Multiple sequence alignment - TraesCS5B01G039400

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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 TraesCS5B01G039400 chr5B 100.000 2594 0 0 1 2594 44356705 44359298 0.000000e+00 4791
1 TraesCS5B01G039400 chr5B 93.905 886 50 3 1709 2594 453094783 453095664 0.000000e+00 1334
2 TraesCS5B01G039400 chr5B 87.162 888 103 10 9 891 188131934 188131053 0.000000e+00 998
3 TraesCS5B01G039400 chr5B 86.338 893 114 7 1 891 105341570 105342456 0.000000e+00 966
4 TraesCS5B01G039400 chr7B 94.382 890 46 4 1706 2594 302119477 302120363 0.000000e+00 1363
5 TraesCS5B01G039400 chr7B 94.250 887 50 1 1708 2594 545894646 545895531 0.000000e+00 1354
6 TraesCS5B01G039400 chr7B 86.735 882 103 13 1 876 394275081 394275954 0.000000e+00 968
7 TraesCS5B01G039400 chr4B 94.144 888 50 2 1708 2594 348833428 348834314 0.000000e+00 1351
8 TraesCS5B01G039400 chr4B 87.981 857 96 7 37 891 373841915 373841064 0.000000e+00 1005
9 TraesCS5B01G039400 chr1B 94.124 885 50 2 1708 2592 152082215 152083097 0.000000e+00 1345
10 TraesCS5B01G039400 chr1B 94.018 886 51 2 1709 2594 391921596 391922479 0.000000e+00 1341
11 TraesCS5B01G039400 chr6B 93.708 890 52 4 1706 2594 131502231 131503117 0.000000e+00 1330
12 TraesCS5B01G039400 chr6B 93.610 892 51 6 1703 2594 561442903 561442018 0.000000e+00 1327
13 TraesCS5B01G039400 chr6B 92.727 440 28 3 999 1438 648435871 648436306 1.310000e-177 632
14 TraesCS5B01G039400 chr6B 96.324 272 8 2 1436 1707 648442794 648443063 1.830000e-121 446
15 TraesCS5B01G039400 chr6B 98.095 105 1 1 893 997 648364195 648364298 5.700000e-42 182
16 TraesCS5B01G039400 chr2B 93.603 891 53 4 1705 2594 400846658 400847545 0.000000e+00 1327
17 TraesCS5B01G039400 chr2B 88.130 893 99 7 1 891 447262463 447263350 0.000000e+00 1055
18 TraesCS5B01G039400 chr2B 86.961 882 104 11 14 891 612976503 612977377 0.000000e+00 981
19 TraesCS5B01G039400 chr3B 88.914 875 84 12 1 870 350337421 350338287 0.000000e+00 1066
20 TraesCS5B01G039400 chr3B 87.903 868 92 11 25 887 802320318 802319459 0.000000e+00 1009
21 TraesCS5B01G039400 chr4D 87.256 871 98 11 25 891 331777649 331778510 0.000000e+00 981
22 TraesCS5B01G039400 chr4D 82.413 688 113 4 1026 1706 30426486 30427172 6.180000e-166 593
23 TraesCS5B01G039400 chr4D 82.096 687 112 10 1026 1706 30445452 30446133 6.220000e-161 577
24 TraesCS5B01G039400 chr4D 79.472 682 132 7 1029 1706 387464005 387463328 6.490000e-131 477
25 TraesCS5B01G039400 chr3D 81.599 788 122 15 928 1707 485062225 485061453 4.710000e-177 630
26 TraesCS5B01G039400 chr3D 81.805 687 114 10 1026 1706 510333817 510334498 1.350000e-157 566
27 TraesCS5B01G039400 chr1D 80.994 684 118 6 1026 1706 411778909 411778235 1.370000e-147 532


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 TraesCS5B01G039400 chr5B 44356705 44359298 2593 False 4791 4791 100.000 1 2594 1 chr5B.!!$F1 2593
1 TraesCS5B01G039400 chr5B 453094783 453095664 881 False 1334 1334 93.905 1709 2594 1 chr5B.!!$F3 885
2 TraesCS5B01G039400 chr5B 188131053 188131934 881 True 998 998 87.162 9 891 1 chr5B.!!$R1 882
3 TraesCS5B01G039400 chr5B 105341570 105342456 886 False 966 966 86.338 1 891 1 chr5B.!!$F2 890
