCTCCAGCAGTG 59.185 52.381 0.00 0.00 0.00 3.66
697 719 0.550914 TTTTGACCCTCCAGCAGTGT 59.449 50.000 0.00 0.00 0.00 3.55
698 720 0.550914 TTTGACCCTCCAGCAGTGTT 59.449 50.000 0.00 0.00 0.00 3.32
699 721 0.550914 TTGACCCTCCAGCAGTGTTT 59.449 50.000 0.00 0.00 0.00 2.83
700 722 0.179020 TGACCCTCCAGCAGTGTTTG 60.179 55.000 0.00 0.00 0.00 2.93
701 723 0.890996 GACCCTCCAGCAGTGTTTGG 60.891 60.000 8.93 8.93 35.74 3.28
702 724 1.352622 ACCCTCCAGCAGTGTTTGGA 61.353 55.000 15.06 15.06 41.06 3.53
703 725 0.178992 CCCTCCAGCAGTGTTTGGAA 60.179 55.000 16.17 4.72 42.61 3.53
704 726 0.954452 CCTCCAGCAGTGTTTGGAAC 59.046 55.000 16.17 0.00 42.61 3.62
705 727 1.679139 CTCCAGCAGTGTTTGGAACA 58.321 50.000 16.17 0.00 42.61 3.18
718 740 6.951062 TGTTTGGAACACATAAATCTCACA 57.049 33.333 0.00 0.00 39.29 3.58
719 741 7.340122 TGTTTGGAACACATAAATCTCACAA 57.660 32.000 0.00 0.00 39.29 3.33
720 742 7.776107 TGTTTGGAACACATAAATCTCACAAA 58.224 30.769 0.00 0.00 39.29 2.83
721 743 8.420222 TGTTTGGAACACATAAATCTCACAAAT 58.580 29.630 0.00 0.00 39.29 2.32
722 744 9.906660 GTTTGGAACACATAAATCTCACAAATA 57.093 29.630 0.00 0.00 39.29 1.40
726 748 9.736023 GGAACACATAAATCTCACAAATAATCC 57.264 33.333 0.00 0.00 0.00 3.01
768 790 5.875930 GGTAACCCTTGATTCGTTTGTATG 58.124 41.667 0.00 0.00 0.00 2.39
769 791 5.644636 GGTAACCCTTGATTCGTTTGTATGA 59.355 40.000 0.00 0.00 0.00 2.15
770 792 6.149807 GGTAACCCTTGATTCGTTTGTATGAA 59.850 38.462 0.00 0.00 33.97 2.57
771 793 6.642707 AACCCTTGATTCGTTTGTATGAAA 57.357 33.333 0.00 0.00 33.22 2.69
772 794 6.642707 ACCCTTGATTCGTTTGTATGAAAA 57.357 33.333 0.00 0.00 33.22 2.29
773 795 7.045126 ACCCTTGATTCGTTTGTATGAAAAA 57.955 32.000 0.00 0.00 33.22 1.94
793 815 6.894339 AAAAAGTTCTCCGGTTTCATATGT 57.106 33.333 0.00 0.00 0.00 2.29
794 816 6.894339 AAAAGTTCTCCGGTTTCATATGTT 57.106 33.333 0.00 0.00 0.00 2.71
795 817 5.880054 AAGTTCTCCGGTTTCATATGTTG 57.120 39.130 0.00 0.00 0.00 3.33
796 818 4.906618 AGTTCTCCGGTTTCATATGTTGT 58.093 39.130 0.00 0.00 0.00 3.32
797 819 4.935808 AGTTCTCCGGTTTCATATGTTGTC 59.064 41.667 0.00 0.00 0.00 3.18
798 820 4.545208 TCTCCGGTTTCATATGTTGTCA 57.455 40.909 0.00 0.00 0.00 3.58
799 821 4.900684 TCTCCGGTTTCATATGTTGTCAA 58.099 39.130 0.00 0.00 0.00 3.18
800 822 4.693566 TCTCCGGTTTCATATGTTGTCAAC 59.306 41.667 8.86 8.86 0.00 3.18
801 823 4.390264 TCCGGTTTCATATGTTGTCAACA 58.610 39.130 20.28 20.28 46.94 3.33
802 824 4.214545 TCCGGTTTCATATGTTGTCAACAC 59.785 41.667 20.41 6.16 45.50 3.32
