Multiple sequence alignment - TraesCS7A01G284200

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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 TraesCS7A01G284200 chr7A 100.000 2978 0 0 1 2978 320966113 320963136 0.000000e+00 5500.0
1 TraesCS7A01G284200 chr7A 94.183 2871 120 6 109 2978 320958131 320955307 0.000000e+00 4333.0
2 TraesCS7A01G284200 chr7A 91.047 2893 208 32 109 2978 385028834 385031698 0.000000e+00 3860.0
3 TraesCS7A01G284200 chr7A 91.069 2777 212 25 109 2858 385020147 385022914 0.000000e+00 3722.0
4 TraesCS7A01G284200 chr7A 90.837 1004 87 5 1977 2976 332764379 332765381 0.000000e+00 1339.0
5 TraesCS7A01G284200 chr7A 90.637 1004 89 5 1977 2976 332758755 332759757 0.000000e+00 1328.0
6 TraesCS7A01G284200 chr7A 92.593 135 8 1 852 986 573305426 573305294 3.030000e-45 193.0
7 TraesCS7A01G284200 chr7A 93.396 106 7 0 1 106 278123661 278123766 1.110000e-34 158.0
8 TraesCS7A01G284200 chr7A 93.443 61 4 0 969 1029 330396594 330396534 1.140000e-14 91.6
9 TraesCS7A01G284200 chr7A 94.737 57 1 2 979 1034 178718813 178718758 1.470000e-13 87.9
10 TraesCS7A01G284200 chr3A 91.166 2898 220 24 105 2978 320477585 320474700 0.000000e+00 3901.0
11 TraesCS7A01G284200 chr3A 90.555 2901 236 21 109 2978 359522708 359525601 0.000000e+00 3805.0
12 TraesCS7A01G284200 chr3A 89.500 1981 181 17 1019 2978 359552974 359554948 0.000000e+00 2481.0
13 TraesCS7A01G284200 chr3A 89.761 1006 92 10 1978 2978 329813128 329814127 0.000000e+00 1277.0
14 TraesCS7A01G284200 chr3A 95.472 795 29 2 103 890 359521903 359522697 0.000000e+00 1262.0
15 TraesCS7A01G284200 chr3A 95.564 789 28 2 109 890 359551919 359552707 0.000000e+00 1256.0
16 TraesCS7A01G284200 chr3A 89.990 979 85 11 2003 2977 540984150 540985119 0.000000e+00 1253.0
17 TraesCS7A01G284200 chr3A 82.510 1052 132 34 1945 2976 283734260 283735279 0.000000e+00 876.0
18 TraesCS7A01G284200 chr3A 87.993 583 58 11 211 787 662486650 662486074 0.000000e+00 678.0
19 TraesCS7A01G284200 chr3A 81.973 821 97 38 109 891 505763471 505762664 0.000000e+00 649.0
20 TraesCS7A01G284200 chr3A 81.265 822 98 43 109 891 505810505 505809701 5.460000e-172 614.0
21 TraesCS7A01G284200 chr3A 76.372 893 139 54 121 986 426164824 426163977 5.940000e-112 414.0
22 TraesCS7A01G284200 chr3A 94.444 144 6 2 1416 1558 353635171 353635029 1.390000e-53 220.0
23 TraesCS7A01G284200 chr3A 92.593 135 8 1 852 986 426172088 426171956 3.030000e-45 193.0
24 TraesCS7A01G284200 chr3A 92.661 109 8 0 1 109 323185783 323185891 1.110000e-34 158.0
25 TraesCS7A01G284200 chr3A 91.176 68 3 3 1935 1999 260323542 260323475 4.090000e-14 89.8
26 TraesCS7A01G284200 chr2A 88.018 1135 101 22 1874 2978 583410861 583409732 0.000000e+00 1310.0