4 TraesCS5B01G039400 chr7B 302119477 302120363 886 False 1363 1363 94.382 1706 2594 1 chr7B.!!$F1 888
5 TraesCS5B01G039400 chr7B 545894646 545895531 885 False 1354 1354 94.250 1708 2594 1 chr7B.!!$F3 886
6 TraesCS5B01G039400 chr7B 394275081 394275954 873 False 968 968 86.735 1 876 1 chr7B.!!$F2 875
7 TraesCS5B01G039400 chr4B 348833428 348834314 886 False 1351 1351 94.144 1708 2594 1 chr4B.!!$F1 886
8 TraesCS5B01G039400 chr4B 373841064 373841915 851 True 1005 1005 87.981 37 891 1 chr4B.!!$R1 854
9 TraesCS5B01G039400 chr1B 152082215 152083097 882 False 1345 1345 94.124 1708 2592 1 chr1B.!!$F1 884
10 TraesCS5B01G039400 chr1B 391921596 391922479 883 False 1341 1341 94.018 1709 2594 1 chr1B.!!$F2 885
11 TraesCS5B01G039400 chr6B 131502231 131503117 886 False 1330 1330 93.708 1706 2594 1 chr6B.!!$F1 888
12 TraesCS5B01G039400 chr6B 561442018 561442903 885 True 1327 1327 93.610 1703 2594 1 chr6B.!!$R1 891
13 TraesCS5B01G039400 chr2B 400846658 400847545 887 False 1327 1327 93.603 1705 2594 1 chr2B.!!$F1 889
14 TraesCS5B01G039400 chr2B 447262463 447263350 887 False 1055 1055 88.130 1 891 1 chr2B.!!$F2 890
15 TraesCS5B01G039400 chr2B 612976503 612977377 874 False 981 981 86.961 14 891 1 chr2B.!!$F3 877
16 TraesCS5B01G039400 chr3B 350337421 350338287 866 False 1066 1066 88.914 1 870 1 chr3B.!!$F1 869
17 TraesCS5B01G039400 chr3B 802319459 802320318 859 True 1009 1009 87.903 25 887 1 chr3B.!!$R1 862
18 TraesCS5B01G039400 chr4D 331777649 331778510 861 False 981 981 87.256 25 891 1 chr4D.!!$F3 866
19 TraesCS5B01G039400 chr4D 30426486 30427172 686 False 593 593 82.413 1026 1706 1 chr4D.!!$F1 680
20 TraesCS5B01G039400 chr4D 30445452 30446133 681 False 577 577 82.096 1026 1706 1 chr4D.!!$F2 680
21 TraesCS5B01G039400 chr4D 387463328 387464005 677 True 477 477 79.472 1029 1706 1 chr4D.!!$R1 677
22 TraesCS5B01G039400 chr3D 485061453 485062225 772 True 630 630 81.599 928 1707 1 chr3D.!!$R1 779
23 TraesCS5B01G039400 chr3D 510333817 510334498 681 False 566 566 81.805 1026 1706 1 chr3D.!!$F1 680
24 TraesCS5B01G039400 chr1D 411778235 411778909 674 True 532 532 80.994 1026 1706 1 chr1D.!!$R1 680

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
148 150 0.027586 AACAACTCGTTGCGCTTGTC 59.972 50.0 9.73 0.0 44.03 3.18 F
980 988 0.035343 GGGGCTTGGTTCAGGTACTC 60.035 60.0 0.00 0.0 34.60 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1004 1014 0.033090 AAACGTGGTTCTCGAGTCCC 59.967 55.0 13.13 13.59 0.0 4.46 R
2511 2533 0.544357 ATCTCCACCGTCAACCTCCA 60.544 55.0 0.00 0.00 0.0 3.86 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
93 95 5.286438 GGAATTACCATGGTAAAAATCGGC 58.714 41.667 34.93 19.95 42.82 5.54
98 100 0.634465 ATGGTAAAAATCGGCCCCCT 59.366 50.000 0.00 0.00 0.00 4.79
124 126 3.136123 CGCACCATTCTGGGCCTG 61.136 66.667 4.53 4.06 43.37 4.85
146 148 4.996113 AACAACTCGTTGCGCTTG 57.004 50.000 9.73 6.07 44.03 4.01
148 150 0.027586 AACAACTCGTTGCGCTTGTC 59.972 50.000 9.73 0.00 44.03 3.18
160 162 3.160585 CTTGTCTGTGGCCCAGGA 58.839 61.111 17.89 3.38 41.83 3.86
336 341 0.392327 GAAGAGCAAGAGGGTGAGGC 60.392 60.000 0.00 0.00 0.00 4.70
517 524 4.835284 TGGTGGCATGTAGATCTTTGTA 57.165 40.909 0.00 0.00 0.00 2.41
537 545 9.729023 CTTTGTAAAGATCATTAACACACACAA 57.271 29.630 0.00 0.00 38.28 3.33