803 825 4.023622 CCGGTTTCATATGTTGTCAACACA 60.024 41.667 20.41 10.08 45.50 3.72
804 826 5.335583 CCGGTTTCATATGTTGTCAACACAT 60.336 40.000 20.41 12.16 45.50 3.21
805 827 6.128145 CCGGTTTCATATGTTGTCAACACATA 60.128 38.462 20.41 10.61 45.50 2.29
806 828 7.301789 CGGTTTCATATGTTGTCAACACATAA 58.698 34.615 20.41 9.87 45.50 1.90
807 829 7.967854 CGGTTTCATATGTTGTCAACACATAAT 59.032 33.333 20.41 7.23 45.50 1.28
808 830 9.289303 GGTTTCATATGTTGTCAACACATAATC 57.711 33.333 20.41 4.01 45.50 1.75
811 833 8.130307 TCATATGTTGTCAACACATAATCTCG 57.870 34.615 20.41 2.34 45.50 4.04
812 834 5.801350 ATGTTGTCAACACATAATCTCGG 57.199 39.130 20.41 0.00 45.50 4.63
813 835 4.000325 TGTTGTCAACACATAATCTCGGG 59.000 43.478 14.48 0.00 36.25 5.14
814 836 4.250464 GTTGTCAACACATAATCTCGGGA 58.750 43.478 10.93 0.00 30.55 5.14
815 837 4.753516 TGTCAACACATAATCTCGGGAT 57.246 40.909 0.00 0.00 0.00 3.85
816 838 5.862678 TGTCAACACATAATCTCGGGATA 57.137 39.130 0.00 0.00 0.00 2.59
817 839 5.842907 TGTCAACACATAATCTCGGGATAG 58.157 41.667 0.00 0.00 0.00 2.08
818 840 5.221441 TGTCAACACATAATCTCGGGATAGG 60.221 44.000 0.00 0.00 0.00 2.57
819 841 5.010719 GTCAACACATAATCTCGGGATAGGA 59.989 44.000 0.00 0.00 0.00 2.94
820 842 5.243954 TCAACACATAATCTCGGGATAGGAG 59.756 44.000 0.00 0.00 0.00 3.69
821 843 3.511934 ACACATAATCTCGGGATAGGAGC 59.488 47.826 0.00 0.00 0.00 4.70
822 844 3.511540 CACATAATCTCGGGATAGGAGCA 59.488 47.826 0.00 0.00 0.00 4.26
823 845 3.511934 ACATAATCTCGGGATAGGAGCAC 59.488 47.826 0.00 0.00 0.00 4.40
824 846 2.088104 AATCTCGGGATAGGAGCACA 57.912 50.000 0.00 0.00 0.00 4.57
825 847 2.088104 ATCTCGGGATAGGAGCACAA 57.912 50.000 0.00 0.00 0.00 3.33
870 892 1.807981 CGTTCTGGTGCGGCGATTA 60.808 57.895 12.98 0.00 0.00 1.75
873 895 2.202690 CTGGTGCGGCGATTACGA 60.203 61.111 12.98 2.29 42.66 3.43
880 902 3.306634 GGCGATTACGAAGGCGAC 58.693 61.111 0.00 0.00 42.66 5.19
911 933 1.626356 CCCTCATTCCTTCCTCGGCA 61.626 60.000 0.00 0.00 0.00 5.69
921 943 1.691195 TTCCTCGGCAGACCAACACA 61.691 55.000 0.00 0.00 34.57 3.72
928 950 1.555075 GGCAGACCAACACAGGATCTA 59.445 52.381 0.00 0.00 35.26 1.98
1048 1071 0.799534 GCGCACGGTCGTAATACACT 60.800 55.000 0.30 0.00 0.00 3.55
1062 1085 6.835488 TCGTAATACACTCATAAACCCTAGGT 59.165 38.462 8.29 0.00 37.65 3.08
1064 1087 7.201848 CGTAATACACTCATAAACCCTAGGTGA 60.202 40.741 8.29 3.37 35.34 4.02
1069 1092 5.187967 CACTCATAAACCCTAGGTGAAGAGT 59.812 44.000 8.29 10.01 35.97 3.24
