Multiple sequence alignment - TraesCS1D01G374500

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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 TraesCS1D01G374500 chr1D 100.000 3513 0 0 1 3513 451951905 451955417 0.000000e+00 6488.0
1 TraesCS1D01G374500 chr1A 94.242 2501 82 14 1043 3513 546512117 546514585 0.000000e+00 3764.0
2 TraesCS1D01G374500 chr1A 88.151 557 40 16 267 819 65898737 65899271 1.060000e-179 640.0
3 TraesCS1D01G374500 chr1B 94.237 1718 70 10 1036 2726 621952250 621953965 0.000000e+00 2597.0
4 TraesCS1D01G374500 chr1B 93.194 720 36 6 2799 3513 621953953 621954664 0.000000e+00 1046.0
5 TraesCS1D01G374500 chr1B 87.805 82 6 4 2729 2807 523134762 523134842 3.730000e-15 93.5
6 TraesCS1D01G374500 chr1B 88.571 70 7 1 2731 2800 32128826 32128894 2.250000e-12 84.2
7 TraesCS1D01G374500 chr3D 95.742 916 22 9 1 906 575557778 575558686 0.000000e+00 1459.0
8 TraesCS1D01G374500 chr3D 94.852 913 27 12 1 903 587656666 587657568 0.000000e+00 1408.0
9 TraesCS1D01G374500 chr3D 94.518 912 23 12 1 903 570149141 570148248 0.000000e+00 1382.0
10 TraesCS1D01G374500 chr3D 97.535 284 5 2 1 284 80257868 80258149 5.270000e-133 484.0
11 TraesCS1D01G374500 chr3D 89.873 316 18 8 599 903 518169370 518169058 9.140000e-106 394.0
12 TraesCS1D01G374500 chr6D 95.400 913 27 6 1 904 33503140 33504046 0.000000e+00 1439.0
13 TraesCS1D01G374500 chr6D 97.193 285 5 3 1 284 28873458 28873740 2.450000e-131 479.0
14 TraesCS1D01G374500 chrUn 94.323 916 21 9 1 906 20592937 20593831 0.000000e+00 1375.0
15 TraesCS1D01G374500 chrUn 90.506 316 17 8 599 903 61000495 61000182 4.220000e-109 405.0
16 TraesCS1D01G374500 chrUn 90.506 316 17 8 599 903 330692008 330692321 4.220000e-109 405.0
17 TraesCS1D01G374500 chr4A 89.189 592 48 10 288 874 142238700 142238120 0.000000e+00 725.0
18 TraesCS1D01G374500 chr3B 89.020 592 49 10 288 874 508712246 508712826 0.000000e+00 719.0
19 TraesCS1D01G374500 chr2A 87.765 613 46 18 267 874 436385290 436385878 0.000000e+00 689.0
20 TraesCS1D01G374500 chr2A 95.000 60 2 1 2727 2786 30196753 30196695 3.730000e-15 93.5
21 TraesCS1D01G374500 chr5D 97.535 284 5 2 1 284 484942040 484941759 5.270000e-133 484.0
22 TraesCS1D01G374500 chr5D 97.193 285 5 3 1 284 45502647 45502365 2.450000e-131 479.0
23 TraesCS1D01G374500 chr5D 83.117 308 45 6 602 902 386101341 386101034 1.240000e-69 274.0
24 TraesCS1D01G374500 chr7D 90.584 308 21 8 599 903 31476498 31476800 5.460000e-108 401.0
25 TraesCS1D01G374500 chr7B 94.203 69 4 0 2728 2796 704799093 704799025 4.800000e-19 106.0
26 TraesCS1D01G374500 chr7B 89.706 68 7 0 2728 2795 641527093 641527026 1.740000e-13 87.9
27 TraesCS1D01G374500 chr6A 82.203 118 18 2 2943 3060 556975499 556975385 8.030000e-17 99.0
28 TraesCS1D01G374500 chr5A 91.667 72 4 2 2728 2798 14492569 14492639 8.030000e-17 99.0
29 TraesCS1D01G374500 chr6B 81.356 118 19 2 2943 3060 620180758 620180644 3.730000e-15 93.5
30 TraesCS1D01G374500 chr2B 91.803 61 5 0 2727 2787 793314610 793314670 6.250000e-13 86.1


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 TraesCS1D01G374500 chr1D 451951905 451955417 3512 False 6488.0 6488 100.0000 1 3513 1 chr1D.!!$F1 3512
1 TraesCS1D01G374500 chr1A 546512117 546514585 2468 False 3764.0 3764 94.2420 1043 3513 1 chr1A.!!$F2 2470