538 546 9.509855 TTTGTAAAGATCATTAACACACACAAC 57.490 29.630 0.00 0.00 0.00 3.32
554 562 1.774254 ACAACATCAGGTGAGGACCAA 59.226 47.619 0.00 0.00 45.98 3.67
556 564 2.554032 CAACATCAGGTGAGGACCAAAC 59.446 50.000 0.00 0.00 45.98 2.93
654 662 1.202879 ACCTTTGCCGAGGACATCAAA 60.203 47.619 9.27 0.00 39.25 2.69
659 667 0.250513 GCCGAGGACATCAAAGAGGT 59.749 55.000 0.00 0.00 0.00 3.85
668 676 0.254178 ATCAAAGAGGTCGCAGCCAT 59.746 50.000 0.00 0.00 0.00 4.40
887 895 3.608662 TTGGACGCCCGTCGAAGT 61.609 61.111 12.99 0.00 45.41 3.01
891 899 2.360350 ACGCCCGTCGAAGTAGGA 60.360 61.111 0.00 0.00 41.67 2.94
892 900 1.926511 GACGCCCGTCGAAGTAGGAA 61.927 60.000 4.97 0.00 41.67 3.36
893 901 1.226603 CGCCCGTCGAAGTAGGAAG 60.227 63.158 0.00 0.00 41.67 3.46
894 902 1.651240 CGCCCGTCGAAGTAGGAAGA 61.651 60.000 0.00 0.00 41.67 2.87
895 903 0.745468 GCCCGTCGAAGTAGGAAGAT 59.255 55.000 0.00 0.00 0.00 2.40
896 904 1.952296 GCCCGTCGAAGTAGGAAGATA 59.048 52.381 0.00 0.00 0.00 1.98
897 905 2.030981 GCCCGTCGAAGTAGGAAGATAG 60.031 54.545 0.00 0.00 0.00 2.08
898 906 3.474600 CCCGTCGAAGTAGGAAGATAGA 58.525 50.000 0.00 0.00 0.00 1.98
899 907 3.499157 CCCGTCGAAGTAGGAAGATAGAG 59.501 52.174 0.00 0.00 0.00 2.43
900 908 4.378774 CCGTCGAAGTAGGAAGATAGAGA 58.621 47.826 0.00 0.00 0.00 3.10
901 909 4.815308 CCGTCGAAGTAGGAAGATAGAGAA 59.185 45.833 0.00 0.00 0.00 2.87
902 910 5.296283 CCGTCGAAGTAGGAAGATAGAGAAA 59.704 44.000 0.00 0.00 0.00 2.52
903 911 6.423862 CGTCGAAGTAGGAAGATAGAGAAAG 58.576 44.000 0.00 0.00 0.00 2.62
904 912 6.258287 CGTCGAAGTAGGAAGATAGAGAAAGA 59.742 42.308 0.00 0.00 0.00 2.52
905 913 7.517734 CGTCGAAGTAGGAAGATAGAGAAAGAG 60.518 44.444 0.00 0.00 0.00 2.85
906 914 6.261381 TCGAAGTAGGAAGATAGAGAAAGAGC 59.739 42.308 0.00 0.00 0.00 4.09
907 915 6.038825 CGAAGTAGGAAGATAGAGAAAGAGCA 59.961 42.308 0.00 0.00 0.00 4.26
908 916 7.415765 CGAAGTAGGAAGATAGAGAAAGAGCAA 60.416 40.741 0.00 0.00 0.00 3.91
909 917 7.107639 AGTAGGAAGATAGAGAAAGAGCAAC 57.892 40.000 0.00 0.00 0.00 4.17
910 918 6.665680 AGTAGGAAGATAGAGAAAGAGCAACA 59.334 38.462 0.00 0.00 0.00 3.33
911 919 6.365970 AGGAAGATAGAGAAAGAGCAACAA 57.634 37.500 0.00 0.00 0.00 2.83
912 920 6.773638 AGGAAGATAGAGAAAGAGCAACAAA 58.226 36.000 0.00 0.00 0.00 2.83
913 921 7.401246 AGGAAGATAGAGAAAGAGCAACAAAT 58.599 34.615 0.00 0.00 0.00 2.32
914 922 7.552330 AGGAAGATAGAGAAAGAGCAACAAATC 59.448 37.037 0.00 0.00 0.00 2.17
915 923 7.552330 GGAAGATAGAGAAAGAGCAACAAATCT 59.448 37.037 0.00 0.00 0.00 2.40
916 924 7.846644 AGATAGAGAAAGAGCAACAAATCTG 57.153 36.000 0.00 0.00 0.00 2.90
917 925 7.619050 AGATAGAGAAAGAGCAACAAATCTGA 58.381 34.615 0.00 0.00 0.00 3.27
918 926 7.765360 AGATAGAGAAAGAGCAACAAATCTGAG 59.235 37.037 0.00 0.00 0.00 3.35
919 927 5.619220 AGAGAAAGAGCAACAAATCTGAGT 58.381 37.500 0.00 0.00 0.00 3.41
920 928 6.060788 AGAGAAAGAGCAACAAATCTGAGTT 58.939 36.000 0.00 0.00 0.00 3.01
921 929 6.545298 AGAGAAAGAGCAACAAATCTGAGTTT 59.455 34.615 0.00 0.00 0.00 2.66
922 930 7.067981 AGAGAAAGAGCAACAAATCTGAGTTTT 59.932 33.333 0.00 0.00 0.00 2.43
923 931 7.550712 AGAAAGAGCAACAAATCTGAGTTTTT 58.449 30.769 0.00 0.00 0.00 1.94
924 932 7.490402 AGAAAGAGCAACAAATCTGAGTTTTTG 59.510 33.333 11.20 11.20 38.49 2.44