1070 1093 6.380274 CACTCATAAACCCTAGGTGAAGAGTA 59.620 42.308 8.29 0.00 34.81 2.59
1101 1124 0.755698 GCGGTGATGGAGGGAGTAGA 60.756 60.000 0.00 0.00 0.00 2.59
1231 1254 1.593787 CTTCTCCGAGAAGCTGGCA 59.406 57.895 22.24 0.00 44.35 4.92
1237 1260 2.431683 GAGAAGCTGGCACACCCA 59.568 61.111 0.00 0.00 42.79 4.51
1274 1297 1.410153 CTCTTGGCAAAGTTTGGTGCT 59.590 47.619 17.11 0.00 40.70 4.40
1315 1339 1.232909 AGGAGGTAGGGGAGAATCGA 58.767 55.000 0.00 0.00 34.37 3.59
1453 1477 5.163854 GGAGGAGTATGAATTCAACAACACG 60.164 44.000 13.09 0.00 0.00 4.49
1489 1513 1.703513 GTCTACAACCTTCCCTTGGGT 59.296 52.381 5.51 0.00 37.44 4.51
1549 1573 0.901827 TCGGCCAGTTCATAGAAGCA 59.098 50.000 2.24 0.00 0.00 3.91
1585 1609 2.026262 TGGGAGTGCAATAGGGAAGTTC 60.026 50.000 0.00 0.00 0.00 3.01
1702 1726 6.350696 GGAGGATGAGAGATGATGAAGATGAG 60.351 46.154 0.00 0.00 0.00 2.90
1714 1738 0.987294 AAGATGAGAGTGGGTGGTGG 59.013 55.000 0.00 0.00 0.00 4.61
1744 1768 7.386851 TCGAGTATGAATTTCTTCCAGACTTT 58.613 34.615 0.00 0.00 0.00 2.66
1766 1790 2.498078 TGTTATACATGTGGTCGGCTCA 59.502 45.455 9.11 0.00 0.00 4.26
1798 1822 6.017109 GCAAAAAGGACTGTGAGATCAAACTA 60.017 38.462 0.00 0.00 0.00 2.24
1864 1889 2.039831 GGGCATAGGAGGGGGTGA 60.040 66.667 0.00 0.00 0.00 4.02
1867 1892 2.072487 GCATAGGAGGGGGTGAGCA 61.072 63.158 0.00 0.00 0.00 4.26
1888 1913 1.203364 AGGAAGGAAGCTGGAGGAGAA 60.203 52.381 0.00 0.00 0.00 2.87
1904 1929 2.490168 GGAGAAGAGGTAGGGAGCTAGG 60.490 59.091 0.00 0.00 32.11 3.02
1913 1938 5.477913 AGGTAGGGAGCTAGGAAATAACAT 58.522 41.667 0.00 0.00 0.00 2.71
1917 1942 4.068599 GGGAGCTAGGAAATAACATGAGC 58.931 47.826 0.00 0.00 0.00 4.26
1926 2138 5.476945 AGGAAATAACATGAGCTTCGGTTTT 59.523 36.000 0.00 0.00 0.00 2.43
1948 2160 0.108329 CCGTTCAAGCGGTAGGACAT 60.108 55.000 0.00 0.00 46.11 3.06
1987 2199 4.113815 CATGGCGGAAGGAGGGCA 62.114 66.667 0.00 0.00 43.20 5.36
2067 2279 4.244862 CGGCAAAGAATAAACAGGCAATT 58.755 39.130 0.00 0.00 0.00 2.32
2124 2336 2.736826 GGGCTCGGAGGAAAGGAGG 61.737 68.421 7.20 0.00 0.00 4.30
2294 2506 1.531149 CCAGGAACACTAACAGCAACG 59.469 52.381 0.00 0.00 0.00 4.10
2308 2520 2.817258 CAGCAACGAAAACCCTAATGGA 59.183 45.455 0.00 0.00 38.00 3.41
2330 2542 1.905894 AGAAGTTCAAGAGGAGGGAGC 59.094 52.381 5.50 0.00 0.00 4.70
2360 2572 0.331616 GTCCCCTTGCCCTAACACAT 59.668 55.000 0.00 0.00 0.00 3.21
2365 2577 2.771943 CCCTTGCCCTAACACATAGAGA 59.228 50.000 0.00 0.00 33.04 3.10
2400 2612 2.742053 GGCAGAAACGAAGCATCAGTAA 59.258 45.455 0.00 0.00 0.00 2.24