2 TraesCS1D01G374500 chr1A 65898737 65899271 534 False 640.0 640 88.1510 267 819 1 chr1A.!!$F1 552
3 TraesCS1D01G374500 chr1B 621952250 621954664 2414 False 1821.5 2597 93.7155 1036 3513 2 chr1B.!!$F3 2477
4 TraesCS1D01G374500 chr3D 575557778 575558686 908 False 1459.0 1459 95.7420 1 906 1 chr3D.!!$F2 905
5 TraesCS1D01G374500 chr3D 587656666 587657568 902 False 1408.0 1408 94.8520 1 903 1 chr3D.!!$F3 902
6 TraesCS1D01G374500 chr3D 570148248 570149141 893 True 1382.0 1382 94.5180 1 903 1 chr3D.!!$R2 902
7 TraesCS1D01G374500 chr6D 33503140 33504046 906 False 1439.0 1439 95.4000 1 904 1 chr6D.!!$F2 903
8 TraesCS1D01G374500 chrUn 20592937 20593831 894 False 1375.0 1375 94.3230 1 906 1 chrUn.!!$F1 905
9 TraesCS1D01G374500 chr4A 142238120 142238700 580 True 725.0 725 89.1890 288 874 1 chr4A.!!$R1 586
10 TraesCS1D01G374500 chr3B 508712246 508712826 580 False 719.0 719 89.0200 288 874 1 chr3B.!!$F1 586
11 TraesCS1D01G374500 chr2A 436385290 436385878 588 False 689.0 689 87.7650 267 874 1 chr2A.!!$F1 607

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
979 1006 0.108992 TAACGCAGGTGAGCTTACGG 60.109 55.0 2.14 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2852 2906 0.326595 TGCCCCTCGCATTGTTAAGA 59.673 50.0 0.0 0.0 44.64 2.1 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
387 390 4.870123 TGATTTTTGCTGCAACCATAGT 57.130 36.364 15.72 0.00 0.00 2.12
388 391 5.212532 TGATTTTTGCTGCAACCATAGTT 57.787 34.783 15.72 0.00 36.33 2.24
809 822 2.127708 AGAAGTTGGGGGCGATCTATT 58.872 47.619 0.00 0.00 0.00 1.73
810 823 2.509964 AGAAGTTGGGGGCGATCTATTT 59.490 45.455 0.00 0.00 0.00 1.40
811 824 2.640316 AGTTGGGGGCGATCTATTTC 57.360 50.000 0.00 0.00 0.00 2.17
855 873 1.140652 TGCGTGGCTCATATCCAATGA 59.859 47.619 0.00 0.00 35.01 2.57
870 897 2.484287 AATGACCTGGGCTGGAACGG 62.484 60.000 0.00 0.00 38.10 4.44
907 934 2.249844 GCCTATAAGCGGCCTAAACA 57.750 50.000 0.00 0.00 41.73 2.83
908 935 2.567985 GCCTATAAGCGGCCTAAACAA 58.432 47.619 0.00 0.00 41.73 2.83
909 936 2.946990 GCCTATAAGCGGCCTAAACAAA 59.053 45.455 0.00 0.00 41.73 2.83
910 937 3.379057 GCCTATAAGCGGCCTAAACAAAA 59.621 43.478 0.00 0.00 41.73 2.44
911 938 4.732647 GCCTATAAGCGGCCTAAACAAAAC 60.733 45.833 0.00 0.00 41.73 2.43
912 939 4.396790 CCTATAAGCGGCCTAAACAAAACA 59.603 41.667 0.00 0.00 0.00 2.83
913 940 4.857509 ATAAGCGGCCTAAACAAAACAA 57.142 36.364 0.00 0.00 0.00 2.83
914 941 2.793278 AGCGGCCTAAACAAAACAAG 57.207 45.000 0.00 0.00 0.00 3.16
915 942 1.339929 AGCGGCCTAAACAAAACAAGG 59.660 47.619 0.00 0.00 0.00 3.61
916 943 1.604438 GCGGCCTAAACAAAACAAGGG 60.604 52.381 0.00 0.00 0.00 3.95
917 944 1.957877 CGGCCTAAACAAAACAAGGGA 59.042 47.619 0.00 0.00 0.00 4.20
918 945 2.362717 CGGCCTAAACAAAACAAGGGAA 59.637 45.455 0.00 0.00 0.00 3.97
919 946 3.181474 CGGCCTAAACAAAACAAGGGAAA 60.181 43.478 0.00 0.00 0.00 3.13
920 947 4.502431 CGGCCTAAACAAAACAAGGGAAAT 60.502 41.667 0.00 0.00 0.00 2.17
921 948 4.754618 GGCCTAAACAAAACAAGGGAAATG 59.245 41.667 0.00 0.00 0.00 2.32
922 949 5.364778 GCCTAAACAAAACAAGGGAAATGT 58.635 37.500 0.00 0.00 0.00 2.71
923 950 5.465390 GCCTAAACAAAACAAGGGAAATGTC 59.535 40.000 0.00 0.00 0.00 3.06
924 951 6.578023 CCTAAACAAAACAAGGGAAATGTCA 58.422 36.000 0.00 0.00 0.00 3.58
