Multiple sequence alignment - TraesCS1B01G070600

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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 TraesCS1B01G070600 chr1B 100.000 3235 0 0 1 3235 55966357 55969591 0.000000e+00 5975.0
1 TraesCS1B01G070600 chr1B 95.610 2392 59 11 876 3235 56010374 56012751 0.000000e+00 3794.0
2 TraesCS1B01G070600 chr1B 97.595 1497 15 4 1758 3235 55990095 55991589 0.000000e+00 2545.0
3 TraesCS1B01G070600 chr1B 92.752 1628 95 10 894 2514 55950754 55952365 0.000000e+00 2331.0
4 TraesCS1B01G070600 chr1B 94.000 950 52 3 1568 2514 55940163 55941110 0.000000e+00 1434.0
5 TraesCS1B01G070600 chr1B 90.617 746 46 10 2512 3235 55941227 55941970 0.000000e+00 968.0
6 TraesCS1B01G070600 chr1B 90.483 746 46 12 2512 3235 55952482 55953224 0.000000e+00 961.0
7 TraesCS1B01G070600 chr1B 95.320 406 7 1 876 1281 55989139 55989532 4.550000e-178 634.0
8 TraesCS1B01G070600 chr1B 92.012 338 15 2 894 1231 55939463 55939788 6.320000e-127 464.0
9 TraesCS1B01G070600 chr1B 90.189 265 22 3 1380 1640 55989842 55990106 3.090000e-90 342.0
10 TraesCS1B01G070600 chr1B 95.522 67 3 0 791 857 55935593 55935659 1.230000e-19 108.0
11 TraesCS1B01G070600 chr1B 98.214 56 1 0 801 856 55988982 55989037 7.390000e-17 99.0
12 TraesCS1B01G070600 chr1B 96.364 55 2 0 802 856 56010240 56010294 1.240000e-14 91.6
13 TraesCS1B01G070600 chr1D 91.723 2066 134 17 1040 3082 36307969 36310020 0.000000e+00 2833.0
14 TraesCS1B01G070600 chr1D 93.789 161 9 1 3075 3235 36311154 36311313 1.160000e-59 241.0
15 TraesCS1B01G070600 chr1D 96.226 106 1 1 894 999 36307866 36307968 1.540000e-38 171.0
16 TraesCS1B01G070600 chr1D 96.471 85 3 0 801 885 36307688 36307772 1.210000e-29 141.0
17 TraesCS1B01G070600 chr1A 92.938 1671 104 10 1086 2745 35529301 35530968 0.000000e+00 2420.0
18 TraesCS1B01G070600 chr1A 92.729 1389 79 6 876 2258 35491162 35492534 0.000000e+00 1986.0
19 TraesCS1B01G070600 chr1A 87.203 758 59 9 2254 2975 35498654 35499409 0.000000e+00 828.0
20 TraesCS1B01G070600 chr1A 91.051 447 38 1 2789 3235 35531141 35531585 1.280000e-168 603.0
21 TraesCS1B01G070600 chr1A 92.012 338 15 2 894 1231 35528823 35529148 6.320000e-127 464.0
22 TraesCS1B01G070600 chr1A 96.364 55 2 0 802 856 35491029 35491083 1.240000e-14 91.6
23 TraesCS1B01G070600 chr5A 80.769 546 78 23 12 545 102999636 102999106 5.030000e-108 401.0
24 TraesCS1B01G070600 chr5A 79.757 494 79 15 1 484 102999603 102999121 4.000000e-89 339.0
25 TraesCS1B01G070600 chr5A 78.158 467 75 22 1 461 2390620 2390175 4.110000e-69 272.0
26 TraesCS1B01G070600 chr7D 79.070 516 82 20 5 507 59394805 59394303 6.690000e-87 331.0
27 TraesCS1B01G070600 chr7D 78.226 496 82 18 6 488 59394760 59394278 8.780000e-76 294.0
28 TraesCS1B01G070600 chr3B 80.841 428 62 14 119 538 96830500 96830085 5.210000e-83 318.0
29 TraesCS1B01G070600 chr3B 78.689 366 58 15 182 538 457158369 457158723 3.250000e-55 226.0
30 TraesCS1B01G070600 chr2D 80.186 429 65 15 119 538 625626287 625626704 1.460000e-78 303.0
31 TraesCS1B01G070600 chr6B 76.514 545 103 20 1 536 26543351 26542823 1.140000e-69 274.0
