Multiple sequence alignment - TraesCS3B01G499900

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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 TraesCS3B01G499900 chr3B 100.000 4442 0 0 1 4442 744513995 744509554 0.000000e+00 8203.0
1 TraesCS3B01G499900 chr3B 97.857 1353 25 2 2346 3695 747385557 747386908 0.000000e+00 2335.0
2 TraesCS3B01G499900 chr3B 92.436 1256 80 5 1004 2257 747384314 747385556 0.000000e+00 1779.0
3 TraesCS3B01G499900 chr3B 92.040 1294 53 26 913 2167 747330230 747331512 0.000000e+00 1773.0
4 TraesCS3B01G499900 chr3B 87.776 1088 106 13 1069 2153 747093709 747094772 0.000000e+00 1247.0
5 TraesCS3B01G499900 chr3B 87.097 1085 119 7 1069 2153 744546729 744545666 0.000000e+00 1208.0
6 TraesCS3B01G499900 chr3B 84.732 1120 149 17 1009 2127 744590517 744591615 0.000000e+00 1101.0
7 TraesCS3B01G499900 chr3B 84.643 1120 150 17 1009 2127 746856441 746855343 0.000000e+00 1096.0
8 TraesCS3B01G499900 chr3B 83.375 1203 160 25 995 2192 747492958 747494125 0.000000e+00 1077.0
9 TraesCS3B01G499900 chr3B 87.689 926 107 7 1065 1987 745203414 745202493 0.000000e+00 1072.0
10 TraesCS3B01G499900 chr3B 86.927 872 91 12 1 866 240265915 240266769 0.000000e+00 957.0
11 TraesCS3B01G499900 chr3B 88.648 784 54 22 2331 3103 747331609 747332368 0.000000e+00 922.0
12 TraesCS3B01G499900 chr3B 97.835 462 8 2 3981 4442 747390033 747390492 0.000000e+00 797.0
13 TraesCS3B01G499900 chr3B 85.857 601 59 12 2645 3238 747095215 747095796 2.270000e-172 616.0
14 TraesCS3B01G499900 chr3B 86.071 560 56 15 2645 3184 744545226 744544669 2.300000e-162 582.0
15 TraesCS3B01G499900 chr3B 84.906 530 68 8 2600 3127 747494466 747494985 3.940000e-145 525.0
16 TraesCS3B01G499900 chr3B 95.849 265 9 1 3692 3956 747386952 747387214 1.140000e-115 427.0
17 TraesCS3B01G499900 chr3B 86.758 219 22 3 2378 2589 745473735 745473517 2.070000e-58 237.0
18 TraesCS3B01G499900 chr3B 86.239 218 26 4 2371 2585 744591681 744591897 2.670000e-57 233.0
19 TraesCS3B01G499900 chr3B 86.239 218 26 4 2371 2585 746855277 746855061 2.670000e-57 233.0
20 TraesCS3B01G499900 chr3B 93.137 102 6 1 4341 4442 50926191 50926291 9.950000e-32 148.0
21 TraesCS3B01G499900 chr3B 90.385 104 10 0 3249 3352 747495021 747495124 2.150000e-28 137.0
22 TraesCS3B01G499900 chr3D 91.852 1215 69 5 968 2167 560269694 560268495 0.000000e+00 1668.0
23 TraesCS3B01G499900 chr3D 92.617 921 46 8 2331 3238 560268396 560267485 0.000000e+00 1304.0
24 TraesCS3B01G499900 chr3D 86.094 1129 131 15 1035 2153 560551529 560552641 0.000000e+00 1192.0
25 TraesCS3B01G499900 chr3D 82.824 1275 165 36 940 2208 560235237 560234011 0.000000e+00 1092.0
26 TraesCS3B01G499900 chr3D 88.613 483 48 6 2650 3126 560285221 560284740 8.280000e-162 580.0
27 TraesCS3B01G499900 chr3D 79.717 848 114 35 2317 3127 560827928 560828754 1.080000e-155 560.0