925 933 5.594926 AGAGCAACAAATCTGAGTTTTTGG 58.405 37.500 15.69 1.99 37.19 3.28
926 934 5.127682 AGAGCAACAAATCTGAGTTTTTGGT 59.872 36.000 17.69 17.69 37.19 3.67
929 937 6.335176 CAACAAATCTGAGTTTTTGGTGTG 57.665 37.500 15.51 7.87 42.71 3.82
930 938 5.913137 ACAAATCTGAGTTTTTGGTGTGA 57.087 34.783 12.61 0.00 37.19 3.58
931 939 5.894807 ACAAATCTGAGTTTTTGGTGTGAG 58.105 37.500 12.61 0.00 37.19 3.51
932 940 5.163519 ACAAATCTGAGTTTTTGGTGTGAGG 60.164 40.000 12.61 0.00 37.19 3.86
933 941 2.297701 TCTGAGTTTTTGGTGTGAGGC 58.702 47.619 0.00 0.00 0.00 4.70
934 942 1.002468 CTGAGTTTTTGGTGTGAGGCG 60.002 52.381 0.00 0.00 0.00 5.52
935 943 0.310854 GAGTTTTTGGTGTGAGGCGG 59.689 55.000 0.00 0.00 0.00 6.13
936 944 1.299850 GTTTTTGGTGTGAGGCGGC 60.300 57.895 0.00 0.00 0.00 6.53
937 945 2.840066 TTTTTGGTGTGAGGCGGCG 61.840 57.895 0.51 0.51 0.00 6.46
942 950 4.760047 GTGTGAGGCGGCGGTGAT 62.760 66.667 9.78 0.00 0.00 3.06
947 955 1.154035 GAGGCGGCGGTGATTTTTG 60.154 57.895 9.78 0.00 0.00 2.44
960 968 1.202348 GATTTTTGGAGGCGTTCAGGG 59.798 52.381 0.00 0.00 0.00 4.45
977 985 3.503099 GGGGGCTTGGTTCAGGTA 58.497 61.111 0.00 0.00 0.00 3.08
979 987 1.498176 GGGGGCTTGGTTCAGGTACT 61.498 60.000 0.00 0.00 43.88 2.73
980 988 0.035343 GGGGCTTGGTTCAGGTACTC 60.035 60.000 0.00 0.00 34.60 2.59
981 989 0.035343 GGGCTTGGTTCAGGTACTCC 60.035 60.000 0.00 0.00 34.60 3.85
983 991 0.690762 GCTTGGTTCAGGTACTCCCA 59.309 55.000 0.00 0.00 34.60 4.37
984 992 1.339151 GCTTGGTTCAGGTACTCCCAG 60.339 57.143 0.00 0.00 34.60 4.45
985 993 1.978580 CTTGGTTCAGGTACTCCCAGT 59.021 52.381 0.00 0.00 34.60 4.00
986 994 3.170717 CTTGGTTCAGGTACTCCCAGTA 58.829 50.000 0.00 0.00 34.60 2.74
987 995 2.816411 TGGTTCAGGTACTCCCAGTAG 58.184 52.381 0.00 0.00 34.60 2.57
989 997 3.012502 TGGTTCAGGTACTCCCAGTAGAT 59.987 47.826 0.00 0.00 34.60 1.98
996 1006 0.399233 ACTCCCAGTAGATCCCAGCC 60.399 60.000 0.00 0.00 0.00 4.85
1013 1023 2.202932 CGCAATGGGGGACTCGAG 60.203 66.667 11.84 11.84 0.00 4.04
1014 1024 2.721167 CGCAATGGGGGACTCGAGA 61.721 63.158 21.68 0.00 0.00 4.04
1019 1029 1.265454 ATGGGGGACTCGAGAACCAC 61.265 60.000 21.68 20.98 0.00 4.16
1024 1034 1.539712 GGGACTCGAGAACCACGTTTT 60.540 52.381 21.68 0.00 0.00 2.43
1038 1048 3.129638 CCACGTTTTTGGAAGGAGTTCAA 59.870 43.478 0.00 0.00 39.24 2.69
1041 1051 3.630312 CGTTTTTGGAAGGAGTTCAAGGA 59.370 43.478 0.00 0.00 33.93 3.36
1045 1055 6.806668 TTTTGGAAGGAGTTCAAGGAAAAT 57.193 33.333 0.00 0.00 33.93 1.82
1062 1072 4.683320 GGAAAATTCAAGAACTTGCAGCTC 59.317 41.667 9.38 3.41 40.24 4.09
1066 1076 3.037431 TCAAGAACTTGCAGCTCTCTC 57.963 47.619 9.38 0.00 40.24 3.20
1070 1080 2.075338 GAACTTGCAGCTCTCTCAAGG 58.925 52.381 14.94 2.98 40.93 3.61
1071 1081 1.346062 ACTTGCAGCTCTCTCAAGGA 58.654 50.000 14.94 0.00 40.93 3.36
1136 1146 2.779506 GCAGGTAAACAAGCTACAGGT 58.220 47.619 0.00 0.00 33.59 4.00
1176 1186 1.040339 AGAGGCCGGTTAGAGCAGAG 61.040 60.000 1.90 0.00 0.00 3.35
1191 1201 1.964552 CAGAGCATGTGGGAAGATCC 58.035 55.000 0.00 0.00 35.23 3.36
1213 1228 2.160646 GGGGGAGTTTGGAGTCCAA 58.839 57.895 21.05 21.05 45.69 3.53
1232 1247 4.073549 CCAATTTTTGGTGTGGAATGCAT 58.926 39.130 0.00 0.00 45.93 3.96
1236 1251 5.798125 TTTTTGGTGTGGAATGCATAGAA 57.202 34.783 0.00 0.00 0.00 2.10