32 TraesCS1B01G070600 chr2B 75.874 572 103 28 4 568 585707184 585707727 3.200000e-65 259.0


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 TraesCS1B01G070600 chr1B 55966357 55969591 3234 False 5975.000000 5975 100.000000 1 3235 1 chr1B.!!$F1 3234
1 TraesCS1B01G070600 chr1B 56010240 56012751 2511 False 1942.800000 3794 95.987000 802 3235 2 chr1B.!!$F5 2433
2 TraesCS1B01G070600 chr1B 55950754 55953224 2470 False 1646.000000 2331 91.617500 894 3235 2 chr1B.!!$F3 2341
3 TraesCS1B01G070600 chr1B 55988982 55991589 2607 False 905.000000 2545 95.329500 801 3235 4 chr1B.!!$F4 2434
4 TraesCS1B01G070600 chr1B 55935593 55941970 6377 False 743.500000 1434 93.037750 791 3235 4 chr1B.!!$F2 2444
5 TraesCS1B01G070600 chr1D 36307688 36311313 3625 False 846.500000 2833 94.552250 801 3235 4 chr1D.!!$F1 2434
6 TraesCS1B01G070600 chr1A 35528823 35531585 2762 False 1162.333333 2420 92.000333 894 3235 3 chr1A.!!$F3 2341
7 TraesCS1B01G070600 chr1A 35491029 35492534 1505 False 1038.800000 1986 94.546500 802 2258 2 chr1A.!!$F2 1456
8 TraesCS1B01G070600 chr1A 35498654 35499409 755 False 828.000000 828 87.203000 2254 2975 1 chr1A.!!$F1 721
9 TraesCS1B01G070600 chr5A 102999106 102999636 530 True 370.000000 401 80.263000 1 545 2 chr5A.!!$R2 544
10 TraesCS1B01G070600 chr7D 59394278 59394805 527 True 312.500000 331 78.648000 5 507 2 chr7D.!!$R1 502
11 TraesCS1B01G070600 chr6B 26542823 26543351 528 True 274.000000 274 76.514000 1 536 1 chr6B.!!$R1 535
12 TraesCS1B01G070600 chr2B 585707184 585707727 543 False 259.000000 259 75.874000 4 568 1 chr2B.!!$F1 564

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
724 923 0.034896 TCCCTTCAGTTTCGTGGCTC 59.965 55.0 0.0 0.0 0.0 4.70 F
726 925 0.035458 CCTTCAGTTTCGTGGCTCCT 59.965 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 6077 1.293179 CATGAGCTGGTGGTCGTCA 59.707 57.895 0.0 0.0 43.09 4.35 R
2268 6887 3.609853 AGTCAAGAACAAGTGTGCAAGA 58.390 40.909 0.0 0.0 0.00 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
32 68 5.347364 ACATTTTCCAAACAGTTGTTCAACG 59.653 36.000 9.54 7.66 37.25 4.10
42 78 6.830114 ACAGTTGTTCAACGTTTTTCAAAA 57.170 29.167 0.00 0.00 0.00 2.44
49 85 7.119997 TGTTCAACGTTTTTCAAAAACTTGTG 58.880 30.769 20.78 15.49 0.00 3.33
71 107 8.880878 TGTGCAACACTTTATATATACACGAT 57.119 30.769 0.00 0.00 45.67 3.73
72 108 8.974408 TGTGCAACACTTTATATATACACGATC 58.026 33.333 0.00 0.00 45.67 3.69
73 109 8.974408 GTGCAACACTTTATATATACACGATCA 58.026 33.333 0.00 0.00 36.32 2.92
74 110 9.535878 TGCAACACTTTATATATACACGATCAA 57.464 29.630 0.00 0.00 0.00 2.57
75 111 9.793245 GCAACACTTTATATATACACGATCAAC 57.207 33.333 0.00 0.00 0.00 3.18
484 659 6.783162 TCCAAATGCTTGTTCAACATTTTTG 58.217 32.000 15.80 0.17 40.94 2.44
485 660 6.373774 TCCAAATGCTTGTTCAACATTTTTGT 59.626 30.769 15.80 0.00 40.94 2.83
486 661 7.550551 TCCAAATGCTTGTTCAACATTTTTGTA 59.449 29.630 15.80 0.00 40.94 2.41
487 662 8.344098 CCAAATGCTTGTTCAACATTTTTGTAT 58.656 29.630 15.80 0.00 40.94 2.29
490 665 9.539825 AATGCTTGTTCAACATTTTTGTATACA 57.460 25.926 0.08 0.08 29.94 2.29
491 666 9.709495 ATGCTTGTTCAACATTTTTGTATACAT 57.291 25.926 6.36 0.00 0.00 2.29