27 TraesCS7A01G284200 chr2A 89.200 1000 100 7 1982 2978 407205293 407204299 0.000000e+00 1242.0
28 TraesCS7A01G284200 chr2A 89.623 318 33 0 1114 1431 268719244 268718927 3.570000e-109 405.0
29 TraesCS7A01G284200 chr2A 93.893 131 7 1 855 985 251307063 251306934 2.340000e-46 196.0
30 TraesCS7A01G284200 chr2A 96.078 51 2 0 1945 1995 331523307 331523357 1.900000e-12 84.2
31 TraesCS7A01G284200 chr1A 88.768 1015 97 14 1975 2978 24084982 24083974 0.000000e+00 1227.0
32 TraesCS7A01G284200 chr1A 88.067 595 56 14 201 787 337226694 337226107 0.000000e+00 691.0
33 TraesCS7A01G284200 chr1A 95.422 415 19 0 1542 1956 259140707 259140293 0.000000e+00 662.0
34 TraesCS7A01G284200 chr1A 95.157 413 20 0 1542 1954 259148945 259148533 0.000000e+00 652.0
35 TraesCS7A01G284200 chr5A 88.812 1010 93 18 1978 2978 488609983 488608985 0.000000e+00 1221.0
36 TraesCS7A01G284200 chr5A 95.884 413 16 1 1542 1954 599479580 599479169 0.000000e+00 667.0
37 TraesCS7A01G284200 chr5A 94.891 137 7 0 1422 1558 301760050 301759914 6.470000e-52 215.0
38 TraesCS7A01G284200 chr5A 92.053 151 9 3 1411 1558 275862311 275862461 3.010000e-50 209.0
39 TraesCS7A01G284200 chr1B 89.412 595 56 7 108 699 363937144 363937734 0.000000e+00 743.0
40 TraesCS7A01G284200 chr4D 88.907 604 50 9 109 699 255560473 255561072 0.000000e+00 728.0
41 TraesCS7A01G284200 chr6A 88.994 318 35 0 1114 1431 310221155 310220838 7.740000e-106 394.0
42 TraesCS7A01G284200 chr6A 88.994 318 34 1 1114 1431 310229229 310228913 2.780000e-105 392.0
43 TraesCS7A01G284200 chr6A 94.340 106 6 0 1 106 390326635 390326740 2.380000e-36 163.0
44 TraesCS7A01G284200 chr6A 93.396 106 7 0 1 106 390185860 390185965 1.110000e-34 158.0
45 TraesCS7A01G284200 chr5B 95.327 107 5 0 3 109 247728024 247728130 1.420000e-38 171.0
46 TraesCS7A01G284200 chr2D 94.495 109 6 0 1 109 555563632 555563740 5.110000e-38 169.0
47 TraesCS7A01G284200 chr2D 92.593 108 8 0 2 109 157805492 157805385 3.970000e-34 156.0
48 TraesCS7A01G284200 chr3D 92.661 109 8 0 1 109 225434444 225434336 1.110000e-34 158.0
49 TraesCS7A01G284200 chr3B 92.661 109 8 0 1 109 590233107 590232999 1.110000e-34 158.0


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 TraesCS7A01G284200 chr7A 320963136 320966113 2977 True 5500.0 5500 100.0000 1 2978 1 chr7A.!!$R3 2977
1 TraesCS7A01G284200 chr7A 320955307 320958131 2824 True 4333.0 4333 94.1830 109 2978 1 chr7A.!!$R2 2869
2 TraesCS7A01G284200 chr7A 385028834 385031698 2864 False 3860.0 3860 91.0470 109 2978 1 chr7A.!!$F5 2869
3 TraesCS7A01G284200 chr7A 385020147 385022914 2767 False 3722.0 3722 91.0690 109 2858 1 chr7A.!!$F4 2749
4 TraesCS7A01G284200 chr7A 332764379 332765381 1002 False 1339.0 1339 90.8370 1977 2976 1 chr7A.!!$F3 999