925 952 7.044798 CCTAAACAAAACAAGGGAAATGTCAA 58.955 34.615 0.00 0.00 0.00 3.18
926 953 7.714813 CCTAAACAAAACAAGGGAAATGTCAAT 59.285 33.333 0.00 0.00 0.00 2.57
927 954 7.552458 AAACAAAACAAGGGAAATGTCAATC 57.448 32.000 0.00 0.00 0.00 2.67
928 955 6.232581 ACAAAACAAGGGAAATGTCAATCA 57.767 33.333 0.00 0.00 0.00 2.57
929 956 6.048509 ACAAAACAAGGGAAATGTCAATCAC 58.951 36.000 0.00 0.00 0.00 3.06
930 957 4.871933 AACAAGGGAAATGTCAATCACC 57.128 40.909 0.00 0.00 0.00 4.02
931 958 3.165071 ACAAGGGAAATGTCAATCACCC 58.835 45.455 0.00 0.00 37.79 4.61
932 959 3.164268 CAAGGGAAATGTCAATCACCCA 58.836 45.455 0.00 0.00 39.73 4.51
933 960 3.541242 AGGGAAATGTCAATCACCCAA 57.459 42.857 0.00 0.00 39.73 4.12
934 961 3.855668 AGGGAAATGTCAATCACCCAAA 58.144 40.909 0.00 0.00 39.73 3.28
935 962 4.230455 AGGGAAATGTCAATCACCCAAAA 58.770 39.130 0.00 0.00 39.73 2.44
936 963 4.657969 AGGGAAATGTCAATCACCCAAAAA 59.342 37.500 0.00 0.00 39.73 1.94
937 964 4.996758 GGGAAATGTCAATCACCCAAAAAG 59.003 41.667 0.00 0.00 37.50 2.27
938 965 4.996758 GGAAATGTCAATCACCCAAAAAGG 59.003 41.667 0.00 0.00 37.03 3.11
939 966 5.221621 GGAAATGTCAATCACCCAAAAAGGA 60.222 40.000 0.00 0.00 41.22 3.36
940 967 5.885449 AATGTCAATCACCCAAAAAGGAA 57.115 34.783 0.00 0.00 41.22 3.36
941 968 4.935352 TGTCAATCACCCAAAAAGGAAG 57.065 40.909 0.00 0.00 41.22 3.46
942 969 3.069443 TGTCAATCACCCAAAAAGGAAGC 59.931 43.478 0.00 0.00 41.22 3.86
943 970 2.295909 TCAATCACCCAAAAAGGAAGCG 59.704 45.455 0.00 0.00 41.22 4.68
944 971 1.995376 ATCACCCAAAAAGGAAGCGT 58.005 45.000 0.00 0.00 41.22 5.07
945 972 2.642154 TCACCCAAAAAGGAAGCGTA 57.358 45.000 0.00 0.00 41.22 4.42
946 973 2.933573 TCACCCAAAAAGGAAGCGTAA 58.066 42.857 0.00 0.00 41.22 3.18
947 974 3.288964 TCACCCAAAAAGGAAGCGTAAA 58.711 40.909 0.00 0.00 41.22 2.01
948 975 3.316868 TCACCCAAAAAGGAAGCGTAAAG 59.683 43.478 0.00 0.00 41.22 1.85
949 976 2.626266 ACCCAAAAAGGAAGCGTAAAGG 59.374 45.455 0.00 0.00 41.22 3.11
950 977 2.609491 CCCAAAAAGGAAGCGTAAAGGC 60.609 50.000 0.00 0.00 41.22 4.35
951 978 4.869700 CCCAAAAAGGAAGCGTAAAGGCT 61.870 47.826 0.00 0.00 41.22 4.58
952 979 3.504520 CCAAAAAGGAAGCGTAAAGGCTA 59.495 43.478 0.00 0.00 43.93 3.93
953 980 4.022676 CCAAAAAGGAAGCGTAAAGGCTAA 60.023 41.667 0.00 0.00 43.93 3.09
954 981 5.336451 CCAAAAAGGAAGCGTAAAGGCTAAT 60.336 40.000 0.00 0.00 43.93 1.73
955 982 5.977489 AAAAGGAAGCGTAAAGGCTAATT 57.023 34.783 0.00 0.00 43.93 1.40
956 983 7.309920 CAAAAAGGAAGCGTAAAGGCTAATTA 58.690 34.615 0.00 0.00 43.93 1.40
957 984 6.432607 AAAGGAAGCGTAAAGGCTAATTAC 57.567 37.500 0.00 0.00 43.93 1.89
965 992 5.183209 CGTAAAGGCTAATTACGTTAACGC 58.817 41.667 27.07 9.23 46.35 4.84
966 993 5.220191 CGTAAAGGCTAATTACGTTAACGCA 60.220 40.000 27.07 12.84 46.35 5.24
967 994 4.852609 AAGGCTAATTACGTTAACGCAG 57.147 40.909 27.07 16.37 44.43 5.18
968 995 3.192466 AGGCTAATTACGTTAACGCAGG 58.808 45.455 27.07 12.49 44.43 4.85
969 996 2.931969 GGCTAATTACGTTAACGCAGGT 59.068 45.455 27.07 10.82 44.43 4.00
970 997 3.242188 GGCTAATTACGTTAACGCAGGTG 60.242 47.826 27.07 14.01 44.43 4.00
971 998 3.613737 GCTAATTACGTTAACGCAGGTGA 59.386 43.478 27.07 5.62 44.43 4.02
972 999 4.259690 GCTAATTACGTTAACGCAGGTGAG 60.260 45.833 27.07 17.35 44.43 3.51