492 667 8.976471 TGCTTGTTCAACATTTTTGTATACATG 58.024 29.630 6.36 4.53 0.00 3.21
493 668 9.190858 GCTTGTTCAACATTTTTGTATACATGA 57.809 29.630 6.36 2.71 0.00 3.07
496 671 9.553418 TGTTCAACATTTTTGTATACATGATCG 57.447 29.630 6.36 0.00 0.00 3.69
497 672 9.767684 GTTCAACATTTTTGTATACATGATCGA 57.232 29.630 6.36 0.00 0.00 3.59
498 673 9.767684 TTCAACATTTTTGTATACATGATCGAC 57.232 29.630 6.36 0.00 0.00 4.20
499 674 8.940952 TCAACATTTTTGTATACATGATCGACA 58.059 29.630 6.36 0.00 0.00 4.35
500 675 9.553418 CAACATTTTTGTATACATGATCGACAA 57.447 29.630 6.36 1.44 0.00 3.18
647 846 3.525268 AAAACACAGAAAACAGGCTGG 57.475 42.857 20.34 1.75 36.47 4.85
648 847 2.435372 AACACAGAAAACAGGCTGGA 57.565 45.000 20.34 0.00 36.47 3.86
649 848 1.972872 ACACAGAAAACAGGCTGGAG 58.027 50.000 20.34 4.17 36.47 3.86
650 849 1.212935 ACACAGAAAACAGGCTGGAGT 59.787 47.619 20.34 2.29 36.47 3.85
651 850 2.301346 CACAGAAAACAGGCTGGAGTT 58.699 47.619 20.34 9.32 36.47 3.01
652 851 2.689983 CACAGAAAACAGGCTGGAGTTT 59.310 45.455 20.34 15.15 39.46 2.66
653 852 2.952310 ACAGAAAACAGGCTGGAGTTTC 59.048 45.455 20.34 21.78 36.98 2.78
654 853 2.294512 CAGAAAACAGGCTGGAGTTTCC 59.705 50.000 24.69 14.15 36.98 3.13
655 854 2.175715 AGAAAACAGGCTGGAGTTTCCT 59.824 45.455 24.69 15.45 36.98 3.36
661 860 3.793144 CTGGAGTTTCCTGCGCGC 61.793 66.667 27.26 27.26 37.46 6.86
662 861 4.617520 TGGAGTTTCCTGCGCGCA 62.618 61.111 34.12 34.12 37.46 6.09
663 862 3.127533 GGAGTTTCCTGCGCGCAT 61.128 61.111 36.48 19.62 32.53 4.73
664 863 2.099062 GAGTTTCCTGCGCGCATG 59.901 61.111 36.48 31.59 0.00 4.06
665 864 3.386867 GAGTTTCCTGCGCGCATGG 62.387 63.158 36.48 33.23 0.00 3.66
666 865 4.481112 GTTTCCTGCGCGCATGGG 62.481 66.667 36.48 31.78 0.00 4.00
684 883 3.047877 CCGTCCAACTGGCGGTTC 61.048 66.667 9.17 0.00 44.28 3.62
685 884 3.047877 CGTCCAACTGGCGGTTCC 61.048 66.667 9.17 0.00 35.74 3.62
686 885 2.671963 GTCCAACTGGCGGTTCCC 60.672 66.667 9.17 0.00 35.74 3.97
687 886 2.852075 TCCAACTGGCGGTTCCCT 60.852 61.111 9.17 0.00 35.74 4.20
688 887 2.115266 CCAACTGGCGGTTCCCTT 59.885 61.111 9.17 0.00 35.74 3.95
689 888 1.971695 CCAACTGGCGGTTCCCTTC 60.972 63.158 9.17 0.00 35.74 3.46
690 889 1.228124 CAACTGGCGGTTCCCTTCA 60.228 57.895 9.17 0.00 35.74 3.02
691 890 1.073199 AACTGGCGGTTCCCTTCAG 59.927 57.895 5.72 0.00 31.69 3.02
692 891 1.705997 AACTGGCGGTTCCCTTCAGT 61.706 55.000 5.72 0.00 36.53 3.41
693 892 1.073199 CTGGCGGTTCCCTTCAGTT 59.927 57.895 0.00 0.00 0.00 3.16
694 893 0.537371 CTGGCGGTTCCCTTCAGTTT 60.537 55.000 0.00 0.00 0.00 2.66
695 894 0.536460 TGGCGGTTCCCTTCAGTTTC 60.536 55.000 0.00 0.00 0.00 2.78
696 895 0.536460 GGCGGTTCCCTTCAGTTTCA 60.536 55.000 0.00 0.00 0.00 2.69
697 896 1.314730 GCGGTTCCCTTCAGTTTCAA 58.685 50.000 0.00 0.00 0.00 2.69
698 897 1.886542 GCGGTTCCCTTCAGTTTCAAT 59.113 47.619 0.00 0.00 0.00 2.57
699 898 2.351738 GCGGTTCCCTTCAGTTTCAATG 60.352 50.000 0.00 0.00 0.00 2.82
700 899 2.228822 CGGTTCCCTTCAGTTTCAATGG 59.771 50.000 0.00 0.00 0.00 3.16
701 900 2.562738 GGTTCCCTTCAGTTTCAATGGG 59.437 50.000 0.00 0.00 36.14 4.00
702 901 1.923356 TCCCTTCAGTTTCAATGGGC 58.077 50.000 0.00 0.00 34.89 5.36