2405 2617 6.475727 GCAGAAACGAAGCATCAGTAATAGTA 59.524 38.462 0.00 0.00 0.00 1.82
2433 2645 4.695455 CGAGAATGAAGCTAAAAAGGGACA 59.305 41.667 0.00 0.00 0.00 4.02
2491 2703 4.022068 GCAACAGATCAGGGTGAATTGAAA 60.022 41.667 6.62 0.00 0.00 2.69
2570 2782 6.540914 CCGGGAACAATGAAAATAGTAAGCTA 59.459 38.462 0.00 0.00 0.00 3.32
2583 2796 1.335132 TAAGCTAGAACTGCCGGGGG 61.335 60.000 2.18 0.00 0.00 5.40
2609 2822 2.675075 CGGCCCGGTGGTTCAAAT 60.675 61.111 0.00 0.00 0.00 2.32
2639 2852 1.531981 ATGGGGAGAGTGGAGGACCT 61.532 60.000 0.00 0.00 37.04 3.85
2693 2906 5.302568 TGACGGAAAAGGAACTAGACAAGTA 59.697 40.000 0.00 0.00 38.49 2.24
2735 2948 0.395311 CAGATGCTTGCATGGGACCT 60.395 55.000 13.18 0.59 0.00 3.85
2784 2997 0.112412 TTTGGAGAAGGGGGCTGAAC 59.888 55.000 0.00 0.00 0.00 3.18
2794 3007 0.107643 GGGGCTGAACCTATCTCTGC 59.892 60.000 0.00 0.00 39.10 4.26
2820 3033 4.630644 CTATGGTAGGAGGCATGTTGAT 57.369 45.455 0.00 0.00 0.00 2.57
2831 3044 4.021229 AGGCATGTTGATGTTGATGTGAT 58.979 39.130 0.00 0.00 31.50 3.06
2846 3059 6.312141 TGATGTGATAGAAGAACATGGGAA 57.688 37.500 0.00 0.00 34.74 3.97
2850 3063 6.962182 TGTGATAGAAGAACATGGGAAGATT 58.038 36.000 0.00 0.00 0.00 2.40
2871 3084 1.294459 GAGGTTGACGGGGGTGTAC 59.706 63.158 0.00 0.00 0.00 2.90
2922 3135 6.043243 AGGAGACTTGGAGAACAATCAAACTA 59.957 38.462 0.00 0.00 37.44 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.308497 TCCTAACCATGAACAAGGAGTTGTA 59.692 40.000 3.07 0.00 46.68 2.41
358 374 4.278419 TGACGATGATGATGTTCTACGGAT 59.722 41.667 0.00 0.00 0.00 4.18
361 377 3.731216 GGTGACGATGATGATGTTCTACG 59.269 47.826 0.00 0.00 0.00 3.51
422 439 1.278127 GTCCCTCGAACTCCAATCCAA 59.722 52.381 0.00 0.00 0.00 3.53
649 671 3.004862 CAATACCTGTTGGGGAACGTAC 58.995 50.000 0.00 0.00 40.03 3.67
665 687 3.706086 AGGGTCAAAATCATGGGCAATAC 59.294 43.478 0.00 0.00 0.00 1.89
666 688 3.960102 GAGGGTCAAAATCATGGGCAATA 59.040 43.478 0.00 0.00 0.00 1.90
667 689 2.767960 GAGGGTCAAAATCATGGGCAAT 59.232 45.455 0.00 0.00 0.00 3.56
668 690 2.178580 GAGGGTCAAAATCATGGGCAA 58.821 47.619 0.00 0.00 0.00 4.52
669 691 1.619432 GGAGGGTCAAAATCATGGGCA 60.619 52.381 0.00 0.00 0.00 5.36
670 692 1.114627 GGAGGGTCAAAATCATGGGC 58.885 55.000 0.00 0.00 0.00 5.36
671 693 2.381911 CTGGAGGGTCAAAATCATGGG 58.618 52.381 0.00 0.00 0.00 4.00
672 694 1.753073 GCTGGAGGGTCAAAATCATGG 59.247 52.381 0.00 0.00 0.00 3.66
673 695 2.426024 CTGCTGGAGGGTCAAAATCATG 59.574 50.000 0.00 0.00 0.00 3.07