28 TraesCS3B01G499900 chr3D 85.379 383 40 7 501 869 143620917 143621297 2.510000e-102 383.0
29 TraesCS3B01G499900 chr3D 92.899 169 12 0 2379 2547 560478889 560479057 3.430000e-61 246.0
30 TraesCS3B01G499900 chr3D 85.398 226 28 4 2371 2592 560332218 560332442 3.460000e-56 230.0
31 TraesCS3B01G499900 chr3D 97.500 40 1 0 2192 2231 560268488 560268449 7.970000e-08 69.4
32 TraesCS3B01G499900 chr3A 87.717 1270 75 16 913 2167 696344975 696343772 0.000000e+00 1406.0
33 TraesCS3B01G499900 chr3A 91.562 1031 67 11 2331 3352 696343674 696342655 0.000000e+00 1404.0
34 TraesCS3B01G499900 chr3A 86.544 1085 125 7 1069 2153 629056478 629057541 0.000000e+00 1175.0
35 TraesCS3B01G499900 chr3A 88.406 483 48 7 2645 3121 629057931 629058411 3.850000e-160 575.0
36 TraesCS3B01G499900 chr3A 91.000 400 25 4 3550 3946 696342119 696341728 3.040000e-146 529.0
37 TraesCS3B01G499900 chr3A 88.788 330 35 2 3371 3698 696342667 696342338 1.920000e-108 403.0
38 TraesCS3B01G499900 chr3A 89.562 297 20 4 3653 3946 629066699 629066987 2.520000e-97 366.0
39 TraesCS3B01G499900 chr3A 91.204 216 19 0 654 869 707134690 707134475 1.210000e-75 294.0
40 TraesCS3B01G499900 chr3A 97.500 40 1 0 2192 2231 696343765 696343726 7.970000e-08 69.4
41 TraesCS3B01G499900 chr5B 87.529 874 92 14 1 869 668812377 668813238 0.000000e+00 994.0
42 TraesCS3B01G499900 chr5B 88.115 488 53 4 50 536 203516659 203516176 3.850000e-160 575.0
43 TraesCS3B01G499900 chr5B 94.059 101 4 2 4342 4442 578825941 578825843 7.700000e-33 152.0
44 TraesCS3B01G499900 chr1B 86.765 884 101 8 1 871 59637780 59636900 0.000000e+00 970.0
45 TraesCS3B01G499900 chr1B 93.007 572 40 0 1 572 476036325 476035754 0.000000e+00 835.0
46 TraesCS3B01G499900 chr2A 86.751 868 89 12 2 866 524837229 524838073 0.000000e+00 942.0
47 TraesCS3B01G499900 chr4D 87.044 849 86 14 2 846 9729087 9728259 0.000000e+00 937.0
48 TraesCS3B01G499900 chr7B 85.550 872 96 15 1 868 417608995 417609840 0.000000e+00 885.0
49 TraesCS3B01G499900 chr7B 87.854 247 27 1 623 866 399792398 399792152 2.020000e-73 287.0
50 TraesCS3B01G499900 chr7B 87.045 247 29 1 623 866 399795231 399795477 4.380000e-70 276.0
51 TraesCS3B01G499900 chr7B 94.059 101 6 0 4342 4442 674474931 674474831 2.140000e-33 154.0
52 TraesCS3B01G499900 chr5D 86.192 688 78 12 193 872 453975026 453974348 0.000000e+00 728.0
53 TraesCS3B01G499900 chr7D 84.082 779 87 22 112 870 137856058 137855297 0.000000e+00 717.0
54 TraesCS3B01G499900 chr7D 91.667 216 18 0 651 866 555227228 555227013 2.600000e-77 300.0
55 TraesCS3B01G499900 chr1D 87.291 598 58 11 50 645 209506643 209507224 0.000000e+00 667.0
56 TraesCS3B01G499900 chr2D 84.330 619 64 22 259 876 460567276 460567862 3.850000e-160 575.0
57 TraesCS3B01G499900 chr2B 89.278 457 44 4 55 510 545000137 544999685 6.450000e-158 568.0