703 902 0.897621 CCCTTCAGTTTCAATGGGCC 59.102 55.000 0.00 0.00 0.00 5.80
704 903 1.631405 CCTTCAGTTTCAATGGGCCA 58.369 50.000 9.61 9.61 0.00 5.36
705 904 2.181975 CCTTCAGTTTCAATGGGCCAT 58.818 47.619 14.78 14.78 0.00 4.40
706 905 2.167075 CCTTCAGTTTCAATGGGCCATC 59.833 50.000 21.48 6.78 0.00 3.51
707 906 1.851304 TCAGTTTCAATGGGCCATCC 58.149 50.000 21.48 5.78 0.00 3.51
718 917 2.482326 GGCCATCCCTTCAGTTTCG 58.518 57.895 0.00 0.00 0.00 3.46
719 918 0.322546 GGCCATCCCTTCAGTTTCGT 60.323 55.000 0.00 0.00 0.00 3.85
720 919 0.804989 GCCATCCCTTCAGTTTCGTG 59.195 55.000 0.00 0.00 0.00 4.35
721 920 1.453155 CCATCCCTTCAGTTTCGTGG 58.547 55.000 0.00 0.00 0.00 4.94
722 921 0.804989 CATCCCTTCAGTTTCGTGGC 59.195 55.000 0.00 0.00 0.00 5.01
723 922 0.693049 ATCCCTTCAGTTTCGTGGCT 59.307 50.000 0.00 0.00 0.00 4.75
724 923 0.034896 TCCCTTCAGTTTCGTGGCTC 59.965 55.000 0.00 0.00 0.00 4.70
725 924 0.955919 CCCTTCAGTTTCGTGGCTCC 60.956 60.000 0.00 0.00 0.00 4.70
726 925 0.035458 CCTTCAGTTTCGTGGCTCCT 59.965 55.000 0.00 0.00 0.00 3.69
727 926 1.433534 CTTCAGTTTCGTGGCTCCTC 58.566 55.000 0.00 0.00 0.00 3.71
728 927 1.001406 CTTCAGTTTCGTGGCTCCTCT 59.999 52.381 0.00 0.00 0.00 3.69
729 928 0.603569 TCAGTTTCGTGGCTCCTCTC 59.396 55.000 0.00 0.00 0.00 3.20
730 929 0.734253 CAGTTTCGTGGCTCCTCTCG 60.734 60.000 0.00 0.00 0.00 4.04
731 930 2.095252 GTTTCGTGGCTCCTCTCGC 61.095 63.158 0.00 0.00 0.00 5.03
732 931 3.626680 TTTCGTGGCTCCTCTCGCG 62.627 63.158 0.00 0.00 38.12 5.87
737 936 4.189188 GGCTCCTCTCGCGCGTAA 62.189 66.667 30.98 17.72 0.00 3.18
738 937 2.950194 GCTCCTCTCGCGCGTAAC 60.950 66.667 30.98 9.67 0.00 2.50
752 951 2.940137 GCGTAACGCGAGAAATAGTTG 58.060 47.619 15.93 0.00 44.55 3.16
753 952 2.840968 GCGTAACGCGAGAAATAGTTGC 60.841 50.000 15.93 0.00 44.55 4.17
756 955 1.012234 CGCGAGAAATAGTTGCGGC 60.012 57.895 0.00 0.00 44.65 6.53
757 956 1.352056 GCGAGAAATAGTTGCGGCC 59.648 57.895 0.00 0.00 0.00 6.13
758 957 2.014594 CGAGAAATAGTTGCGGCCC 58.985 57.895 0.00 0.00 0.00 5.80
759 958 0.462047 CGAGAAATAGTTGCGGCCCT 60.462 55.000 0.00 0.00 0.00 5.19
760 959 1.751437 GAGAAATAGTTGCGGCCCTT 58.249 50.000 0.00 0.00 0.00 3.95
761 960 2.092323 GAGAAATAGTTGCGGCCCTTT 58.908 47.619 0.00 0.00 0.00 3.11
762 961 2.492088 GAGAAATAGTTGCGGCCCTTTT 59.508 45.455 0.00 0.00 0.00 2.27
763 962 2.897326 AGAAATAGTTGCGGCCCTTTTT 59.103 40.909 0.00 1.45 0.00 1.94
764 963 2.741759 AATAGTTGCGGCCCTTTTTG 57.258 45.000 0.00 0.00 0.00 2.44
765 964 1.627864 ATAGTTGCGGCCCTTTTTGT 58.372 45.000 0.00 0.00 0.00 2.83
766 965 0.671251 TAGTTGCGGCCCTTTTTGTG 59.329 50.000 0.00 0.00 0.00 3.33
767 966 1.142965 GTTGCGGCCCTTTTTGTGT 59.857 52.632 0.00 0.00 0.00 3.72
768 967 0.874175 GTTGCGGCCCTTTTTGTGTC 60.874 55.000 0.00 0.00 0.00 3.67
769 968 1.323271 TTGCGGCCCTTTTTGTGTCA 61.323 50.000 0.00 0.00 0.00 3.58
770 969 1.112315 TGCGGCCCTTTTTGTGTCAT 61.112 50.000 0.00 0.00 0.00 3.06
771 970 0.388520 GCGGCCCTTTTTGTGTCATC 60.389 55.000 0.00 0.00 0.00 2.92
772 971 1.247567 CGGCCCTTTTTGTGTCATCT 58.752 50.000 0.00 0.00 0.00 2.90
773 972 2.432444 CGGCCCTTTTTGTGTCATCTA 58.568 47.619 0.00 0.00 0.00 1.98