1237 1252 5.999205 TTTTGGTGTGGAATGCATAGAAT 57.001 34.783 0.00 0.00 0.00 2.40
1243 1258 1.955778 TGGAATGCATAGAATTGGGCG 59.044 47.619 0.00 0.00 0.00 6.13
1250 1265 2.862541 CATAGAATTGGGCGGGAATCA 58.137 47.619 0.00 0.00 0.00 2.57
1251 1266 3.424703 CATAGAATTGGGCGGGAATCAT 58.575 45.455 0.00 0.00 0.00 2.45
1269 1284 8.753133 GGGAATCATTTTCTCTTTACTTTCCAT 58.247 33.333 0.00 0.00 32.45 3.41
1317 1332 0.842635 ATGCTGGACCCTGGAGATTC 59.157 55.000 0.00 0.00 0.00 2.52
1327 1342 3.074390 ACCCTGGAGATTCAACAATGACA 59.926 43.478 0.00 0.00 34.61 3.58
1353 1368 2.099098 GGTAATGGAGGATTTTGTGCCG 59.901 50.000 0.00 0.00 0.00 5.69
1362 1377 3.008049 AGGATTTTGTGCCGAGTAGAACT 59.992 43.478 0.00 0.00 0.00 3.01
1443 1458 2.098117 GGGGATGATGAGCAAAGAAACG 59.902 50.000 0.00 0.00 0.00 3.60
1447 1462 3.071874 TGATGAGCAAAGAAACGGGAT 57.928 42.857 0.00 0.00 0.00 3.85
1479 1494 5.644206 GGGAGAACAAGTTGGAGAAGTTATC 59.356 44.000 7.96 0.00 31.64 1.75
1497 1512 0.824109 TCGATGTGGACCTGGATGTC 59.176 55.000 0.00 0.00 34.42 3.06
1566 1581 7.862274 AGATATCACAGTCCCAATTATGAGA 57.138 36.000 5.32 0.00 0.00 3.27
1570 1585 9.872684 ATATCACAGTCCCAATTATGAGATTTT 57.127 29.630 0.00 0.00 0.00 1.82
1607 1622 6.139679 TGGGGAATAAGAAGAACATGAACT 57.860 37.500 0.00 0.00 0.00 3.01
1608 1623 7.265599 TGGGGAATAAGAAGAACATGAACTA 57.734 36.000 0.00 0.00 0.00 2.24
1610 1625 7.037586 TGGGGAATAAGAAGAACATGAACTAGT 60.038 37.037 0.00 0.00 0.00 2.57
1631 1646 6.715347 AGTAAATGAAATGATACTTGGGGC 57.285 37.500 0.00 0.00 28.69 5.80
1635 1650 3.620488 TGAAATGATACTTGGGGCAGAC 58.380 45.455 0.00 0.00 0.00 3.51
1647 1662 0.103937 GGGCAGACGATGAAGAGGAG 59.896 60.000 0.00 0.00 0.00 3.69
1654 1671 3.053991 AGACGATGAAGAGGAGAAGAGGA 60.054 47.826 0.00 0.00 0.00 3.71
1655 1672 3.697045 GACGATGAAGAGGAGAAGAGGAA 59.303 47.826 0.00 0.00 0.00 3.36
1695 1713 5.734720 TGCGGAAAAGATTGTCTCTCTTAT 58.265 37.500 0.00 0.00 32.72 1.73
1754 1773 2.159085 ACATTTTGGGCCGAACGAAAAA 60.159 40.909 5.46 2.49 33.01 1.94
1788 1807 8.166422 TCATACATATGACACTTCTATGACGT 57.834 34.615 10.38 0.00 37.76 4.34
1962 1983 1.078356 GAAGCGAGGGGGAGGAAAC 60.078 63.158 0.00 0.00 0.00 2.78
2056 2077 1.876416 GCGTTGGCTCTAACTGAACCA 60.876 52.381 0.00 0.00 39.00 3.67
2099 2120 1.904287 AAACCCGAGCAATTGCACTA 58.096 45.000 30.89 0.00 45.16 2.74
2160 2181 3.670625 CTGTTAACTGAACCCGATGGAA 58.329 45.455 7.22 0.00 37.22 3.53
2255 2277 2.111043 AGTGAGTGGTGGCGTTGG 59.889 61.111 0.00 0.00 0.00 3.77
2267 2289 0.749454 GGCGTTGGCTCTGGATGAAT 60.749 55.000 0.00 0.00 39.81 2.57
2275 2297 2.334023 GCTCTGGATGAATAGGACCCT 58.666 52.381 0.00 0.00 0.00 4.34
2295 2317 1.082019 TGGTGTGGAGGGCTGGATA 59.918 57.895 0.00 0.00 0.00 2.59
2418 2440 1.221021 GACGATGGAGGGGTGGTTC 59.779 63.158 0.00 0.00 0.00 3.62
2428 2450 2.772515 GAGGGGTGGTTCAATAGTAGCT 59.227 50.000 0.00 0.00 0.00 3.32
2461 2483 1.153289 CGGTGGAGGCTGGATGAAG 60.153 63.158 0.00 0.00 0.00 3.02
2518 2540 2.121963 TGGAGGCTGGTGGAGGTT 60.122 61.111 0.00 0.00 0.00 3.50
2578 2600 3.315949 GTACGCCACACCCCTCCA 61.316 66.667 0.00 0.00 0.00 3.86
2579 2601 3.315949 TACGCCACACCCCTCCAC 61.316 66.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 71 5.737922 GCCGATTTTTACCATGGTAATTCCC 60.738 44.000 32.67 21.60 39.87 3.97