58 TraesCS3B01G499900 chr2B 93.137 102 6 1 4341 4442 95550718 95550618 9.950000e-32 148.0
59 TraesCS3B01G499900 chr2B 87.912 91 11 0 2093 2183 218522178 218522088 1.690000e-19 108.0
60 TraesCS3B01G499900 chr4A 85.185 405 52 7 465 863 130452153 130451751 4.140000e-110 409.0


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 TraesCS3B01G499900 chr3B 744509554 744513995 4441 True 8203.000000 8203 100.000000 1 4442 1 chr3B.!!$R1 4441
1 TraesCS3B01G499900 chr3B 747330230 747332368 2138 False 1347.500000 1773 90.344000 913 3103 2 chr3B.!!$F5 2190
2 TraesCS3B01G499900 chr3B 747384314 747390492 6178 False 1334.500000 2335 95.994250 1004 4442 4 chr3B.!!$F6 3438
3 TraesCS3B01G499900 chr3B 745202493 745203414 921 True 1072.000000 1072 87.689000 1065 1987 1 chr3B.!!$R2 922
4 TraesCS3B01G499900 chr3B 240265915 240266769 854 False 957.000000 957 86.927000 1 866 1 chr3B.!!$F2 865
5 TraesCS3B01G499900 chr3B 747093709 747095796 2087 False 931.500000 1247 86.816500 1069 3238 2 chr3B.!!$F4 2169
6 TraesCS3B01G499900 chr3B 744544669 744546729 2060 True 895.000000 1208 86.584000 1069 3184 2 chr3B.!!$R4 2115
7 TraesCS3B01G499900 chr3B 744590517 744591897 1380 False 667.000000 1101 85.485500 1009 2585 2 chr3B.!!$F3 1576
8 TraesCS3B01G499900 chr3B 746855061 746856441 1380 True 664.500000 1096 85.441000 1009 2585 2 chr3B.!!$R5 1576
9 TraesCS3B01G499900 chr3B 747492958 747495124 2166 False 579.666667 1077 86.222000 995 3352 3 chr3B.!!$F7 2357
10 TraesCS3B01G499900 chr3D 560551529 560552641 1112 False 1192.000000 1192 86.094000 1035 2153 1 chr3D.!!$F4 1118
11 TraesCS3B01G499900 chr3D 560234011 560235237 1226 True 1092.000000 1092 82.824000 940 2208 1 chr3D.!!$R1 1268
12 TraesCS3B01G499900 chr3D 560267485 560269694 2209 True 1013.800000 1668 93.989667 968 3238 3 chr3D.!!$R3 2270
13 TraesCS3B01G499900 chr3D 560827928 560828754 826 False 560.000000 560 79.717000 2317 3127 1 chr3D.!!$F5 810
14 TraesCS3B01G499900 chr3A 629056478 629058411 1933 False 875.000000 1175 87.475000 1069 3121 2 chr3A.!!$F2 2052
15 TraesCS3B01G499900 chr3A 696341728 696344975 3247 True 762.280000 1406 91.313400 913 3946 5 chr3A.!!$R2 3033
16 TraesCS3B01G499900 chr5B 668812377 668813238 861 False 994.000000 994 87.529000 1 869 1 chr5B.!!$F1 868
17 TraesCS3B01G499900 chr1B 59636900 59637780 880 True 970.000000 970 86.765000 1 871 1 chr1B.!!$R1 870
18 TraesCS3B01G499900 chr1B 476035754 476036325 571 True 835.000000 835 93.007000 1 572 1 chr1B.!!$R2 571
19 TraesCS3B01G499900 chr2A 524837229 524838073 844 False 942.000000 942 86.751000 2 866 1 chr2A.!!$F1 864
20 TraesCS3B01G499900 chr4D 9728259 9729087 828 True 937.000000 937 87.044000 2 846 1 chr4D.!!$R1 844
21 TraesCS3B01G499900 chr7B 417608995 417609840 845 False 885.000000 885 85.550000 1 868 1 chr7B.!!$F2 867