774 973 2.817258 CGGCCCTTTTTGTGTCATCTAA 59.183 45.455 0.00 0.00 0.00 2.10
775 974 3.119849 CGGCCCTTTTTGTGTCATCTAAG 60.120 47.826 0.00 0.00 0.00 2.18
776 975 3.367395 GGCCCTTTTTGTGTCATCTAAGC 60.367 47.826 0.00 0.00 0.00 3.09
777 976 3.367395 GCCCTTTTTGTGTCATCTAAGCC 60.367 47.826 0.00 0.00 0.00 4.35
778 977 3.826157 CCCTTTTTGTGTCATCTAAGCCA 59.174 43.478 0.00 0.00 0.00 4.75
779 978 4.463891 CCCTTTTTGTGTCATCTAAGCCAT 59.536 41.667 0.00 0.00 0.00 4.40
780 979 5.047092 CCCTTTTTGTGTCATCTAAGCCATT 60.047 40.000 0.00 0.00 0.00 3.16
781 980 6.458210 CCTTTTTGTGTCATCTAAGCCATTT 58.542 36.000 0.00 0.00 0.00 2.32
782 981 6.930722 CCTTTTTGTGTCATCTAAGCCATTTT 59.069 34.615 0.00 0.00 0.00 1.82
783 982 7.116805 CCTTTTTGTGTCATCTAAGCCATTTTC 59.883 37.037 0.00 0.00 0.00 2.29
784 983 5.643379 TTGTGTCATCTAAGCCATTTTCC 57.357 39.130 0.00 0.00 0.00 3.13
785 984 4.661222 TGTGTCATCTAAGCCATTTTCCA 58.339 39.130 0.00 0.00 0.00 3.53
786 985 4.458989 TGTGTCATCTAAGCCATTTTCCAC 59.541 41.667 0.00 0.00 0.00 4.02
787 986 4.702131 GTGTCATCTAAGCCATTTTCCACT 59.298 41.667 0.00 0.00 0.00 4.00
788 987 4.943705 TGTCATCTAAGCCATTTTCCACTC 59.056 41.667 0.00 0.00 0.00 3.51
789 988 5.189180 GTCATCTAAGCCATTTTCCACTCT 58.811 41.667 0.00 0.00 0.00 3.24
892 4867 2.125106 GAGGAAACCCTCGCGCAT 60.125 61.111 8.75 0.00 40.68 4.73
933 4908 3.621394 GCTCTCGCAATCGCCGTC 61.621 66.667 0.00 0.00 35.78 4.79
934 4909 3.315521 CTCTCGCAATCGCCGTCG 61.316 66.667 0.00 0.00 35.26 5.12
1055 5030 2.341543 CTCAGGTGCTGTCTGCGT 59.658 61.111 0.00 0.00 46.63 5.24
1439 5927 2.584608 CCGATCCCCTTTGACGCT 59.415 61.111 0.00 0.00 0.00 5.07
1515 6003 0.534877 TGGAAGCAGTTGCATCGTGT 60.535 50.000 6.90 0.00 45.16 4.49
1589 6077 1.686110 GTGGACGTGGATCTCCCCT 60.686 63.158 0.00 0.00 34.29 4.79
1649 6137 5.407407 TGGACTCTTTCTACAATGAGGAC 57.593 43.478 0.00 0.00 37.87 3.85
1650 6138 4.223032 TGGACTCTTTCTACAATGAGGACC 59.777 45.833 0.00 0.00 37.87 4.46
1652 6140 5.280011 GGACTCTTTCTACAATGAGGACCAA 60.280 44.000 0.00 0.00 37.87 3.67
1757 6245 2.804933 GCGCAGAGATAGGAAGGGAAAG 60.805 54.545 0.30 0.00 0.00 2.62
2002 6618 3.561310 GCGAATCATGCACTATTCCTTGA 59.439 43.478 14.22 1.72 0.00 3.02
2105 6721 7.598869 TCTCTTGAGTATGTCAACATGTGTAAC 59.401 37.037 0.00 0.00 40.45 2.50
2880 7781 0.179113 ACACAAGGGCGTGCTTTTTG 60.179 50.000 0.00 0.00 40.73 2.44
3022 7923 2.751806 GGAGTTTCTTCCTTGCCATGAG 59.248 50.000 0.00 0.00 34.27 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 34 7.341446 AGTTTTTGAAAAACGTTGAACAACTG 58.659 30.769 23.06 10.59 39.08 3.16
32 68 6.426327 AGTGTTGCACAAGTTTTTGAAAAAC 58.574 32.000 22.22 22.22 36.74 2.43
49 85 9.793245 GTTGATCGTGTATATATAAAGTGTTGC 57.207 33.333 0.00 0.00 0.00 4.17
292 393 9.030301 CGTGTATATGTGATATGTTGAACAAGA 57.970 33.333 0.62 0.00 0.00 3.02
467 642 9.190858 TCATGTATACAAAAATGTTGAACAAGC 57.809 29.630 10.14 0.00 0.00 4.01
626 825 3.513515 TCCAGCCTGTTTTCTGTGTTTTT 59.486 39.130 0.00 0.00 0.00 1.94
627 826 3.096092 TCCAGCCTGTTTTCTGTGTTTT 58.904 40.909 0.00 0.00 0.00 2.43
628 827 2.689983 CTCCAGCCTGTTTTCTGTGTTT 59.310 45.455 0.00 0.00 0.00 2.83