135 137 2.243957 CCACAGACAAGCGCAACGA 61.244 57.895 11.47 0.00 0.00 3.85
209 213 1.852067 CTGCCCGTGCACAGGTAAAC 61.852 60.000 20.15 4.35 44.23 2.01
251 256 1.138568 CCCTCATCTTCCCTGCTCAT 58.861 55.000 0.00 0.00 0.00 2.90
517 524 7.939782 TGATGTTGTGTGTGTTAATGATCTTT 58.060 30.769 0.00 0.00 0.00 2.52
535 543 2.554032 GTTTGGTCCTCACCTGATGTTG 59.446 50.000 0.00 0.00 44.17 3.33
537 545 1.270839 CGTTTGGTCCTCACCTGATGT 60.271 52.381 0.00 0.00 44.17 3.06
538 546 1.001974 TCGTTTGGTCCTCACCTGATG 59.998 52.381 0.00 0.00 44.17 3.07
637 645 2.426522 CTCTTTGATGTCCTCGGCAAA 58.573 47.619 0.00 0.00 0.00 3.68
697 705 2.829003 CTGGCAGCTGCATGGGAG 60.829 66.667 37.63 20.72 44.36 4.30
787 795 4.152284 TCTTCATGAAGATCTGCATGCT 57.848 40.909 31.68 4.13 42.06 3.79
870 878 2.203972 CTACTTCGACGGGCGTCCAA 62.204 60.000 6.96 0.00 41.76 3.53
878 886 4.378774 TCTCTATCTTCCTACTTCGACGG 58.621 47.826 0.00 0.00 0.00 4.79
887 895 7.482169 TTGTTGCTCTTTCTCTATCTTCCTA 57.518 36.000 0.00 0.00 0.00 2.94
891 899 8.099537 TCAGATTTGTTGCTCTTTCTCTATCTT 58.900 33.333 0.00 0.00 0.00 2.40
892 900 7.619050 TCAGATTTGTTGCTCTTTCTCTATCT 58.381 34.615 0.00 0.00 0.00 1.98
893 901 7.548780 ACTCAGATTTGTTGCTCTTTCTCTATC 59.451 37.037 0.00 0.00 0.00 2.08
894 902 7.393216 ACTCAGATTTGTTGCTCTTTCTCTAT 58.607 34.615 0.00 0.00 0.00 1.98
895 903 6.763355 ACTCAGATTTGTTGCTCTTTCTCTA 58.237 36.000 0.00 0.00 0.00 2.43
896 904 5.619220 ACTCAGATTTGTTGCTCTTTCTCT 58.381 37.500 0.00 0.00 0.00 3.10
897 905 5.938438 ACTCAGATTTGTTGCTCTTTCTC 57.062 39.130 0.00 0.00 0.00 2.87
898 906 6.705863 AAACTCAGATTTGTTGCTCTTTCT 57.294 33.333 0.00 0.00 0.00 2.52
899 907 7.254218 CCAAAAACTCAGATTTGTTGCTCTTTC 60.254 37.037 0.00 0.00 35.30 2.62
900 908 6.536224 CCAAAAACTCAGATTTGTTGCTCTTT 59.464 34.615 0.00 0.00 35.30 2.52
901 909 6.044682 CCAAAAACTCAGATTTGTTGCTCTT 58.955 36.000 0.00 0.00 35.30 2.85
902 910 5.127682 ACCAAAAACTCAGATTTGTTGCTCT 59.872 36.000 0.00 0.00 35.30 4.09
903 911 5.232838 CACCAAAAACTCAGATTTGTTGCTC 59.767 40.000 0.00 0.00 35.30 4.26
904 912 5.111293 CACCAAAAACTCAGATTTGTTGCT 58.889 37.500 0.00 0.00 35.30 3.91
905 913 4.869861 ACACCAAAAACTCAGATTTGTTGC 59.130 37.500 5.57 0.00 33.72 4.17
906 914 6.098679 TCACACCAAAAACTCAGATTTGTTG 58.901 36.000 6.85 5.68 35.73 3.33
907 915 6.279513 TCACACCAAAAACTCAGATTTGTT 57.720 33.333 6.85 0.00 35.30 2.83
908 916 5.163519 CCTCACACCAAAAACTCAGATTTGT 60.164 40.000 6.85 0.00 35.30 2.83
909 917 5.284079 CCTCACACCAAAAACTCAGATTTG 58.716 41.667 1.99 1.99 36.52 2.32
910 918 4.202151 GCCTCACACCAAAAACTCAGATTT 60.202 41.667 0.00 0.00 0.00 2.17
911 919 3.319122 GCCTCACACCAAAAACTCAGATT 59.681 43.478 0.00 0.00 0.00 2.40
912 920 2.887152 GCCTCACACCAAAAACTCAGAT 59.113 45.455 0.00 0.00 0.00 2.90
913 921 2.297701 GCCTCACACCAAAAACTCAGA 58.702 47.619 0.00 0.00 0.00 3.27
914 922 1.002468 CGCCTCACACCAAAAACTCAG 60.002 52.381 0.00 0.00 0.00 3.35
915 923 1.021202 CGCCTCACACCAAAAACTCA 58.979 50.000 0.00 0.00 0.00 3.41
916 924 0.310854 CCGCCTCACACCAAAAACTC 59.689 55.000 0.00 0.00 0.00 3.01
917 925 1.734388 GCCGCCTCACACCAAAAACT 61.734 55.000 0.00 0.00 0.00 2.66
918 926 1.299850 GCCGCCTCACACCAAAAAC 60.300 57.895 0.00 0.00 0.00 2.43
919 927 2.840066 CGCCGCCTCACACCAAAAA 61.840 57.895 0.00 0.00 0.00 1.94