5 TraesCS7A01G284200 chr7A 332758755 332759757 1002 False 1328.0 1328 90.6370 1977 2976 1 chr7A.!!$F2 999
6 TraesCS7A01G284200 chr3A 320474700 320477585 2885 True 3901.0 3901 91.1660 105 2978 1 chr3A.!!$R2 2873
7 TraesCS7A01G284200 chr3A 359521903 359525601 3698 False 2533.5 3805 93.0135 103 2978 2 chr3A.!!$F5 2875
8 TraesCS7A01G284200 chr3A 359551919 359554948 3029 False 1868.5 2481 92.5320 109 2978 2 chr3A.!!$F6 2869
9 TraesCS7A01G284200 chr3A 329813128 329814127 999 False 1277.0 1277 89.7610 1978 2978 1 chr3A.!!$F3 1000
10 TraesCS7A01G284200 chr3A 540984150 540985119 969 False 1253.0 1253 89.9900 2003 2977 1 chr3A.!!$F4 974
11 TraesCS7A01G284200 chr3A 283734260 283735279 1019 False 876.0 876 82.5100 1945 2976 1 chr3A.!!$F1 1031
12 TraesCS7A01G284200 chr3A 662486074 662486650 576 True 678.0 678 87.9930 211 787 1 chr3A.!!$R8 576
13 TraesCS7A01G284200 chr3A 505762664 505763471 807 True 649.0 649 81.9730 109 891 1 chr3A.!!$R6 782
14 TraesCS7A01G284200 chr3A 505809701 505810505 804 True 614.0 614 81.2650 109 891 1 chr3A.!!$R7 782
15 TraesCS7A01G284200 chr3A 426163977 426164824 847 True 414.0 414 76.3720 121 986 1 chr3A.!!$R4 865
16 TraesCS7A01G284200 chr2A 583409732 583410861 1129 True 1310.0 1310 88.0180 1874 2978 1 chr2A.!!$R4 1104
17 TraesCS7A01G284200 chr2A 407204299 407205293 994 True 1242.0 1242 89.2000 1982 2978 1 chr2A.!!$R3 996
18 TraesCS7A01G284200 chr1A 24083974 24084982 1008 True 1227.0 1227 88.7680 1975 2978 1 chr1A.!!$R1 1003
19 TraesCS7A01G284200 chr1A 337226107 337226694 587 True 691.0 691 88.0670 201 787 1 chr1A.!!$R4 586
20 TraesCS7A01G284200 chr5A 488608985 488609983 998 True 1221.0 1221 88.8120 1978 2978 1 chr5A.!!$R2 1000
21 TraesCS7A01G284200 chr1B 363937144 363937734 590 False 743.0 743 89.4120 108 699 1 chr1B.!!$F1 591
22 TraesCS7A01G284200 chr4D 255560473 255561072 599 False 728.0 728 88.9070 109 699 1 chr4D.!!$F1 590

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
637 656 0.245266 TATCAGCGCGTCCAACTTCA 59.755 50.0 8.43 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 3063 0.252197 GATGCGGTGTAGGGGAAGTT 59.748 55.0 0.0 0.0 0.0 2.66 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
24 25 7.066374 GTTTGCCTCACTATCTTCTGTAAAG 57.934 40.000 0.00 0.00 0.00 1.85
25 26 6.360370 TTGCCTCACTATCTTCTGTAAAGT 57.640 37.500 0.00 0.00 0.00 2.66
26 27 6.360370 TGCCTCACTATCTTCTGTAAAGTT 57.640 37.500 0.00 0.00 0.00 2.66
27 28 6.398918 TGCCTCACTATCTTCTGTAAAGTTC 58.601 40.000 0.00 0.00 0.00 3.01
28 29 6.211584 TGCCTCACTATCTTCTGTAAAGTTCT 59.788 38.462 0.00 0.00 0.00 3.01
29 30 6.533367 GCCTCACTATCTTCTGTAAAGTTCTG 59.467 42.308 0.00 0.00 0.00 3.02