22 TraesCS3B01G499900 chr5D 453974348 453975026 678 True 728.000000 728 86.192000 193 872 1 chr5D.!!$R1 679
23 TraesCS3B01G499900 chr7D 137855297 137856058 761 True 717.000000 717 84.082000 112 870 1 chr7D.!!$R1 758
24 TraesCS3B01G499900 chr1D 209506643 209507224 581 False 667.000000 667 87.291000 50 645 1 chr1D.!!$F1 595
25 TraesCS3B01G499900 chr2D 460567276 460567862 586 False 575.000000 575 84.330000 259 876 1 chr2D.!!$F1 617

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
675 711 1.754803 CTAGTATTCACCCACGGCTCA 59.245 52.381 0.00 0.0 0.00 4.26 F
846 887 2.817258 TCAACCGGCTCAAGTTTAATGG 59.183 45.455 0.00 0.0 0.00 3.16 F
898 939 3.632145 CCACTCCAAAAAGCAGTTACTGT 59.368 43.478 14.23 0.0 33.43 3.55 F
2249 2371 0.485543 TGTCCCTGGGTGTCTCTGTA 59.514 55.000 13.56 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 1911 1.452108 CAGGACGGGGCATCTTTCC 60.452 63.158 0.00 0.00 0.00 3.13 R
2133 2234 1.723608 TACCACGACGACGGTGTTGT 61.724 55.000 19.45 1.88 44.46 3.32 R
2854 3193 4.101448 GCTCCAGCACCCGACCAT 62.101 66.667 0.00 0.00 41.59 3.55 R
3774 4549 0.248565 TCTCTGCCAGCACAGCTTAG 59.751 55.000 0.00 0.00 36.40 2.18 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
70 72 6.018180 CACCTACAAAGTGACAGTAAAGTTCC 60.018 42.308 0.00 0.00 37.42 3.62
209 212 6.649155 TGTGCCTAATTTAATCAGTGCTCTA 58.351 36.000 0.00 0.00 0.00 2.43
277 284 5.625656 GCTCAAGCTAGGAACTGACACTTAT 60.626 44.000 0.00 0.00 41.52 1.73
281 288 7.832685 TCAAGCTAGGAACTGACACTTATAGTA 59.167 37.037 0.00 0.00 41.52 1.82
323 330 3.587506 AGATCCATCCATCATGCTCATCA 59.412 43.478 0.00 0.00 0.00 3.07
452 459 4.988716 ACGACAGGGACGGAGGCA 62.989 66.667 0.00 0.00 34.93 4.75
456 463 2.997315 CAGGGACGGAGGCAGTGA 60.997 66.667 0.00 0.00 0.00 3.41
467 474 2.032681 GCAGTGAAGGAGGGCGTT 59.967 61.111 0.00 0.00 0.00 4.84
631 660 3.635191 TGCGACCAGGTCATGCCA 61.635 61.111 20.13 7.66 40.61 4.92
669 705 3.181454 CCCATGGACTAGTATTCACCCAC 60.181 52.174 15.22 0.00 0.00 4.61
675 711 1.754803 CTAGTATTCACCCACGGCTCA 59.245 52.381 0.00 0.00 0.00 4.26
682 718 4.722700 CCCACGGCTCAACCAGGG 62.723 72.222 0.00 0.00 44.61 4.45
743 780 4.746115 AGTCAGCAAATACGTACACGAAAA 59.254 37.500 9.04 0.00 43.02 2.29
843 884 2.875933 CTGTCAACCGGCTCAAGTTTAA 59.124 45.455 0.00 0.00 0.00 1.52
846 887 2.817258 TCAACCGGCTCAAGTTTAATGG 59.183 45.455 0.00 0.00 0.00 3.16
855 896 4.628333 GCTCAAGTTTAATGGCGTACAGTA 59.372 41.667 0.00 0.00 0.00 2.74
872 913 9.654417 GCGTACAGTAAATTTTTCTCTTTTGTA 57.346 29.630 0.00 0.00 0.00 2.41
882 923 9.764363 AATTTTTCTCTTTTGTATTTCCACTCC 57.236 29.630 0.00 0.00 0.00 3.85
883 924 7.889873 TTTTCTCTTTTGTATTTCCACTCCA 57.110 32.000 0.00 0.00 0.00 3.86
884 925 7.889873 TTTCTCTTTTGTATTTCCACTCCAA 57.110 32.000 0.00 0.00 0.00 3.53
885 926 7.889873 TTCTCTTTTGTATTTCCACTCCAAA 57.110 32.000 0.00 0.00 0.00 3.28
886 927 7.889873 TCTCTTTTGTATTTCCACTCCAAAA 57.110 32.000 0.00 0.00 34.77 2.44