973 1000 1.421382 TTACGTTAACGCAGGTGAGC 58.579 50.000 27.07 0.00 44.43 4.26
974 1001 0.599558 TACGTTAACGCAGGTGAGCT 59.400 50.000 27.07 7.51 44.43 4.09
975 1002 0.249741 ACGTTAACGCAGGTGAGCTT 60.250 50.000 27.07 1.11 44.43 3.74
976 1003 1.000060 ACGTTAACGCAGGTGAGCTTA 60.000 47.619 27.07 0.00 44.43 3.09
977 1004 1.389106 CGTTAACGCAGGTGAGCTTAC 59.611 52.381 16.05 0.00 0.00 2.34
978 1005 1.389106 GTTAACGCAGGTGAGCTTACG 59.611 52.381 2.14 2.70 0.00 3.18
979 1006 0.108992 TAACGCAGGTGAGCTTACGG 60.109 55.000 2.14 0.00 0.00 4.02
980 1007 2.095978 AACGCAGGTGAGCTTACGGT 62.096 55.000 2.14 0.00 0.00 4.83
981 1008 1.805945 CGCAGGTGAGCTTACGGTC 60.806 63.158 2.14 0.00 38.14 4.79
982 1009 1.292223 GCAGGTGAGCTTACGGTCA 59.708 57.895 2.14 0.00 44.73 4.02
986 1013 4.806571 TGAGCTTACGGTCATCGC 57.193 55.556 0.00 0.00 42.30 4.58
987 1014 1.226575 TGAGCTTACGGTCATCGCG 60.227 57.895 0.00 0.00 42.30 5.87
988 1015 2.577785 GAGCTTACGGTCATCGCGC 61.578 63.158 0.00 0.00 43.89 6.86
989 1016 2.582498 GCTTACGGTCATCGCGCT 60.582 61.111 5.56 0.00 43.89 5.92
990 1017 2.577785 GCTTACGGTCATCGCGCTC 61.578 63.158 5.56 0.00 43.89 5.03
991 1018 1.064296 CTTACGGTCATCGCGCTCT 59.936 57.895 5.56 0.00 43.89 4.09
992 1019 1.202973 CTTACGGTCATCGCGCTCTG 61.203 60.000 5.56 2.31 43.89 3.35
993 1020 3.751401 TACGGTCATCGCGCTCTGC 62.751 63.158 5.56 0.00 43.89 4.26
994 1021 4.862092 CGGTCATCGCGCTCTGCT 62.862 66.667 5.56 0.00 43.27 4.24
995 1022 2.413351 GGTCATCGCGCTCTGCTA 59.587 61.111 5.56 0.00 43.27 3.49
996 1023 1.006805 GGTCATCGCGCTCTGCTAT 60.007 57.895 5.56 0.00 43.27 2.97
997 1024 1.006314 GGTCATCGCGCTCTGCTATC 61.006 60.000 5.56 0.00 43.27 2.08
998 1025 0.318191 GTCATCGCGCTCTGCTATCA 60.318 55.000 5.56 0.00 43.27 2.15
999 1026 0.600057 TCATCGCGCTCTGCTATCAT 59.400 50.000 5.56 0.00 43.27 2.45
1000 1027 1.812571 TCATCGCGCTCTGCTATCATA 59.187 47.619 5.56 0.00 43.27 2.15
1001 1028 2.228822 TCATCGCGCTCTGCTATCATAA 59.771 45.455 5.56 0.00 43.27 1.90
1002 1029 2.338140 TCGCGCTCTGCTATCATAAG 57.662 50.000 5.56 0.00 43.27 1.73
1003 1030 0.712775 CGCGCTCTGCTATCATAAGC 59.287 55.000 5.56 0.00 43.27 3.09
1004 1031 1.668337 CGCGCTCTGCTATCATAAGCT 60.668 52.381 5.56 0.00 43.19 3.74
1005 1032 2.411904 GCGCTCTGCTATCATAAGCTT 58.588 47.619 3.48 3.48 43.19 3.74
1006 1033 2.805099 GCGCTCTGCTATCATAAGCTTT 59.195 45.455 3.20 0.00 43.19 3.51
1007 1034 3.363772 GCGCTCTGCTATCATAAGCTTTG 60.364 47.826 3.20 3.18 43.19 2.77
1008 1035 3.186001 CGCTCTGCTATCATAAGCTTTGG 59.814 47.826 3.20 0.00 43.19 3.28
1009 1036 3.058363 GCTCTGCTATCATAAGCTTTGGC 60.058 47.826 3.20 0.00 43.19 4.52
1010 1037 4.132336 CTCTGCTATCATAAGCTTTGGCA 58.868 43.478 3.20 5.43 43.19 4.92
1011 1038 3.879295 TCTGCTATCATAAGCTTTGGCAC 59.121 43.478 3.20 0.00 43.19 5.01
1012 1039 2.613595 TGCTATCATAAGCTTTGGCACG 59.386 45.455 3.20 0.00 43.19 5.34
1013 1040 2.603173 GCTATCATAAGCTTTGGCACGC 60.603 50.000 3.20 0.00 41.70 5.34
1014 1041 0.740737 ATCATAAGCTTTGGCACGCC 59.259 50.000 3.20 0.00 41.70 5.68
1015 1042 1.139520 CATAAGCTTTGGCACGCCC 59.860 57.895 3.20 0.00 41.70 6.13
1016 1043 2.406616 ATAAGCTTTGGCACGCCCG 61.407 57.895 3.20 0.00 41.70 6.13
1037 1064 3.941188 CGCTGGTGTGTGGGGTCT 61.941 66.667 0.00 0.00 0.00 3.85
1908 1935 3.822192 CGTCGACGCCATCAGGGA 61.822 66.667 26.59 0.00 40.01 4.20