30 31 6.533367 CCTCACTATCTTCTGTAAAGTTCTGC 59.467 42.308 0.00 0.00 0.00 4.26
31 32 6.398918 TCACTATCTTCTGTAAAGTTCTGCC 58.601 40.000 0.00 0.00 0.00 4.85
32 33 6.211584 TCACTATCTTCTGTAAAGTTCTGCCT 59.788 38.462 0.00 0.00 0.00 4.75
33 34 6.312426 CACTATCTTCTGTAAAGTTCTGCCTG 59.688 42.308 0.00 0.00 0.00 4.85
34 35 4.008074 TCTTCTGTAAAGTTCTGCCTGG 57.992 45.455 0.00 0.00 0.00 4.45
35 36 2.185004 TCTGTAAAGTTCTGCCTGGC 57.815 50.000 12.87 12.87 0.00 4.85
36 37 1.419762 TCTGTAAAGTTCTGCCTGGCA 59.580 47.619 21.96 21.96 36.92 4.92
37 38 2.040278 TCTGTAAAGTTCTGCCTGGCAT 59.960 45.455 23.64 8.76 38.13 4.40
38 39 3.263170 TCTGTAAAGTTCTGCCTGGCATA 59.737 43.478 23.64 12.92 38.13 3.14
39 40 4.009675 CTGTAAAGTTCTGCCTGGCATAA 58.990 43.478 23.64 18.74 38.13 1.90
40 41 4.009675 TGTAAAGTTCTGCCTGGCATAAG 58.990 43.478 23.64 11.14 38.13 1.73
41 42 3.439857 AAAGTTCTGCCTGGCATAAGA 57.560 42.857 23.64 13.56 38.13 2.10
42 43 2.706339 AGTTCTGCCTGGCATAAGAG 57.294 50.000 23.64 10.33 38.13 2.85
43 44 2.191400 AGTTCTGCCTGGCATAAGAGA 58.809 47.619 23.64 12.76 38.13 3.10
44 45 2.776536 AGTTCTGCCTGGCATAAGAGAT 59.223 45.455 23.64 5.80 38.13 2.75
45 46 3.969976 AGTTCTGCCTGGCATAAGAGATA 59.030 43.478 23.64 4.08 38.13 1.98
46 47 4.596643 AGTTCTGCCTGGCATAAGAGATAT 59.403 41.667 23.64 4.37 38.13 1.63
47 48 4.548451 TCTGCCTGGCATAAGAGATATG 57.452 45.455 23.64 6.36 43.64 1.78
48 49 4.162651 TCTGCCTGGCATAAGAGATATGA 58.837 43.478 23.64 8.84 43.52 2.15
59 60 9.638239 GGCATAAGAGATATGACTCTAAAAGAG 57.362 37.037 2.39 2.39 45.25 2.85
67 68 9.883142 AGATATGACTCTAAAAGAGAAACAAGG 57.117 33.333 10.80 0.00 45.07 3.61
68 69 9.877178 GATATGACTCTAAAAGAGAAACAAGGA 57.123 33.333 10.80 0.70 45.07 3.36
69 70 9.883142 ATATGACTCTAAAAGAGAAACAAGGAG 57.117 33.333 10.80 0.00 45.07 3.69
70 71 7.361457 TGACTCTAAAAGAGAAACAAGGAGA 57.639 36.000 10.80 0.00 45.07 3.71
71 72 7.210873 TGACTCTAAAAGAGAAACAAGGAGAC 58.789 38.462 10.80 0.00 45.07 3.36
72 73 7.125792 ACTCTAAAAGAGAAACAAGGAGACA 57.874 36.000 10.80 0.00 45.07 3.41
73 74 7.213678 ACTCTAAAAGAGAAACAAGGAGACAG 58.786 38.462 10.80 0.00 45.07 3.51
74 75 7.070074 ACTCTAAAAGAGAAACAAGGAGACAGA 59.930 37.037 10.80 0.00 45.07 3.41
75 76 7.967908 TCTAAAAGAGAAACAAGGAGACAGAT 58.032 34.615 0.00 0.00 0.00 2.90
76 77 9.090103 TCTAAAAGAGAAACAAGGAGACAGATA 57.910 33.333 0.00 0.00 0.00 1.98
77 78 9.712305 CTAAAAGAGAAACAAGGAGACAGATAA 57.288 33.333 0.00 0.00 0.00 1.75
78 79 7.971183 AAAGAGAAACAAGGAGACAGATAAC 57.029 36.000 0.00 0.00 0.00 1.89
79 80 6.672266 AGAGAAACAAGGAGACAGATAACA 57.328 37.500 0.00 0.00 0.00 2.41
80 81 7.067496 AGAGAAACAAGGAGACAGATAACAA 57.933 36.000 0.00 0.00 0.00 2.83
81 82 7.158021 AGAGAAACAAGGAGACAGATAACAAG 58.842 38.462 0.00 0.00 0.00 3.16