887 928 8.299990 TCTCTTTTGTATTTCCACTCCAAAAA 57.700 30.769 0.00 0.00 35.36 1.94
888 929 8.413229 TCTCTTTTGTATTTCCACTCCAAAAAG 58.587 33.333 0.00 0.00 35.36 2.27
889 930 6.983890 TCTTTTGTATTTCCACTCCAAAAAGC 59.016 34.615 0.00 0.00 35.36 3.51
890 931 5.860941 TTGTATTTCCACTCCAAAAAGCA 57.139 34.783 0.00 0.00 0.00 3.91
891 932 5.452078 TGTATTTCCACTCCAAAAAGCAG 57.548 39.130 0.00 0.00 0.00 4.24
892 933 4.892934 TGTATTTCCACTCCAAAAAGCAGT 59.107 37.500 0.00 0.00 0.00 4.40
893 934 5.362430 TGTATTTCCACTCCAAAAAGCAGTT 59.638 36.000 0.00 0.00 0.00 3.16
894 935 6.547880 TGTATTTCCACTCCAAAAAGCAGTTA 59.452 34.615 0.00 0.00 0.00 2.24
895 936 4.911514 TTCCACTCCAAAAAGCAGTTAC 57.088 40.909 0.00 0.00 0.00 2.50
896 937 4.164843 TCCACTCCAAAAAGCAGTTACT 57.835 40.909 0.00 0.00 0.00 2.24
897 938 3.882888 TCCACTCCAAAAAGCAGTTACTG 59.117 43.478 8.18 8.18 34.12 2.74
898 939 3.632145 CCACTCCAAAAAGCAGTTACTGT 59.368 43.478 14.23 0.00 33.43 3.55
899 940 4.097892 CCACTCCAAAAAGCAGTTACTGTT 59.902 41.667 14.23 4.90 33.43 3.16
900 941 5.036737 CACTCCAAAAAGCAGTTACTGTTG 58.963 41.667 14.23 9.85 33.43 3.33
901 942 4.947388 ACTCCAAAAAGCAGTTACTGTTGA 59.053 37.500 14.23 0.59 33.43 3.18
902 943 5.066505 ACTCCAAAAAGCAGTTACTGTTGAG 59.933 40.000 14.23 11.94 33.43 3.02
903 944 4.947388 TCCAAAAAGCAGTTACTGTTGAGT 59.053 37.500 14.23 0.00 33.43 3.41
904 945 6.116806 TCCAAAAAGCAGTTACTGTTGAGTA 58.883 36.000 14.23 0.00 33.43 2.59
905 946 6.770785 TCCAAAAAGCAGTTACTGTTGAGTAT 59.229 34.615 14.23 0.00 34.53 2.12
906 947 7.284489 TCCAAAAAGCAGTTACTGTTGAGTATT 59.716 33.333 14.23 0.00 34.53 1.89
907 948 7.920682 CCAAAAAGCAGTTACTGTTGAGTATTT 59.079 33.333 14.23 2.48 34.53 1.40
908 949 8.745837 CAAAAAGCAGTTACTGTTGAGTATTTG 58.254 33.333 14.23 10.75 34.53 2.32
909 950 7.801716 AAAGCAGTTACTGTTGAGTATTTGA 57.198 32.000 14.23 0.00 34.53 2.69
910 951 7.801716 AAGCAGTTACTGTTGAGTATTTGAA 57.198 32.000 14.23 0.00 34.53 2.69
911 952 7.986085 AGCAGTTACTGTTGAGTATTTGAAT 57.014 32.000 14.23 0.00 34.53 2.57
991 1032 4.365111 GACATGCCCTGCCCACCA 62.365 66.667 0.00 0.00 0.00 4.17
1067 1133 4.715130 CCGTCACCCTCCTCCCCA 62.715 72.222 0.00 0.00 0.00 4.96
2133 2234 3.561313 GGACAGCAAGAGTTGGGGATTAA 60.561 47.826 0.00 0.00 0.00 1.40
2248 2370 0.833834 CTGTCCCTGGGTGTCTCTGT 60.834 60.000 13.56 0.00 0.00 3.41
2249 2371 0.485543 TGTCCCTGGGTGTCTCTGTA 59.514 55.000 13.56 0.00 0.00 2.74
2250 2372 1.078823 TGTCCCTGGGTGTCTCTGTAT 59.921 52.381 13.56 0.00 0.00 2.29
2251 2373 1.757699 GTCCCTGGGTGTCTCTGTATC 59.242 57.143 13.56 0.00 0.00 2.24
2252 2374 1.646447 TCCCTGGGTGTCTCTGTATCT 59.354 52.381 13.56 0.00 0.00 1.98
2253 2375 1.759445 CCCTGGGTGTCTCTGTATCTG 59.241 57.143 3.97 0.00 0.00 2.90
2254 2376 2.461695 CCTGGGTGTCTCTGTATCTGT 58.538 52.381 0.00 0.00 0.00 3.41
2256 2378 3.634448 CCTGGGTGTCTCTGTATCTGTAG 59.366 52.174 0.00 0.00 0.00 2.74