2203 2230 3.083997 AAAGGGCTCGGCGAGGAT 61.084 61.111 35.03 6.26 0.00 3.24
2239 2266 1.878102 GCCTGCTTCGTCTTGGAGAAA 60.878 52.381 0.00 0.00 0.00 2.52
2372 2399 3.084039 TCTTGACATTTCCAGTCCATGC 58.916 45.455 0.00 0.00 35.15 4.06
2459 2508 3.983344 CCAGAAGCATTTAGTTGTGCAAC 59.017 43.478 6.94 6.94 43.63 4.17
2468 2517 2.292103 AGTTGTGCAACGCAAAATGT 57.708 40.000 9.10 0.00 45.50 2.71
2487 2536 8.950210 CAAAATGTATAATGCTCCTGGGTATAG 58.050 37.037 0.00 0.00 0.00 1.31
2490 2539 6.319715 TGTATAATGCTCCTGGGTATAGTGA 58.680 40.000 0.00 0.00 0.00 3.41
2605 2654 5.858581 GTGTGCAGTTTATCAATCTTTCCAC 59.141 40.000 0.00 0.00 0.00 4.02
2630 2684 5.644636 ACCACTTTCAGAACTGTCGTTTTTA 59.355 36.000 1.73 0.00 32.39 1.52
2646 2700 5.530543 TCGTTTTTAAAAATAGTCACCGGGT 59.469 36.000 16.02 0.00 0.00 5.28
2653 2707 1.192428 ATAGTCACCGGGTGAGGAAC 58.808 55.000 29.42 18.09 43.57 3.62
2663 2717 2.847234 TGAGGAACCGCCACCTGT 60.847 61.111 0.00 0.00 40.02 4.00
2664 2718 2.358737 GAGGAACCGCCACCTGTG 60.359 66.667 0.00 0.00 40.02 3.66
2707 2761 8.122952 CAGAAAGAATGATCCGGTTTATGTAAC 58.877 37.037 0.00 0.00 35.94 2.50
2725 2779 4.334759 TGTAACAAACCGAATCGAAAACCA 59.665 37.500 3.36 0.00 0.00 3.67
2726 2780 4.373348 AACAAACCGAATCGAAAACCAA 57.627 36.364 3.36 0.00 0.00 3.67
2760 2814 1.678970 GGCTCGCACCCTTTTCCAT 60.679 57.895 0.00 0.00 0.00 3.41
2776 2830 8.022550 CCCTTTTCCATTAATTTTGCAATCAAC 58.977 33.333 0.00 0.00 30.75 3.18
2777 2831 8.566260 CCTTTTCCATTAATTTTGCAATCAACA 58.434 29.630 0.00 0.00 30.75 3.33
2836 2890 6.227522 TGATTCAGTTTACGATGAGAAACCA 58.772 36.000 0.00 0.00 36.41 3.67
2852 2906 7.044798 TGAGAAACCAAAACCGAATCAAAAAT 58.955 30.769 0.00 0.00 0.00 1.82
2966 3021 7.087007 TGAAGTGATATGATCGTAGAGAATGC 58.913 38.462 0.41 0.00 43.63 3.56
2967 3022 6.581171 AGTGATATGATCGTAGAGAATGCA 57.419 37.500 0.41 0.00 43.63 3.96
2993 3048 0.899720 GGACATACCTCCACCAACGA 59.100 55.000 0.00 0.00 35.41 3.85
3081 3136 2.225491 TGCTACTGAATGGCGTTTTGAC 59.775 45.455 0.00 0.00 37.70 3.18
3089 3144 1.600023 TGGCGTTTTGACGGAGAATT 58.400 45.000 0.93 0.00 0.00 2.17
3140 3195 0.548510 GGGAGGGGATGAAGACAAGG 59.451 60.000 0.00 0.00 0.00 3.61
3148 3203 2.087646 GATGAAGACAAGGACAAGGCC 58.912 52.381 0.00 0.00 0.00 5.19
3210 3291 3.446570 GGCAGCTGCATGGTGTCC 61.447 66.667 37.63 15.84 45.23 4.02
3284 3365 3.305398 AAGAAAAACACACGCAACCAA 57.695 38.095 0.00 0.00 0.00 3.67
3384 3465 9.032420 GTAGTGTAATCTGAGTATAAGGCAAAC 57.968 37.037 0.00 0.00 0.00 2.93
3414 3498 9.906660 CAACTAGGAGTATTTCTCATACAGATC 57.093 37.037 0.00 0.00 44.40 2.75
3428 3512 9.566331 TCTCATACAGATCTCCCCATTAAATAT 57.434 33.333 0.00 0.00 0.00 1.28
3456 3540 1.034838 ACAACCAACAAGCGCTCCAA 61.035 50.000 12.06 0.00 0.00 3.53
3509 3595 7.480542 GTCAGCATAAACGTACACCTAAAAATG 59.519 37.037 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
715 723 4.779733 GCCTCCTGTCCCCTCCGA 62.780 72.222 0.00 0.00 0.00 4.55
906 933 5.466393 GGTGATTGACATTTCCCTTGTTTTG 59.534 40.000 0.00 0.00 0.00 2.44
907 934 5.454613 GGGTGATTGACATTTCCCTTGTTTT 60.455 40.000 0.00 0.00 32.89 2.43
908 935 4.040339 GGGTGATTGACATTTCCCTTGTTT 59.960 41.667 0.00 0.00 32.89 2.83
909 936 3.578282 GGGTGATTGACATTTCCCTTGTT 59.422 43.478 0.00 0.00 32.89 2.83
910 937 3.165071 GGGTGATTGACATTTCCCTTGT 58.835 45.455 0.00 0.00 32.89 3.16