82 83 6.831976 AGAAACAAGGAGACAGATAACAAGT 58.168 36.000 0.00 0.00 0.00 3.16
83 84 7.283329 AGAAACAAGGAGACAGATAACAAGTT 58.717 34.615 0.00 0.00 0.00 2.66
84 85 7.775561 AGAAACAAGGAGACAGATAACAAGTTT 59.224 33.333 0.00 0.00 0.00 2.66
85 86 7.497925 AACAAGGAGACAGATAACAAGTTTC 57.502 36.000 0.00 0.00 0.00 2.78
86 87 6.591935 ACAAGGAGACAGATAACAAGTTTCA 58.408 36.000 0.00 0.00 0.00 2.69
87 88 6.483640 ACAAGGAGACAGATAACAAGTTTCAC 59.516 38.462 0.00 0.00 0.00 3.18
88 89 6.174720 AGGAGACAGATAACAAGTTTCACA 57.825 37.500 0.00 0.00 0.00 3.58
89 90 6.591935 AGGAGACAGATAACAAGTTTCACAA 58.408 36.000 0.00 0.00 0.00 3.33
90 91 7.054124 AGGAGACAGATAACAAGTTTCACAAA 58.946 34.615 0.00 0.00 0.00 2.83
91 92 7.721399 AGGAGACAGATAACAAGTTTCACAAAT 59.279 33.333 0.00 0.00 0.00 2.32
92 93 8.999431 GGAGACAGATAACAAGTTTCACAAATA 58.001 33.333 0.00 0.00 0.00 1.40
183 186 2.223456 CGTGTGTTTCATTTGTGCCTGA 60.223 45.455 0.00 0.00 0.00 3.86
199 202 4.686091 GTGCCTGACCTTTTATTTTTGCTC 59.314 41.667 0.00 0.00 0.00 4.26
243 249 7.977293 CCATCATCTCATAAATCTTTTGCAACA 59.023 33.333 0.00 0.00 0.00 3.33
622 641 2.025793 TGTGAGCCCGGGAAAATTATCA 60.026 45.455 29.31 12.55 0.00 2.15
637 656 0.245266 TATCAGCGCGTCCAACTTCA 59.755 50.000 8.43 0.00 0.00 3.02
850 930 1.480683 CCTAGGCCTCGATCCCACTTA 60.481 57.143 9.68 0.00 0.00 2.24
876 956 1.903183 CTCCCTCGTTTCCTTCCTCTT 59.097 52.381 0.00 0.00 0.00 2.85
924 1805 0.399233 CGATCCCCTCCTCTTTCCCT 60.399 60.000 0.00 0.00 0.00 4.20
994 1877 4.254709 ACCACGAGCAGCCAAGCA 62.255 61.111 0.00 0.00 36.85 3.91
1247 2266 0.318441 CTCCTCGCTTCAAGTCCACA 59.682 55.000 0.00 0.00 0.00 4.17
1258 2277 1.045407 AAGTCCACACCGTCAAGCTA 58.955 50.000 0.00 0.00 0.00 3.32
1308 2327 0.544833 TTCCACCCCGTACCTGCTTA 60.545 55.000 0.00 0.00 0.00 3.09
1344 2363 1.613520 CCGCCGTCTAGGATCCATAGA 60.614 57.143 15.82 14.53 45.00 1.98
1348 2367 3.321111 GCCGTCTAGGATCCATAGAAACA 59.679 47.826 15.82 0.00 45.00 2.83
1355 2374 2.614057 GGATCCATAGAAACACCTTGCG 59.386 50.000 6.95 0.00 0.00 4.85
1398 2417 1.071471 CTGGCGTCTTCAACCACCT 59.929 57.895 0.00 0.00 0.00 4.00
1408 2427 2.208349 AACCACCTGAGGCCCTCT 59.792 61.111 12.94 0.00 0.00 3.69
1425 2444 3.958147 CTTCCGTGCCATCGCTGGT 62.958 63.158 7.21 0.00 45.10 4.00
1549 2568 1.466025 AACTACCACCGCTCCGAACA 61.466 55.000 0.00 0.00 0.00 3.18
1670 2689 4.477975 CGGAGACCTCGGACACGC 62.478 72.222 0.00 0.00 40.69 5.34
1678 2697 1.287815 CTCGGACACGCCAAGTACA 59.712 57.895 0.00 0.00 40.69 2.90
1733 2752 2.652530 GACGACCCAAGTACCGCA 59.347 61.111 0.00 0.00 0.00 5.69
1758 2777 2.880890 ACGTTTGTACCTCTACTGTCGT 59.119 45.455 0.00 0.00 0.00 4.34
1779 2798 0.179119 GTGGATCCGACAAGTACCCG 60.179 60.000 7.39 0.00 0.00 5.28
1803 2822 3.385755 ACAACAAGTGTACCTCTACCGTT 59.614 43.478 0.00 0.00 39.29 4.44