920 928 3.283684 CGCCGCCTCACACCAAAA 61.284 61.111 0.00 0.00 0.00 2.44
925 933 4.760047 ATCACCGCCGCCTCACAC 62.760 66.667 0.00 0.00 0.00 3.82
926 934 3.545124 AAATCACCGCCGCCTCACA 62.545 57.895 0.00 0.00 0.00 3.58
927 935 1.862602 AAAAATCACCGCCGCCTCAC 61.863 55.000 0.00 0.00 0.00 3.51
928 936 1.602323 AAAAATCACCGCCGCCTCA 60.602 52.632 0.00 0.00 0.00 3.86
929 937 1.154035 CAAAAATCACCGCCGCCTC 60.154 57.895 0.00 0.00 0.00 4.70
930 938 2.635443 CCAAAAATCACCGCCGCCT 61.635 57.895 0.00 0.00 0.00 5.52
931 939 2.126110 CCAAAAATCACCGCCGCC 60.126 61.111 0.00 0.00 0.00 6.13
932 940 1.154035 CTCCAAAAATCACCGCCGC 60.154 57.895 0.00 0.00 0.00 6.53
933 941 1.506262 CCTCCAAAAATCACCGCCG 59.494 57.895 0.00 0.00 0.00 6.46
934 942 1.215382 GCCTCCAAAAATCACCGCC 59.785 57.895 0.00 0.00 0.00 6.13
935 943 1.154035 CGCCTCCAAAAATCACCGC 60.154 57.895 0.00 0.00 0.00 5.68
936 944 0.596082 AACGCCTCCAAAAATCACCG 59.404 50.000 0.00 0.00 0.00 4.94
937 945 1.611491 TGAACGCCTCCAAAAATCACC 59.389 47.619 0.00 0.00 0.00 4.02
938 946 2.351738 CCTGAACGCCTCCAAAAATCAC 60.352 50.000 0.00 0.00 0.00 3.06
939 947 1.885887 CCTGAACGCCTCCAAAAATCA 59.114 47.619 0.00 0.00 0.00 2.57
940 948 1.202348 CCCTGAACGCCTCCAAAAATC 59.798 52.381 0.00 0.00 0.00 2.17
941 949 1.256812 CCCTGAACGCCTCCAAAAAT 58.743 50.000 0.00 0.00 0.00 1.82
942 950 0.825840 CCCCTGAACGCCTCCAAAAA 60.826 55.000 0.00 0.00 0.00 1.94
960 968 1.001269 GTACCTGAACCAAGCCCCC 60.001 63.158 0.00 0.00 0.00 5.40
963 971 0.035343 GGGAGTACCTGAACCAAGCC 60.035 60.000 0.00 0.00 35.85 4.35
965 973 1.978580 ACTGGGAGTACCTGAACCAAG 59.021 52.381 5.06 0.00 40.42 3.61
969 977 3.637694 GGATCTACTGGGAGTACCTGAAC 59.362 52.174 5.06 0.00 40.42 3.18
971 979 2.177233 GGGATCTACTGGGAGTACCTGA 59.823 54.545 5.06 0.00 40.42 3.86
972 980 2.091278 TGGGATCTACTGGGAGTACCTG 60.091 54.545 0.00 0.00 43.37 4.00
973 981 2.178106 CTGGGATCTACTGGGAGTACCT 59.822 54.545 0.00 0.00 41.11 3.08
974 982 2.599677 CTGGGATCTACTGGGAGTACC 58.400 57.143 0.00 0.00 40.81 3.34
975 983 1.964933 GCTGGGATCTACTGGGAGTAC 59.035 57.143 0.00 0.00 0.00 2.73
976 984 1.133136 GGCTGGGATCTACTGGGAGTA 60.133 57.143 0.00 0.00 0.00 2.59
977 985 0.399233 GGCTGGGATCTACTGGGAGT 60.399 60.000 0.00 0.00 0.00 3.85
979 987 1.457643 CGGCTGGGATCTACTGGGA 60.458 63.158 0.00 0.00 0.00 4.37
980 988 3.142393 CGGCTGGGATCTACTGGG 58.858 66.667 0.00 0.00 0.00 4.45
981 989 1.971505 TTGCGGCTGGGATCTACTGG 61.972 60.000 0.00 0.00 0.00 4.00
983 991 0.107456 CATTGCGGCTGGGATCTACT 59.893 55.000 0.00 0.00 0.00 2.57
984 992 0.886490 CCATTGCGGCTGGGATCTAC 60.886 60.000 0.00 0.00 0.00 2.59
985 993 1.451504 CCATTGCGGCTGGGATCTA 59.548 57.895 0.00 0.00 0.00 1.98
986 994 2.194056 CCATTGCGGCTGGGATCT 59.806 61.111 0.00 0.00 0.00 2.75
996 1006 2.202932 CTCGAGTCCCCCATTGCG 60.203 66.667 3.62 0.00 0.00 4.85
1004 1014 0.033090 AAACGTGGTTCTCGAGTCCC 59.967 55.000 13.13 13.59 0.00 4.46
1010 1020 2.286772 CCTTCCAAAAACGTGGTTCTCG 60.287 50.000 0.00 0.00 39.88 4.04
1013 1023 2.686405 ACTCCTTCCAAAAACGTGGTTC 59.314 45.455 0.00 0.00 39.88 3.62
1014 1024 2.730382 ACTCCTTCCAAAAACGTGGTT 58.270 42.857 0.00 0.00 39.88 3.67
1019 1029 3.630312 TCCTTGAACTCCTTCCAAAAACG 59.370 43.478 0.00 0.00 0.00 3.60