2257 2379 4.274147 CTGGGTGTCTCTGTATCTGTAGT 58.726 47.826 0.00 0.00 0.00 2.73
2258 2380 5.437946 CTGGGTGTCTCTGTATCTGTAGTA 58.562 45.833 0.00 0.00 0.00 1.82
2259 2381 6.014771 TGGGTGTCTCTGTATCTGTAGTAT 57.985 41.667 0.00 0.00 0.00 2.12
2260 2382 7.145474 TGGGTGTCTCTGTATCTGTAGTATA 57.855 40.000 0.00 0.00 0.00 1.47
2261 2383 7.756614 TGGGTGTCTCTGTATCTGTAGTATAT 58.243 38.462 0.00 0.00 0.00 0.86
2262 2384 8.887393 TGGGTGTCTCTGTATCTGTAGTATATA 58.113 37.037 0.00 0.00 0.00 0.86
2263 2385 9.908747 GGGTGTCTCTGTATCTGTAGTATATAT 57.091 37.037 0.00 0.00 0.00 0.86
2854 3193 1.404181 CCTCAAGTTCATCGCGGAGAA 60.404 52.381 6.13 8.25 0.00 2.87
2855 3194 2.544685 CTCAAGTTCATCGCGGAGAAT 58.455 47.619 6.13 0.00 0.00 2.40
2913 3252 1.347707 ACGAATGTTTCTCCTCTGGCA 59.652 47.619 0.00 0.00 0.00 4.92
3284 3642 5.425196 AAACCTGCATTTCTATTGGCATT 57.575 34.783 0.00 0.00 35.45 3.56
3771 4546 3.451526 TGCATAGTGAAAGATGAGCTCG 58.548 45.455 9.64 0.00 0.00 5.03
3772 4547 2.799412 GCATAGTGAAAGATGAGCTCGG 59.201 50.000 9.64 0.00 0.00 4.63
3773 4548 2.586258 TAGTGAAAGATGAGCTCGGC 57.414 50.000 9.64 3.18 0.00 5.54
3774 4549 0.107945 AGTGAAAGATGAGCTCGGCC 60.108 55.000 9.64 0.00 0.00 6.13
3775 4550 0.107945 GTGAAAGATGAGCTCGGCCT 60.108 55.000 9.64 2.81 0.00 5.19
3776 4551 1.137086 GTGAAAGATGAGCTCGGCCTA 59.863 52.381 9.64 0.00 0.00 3.93
3795 4576 1.766625 AAGCTGTGCTGGCAGAGAGT 61.767 55.000 20.86 6.57 39.62 3.24
3903 4686 9.573133 CTTCATGGTAGAATCAAAATGGTTTAC 57.427 33.333 0.00 0.00 0.00 2.01
3970 4810 4.922206 AGAATTGATACACCTTCCAAGCA 58.078 39.130 0.00 0.00 0.00 3.91
3972 4812 4.574674 ATTGATACACCTTCCAAGCAGA 57.425 40.909 0.00 0.00 0.00 4.26
3976 4816 5.614308 TGATACACCTTCCAAGCAGATATG 58.386 41.667 0.00 0.00 0.00 1.78
3977 4817 3.287867 ACACCTTCCAAGCAGATATGG 57.712 47.619 0.00 0.00 38.09 2.74
3978 4818 2.578021 ACACCTTCCAAGCAGATATGGT 59.422 45.455 0.00 0.00 37.94 3.55
3979 4819 3.209410 CACCTTCCAAGCAGATATGGTC 58.791 50.000 0.00 0.00 37.94 4.02
3983 7560 4.590647 CCTTCCAAGCAGATATGGTCTAGA 59.409 45.833 0.00 0.00 37.94 2.43
4041 7618 1.550065 CTTCGTCTGTCGCATGGTAG 58.450 55.000 0.00 0.00 39.67 3.18
4175 7752 3.322254 CCTACAATCGCCACTAGGATCTT 59.678 47.826 0.00 0.00 36.89 2.40
4329 7906 2.797491 GCATGGTCGCCATCTTTTAAC 58.203 47.619 8.21 0.00 43.15 2.01
4331 7908 2.570415 TGGTCGCCATCTTTTAACCA 57.430 45.000 0.00 0.00 34.54 3.67
4416 7993 2.213499 GCGTCTTTGGTCATGGGATAG 58.787 52.381 0.00 0.00 0.00 2.08
4434 8011 4.764823 GGATAGACCAAACCAAACATGACA 59.235 41.667 0.00 0.00 38.79 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 55 4.369182 CACTCGGAACTTTACTGTCACTT 58.631 43.478 0.00 0.00 0.00 3.16
70 72 1.402613 TGCCATTGATTCATGCACTCG 59.597 47.619 0.00 0.00 0.00 4.18
209 212 6.531503 TCTTAGCAGCAGTAGTATTGAAGT 57.468 37.500 0.00 0.00 0.00 3.01
277 284 3.671008 ACAAGTGCGTCAACCATACTA 57.329 42.857 0.00 0.00 0.00 1.82