674 696 2.042162 ACTGCTGGAGGGTCAAAATCAT 59.958 45.455 0.14 0.00 0.00 2.45
675 697 1.425066 ACTGCTGGAGGGTCAAAATCA 59.575 47.619 0.14 0.00 0.00 2.57
676 698 1.815003 CACTGCTGGAGGGTCAAAATC 59.185 52.381 0.14 0.00 0.00 2.17
677 699 1.145738 ACACTGCTGGAGGGTCAAAAT 59.854 47.619 0.00 0.00 29.32 1.82
678 700 0.550914 ACACTGCTGGAGGGTCAAAA 59.449 50.000 0.00 0.00 29.32 2.44
679 701 0.550914 AACACTGCTGGAGGGTCAAA 59.449 50.000 4.02 0.00 37.31 2.69
680 702 0.550914 AAACACTGCTGGAGGGTCAA 59.449 50.000 4.02 0.00 37.31 3.18
681 703 0.179020 CAAACACTGCTGGAGGGTCA 60.179 55.000 4.02 0.00 37.31 4.02
682 704 0.890996 CCAAACACTGCTGGAGGGTC 60.891 60.000 4.02 0.00 37.31 4.46
683 705 1.151450 CCAAACACTGCTGGAGGGT 59.849 57.895 0.00 0.00 41.62 4.34
684 706 0.178992 TTCCAAACACTGCTGGAGGG 60.179 55.000 0.00 0.00 42.61 4.30
685 707 0.954452 GTTCCAAACACTGCTGGAGG 59.046 55.000 0.14 0.00 42.61 4.30
686 708 1.679139 TGTTCCAAACACTGCTGGAG 58.321 50.000 0.00 0.00 42.61 3.86
687 709 3.892633 TGTTCCAAACACTGCTGGA 57.107 47.368 0.00 0.00 40.03 3.86
695 717 6.951062 TGTGAGATTTATGTGTTCCAAACA 57.049 33.333 0.00 0.00 39.52 2.83
696 718 8.816640 ATTTGTGAGATTTATGTGTTCCAAAC 57.183 30.769 0.00 0.00 0.00 2.93
700 722 9.736023 GGATTATTTGTGAGATTTATGTGTTCC 57.264 33.333 0.00 0.00 0.00 3.62
744 766 3.151554 ACAAACGAATCAAGGGTTACCC 58.848 45.455 13.56 13.56 45.90 3.69
745 767 5.644636 TCATACAAACGAATCAAGGGTTACC 59.355 40.000 0.00 0.00 0.00 2.85
746 768 6.730960 TCATACAAACGAATCAAGGGTTAC 57.269 37.500 0.00 0.00 0.00 2.50
747 769 7.747155 TTTCATACAAACGAATCAAGGGTTA 57.253 32.000 0.00 0.00 0.00 2.85
748 770 6.642707 TTTCATACAAACGAATCAAGGGTT 57.357 33.333 0.00 0.00 0.00 4.11
749 771 6.642707 TTTTCATACAAACGAATCAAGGGT 57.357 33.333 0.00 0.00 0.00 4.34
770 792 6.894339 ACATATGAAACCGGAGAACTTTTT 57.106 33.333 9.46 0.00 0.00 1.94
771 793 6.264518 ACAACATATGAAACCGGAGAACTTTT 59.735 34.615 9.46 0.00 0.00 2.27
772 794 5.768164 ACAACATATGAAACCGGAGAACTTT 59.232 36.000 9.46 0.00 0.00 2.66
773 795 5.313712 ACAACATATGAAACCGGAGAACTT 58.686 37.500 9.46 0.00 0.00 2.66
774 796 4.906618 ACAACATATGAAACCGGAGAACT 58.093 39.130 9.46 0.00 0.00 3.01
775 797 4.693566 TGACAACATATGAAACCGGAGAAC 59.306 41.667 9.46 0.00 0.00 3.01
776 798 4.900684 TGACAACATATGAAACCGGAGAA 58.099 39.130 9.46 0.00 0.00 2.87
777 799 4.545208 TGACAACATATGAAACCGGAGA 57.455 40.909 9.46 0.00 0.00 3.71
778 800 4.454161 TGTTGACAACATATGAAACCGGAG 59.546 41.667 17.02 0.00 36.25 4.63