2009 3063 0.109458 CGAACGTCCCGAGAATGTCA 60.109 55.000 4.54 0.00 0.00 3.58
2044 3100 3.664495 TCGAACTCGAACCGCTCT 58.336 55.556 0.00 0.00 46.30 4.09
2054 3111 2.138320 CGAACCGCTCTGATAATGCAT 58.862 47.619 0.00 0.00 0.00 3.96
2217 3314 0.893270 CATCTTTTGACACGCCCCCA 60.893 55.000 0.00 0.00 0.00 4.96
2233 3330 3.244875 GCCCCCATCATTTTTCCTTTTGT 60.245 43.478 0.00 0.00 0.00 2.83
2325 3425 1.507742 ACCCCTTTTCCTTTCCACCAT 59.492 47.619 0.00 0.00 0.00 3.55
2348 3454 4.114794 GGTGACAAATGCTTCATATTGCC 58.885 43.478 0.00 0.00 0.00 4.52
2394 3504 6.822667 TGCATAAACTTGTTCATGTCATCT 57.177 33.333 0.00 0.00 0.00 2.90
2410 3520 7.283580 TCATGTCATCTGCATCATGATAACAAA 59.716 33.333 8.15 0.00 40.73 2.83
2554 3669 2.557924 CACCTCTTGCCATGCTAACAAA 59.442 45.455 0.00 0.00 0.00 2.83
2809 3941 0.528901 TTGGATCCGGTAACATCGCG 60.529 55.000 7.39 0.00 0.00 5.87
2814 3946 0.319727 TCCGGTAACATCGCGTTTGT 60.320 50.000 5.77 8.92 39.14 2.83
2815 3947 0.179235 CCGGTAACATCGCGTTTGTG 60.179 55.000 15.97 9.41 39.14 3.33
2816 3948 0.785378 CGGTAACATCGCGTTTGTGA 59.215 50.000 15.97 7.84 39.14 3.58
2817 3949 1.201769 CGGTAACATCGCGTTTGTGAG 60.202 52.381 15.97 6.55 39.14 3.51
2818 3950 1.127951 GGTAACATCGCGTTTGTGAGG 59.872 52.381 15.97 0.00 41.89 3.86
2819 3951 2.063266 GTAACATCGCGTTTGTGAGGA 58.937 47.619 15.97 2.85 38.63 3.71
2820 3952 1.808411 AACATCGCGTTTGTGAGGAT 58.192 45.000 15.97 0.49 38.63 3.24
2821 3953 1.359848 ACATCGCGTTTGTGAGGATC 58.640 50.000 14.84 0.00 38.63 3.36
2822 3954 0.652592 CATCGCGTTTGTGAGGATCC 59.347 55.000 5.77 2.48 38.63 3.36
2861 4008 2.029020 TGTCTTCCTCATGGACTCGTTG 60.029 50.000 0.00 0.00 43.06 4.10
2938 4085 0.107993 TGCTTGCTAGATGCTCGCTT 60.108 50.000 0.00 0.00 43.37 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.651225 ACTTTACAGAAGATAGTGAGGCAAAC 59.349 38.462 0.00 0.00 0.00 2.93
1 2 6.769512 ACTTTACAGAAGATAGTGAGGCAAA 58.230 36.000 0.00 0.00 0.00 3.68
2 3 6.360370 ACTTTACAGAAGATAGTGAGGCAA 57.640 37.500 0.00 0.00 0.00 4.52
3 4 6.211584 AGAACTTTACAGAAGATAGTGAGGCA 59.788 38.462 0.00 0.00 0.00 4.75
4 5 6.533367 CAGAACTTTACAGAAGATAGTGAGGC 59.467 42.308 0.00 0.00 0.00 4.70
5 6 6.533367 GCAGAACTTTACAGAAGATAGTGAGG 59.467 42.308 0.00 0.00 0.00 3.86
6 7 6.533367 GGCAGAACTTTACAGAAGATAGTGAG 59.467 42.308 0.00 0.00 0.00 3.51
7 8 6.211584 AGGCAGAACTTTACAGAAGATAGTGA 59.788 38.462 0.00 0.00 0.00 3.41
8 9 6.312426 CAGGCAGAACTTTACAGAAGATAGTG 59.688 42.308 0.00 0.00 0.00 2.74
9 10 6.402222 CAGGCAGAACTTTACAGAAGATAGT 58.598 40.000 0.00 0.00 0.00 2.12
10 11 5.814705 CCAGGCAGAACTTTACAGAAGATAG 59.185 44.000 0.00 0.00 0.00 2.08
11 12 5.734720 CCAGGCAGAACTTTACAGAAGATA 58.265 41.667 0.00 0.00 0.00 1.98