1024 1034 5.896678 TGAATTTTCCTTGAACTCCTTCCAA 59.103 36.000 0.00 0.00 0.00 3.53
1038 1048 4.343239 AGCTGCAAGTTCTTGAATTTTCCT 59.657 37.500 15.52 0.45 35.30 3.36
1066 1076 4.704057 CCTGATTCCCTTTTTCTCTCCTTG 59.296 45.833 0.00 0.00 0.00 3.61
1070 1080 5.359292 CCAATCCTGATTCCCTTTTTCTCTC 59.641 44.000 0.00 0.00 0.00 3.20
1071 1081 5.015603 TCCAATCCTGATTCCCTTTTTCTCT 59.984 40.000 0.00 0.00 0.00 3.10
1119 1129 4.694037 CCTACAACCTGTAGCTTGTTTACC 59.306 45.833 8.09 0.00 46.72 2.85
1124 1134 5.071384 AGTTTACCTACAACCTGTAGCTTGT 59.929 40.000 8.09 0.00 46.72 3.16
1136 1146 6.434652 CCTCTCTGAGAGAAGTTTACCTACAA 59.565 42.308 31.14 0.00 45.07 2.41
1176 1186 1.396653 CCAAGGATCTTCCCACATGC 58.603 55.000 0.00 0.00 37.19 4.06
1213 1228 5.999205 TCTATGCATTCCACACCAAAAAT 57.001 34.783 3.54 0.00 0.00 1.82
1232 1247 3.593442 AATGATTCCCGCCCAATTCTA 57.407 42.857 0.00 0.00 0.00 2.10
1236 1251 2.695147 GAGAAAATGATTCCCGCCCAAT 59.305 45.455 0.00 0.00 0.00 3.16
1237 1252 2.099405 GAGAAAATGATTCCCGCCCAA 58.901 47.619 0.00 0.00 0.00 4.12
1243 1258 8.122472 TGGAAAGTAAAGAGAAAATGATTCCC 57.878 34.615 0.00 0.00 33.37 3.97
1275 1290 4.777896 TCTAGTGCCTTATCCTTGTCAGTT 59.222 41.667 0.00 0.00 0.00 3.16
1327 1342 5.337491 GCACAAAATCCTCCATTACCAACAT 60.337 40.000 0.00 0.00 0.00 2.71
1335 1350 2.094675 CTCGGCACAAAATCCTCCATT 58.905 47.619 0.00 0.00 0.00 3.16
1443 1458 1.490490 TGTTCTCCCACTGCATATCCC 59.510 52.381 0.00 0.00 0.00 3.85
1447 1462 3.411446 CAACTTGTTCTCCCACTGCATA 58.589 45.455 0.00 0.00 0.00 3.14
1479 1494 3.369381 GACATCCAGGTCCACATCG 57.631 57.895 0.00 0.00 0.00 3.84
1497 1512 3.022557 ACTCCCATTGAATCACCATGG 57.977 47.619 11.19 11.19 0.00 3.66
1586 1601 9.886132 TTACTAGTTCATGTTCTTCTTATTCCC 57.114 33.333 0.00 0.00 0.00 3.97
1605 1620 7.502561 GCCCCAAGTATCATTTCATTTACTAGT 59.497 37.037 0.00 0.00 0.00 2.57
1607 1622 7.350382 TGCCCCAAGTATCATTTCATTTACTA 58.650 34.615 0.00 0.00 0.00 1.82
1608 1623 6.194235 TGCCCCAAGTATCATTTCATTTACT 58.806 36.000 0.00 0.00 0.00 2.24
1610 1625 6.321181 GTCTGCCCCAAGTATCATTTCATTTA 59.679 38.462 0.00 0.00 0.00 1.40
1631 1646 3.066621 CCTCTTCTCCTCTTCATCGTCTG 59.933 52.174 0.00 0.00 0.00 3.51
1635 1650 4.727507 TTTCCTCTTCTCCTCTTCATCG 57.272 45.455 0.00 0.00 0.00 3.84
1655 1672 7.841915 TTTCCGCATTTTCTTTCTTCTTTTT 57.158 28.000 0.00 0.00 0.00 1.94
1672 1690 3.685139 AGAGAGACAATCTTTTCCGCA 57.315 42.857 0.00 0.00 38.84 5.69
1788 1807 5.768662 TGATACCGGGTTTTGTCACAATTAA 59.231 36.000 4.31 0.00 0.00 1.40
1942 1962 1.553690 TTTCCTCCCCCTCGCTTCTG 61.554 60.000 0.00 0.00 0.00 3.02
2015 2036 0.587768 TCGCACGTGTACGAGAGAAA 59.412 50.000 18.38 0.00 43.02 2.52
2056 2077 3.397613 GAGCCCAATGCCTCGCTCT 62.398 63.158 0.00 0.00 43.51 4.09
2255 2277 2.038295 CAGGGTCCTATTCATCCAGAGC 59.962 54.545 0.00 0.00 0.00 4.09
2275 2297 3.569210 CCAGCCCTCCACACCACA 61.569 66.667 0.00 0.00 0.00 4.17
2295 2317 1.978580 CCCCTCCACTGTCTACTGTTT 59.021 52.381 0.00 0.00 0.00 2.83
2418 2440 3.551046 CGCTACTCCACCAGCTACTATTG 60.551 52.174 0.00 0.00 35.57 1.90
2428 2450 4.063967 CCGTGCGCTACTCCACCA 62.064 66.667 9.73 0.00 0.00 4.17
2511 2533 0.544357 ATCTCCACCGTCAACCTCCA 60.544 55.000 0.00 0.00 0.00 3.86
2518 2540 1.338107 ACTGTTCATCTCCACCGTCA 58.662 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.