779 801 4.214545 GTGTTGACAACATATGAAACCGGA 59.785 41.667 23.14 0.00 44.35 5.14
780 802 4.023622 TGTGTTGACAACATATGAAACCGG 60.024 41.667 23.14 0.00 44.35 5.28
781 803 5.102020 TGTGTTGACAACATATGAAACCG 57.898 39.130 23.14 0.00 44.35 4.44
782 804 9.289303 GATTATGTGTTGACAACATATGAAACC 57.711 33.333 30.06 16.81 42.23 3.27
785 807 8.603181 CGAGATTATGTGTTGACAACATATGAA 58.397 33.333 30.06 21.90 42.23 2.57
786 808 7.224557 CCGAGATTATGTGTTGACAACATATGA 59.775 37.037 30.06 25.08 42.23 2.15
787 809 7.347448 CCGAGATTATGTGTTGACAACATATG 58.653 38.462 30.06 17.35 42.23 1.78
788 810 6.483307 CCCGAGATTATGTGTTGACAACATAT 59.517 38.462 27.04 27.04 44.35 1.78
789 811 5.815222 CCCGAGATTATGTGTTGACAACATA 59.185 40.000 23.14 20.74 44.35 2.29
790 812 4.635765 CCCGAGATTATGTGTTGACAACAT 59.364 41.667 23.14 11.50 44.35 2.71
791 813 4.000325 CCCGAGATTATGTGTTGACAACA 59.000 43.478 17.02 17.02 39.52 3.33
792 814 4.250464 TCCCGAGATTATGTGTTGACAAC 58.750 43.478 11.54 11.54 35.11 3.32
793 815 4.545208 TCCCGAGATTATGTGTTGACAA 57.455 40.909 0.00 0.00 35.11 3.18
794 816 4.753516 ATCCCGAGATTATGTGTTGACA 57.246 40.909 0.00 0.00 36.22 3.58
795 817 5.010719 TCCTATCCCGAGATTATGTGTTGAC 59.989 44.000 0.00 0.00 33.67 3.18
796 818 5.144832 TCCTATCCCGAGATTATGTGTTGA 58.855 41.667 0.00 0.00 33.67 3.18
797 819 5.468540 TCCTATCCCGAGATTATGTGTTG 57.531 43.478 0.00 0.00 33.67 3.33
798 820 4.021016 GCTCCTATCCCGAGATTATGTGTT 60.021 45.833 0.00 0.00 33.67 3.32
799 821 3.511934 GCTCCTATCCCGAGATTATGTGT 59.488 47.826 0.00 0.00 33.67 3.72
800 822 3.511540 TGCTCCTATCCCGAGATTATGTG 59.488 47.826 0.00 0.00 33.67 3.21
801 823 3.511934 GTGCTCCTATCCCGAGATTATGT 59.488 47.826 0.00 0.00 33.67 2.29
802 824 3.511540 TGTGCTCCTATCCCGAGATTATG 59.488 47.826 0.00 0.00 33.67 1.90
803 825 3.779444 TGTGCTCCTATCCCGAGATTAT 58.221 45.455 0.00 0.00 33.67 1.28
804 826 3.238788 TGTGCTCCTATCCCGAGATTA 57.761 47.619 0.00 0.00 33.67 1.75
805 827 2.088104 TGTGCTCCTATCCCGAGATT 57.912 50.000 0.00 0.00 33.67 2.40
806 828 1.967066 CTTGTGCTCCTATCCCGAGAT 59.033 52.381 0.00 0.00 36.44 2.75
807 829 1.403814 CTTGTGCTCCTATCCCGAGA 58.596 55.000 0.00 0.00 0.00 4.04
808 830 0.390860 CCTTGTGCTCCTATCCCGAG 59.609 60.000 0.00 0.00 0.00 4.63
809 831 0.325296 ACCTTGTGCTCCTATCCCGA 60.325 55.000 0.00 0.00 0.00 5.14
810 832 0.105039 GACCTTGTGCTCCTATCCCG 59.895 60.000 0.00 0.00 0.00 5.14
811 833 0.470341 GGACCTTGTGCTCCTATCCC 59.530 60.000 0.00 0.00 0.00 3.85
812 834 0.105039 CGGACCTTGTGCTCCTATCC 59.895 60.000 0.00 0.00 0.00 2.59