629 828 2.301346 CTCCAGCCTGTTTTCTGTGTT 58.699 47.619 0.00 0.00 0.00 3.32
630 829 1.212935 ACTCCAGCCTGTTTTCTGTGT 59.787 47.619 0.00 0.00 0.00 3.72
631 830 1.972872 ACTCCAGCCTGTTTTCTGTG 58.027 50.000 0.00 0.00 0.00 3.66
632 831 2.736670 AACTCCAGCCTGTTTTCTGT 57.263 45.000 0.00 0.00 0.00 3.41
633 832 2.294512 GGAAACTCCAGCCTGTTTTCTG 59.705 50.000 9.32 0.00 36.64 3.02
634 833 2.175715 AGGAAACTCCAGCCTGTTTTCT 59.824 45.455 9.32 0.00 39.61 2.52
635 834 2.294512 CAGGAAACTCCAGCCTGTTTTC 59.705 50.000 0.00 0.00 43.25 2.29
636 835 2.310538 CAGGAAACTCCAGCCTGTTTT 58.689 47.619 0.00 0.00 43.25 2.43
637 836 1.986882 CAGGAAACTCCAGCCTGTTT 58.013 50.000 0.00 0.00 43.25 2.83
638 837 3.733709 CAGGAAACTCCAGCCTGTT 57.266 52.632 0.00 0.00 43.25 3.16
639 838 2.738213 CGCAGGAAACTCCAGCCTGT 62.738 60.000 0.00 0.00 45.08 4.00
640 839 2.037136 CGCAGGAAACTCCAGCCTG 61.037 63.158 0.00 0.00 45.08 4.85
641 840 2.348998 CGCAGGAAACTCCAGCCT 59.651 61.111 4.68 0.00 45.08 4.58
642 841 3.435186 GCGCAGGAAACTCCAGCC 61.435 66.667 0.30 0.00 45.08 4.85
643 842 3.793144 CGCGCAGGAAACTCCAGC 61.793 66.667 8.75 0.21 44.53 4.85
644 843 3.793144 GCGCGCAGGAAACTCCAG 61.793 66.667 29.10 0.00 39.61 3.86
645 844 3.899981 ATGCGCGCAGGAAACTCCA 62.900 57.895 38.44 11.80 39.61 3.86
646 845 3.127533 ATGCGCGCAGGAAACTCC 61.128 61.111 38.44 2.63 40.21 3.85
647 846 2.099062 CATGCGCGCAGGAAACTC 59.901 61.111 39.65 3.38 40.21 3.01
648 847 3.434319 CCATGCGCGCAGGAAACT 61.434 61.111 43.14 22.29 46.44 2.66
649 848 4.481112 CCCATGCGCGCAGGAAAC 62.481 66.667 43.14 9.19 0.00 2.78
660 859 3.443045 CAGTTGGACGGCCCATGC 61.443 66.667 3.83 0.00 46.10 4.06
661 860 2.751436 CCAGTTGGACGGCCCATG 60.751 66.667 3.83 0.00 46.10 3.66
662 861 4.740822 GCCAGTTGGACGGCCCAT 62.741 66.667 3.83 0.00 46.10 4.00
668 867 3.047877 GGAACCGCCAGTTGGACG 61.048 66.667 1.45 5.29 39.40 4.79
669 868 2.671963 GGGAACCGCCAGTTGGAC 60.672 66.667 1.45 0.00 40.86 4.02
681 880 2.029020 GCCCATTGAAACTGAAGGGAAC 60.029 50.000 0.00 0.00 38.60 3.62
682 881 2.247358 GCCCATTGAAACTGAAGGGAA 58.753 47.619 0.00 0.00 38.60 3.97
683 882 1.549950 GGCCCATTGAAACTGAAGGGA 60.550 52.381 0.00 0.00 38.60 4.20
684 883 0.897621 GGCCCATTGAAACTGAAGGG 59.102 55.000 0.00 0.00 39.33 3.95
685 884 1.631405 TGGCCCATTGAAACTGAAGG 58.369 50.000 0.00 0.00 0.00 3.46
686 885 2.167075 GGATGGCCCATTGAAACTGAAG 59.833 50.000 0.00 0.00 34.14 3.02
687 886 2.178580 GGATGGCCCATTGAAACTGAA 58.821 47.619 0.00 0.00 34.14 3.02
688 887 1.851304 GGATGGCCCATTGAAACTGA 58.149 50.000 0.00 0.00 34.14 3.41
700 899 0.322546 ACGAAACTGAAGGGATGGCC 60.323 55.000 0.00 0.00 0.00 5.36
701 900 0.804989 CACGAAACTGAAGGGATGGC 59.195 55.000 0.00 0.00 0.00 4.40
702 901 1.453155 CCACGAAACTGAAGGGATGG 58.547 55.000 0.00 0.00 0.00 3.51
703 902 0.804989 GCCACGAAACTGAAGGGATG 59.195 55.000 0.00 0.00 0.00 3.51
704 903 0.693049 AGCCACGAAACTGAAGGGAT 59.307 50.000 0.00 0.00 0.00 3.85
705 904 0.034896 GAGCCACGAAACTGAAGGGA 59.965 55.000 0.00 0.00 0.00 4.20
706 905 0.955919 GGAGCCACGAAACTGAAGGG 60.956 60.000 0.00 0.00 0.00 3.95
707 906 0.035458 AGGAGCCACGAAACTGAAGG 59.965 55.000 0.00 0.00 0.00 3.46