911 938 3.164268 TGGGTGATTGACATTTCCCTTG 58.836 45.455 0.00 0.00 36.23 3.61
912 939 3.541242 TGGGTGATTGACATTTCCCTT 57.459 42.857 0.00 0.00 36.23 3.95
913 940 3.541242 TTGGGTGATTGACATTTCCCT 57.459 42.857 0.00 0.00 36.23 4.20
914 941 4.615588 TTTTGGGTGATTGACATTTCCC 57.384 40.909 0.00 0.00 35.85 3.97
915 942 4.996758 CCTTTTTGGGTGATTGACATTTCC 59.003 41.667 0.00 0.00 0.00 3.13
916 943 5.852827 TCCTTTTTGGGTGATTGACATTTC 58.147 37.500 0.00 0.00 36.20 2.17
917 944 5.885449 TCCTTTTTGGGTGATTGACATTT 57.115 34.783 0.00 0.00 36.20 2.32
918 945 5.742838 GCTTCCTTTTTGGGTGATTGACATT 60.743 40.000 0.00 0.00 36.20 2.71
919 946 4.262592 GCTTCCTTTTTGGGTGATTGACAT 60.263 41.667 0.00 0.00 36.20 3.06
920 947 3.069443 GCTTCCTTTTTGGGTGATTGACA 59.931 43.478 0.00 0.00 36.20 3.58
921 948 3.653344 GCTTCCTTTTTGGGTGATTGAC 58.347 45.455 0.00 0.00 36.20 3.18
922 949 2.295909 CGCTTCCTTTTTGGGTGATTGA 59.704 45.455 0.00 0.00 36.20 2.57
923 950 2.035832 ACGCTTCCTTTTTGGGTGATTG 59.964 45.455 0.00 0.00 36.20 2.67
924 951 2.316108 ACGCTTCCTTTTTGGGTGATT 58.684 42.857 0.00 0.00 36.20 2.57
925 952 1.995376 ACGCTTCCTTTTTGGGTGAT 58.005 45.000 0.00 0.00 36.20 3.06
926 953 2.642154 TACGCTTCCTTTTTGGGTGA 57.358 45.000 0.00 0.00 36.20 4.02
927 954 3.552068 CCTTTACGCTTCCTTTTTGGGTG 60.552 47.826 0.00 0.00 36.20 4.61
928 955 2.626266 CCTTTACGCTTCCTTTTTGGGT 59.374 45.455 0.00 0.00 36.20 4.51
929 956 2.609491 GCCTTTACGCTTCCTTTTTGGG 60.609 50.000 0.00 0.00 36.20 4.12
930 957 2.296190 AGCCTTTACGCTTCCTTTTTGG 59.704 45.455 0.00 0.00 34.73 3.28
931 958 3.643159 AGCCTTTACGCTTCCTTTTTG 57.357 42.857 0.00 0.00 34.73 2.44
932 959 5.977489 ATTAGCCTTTACGCTTCCTTTTT 57.023 34.783 0.00 0.00 40.39 1.94
933 960 5.977489 AATTAGCCTTTACGCTTCCTTTT 57.023 34.783 0.00 0.00 40.39 2.27
934 961 5.064325 CGTAATTAGCCTTTACGCTTCCTTT 59.936 40.000 9.55 0.00 43.50 3.11
935 962 4.569564 CGTAATTAGCCTTTACGCTTCCTT 59.430 41.667 9.55 0.00 43.50 3.36
936 963 4.117685 CGTAATTAGCCTTTACGCTTCCT 58.882 43.478 9.55 0.00 43.50 3.36
937 964 4.448363 CGTAATTAGCCTTTACGCTTCC 57.552 45.455 9.55 0.00 43.50 3.46
943 970 6.093532 TGCGTTAACGTAATTAGCCTTTAC 57.906 37.500 27.28 7.58 42.22 2.01
944 971 5.291614 CCTGCGTTAACGTAATTAGCCTTTA 59.708 40.000 27.28 0.00 42.22 1.85
945 972 4.093850 CCTGCGTTAACGTAATTAGCCTTT 59.906 41.667 27.28 0.00 42.22 3.11
946 973 3.619929 CCTGCGTTAACGTAATTAGCCTT 59.380 43.478 27.28 0.00 42.22 4.35
947 974 3.192466 CCTGCGTTAACGTAATTAGCCT 58.808 45.455 27.28 0.00 42.22 4.58
948 975 2.931969 ACCTGCGTTAACGTAATTAGCC 59.068 45.455 27.28 10.03 42.22 3.93
949 976 3.613737 TCACCTGCGTTAACGTAATTAGC 59.386 43.478 27.28 10.70 42.22 3.09
950 977 4.259690 GCTCACCTGCGTTAACGTAATTAG 60.260 45.833 27.28 17.71 42.22 1.73
951 978 3.613737 GCTCACCTGCGTTAACGTAATTA 59.386 43.478 27.28 9.32 42.22 1.40
952 979 2.414138 GCTCACCTGCGTTAACGTAATT 59.586 45.455 27.28 11.05 42.22 1.40
953 980 1.997606 GCTCACCTGCGTTAACGTAAT 59.002 47.619 27.28 12.53 42.22 1.89
954 981 1.000060 AGCTCACCTGCGTTAACGTAA 60.000 47.619 27.28 15.94 42.22 3.18
955 982 0.599558 AGCTCACCTGCGTTAACGTA 59.400 50.000 27.28 22.66 42.22 3.57
956 983 0.249741 AAGCTCACCTGCGTTAACGT 60.250 50.000 27.28 6.45 42.22 3.99
957 984 1.389106 GTAAGCTCACCTGCGTTAACG 59.611 52.381 23.40 23.40 43.27 3.18