813 835 0.824759 ACGGACCTTGTGCTCCTATC 59.175 55.000 0.00 0.00 0.00 2.08
814 836 0.824759 GACGGACCTTGTGCTCCTAT 59.175 55.000 0.00 0.00 0.00 2.57
815 837 1.255667 GGACGGACCTTGTGCTCCTA 61.256 60.000 0.00 0.00 35.41 2.94
816 838 2.584391 GGACGGACCTTGTGCTCCT 61.584 63.158 0.00 0.00 35.41 3.69
817 839 2.047179 GGACGGACCTTGTGCTCC 60.047 66.667 0.00 0.00 35.41 4.70
818 840 2.047179 GGGACGGACCTTGTGCTC 60.047 66.667 0.00 0.00 38.98 4.26
886 908 1.221840 GAAGGAATGAGGGCTCGCA 59.778 57.895 0.00 0.00 0.00 5.10
897 919 0.909610 TGGTCTGCCGAGGAAGGAAT 60.910 55.000 0.00 0.00 37.67 3.01
911 933 3.041946 GGGATAGATCCTGTGTTGGTCT 58.958 50.000 8.45 0.00 46.35 3.85
928 950 3.178611 GCCGGGAAGGATGGGGAT 61.179 66.667 2.18 0.00 45.00 3.85
956 978 2.532256 CGATCTACGCCGACGACCT 61.532 63.158 0.00 0.00 43.93 3.85
1048 1071 5.897824 CCTACTCTTCACCTAGGGTTTATGA 59.102 44.000 14.81 4.16 31.02 2.15
1062 1085 0.640495 CCCCTACCCCCTACTCTTCA 59.360 60.000 0.00 0.00 0.00 3.02
1064 1087 2.033831 CCCCCTACCCCCTACTCTT 58.966 63.158 0.00 0.00 0.00 2.85
1101 1124 2.451294 GCCCCCTCATCATCCCCT 60.451 66.667 0.00 0.00 0.00 4.79
1200 1223 0.955919 GGAGAAGAGTTTGCCCACCG 60.956 60.000 0.00 0.00 0.00 4.94
1231 1254 2.238144 CAAGGAGATCACATCTGGGTGT 59.762 50.000 0.00 0.00 40.38 4.16
1237 1260 4.161942 CCAAGAGACAAGGAGATCACATCT 59.838 45.833 0.00 0.00 43.70 2.90
1242 1265 2.259917 TGCCAAGAGACAAGGAGATCA 58.740 47.619 0.00 0.00 0.00 2.92
1274 1297 5.302059 CCTTACAGTCTATCCCTTTGATCGA 59.698 44.000 0.00 0.00 34.76 3.59
1315 1339 3.773860 TGCAAGAACGTGAACACAAAT 57.226 38.095 5.80 0.00 0.00 2.32
1453 1477 1.212751 GACTCGCACCCAAATTGGC 59.787 57.895 6.48 0.00 35.79 4.52
1489 1513 3.795877 TGCTGATTCTGCGTTCATCATA 58.204 40.909 10.45 0.00 0.00 2.15
1561 1585 1.891933 TCCCTATTGCACTCCCATCA 58.108 50.000 0.00 0.00 0.00 3.07
1585 1609 7.338710 TCCTCATTCTTACTTTGACCCTAATG 58.661 38.462 0.00 0.00 0.00 1.90
1642 1666 2.466547 TCTGCTCATCATCCTCCTCA 57.533 50.000 0.00 0.00 0.00 3.86
1702 1726 1.375326 GAACCTCCACCACCCACTC 59.625 63.158 0.00 0.00 0.00 3.51
1714 1738 6.106673 TGGAAGAAATTCATACTCGAACCTC 58.893 40.000 0.00 0.00 0.00 3.85
1744 1768 3.055747 TGAGCCGACCACATGTATAACAA 60.056 43.478 0.00 0.00 0.00 2.83
1766 1790 2.821969 CACAGTCCTTTTTGCTATGCCT 59.178 45.455 0.00 0.00 0.00 4.75
1798 1822 2.058675 CGGTGTCTCCCCTTTCTGT 58.941 57.895 0.00 0.00 0.00 3.41
1864 1889 0.327591 CTCCAGCTTCCTTCCTTGCT 59.672 55.000 0.00 0.00 36.04 3.91