708 907 1.001406 AGAGGAGCCACGAAACTGAAG 59.999 52.381 0.00 0.00 0.00 3.02
709 908 1.000955 GAGAGGAGCCACGAAACTGAA 59.999 52.381 0.00 0.00 0.00 3.02
710 909 0.603569 GAGAGGAGCCACGAAACTGA 59.396 55.000 0.00 0.00 0.00 3.41
711 910 0.734253 CGAGAGGAGCCACGAAACTG 60.734 60.000 0.00 0.00 0.00 3.16
712 911 1.587054 CGAGAGGAGCCACGAAACT 59.413 57.895 0.00 0.00 0.00 2.66
713 912 2.095252 GCGAGAGGAGCCACGAAAC 61.095 63.158 0.00 0.00 0.00 2.78
714 913 2.261671 GCGAGAGGAGCCACGAAA 59.738 61.111 0.00 0.00 0.00 3.46
715 914 4.116328 CGCGAGAGGAGCCACGAA 62.116 66.667 0.00 0.00 0.00 3.85
720 919 4.189188 TTACGCGCGAGAGGAGCC 62.189 66.667 39.36 0.00 38.34 4.70
721 920 2.950194 GTTACGCGCGAGAGGAGC 60.950 66.667 39.36 14.50 38.19 4.70
722 921 2.648102 CGTTACGCGCGAGAGGAG 60.648 66.667 39.36 17.78 34.13 3.69
733 932 2.591309 CGCAACTATTTCTCGCGTTACG 60.591 50.000 5.77 0.00 40.99 3.18
734 933 2.284855 CCGCAACTATTTCTCGCGTTAC 60.285 50.000 5.77 0.00 44.23 2.50
735 934 1.921887 CCGCAACTATTTCTCGCGTTA 59.078 47.619 5.77 0.00 44.23 3.18
736 935 0.719465 CCGCAACTATTTCTCGCGTT 59.281 50.000 5.77 0.00 44.23 4.84
737 936 1.693083 GCCGCAACTATTTCTCGCGT 61.693 55.000 5.77 0.00 44.23 6.01
738 937 1.012234 GCCGCAACTATTTCTCGCG 60.012 57.895 0.00 0.00 45.25 5.87
739 938 1.352056 GGCCGCAACTATTTCTCGC 59.648 57.895 0.00 0.00 0.00 5.03
740 939 0.462047 AGGGCCGCAACTATTTCTCG 60.462 55.000 0.00 0.00 0.00 4.04
741 940 1.751437 AAGGGCCGCAACTATTTCTC 58.249 50.000 0.00 0.00 0.00 2.87
742 941 2.215942 AAAGGGCCGCAACTATTTCT 57.784 45.000 0.00 0.00 0.00 2.52
743 942 2.993220 CAAAAAGGGCCGCAACTATTTC 59.007 45.455 0.00 0.00 0.00 2.17
744 943 2.367241 ACAAAAAGGGCCGCAACTATTT 59.633 40.909 0.00 0.00 0.00 1.40
745 944 1.967779 ACAAAAAGGGCCGCAACTATT 59.032 42.857 0.00 0.00 0.00 1.73
746 945 1.272212 CACAAAAAGGGCCGCAACTAT 59.728 47.619 0.00 0.00 0.00 2.12
747 946 0.671251 CACAAAAAGGGCCGCAACTA 59.329 50.000 0.00 0.00 0.00 2.24
748 947 1.326951 ACACAAAAAGGGCCGCAACT 61.327 50.000 0.00 0.00 0.00 3.16
749 948 0.874175 GACACAAAAAGGGCCGCAAC 60.874 55.000 0.00 0.00 0.00 4.17
750 949 1.323271 TGACACAAAAAGGGCCGCAA 61.323 50.000 0.00 0.00 0.00 4.85
751 950 1.112315 ATGACACAAAAAGGGCCGCA 61.112 50.000 0.00 0.00 0.00 5.69
752 951 0.388520 GATGACACAAAAAGGGCCGC 60.389 55.000 0.00 0.00 0.00 6.53
753 952 1.247567 AGATGACACAAAAAGGGCCG 58.752 50.000 0.00 0.00 0.00 6.13
754 953 3.367395 GCTTAGATGACACAAAAAGGGCC 60.367 47.826 0.00 0.00 0.00 5.80
755 954 3.367395 GGCTTAGATGACACAAAAAGGGC 60.367 47.826 0.00 0.00 0.00 5.19
756 955 3.826157 TGGCTTAGATGACACAAAAAGGG 59.174 43.478 0.00 0.00 0.00 3.95
757 956 5.649782 ATGGCTTAGATGACACAAAAAGG 57.350 39.130 0.00 0.00 0.00 3.11
758 957 7.116805 GGAAAATGGCTTAGATGACACAAAAAG 59.883 37.037 0.00 0.00 0.00 2.27
759 958 6.928492 GGAAAATGGCTTAGATGACACAAAAA 59.072 34.615 0.00 0.00 0.00 1.94
760 959 6.041409 TGGAAAATGGCTTAGATGACACAAAA 59.959 34.615 0.00 0.00 0.00 2.44
761 960 5.538053 TGGAAAATGGCTTAGATGACACAAA 59.462 36.000 0.00 0.00 0.00 2.83
762 961 5.048083 GTGGAAAATGGCTTAGATGACACAA 60.048 40.000 0.00 0.00 0.00 3.33
763 962 4.458989 GTGGAAAATGGCTTAGATGACACA 59.541 41.667 0.00 0.00 0.00 3.72