281 288 2.831685 TCTACAAGTGCGTCAACCAT 57.168 45.000 0.00 0.00 0.00 3.55
323 330 1.005687 AGGTTCTACCGGTCTAGCACT 59.994 52.381 12.40 0.26 44.90 4.40
452 459 2.750350 CCAACGCCCTCCTTCACT 59.250 61.111 0.00 0.00 0.00 3.41
456 463 1.978617 CATTGCCAACGCCCTCCTT 60.979 57.895 0.00 0.00 0.00 3.36
648 684 3.492656 CGTGGGTGAATACTAGTCCATGG 60.493 52.174 4.97 4.97 0.00 3.66
649 685 3.492656 CCGTGGGTGAATACTAGTCCATG 60.493 52.174 0.00 4.95 0.00 3.66
675 711 3.503839 TTTGACCGCCCCCTGGTT 61.504 61.111 0.00 0.00 40.63 3.67
743 780 6.285990 GGTTCACTTTGGTCCATATATACGT 58.714 40.000 0.00 0.00 0.00 3.57
843 884 7.448748 AAGAGAAAAATTTACTGTACGCCAT 57.551 32.000 0.00 0.00 0.00 4.40
846 887 8.556517 ACAAAAGAGAAAAATTTACTGTACGC 57.443 30.769 0.00 0.00 0.00 4.42
872 913 5.598417 AGTAACTGCTTTTTGGAGTGGAAAT 59.402 36.000 0.00 0.00 46.85 2.17
875 916 3.882888 CAGTAACTGCTTTTTGGAGTGGA 59.117 43.478 0.00 0.00 46.85 4.02
876 917 3.632145 ACAGTAACTGCTTTTTGGAGTGG 59.368 43.478 0.00 0.00 46.85 4.00
877 918 4.900635 ACAGTAACTGCTTTTTGGAGTG 57.099 40.909 0.00 0.00 46.85 3.51
878 919 8.065502 TACTCAACAGTAACTGCTTTTTGGAGT 61.066 37.037 0.00 0.00 40.49 3.85
879 920 5.066505 ACTCAACAGTAACTGCTTTTTGGAG 59.933 40.000 0.00 0.00 40.20 3.86
880 921 4.947388 ACTCAACAGTAACTGCTTTTTGGA 59.053 37.500 0.00 0.00 34.37 3.53
881 922 5.248870 ACTCAACAGTAACTGCTTTTTGG 57.751 39.130 0.00 0.00 34.37 3.28
882 923 8.745837 CAAATACTCAACAGTAACTGCTTTTTG 58.254 33.333 0.00 0.00 38.66 2.44
883 924 8.682710 TCAAATACTCAACAGTAACTGCTTTTT 58.317 29.630 0.00 0.00 38.66 1.94
884 925 8.220755 TCAAATACTCAACAGTAACTGCTTTT 57.779 30.769 0.00 0.00 38.66 2.27
885 926 7.801716 TCAAATACTCAACAGTAACTGCTTT 57.198 32.000 0.00 0.00 38.66 3.51
886 927 7.801716 TTCAAATACTCAACAGTAACTGCTT 57.198 32.000 0.00 0.00 38.66 3.91
887 928 7.986085 ATTCAAATACTCAACAGTAACTGCT 57.014 32.000 0.00 0.00 38.66 4.24
888 929 9.463443 AAAATTCAAATACTCAACAGTAACTGC 57.537 29.630 0.00 0.00 38.66 4.40
896 937 9.691362 GGCTAAAGAAAATTCAAATACTCAACA 57.309 29.630 0.00 0.00 0.00 3.33
897 938 8.850452 CGGCTAAAGAAAATTCAAATACTCAAC 58.150 33.333 0.00 0.00 0.00 3.18
898 939 8.788806 TCGGCTAAAGAAAATTCAAATACTCAA 58.211 29.630 0.00 0.00 0.00 3.02
899 940 8.330466 TCGGCTAAAGAAAATTCAAATACTCA 57.670 30.769 0.00 0.00 0.00 3.41
900 941 9.278734 CTTCGGCTAAAGAAAATTCAAATACTC 57.721 33.333 0.00 0.00 0.00 2.59
901 942 7.755373 GCTTCGGCTAAAGAAAATTCAAATACT 59.245 33.333 3.26 0.00 38.08 2.12
902 943 7.885681 GCTTCGGCTAAAGAAAATTCAAATAC 58.114 34.615 3.26 0.00 38.08 1.89
904 945 6.951256 GCTTCGGCTAAAGAAAATTCAAAT 57.049 33.333 3.26 0.00 38.08 2.32
934 975 1.002134 ACGTTGGAATCAGGCCCAG 60.002 57.895 0.00 0.00 33.43 4.45
990 1031 1.000283 GAGGAGTGAGTGAGTGGTGTG 60.000 57.143 0.00 0.00 0.00 3.82
991 1032 1.333177 GAGGAGTGAGTGAGTGGTGT 58.667 55.000 0.00 0.00 0.00 4.16