1867 1892 1.203364 TCTCCTCCAGCTTCCTTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
1888 1913 5.149239 GTTATTTCCTAGCTCCCTACCTCT 58.851 45.833 0.00 0.00 0.00 3.69
1904 1929 6.469275 GCTAAAACCGAAGCTCATGTTATTTC 59.531 38.462 0.00 0.00 35.80 2.17
1941 2153 0.824109 CGCTCCCACTTCATGTCCTA 59.176 55.000 0.00 0.00 0.00 2.94
1948 2160 0.687757 AGGCTATCGCTCCCACTTCA 60.688 55.000 0.00 0.00 36.09 3.02
1987 2199 2.683933 ATCGCCACTTCCCCTCGT 60.684 61.111 0.00 0.00 0.00 4.18
2049 2261 5.609423 TGTGCAATTGCCTGTTTATTCTTT 58.391 33.333 26.94 0.00 41.18 2.52
2067 2279 2.668632 GGGACTCCCGAATGTGCA 59.331 61.111 0.00 0.00 32.13 4.57
2100 2312 2.169590 TTTCCTCCGAGCCCTCCTCT 62.170 60.000 0.00 0.00 38.49 3.69
2294 2506 7.284919 TGAACTTCTTTCCATTAGGGTTTTC 57.715 36.000 0.00 0.00 38.11 2.29
2308 2520 3.244735 GCTCCCTCCTCTTGAACTTCTTT 60.245 47.826 0.00 0.00 0.00 2.52
2360 2572 1.146774 CCCCAGGATCTGCTCTCTCTA 59.853 57.143 0.00 0.00 0.00 2.43
2365 2577 2.041762 TGCCCCAGGATCTGCTCT 59.958 61.111 0.00 0.00 0.00 4.09
2400 2612 7.569639 TTAGCTTCATTCTCGTCACTACTAT 57.430 36.000 0.00 0.00 0.00 2.12
2405 2617 5.409826 CCTTTTTAGCTTCATTCTCGTCACT 59.590 40.000 0.00 0.00 0.00 3.41
2433 2645 1.692042 CCCTCCATGCCCTCACTCT 60.692 63.158 0.00 0.00 0.00 3.24
2491 2703 2.540265 CAGAGTTGGTCTGCTTGTCT 57.460 50.000 0.00 0.00 46.41 3.41
2544 2756 5.124936 GCTTACTATTTTCATTGTTCCCGGT 59.875 40.000 0.00 0.00 0.00 5.28
2570 2782 3.966543 CCAACCCCCGGCAGTTCT 61.967 66.667 0.00 0.00 0.00 3.01
2589 2802 2.335092 TTTGAACCACCGGGCCGTTA 62.335 55.000 26.32 0.00 37.90 3.18
2600 2813 5.011943 CCCATTTCAAGGAGAATTTGAACCA 59.988 40.000 0.31 0.00 42.44 3.67
2639 2852 8.162878 AGTTTCCGATATAAAGAGTACATCGA 57.837 34.615 10.14 0.00 40.62 3.59
2693 2906 7.293771 TCTGAGTTAGACCTAGAGACCATCTAT 59.706 40.741 0.00 0.00 39.82 1.98
2735 2948 1.000019 CCCCTACTCCGTCCAGTCA 60.000 63.158 0.00 0.00 0.00 3.41
2784 2997 3.360867 ACCATAGGATCGCAGAGATAGG 58.639 50.000 0.00 0.00 43.63 2.57
2815 3028 8.032952 TGTTCTTCTATCACATCAACATCAAC 57.967 34.615 0.00 0.00 0.00 3.18
2820 3033 5.882000 CCCATGTTCTTCTATCACATCAACA 59.118 40.000 0.00 0.00 0.00 3.33
2831 3044 6.387192 TCCAAATCTTCCCATGTTCTTCTA 57.613 37.500 0.00 0.00 0.00 2.10
2846 3059 0.328258 CCCCGTCAACCTCCAAATCT 59.672 55.000 0.00 0.00 0.00 2.40
2850 3063 2.448931 ACCCCCGTCAACCTCCAA 60.449 61.111 0.00 0.00 0.00 3.53
2871 3084 2.223782 CCTCTCTGCTTCTGATTCTCCG 60.224 54.545 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.