12 13 4.583871 CCAGGCAGAACTTTACAGAAGAT 58.416 43.478 0.00 0.00 0.00 2.40
13 14 3.807209 GCCAGGCAGAACTTTACAGAAGA 60.807 47.826 6.55 0.00 0.00 2.87
14 15 2.485814 GCCAGGCAGAACTTTACAGAAG 59.514 50.000 6.55 0.00 0.00 2.85
15 16 2.158682 TGCCAGGCAGAACTTTACAGAA 60.159 45.455 11.22 0.00 33.32 3.02
16 17 1.419762 TGCCAGGCAGAACTTTACAGA 59.580 47.619 11.22 0.00 33.32 3.41
17 18 1.896220 TGCCAGGCAGAACTTTACAG 58.104 50.000 11.22 0.00 33.32 2.74
18 19 2.584835 ATGCCAGGCAGAACTTTACA 57.415 45.000 21.51 0.00 43.65 2.41
19 20 4.261801 TCTTATGCCAGGCAGAACTTTAC 58.738 43.478 21.51 0.00 43.65 2.01
20 21 4.225042 TCTCTTATGCCAGGCAGAACTTTA 59.775 41.667 21.51 2.86 43.65 1.85
21 22 3.009473 TCTCTTATGCCAGGCAGAACTTT 59.991 43.478 21.51 4.00 43.65 2.66
22 23 2.573462 TCTCTTATGCCAGGCAGAACTT 59.427 45.455 21.51 4.83 43.65 2.66
23 24 2.191400 TCTCTTATGCCAGGCAGAACT 58.809 47.619 21.51 5.26 43.65 3.01
24 25 2.698855 TCTCTTATGCCAGGCAGAAC 57.301 50.000 21.51 0.00 43.65 3.01
25 26 4.594491 TCATATCTCTTATGCCAGGCAGAA 59.406 41.667 20.42 20.42 43.65 3.02
26 27 4.020751 GTCATATCTCTTATGCCAGGCAGA 60.021 45.833 21.51 13.59 43.65 4.26
27 28 4.020396 AGTCATATCTCTTATGCCAGGCAG 60.020 45.833 21.51 6.55 43.65 4.85
28 29 3.906218 AGTCATATCTCTTATGCCAGGCA 59.094 43.478 18.99 18.99 44.86 4.75
29 30 4.222588 AGAGTCATATCTCTTATGCCAGGC 59.777 45.833 3.66 3.66 41.36 4.85
30 31 5.999205 AGAGTCATATCTCTTATGCCAGG 57.001 43.478 0.00 0.00 41.36 4.45
31 32 9.421806 CTTTTAGAGTCATATCTCTTATGCCAG 57.578 37.037 1.61 0.00 43.46 4.85
32 33 9.147732 TCTTTTAGAGTCATATCTCTTATGCCA 57.852 33.333 1.61 0.00 43.46 4.92
33 34 9.638239 CTCTTTTAGAGTCATATCTCTTATGCC 57.362 37.037 1.61 0.00 43.46 4.40
41 42 9.883142 CCTTGTTTCTCTTTTAGAGTCATATCT 57.117 33.333 3.82 0.00 42.83 1.98
42 43 9.877178 TCCTTGTTTCTCTTTTAGAGTCATATC 57.123 33.333 3.82 0.00 42.83 1.63
43 44 9.883142 CTCCTTGTTTCTCTTTTAGAGTCATAT 57.117 33.333 3.82 0.00 42.83 1.78
44 45 9.090103 TCTCCTTGTTTCTCTTTTAGAGTCATA 57.910 33.333 3.82 0.00 42.83 2.15
45 46 7.875554 GTCTCCTTGTTTCTCTTTTAGAGTCAT 59.124 37.037 3.82 0.00 42.83 3.06
46 47 7.147724 TGTCTCCTTGTTTCTCTTTTAGAGTCA 60.148 37.037 3.82 0.00 42.83 3.41
47 48 7.210873 TGTCTCCTTGTTTCTCTTTTAGAGTC 58.789 38.462 3.82 0.00 42.83 3.36
48 49 7.070074 TCTGTCTCCTTGTTTCTCTTTTAGAGT 59.930 37.037 3.82 0.00 42.83 3.24
49 50 7.437748 TCTGTCTCCTTGTTTCTCTTTTAGAG 58.562 38.462 0.00 0.00 43.64 2.43
50 51 7.361457 TCTGTCTCCTTGTTTCTCTTTTAGA 57.639 36.000 0.00 0.00 0.00 2.10
51 52 9.712305 TTATCTGTCTCCTTGTTTCTCTTTTAG 57.288 33.333 0.00 0.00 0.00 1.85
52 53 9.490379 GTTATCTGTCTCCTTGTTTCTCTTTTA 57.510 33.333 0.00 0.00 0.00 1.52
53 54 7.993183 TGTTATCTGTCTCCTTGTTTCTCTTTT 59.007 33.333 0.00 0.00 0.00 2.27