764 963 4.702131 AGTGGAAAATGGCTTAGATGACAC 59.298 41.667 0.00 0.00 0.00 3.67
765 964 4.922206 AGTGGAAAATGGCTTAGATGACA 58.078 39.130 0.00 0.00 0.00 3.58
766 965 5.189180 AGAGTGGAAAATGGCTTAGATGAC 58.811 41.667 0.00 0.00 0.00 3.06
767 966 5.441718 AGAGTGGAAAATGGCTTAGATGA 57.558 39.130 0.00 0.00 0.00 2.92
768 967 5.067023 GGAAGAGTGGAAAATGGCTTAGATG 59.933 44.000 0.00 0.00 0.00 2.90
769 968 5.196695 GGAAGAGTGGAAAATGGCTTAGAT 58.803 41.667 0.00 0.00 0.00 1.98
770 969 4.042809 TGGAAGAGTGGAAAATGGCTTAGA 59.957 41.667 0.00 0.00 0.00 2.10
771 970 4.335416 TGGAAGAGTGGAAAATGGCTTAG 58.665 43.478 0.00 0.00 0.00 2.18
772 971 4.380843 TGGAAGAGTGGAAAATGGCTTA 57.619 40.909 0.00 0.00 0.00 3.09
773 972 3.243359 TGGAAGAGTGGAAAATGGCTT 57.757 42.857 0.00 0.00 0.00 4.35
774 973 2.978156 TGGAAGAGTGGAAAATGGCT 57.022 45.000 0.00 0.00 0.00 4.75
775 974 2.098117 CGATGGAAGAGTGGAAAATGGC 59.902 50.000 0.00 0.00 0.00 4.40
776 975 2.098117 GCGATGGAAGAGTGGAAAATGG 59.902 50.000 0.00 0.00 0.00 3.16
777 976 2.223112 CGCGATGGAAGAGTGGAAAATG 60.223 50.000 0.00 0.00 0.00 2.32
778 977 2.009774 CGCGATGGAAGAGTGGAAAAT 58.990 47.619 0.00 0.00 0.00 1.82
779 978 1.001520 TCGCGATGGAAGAGTGGAAAA 59.998 47.619 3.71 0.00 0.00 2.29
780 979 0.606096 TCGCGATGGAAGAGTGGAAA 59.394 50.000 3.71 0.00 0.00 3.13
781 980 0.173481 CTCGCGATGGAAGAGTGGAA 59.827 55.000 10.36 0.00 0.00 3.53
782 981 1.667154 CCTCGCGATGGAAGAGTGGA 61.667 60.000 10.36 0.00 0.00 4.02
783 982 1.227089 CCTCGCGATGGAAGAGTGG 60.227 63.158 10.36 0.00 0.00 4.00
784 983 1.880340 GCCTCGCGATGGAAGAGTG 60.880 63.158 23.26 4.26 0.00 3.51
785 984 1.680522 ATGCCTCGCGATGGAAGAGT 61.681 55.000 23.26 0.37 0.00 3.24
786 985 0.943359 GATGCCTCGCGATGGAAGAG 60.943 60.000 23.26 5.64 0.00 2.85
787 986 1.068083 GATGCCTCGCGATGGAAGA 59.932 57.895 23.26 10.03 0.00 2.87
788 987 0.531532 AAGATGCCTCGCGATGGAAG 60.532 55.000 23.26 7.02 0.00 3.46
789 988 0.107703 AAAGATGCCTCGCGATGGAA 60.108 50.000 23.26 16.05 0.00 3.53
891 4866 2.764128 ATGGTCGGTGGCGGAGAT 60.764 61.111 0.00 0.00 0.00 2.75
892 4867 3.770040 CATGGTCGGTGGCGGAGA 61.770 66.667 0.00 0.00 0.00 3.71
1055 5030 1.438651 GTAAACAGCATGCCACGAGA 58.561 50.000 15.66 0.00 42.53 4.04
1205 5180 4.035102 GCAGCGGAAGGGGGACTT 62.035 66.667 0.00 0.00 43.65 3.01
1394 5878 1.079405 ACCGCCCTGACATTGTACG 60.079 57.895 0.00 0.00 0.00 3.67
1499 5987 0.318107 GCAACACGATGCAACTGCTT 60.318 50.000 2.95 0.00 45.70 3.91
1589 6077 1.293179 CATGAGCTGGTGGTCGTCA 59.707 57.895 0.00 0.00 43.09 4.35
1649 6137 4.613622 CGAAGCACATAGAACAAACCTTGG 60.614 45.833 0.00 0.00 34.12 3.61
1650 6138 4.466828 CGAAGCACATAGAACAAACCTTG 58.533 43.478 0.00 0.00 0.00 3.61
1757 6245 4.530161 AGGATGTACATGCTAGAAGGATCC 59.470 45.833 26.44 11.35 37.74 3.36
2002 6618 7.147759 TGGCAAAACACATGGTGCTATTATAAT 60.148 33.333 2.97 2.97 36.98 1.28
2268 6887 3.609853 AGTCAAGAACAAGTGTGCAAGA 58.390 40.909 0.00 0.00 0.00 3.02
2901 7802 5.305585 ACATAATAGGAAGTGGCGGTAATG 58.694 41.667 0.00 0.00 0.00 1.90
3022 7923 2.888834 AAGATTGCAAACCACACCAC 57.111 45.000 1.71 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.