1055 1119 3.208592 TGGAGTGGGGAGGAGGGT 61.209 66.667 0.00 0.00 0.00 4.34
1059 1123 4.715130 CCGGTGGAGTGGGGAGGA 62.715 72.222 0.00 0.00 0.00 3.71
1273 1345 4.115199 ATGCGGTCCAAGCCTCCC 62.115 66.667 0.00 0.00 0.00 4.30
1557 1629 2.273449 GGTGCTCCTCCATGGTGG 59.727 66.667 24.44 24.44 39.43 4.61
1831 1911 1.452108 CAGGACGGGGCATCTTTCC 60.452 63.158 0.00 0.00 0.00 3.13
1897 1977 2.125753 CGCAGTCTCTGGCTGACC 60.126 66.667 3.15 0.00 36.12 4.02
2133 2234 1.723608 TACCACGACGACGGTGTTGT 61.724 55.000 19.45 1.88 44.46 3.32
2305 2427 5.163311 GCCAATTAAATTAGCCCAAGGACAT 60.163 40.000 0.00 0.00 0.00 3.06
2306 2428 4.161377 GCCAATTAAATTAGCCCAAGGACA 59.839 41.667 0.00 0.00 0.00 4.02
2854 3193 4.101448 GCTCCAGCACCCGACCAT 62.101 66.667 0.00 0.00 41.59 3.55
2913 3252 2.961062 GCTTGGCCCTCACATTATCATT 59.039 45.455 0.00 0.00 0.00 2.57
3218 3576 3.181493 GCAACCACATCCAGAAAGCATAG 60.181 47.826 0.00 0.00 0.00 2.23
3284 3642 6.764379 TCATGTAACACCACATACAGAAAGA 58.236 36.000 0.00 0.00 37.02 2.52
3771 4546 3.136791 GCCAGCACAGCTTAGGCC 61.137 66.667 8.67 0.00 40.45 5.19
3772 4547 2.360350 TGCCAGCACAGCTTAGGC 60.360 61.111 12.02 12.02 44.63 3.93
3773 4548 0.743701 CTCTGCCAGCACAGCTTAGG 60.744 60.000 0.00 0.00 36.40 2.69
3774 4549 0.248565 TCTCTGCCAGCACAGCTTAG 59.751 55.000 0.00 0.00 36.40 2.18
3775 4550 0.248565 CTCTCTGCCAGCACAGCTTA 59.751 55.000 0.00 0.00 36.40 3.09
3776 4551 1.003597 CTCTCTGCCAGCACAGCTT 60.004 57.895 0.00 0.00 36.40 3.74
3795 4576 1.237163 CCTCCTGCCCCCTCTGATA 59.763 63.158 0.00 0.00 0.00 2.15
3874 4657 6.127535 ACCATTTTGATTCTACCATGAAGCTG 60.128 38.462 0.00 0.00 33.95 4.24
3913 4696 5.764686 ACATTCACAGCAAAGAGTTGTATCA 59.235 36.000 0.00 0.00 39.90 2.15
3956 4739 3.780294 ACCATATCTGCTTGGAAGGTGTA 59.220 43.478 0.00 0.00 36.79 2.90
3957 4740 2.578021 ACCATATCTGCTTGGAAGGTGT 59.422 45.455 0.00 0.00 36.79 4.16
3959 4742 3.118531 AGACCATATCTGCTTGGAAGGT 58.881 45.455 0.00 0.00 35.81 3.50
3970 4810 5.020132 GGTGTGGCTATCTAGACCATATCT 58.980 45.833 4.03 0.00 41.95 1.98
3972 4812 4.752063 TGGTGTGGCTATCTAGACCATAT 58.248 43.478 4.03 0.00 34.00 1.78
3976 4816 2.965831 TCATGGTGTGGCTATCTAGACC 59.034 50.000 0.00 0.00 0.00 3.85
3977 4817 4.372656 GTTCATGGTGTGGCTATCTAGAC 58.627 47.826 0.00 0.00 0.00 2.59
3978 4818 3.388024 GGTTCATGGTGTGGCTATCTAGA 59.612 47.826 0.00 0.00 0.00 2.43
3979 4819 3.733337 GGTTCATGGTGTGGCTATCTAG 58.267 50.000 0.00 0.00 0.00 2.43
3983 7560 0.618458 ACGGTTCATGGTGTGGCTAT 59.382 50.000 0.00 0.00 0.00 2.97
4041 7618 0.951040 CGACTTGGCTTGAGGTGGAC 60.951 60.000 0.00 0.00 0.00 4.02
4175 7752 1.999735 GATGAAGCATCGTCGGAAACA 59.000 47.619 0.00 0.00 32.20 2.83
4238 7815 1.145819 GCTTCAGCCTAGGAGCCTG 59.854 63.158 14.75 10.81 34.31 4.85
4416 7993 3.118956 TGGTTGTCATGTTTGGTTTGGTC 60.119 43.478 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.