958 985 1.389106 CGTAAGCTCACCTGCGTTAAC 59.611 52.381 0.00 0.00 38.13 2.01
959 986 1.670674 CCGTAAGCTCACCTGCGTTAA 60.671 52.381 0.00 0.00 38.13 2.01
960 987 0.108992 CCGTAAGCTCACCTGCGTTA 60.109 55.000 0.00 0.00 38.13 3.18
961 988 1.374252 CCGTAAGCTCACCTGCGTT 60.374 57.895 0.00 0.00 38.13 4.84
962 989 2.261671 CCGTAAGCTCACCTGCGT 59.738 61.111 0.00 0.00 38.13 5.24
963 990 1.805945 GACCGTAAGCTCACCTGCG 60.806 63.158 0.00 0.00 38.13 5.18
964 991 0.108138 ATGACCGTAAGCTCACCTGC 60.108 55.000 0.00 0.00 0.00 4.85
965 992 1.799181 CGATGACCGTAAGCTCACCTG 60.799 57.143 0.00 0.00 0.00 4.00
966 993 0.456221 CGATGACCGTAAGCTCACCT 59.544 55.000 0.00 0.00 0.00 4.00
967 994 1.146358 GCGATGACCGTAAGCTCACC 61.146 60.000 0.00 0.00 41.15 4.02
968 995 1.472276 CGCGATGACCGTAAGCTCAC 61.472 60.000 0.00 0.00 41.15 3.51
969 996 1.226575 CGCGATGACCGTAAGCTCA 60.227 57.895 0.00 0.00 41.15 4.26
970 997 2.577785 GCGCGATGACCGTAAGCTC 61.578 63.158 12.10 0.00 41.15 4.09
971 998 2.582498 GCGCGATGACCGTAAGCT 60.582 61.111 12.10 0.00 41.15 3.74
972 999 2.577785 GAGCGCGATGACCGTAAGC 61.578 63.158 12.10 0.00 41.15 3.09
973 1000 1.064296 AGAGCGCGATGACCGTAAG 59.936 57.895 12.10 0.00 41.15 2.34
974 1001 1.226575 CAGAGCGCGATGACCGTAA 60.227 57.895 12.10 0.00 41.15 3.18
975 1002 2.407616 CAGAGCGCGATGACCGTA 59.592 61.111 12.10 0.00 41.15 4.02
985 1012 2.077413 AGCTTATGATAGCAGAGCGC 57.923 50.000 0.00 0.00 43.68 5.92
986 1013 3.186001 CCAAAGCTTATGATAGCAGAGCG 59.814 47.826 0.00 1.22 43.68 5.03
987 1014 3.058363 GCCAAAGCTTATGATAGCAGAGC 60.058 47.826 0.00 10.24 43.68 4.09
988 1015 4.024218 GTGCCAAAGCTTATGATAGCAGAG 60.024 45.833 0.00 0.00 43.68 3.35
989 1016 3.879295 GTGCCAAAGCTTATGATAGCAGA 59.121 43.478 0.00 0.00 43.68 4.26
990 1017 3.303593 CGTGCCAAAGCTTATGATAGCAG 60.304 47.826 0.00 0.00 43.68 4.24
991 1018 2.613595 CGTGCCAAAGCTTATGATAGCA 59.386 45.455 0.00 0.00 43.68 3.49
992 1019 2.603173 GCGTGCCAAAGCTTATGATAGC 60.603 50.000 0.00 0.00 40.80 2.97
993 1020 2.031682 GGCGTGCCAAAGCTTATGATAG 60.032 50.000 5.89 0.00 40.80 2.08
994 1021 1.946768 GGCGTGCCAAAGCTTATGATA 59.053 47.619 5.89 0.00 40.80 2.15
995 1022 0.740737 GGCGTGCCAAAGCTTATGAT 59.259 50.000 5.89 0.00 40.80 2.45
996 1023 1.312371 GGGCGTGCCAAAGCTTATGA 61.312 55.000 13.76 0.00 40.80 2.15
997 1024 1.139520 GGGCGTGCCAAAGCTTATG 59.860 57.895 13.76 0.28 40.80 1.90
998 1025 2.406616 CGGGCGTGCCAAAGCTTAT 61.407 57.895 13.76 0.00 40.80 1.73
999 1026 3.053291 CGGGCGTGCCAAAGCTTA 61.053 61.111 13.76 0.00 40.80 3.09
1020 1047 3.883744 GAGACCCCACACACCAGCG 62.884 68.421 0.00 0.00 0.00 5.18
1021 1048 2.032681 GAGACCCCACACACCAGC 59.967 66.667 0.00 0.00 0.00 4.85
1022 1049 1.071471 GTGAGACCCCACACACCAG 59.929 63.158 0.00 0.00 37.04 4.00
1023 1050 1.383943 AGTGAGACCCCACACACCA 60.384 57.895 0.00 0.00 39.42 4.17
1024 1051 1.122019 AGAGTGAGACCCCACACACC 61.122 60.000 0.00 0.00 39.42 4.16
1025 1052 0.318762 GAGAGTGAGACCCCACACAC 59.681 60.000 0.00 0.00 39.42 3.82
1026 1053 0.105709 TGAGAGTGAGACCCCACACA 60.106 55.000 0.00 0.00 39.42 3.72
1027 1054 0.318762 GTGAGAGTGAGACCCCACAC 59.681 60.000 0.00 0.00 39.42 3.82
1028 1055 0.832135 GGTGAGAGTGAGACCCCACA 60.832 60.000 0.00 0.00 39.42 4.17
1029 1056 1.545706 GGGTGAGAGTGAGACCCCAC 61.546 65.000 0.00 0.00 43.30 4.61
1030 1057 1.229209 GGGTGAGAGTGAGACCCCA 60.229 63.158 0.00 0.00 43.30 4.96
1031 1058 3.715015 GGGTGAGAGTGAGACCCC 58.285 66.667 0.00 0.00 43.30 4.95
1033 1060 0.107945 GCATGGGTGAGAGTGAGACC 60.108 60.000 0.00 0.00 0.00 3.85
1034 1061 0.901124 AGCATGGGTGAGAGTGAGAC 59.099 55.000 0.00 0.00 0.00 3.36
1035 1062 1.552337 GAAGCATGGGTGAGAGTGAGA 59.448 52.381 0.00 0.00 0.00 3.27
1036 1063 1.406614 GGAAGCATGGGTGAGAGTGAG 60.407 57.143 0.00 0.00 0.00 3.51
1037 1064 0.615331 GGAAGCATGGGTGAGAGTGA 59.385 55.000 0.00 0.00 0.00 3.41
1048 1075 1.554392 CTCTCGAGTTCGGAAGCATG 58.446 55.000 13.13 0.00 40.29 4.06
1445 1472 2.433318 GCAGACGAGGCAGTGGAC 60.433 66.667 0.00 0.00 0.00 4.02
1908 1935 2.186384 GCATGTCGGAGAGCAGCT 59.814 61.111 0.00 0.00 36.95 4.24
1955 1982 2.271800 CTTGATCAGGACGTTGTAGCC 58.728 52.381 0.00 0.00 0.00 3.93
2203 2230 4.722700 GCTTCCTCCGCCTTGCCA 62.723 66.667 0.00 0.00 0.00 4.92
2239 2266 2.610859 ACCCCACTCTCCGCCATT 60.611 61.111 0.00 0.00 0.00 3.16
2459 2508 4.539870 CCAGGAGCATTATACATTTTGCG 58.460 43.478 0.00 0.00 40.00 4.85
2468 2517 6.319715 TGTCACTATACCCAGGAGCATTATA 58.680 40.000 0.00 0.00 0.00 0.98
2487 2536 5.105752 AGACTCGCATCTTTTATCTGTCAC 58.894 41.667 0.00 0.00 0.00 3.67
2490 2539 6.754209 CAGTAAGACTCGCATCTTTTATCTGT 59.246 38.462 6.35 0.00 39.65 3.41
2605 2654 2.550978 ACGACAGTTCTGAAAGTGGTG 58.449 47.619 6.83 3.51 39.69 4.17
2630 2684 2.640826 TCCTCACCCGGTGACTATTTTT 59.359 45.455 16.73 0.00 37.67 1.94
2646 2700 2.847234 ACAGGTGGCGGTTCCTCA 60.847 61.111 0.00 0.00 35.26 3.86
2653 2707 0.671796 TCGATATACACAGGTGGCGG 59.328 55.000 4.24 0.00 34.19 6.13
2707 2761 5.898630 AAATTGGTTTTCGATTCGGTTTG 57.101 34.783 6.18 0.00 0.00 2.93
2753 2807 9.334947 TCTGTTGATTGCAAAATTAATGGAAAA 57.665 25.926 1.71 0.00 35.42 2.29
2776 2830 9.552114 GATTCAAAACAGACTGATGTATTTCTG 57.448 33.333 10.08 0.00 41.14 3.02
2777 2831 8.446273 CGATTCAAAACAGACTGATGTATTTCT 58.554 33.333 10.08 0.00 31.70 2.52
2852 2906 0.326595 TGCCCCTCGCATTGTTAAGA 59.673 50.000 0.00 0.00 44.64 2.10
2893 2948 3.760035 GCGACGCTTCTCCCTGGA 61.760 66.667 13.73 0.00 0.00 3.86
2966 3021 2.179427 TGGAGGTATGTCCACTCACTG 58.821 52.381 0.00 0.00 41.99 3.66
2967 3022 2.623418 TGGAGGTATGTCCACTCACT 57.377 50.000 0.00 0.00 41.99 3.41
2993 3048 2.551270 TCTCTTTGGGCTATGACCACT 58.449 47.619 0.00 0.00 42.46 4.00
3081 3136 3.674997 TGAGGTTTCTCCAAATTCTCCG 58.325 45.455 0.00 0.00 39.23 4.63
3089 3144 4.408921 TGAACTTCTCTGAGGTTTCTCCAA 59.591 41.667 4.59 0.00 39.23 3.53
3210 3291 5.043903 ACAGATGATGGTCGTCGAATTTAG 58.956 41.667 0.00 0.00 37.48 1.85
3269 3350 2.926838 GTTGAATTGGTTGCGTGTGTTT 59.073 40.909 0.00 0.00 0.00 2.83
3284 3365 3.228188 TGAAGTGCCCTTCTGTTGAAT 57.772 42.857 10.38 0.00 46.07 2.57
3303 3384 8.099537 AGTCTATTTTGTATCTCTGGCCATATG 58.900 37.037 5.51 0.00 0.00 1.78
3384 3465 5.344743 TGAGAAATACTCCTAGTTGGCAG 57.655 43.478 0.00 0.00 44.34 4.85
3395 3476 6.495181 TGGGGAGATCTGTATGAGAAATACTC 59.505 42.308 0.00 0.00 45.11 2.59
3414 3498 8.862325 TGTACAATAGCATATTTAATGGGGAG 57.138 34.615 0.00 0.00 0.00 4.30
3428 3512 3.058570 CGCTTGTTGGTTGTACAATAGCA 60.059 43.478 12.26 9.55 39.11 3.49


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

AutoCloner maintained by Alex Coulton.