54 55 7.509546 TGTTATCTGTCTCCTTGTTTCTCTTT 58.490 34.615 0.00 0.00 0.00 2.52
55 56 7.067496 TGTTATCTGTCTCCTTGTTTCTCTT 57.933 36.000 0.00 0.00 0.00 2.85
56 57 6.672266 TGTTATCTGTCTCCTTGTTTCTCT 57.328 37.500 0.00 0.00 0.00 3.10
57 58 6.931840 ACTTGTTATCTGTCTCCTTGTTTCTC 59.068 38.462 0.00 0.00 0.00 2.87
58 59 6.831976 ACTTGTTATCTGTCTCCTTGTTTCT 58.168 36.000 0.00 0.00 0.00 2.52
59 60 7.497925 AACTTGTTATCTGTCTCCTTGTTTC 57.502 36.000 0.00 0.00 0.00 2.78
60 61 7.556275 TGAAACTTGTTATCTGTCTCCTTGTTT 59.444 33.333 0.00 0.00 0.00 2.83
61 62 7.012421 GTGAAACTTGTTATCTGTCTCCTTGTT 59.988 37.037 0.00 0.00 0.00 2.83
62 63 6.483640 GTGAAACTTGTTATCTGTCTCCTTGT 59.516 38.462 0.00 0.00 0.00 3.16
63 64 6.483307 TGTGAAACTTGTTATCTGTCTCCTTG 59.517 38.462 0.00 0.00 38.04 3.61
64 65 6.591935 TGTGAAACTTGTTATCTGTCTCCTT 58.408 36.000 0.00 0.00 38.04 3.36
65 66 6.174720 TGTGAAACTTGTTATCTGTCTCCT 57.825 37.500 0.00 0.00 38.04 3.69
66 67 6.861065 TTGTGAAACTTGTTATCTGTCTCC 57.139 37.500 0.00 0.00 38.04 3.71
77 78 9.554724 CGTTGCTTATATATTTGTGAAACTTGT 57.445 29.630 0.00 0.00 38.04 3.16
78 79 9.767684 TCGTTGCTTATATATTTGTGAAACTTG 57.232 29.630 0.00 0.00 38.04 3.16
84 85 9.758651 ACACTATCGTTGCTTATATATTTGTGA 57.241 29.630 0.00 0.00 0.00 3.58
85 86 9.797473 CACACTATCGTTGCTTATATATTTGTG 57.203 33.333 0.00 0.00 0.00 3.33
86 87 9.758651 TCACACTATCGTTGCTTATATATTTGT 57.241 29.630 0.00 0.00 0.00 2.83
88 89 8.912658 CGTCACACTATCGTTGCTTATATATTT 58.087 33.333 0.00 0.00 0.00 1.40
89 90 7.061905 GCGTCACACTATCGTTGCTTATATATT 59.938 37.037 0.00 0.00 0.00 1.28
90 91 6.527023 GCGTCACACTATCGTTGCTTATATAT 59.473 38.462 0.00 0.00 0.00 0.86
91 92 5.854866 GCGTCACACTATCGTTGCTTATATA 59.145 40.000 0.00 0.00 0.00 0.86
92 93 4.680110 GCGTCACACTATCGTTGCTTATAT 59.320 41.667 0.00 0.00 0.00 0.86
93 94 4.039703 GCGTCACACTATCGTTGCTTATA 58.960 43.478 0.00 0.00 0.00 0.98
94 95 2.858344 GCGTCACACTATCGTTGCTTAT 59.142 45.455 0.00 0.00 0.00 1.73
95 96 2.256174 GCGTCACACTATCGTTGCTTA 58.744 47.619 0.00 0.00 0.00 3.09
96 97 1.068474 GCGTCACACTATCGTTGCTT 58.932 50.000 0.00 0.00 0.00 3.91
97 98 0.736325 GGCGTCACACTATCGTTGCT 60.736 55.000 0.00 0.00 0.00 3.91
98 99 1.708027 GGCGTCACACTATCGTTGC 59.292 57.895 0.00 0.00 0.00 4.17
99 100 0.731514 ACGGCGTCACACTATCGTTG 60.732 55.000 6.77 0.00 0.00 4.10
100 101 0.731514 CACGGCGTCACACTATCGTT 60.732 55.000 10.85 0.00 0.00 3.85
101 102 1.154093 CACGGCGTCACACTATCGT 60.154 57.895 10.85 0.00 0.00 3.73
183 186 6.100404 TGATGCAGAGCAAAAATAAAAGGT 57.900 33.333 0.00 0.00 43.62 3.50
199 202 2.558359 ATGGCATGATGACATGATGCAG 59.442 45.455 31.93 4.59 46.11 4.41
243 249 7.902920 AGATCCATGCCATTTATTTAGTTGT 57.097 32.000 0.00 0.00 0.00 3.32
622 641 1.298859 GGAATGAAGTTGGACGCGCT 61.299 55.000 5.73 0.00 0.00 5.92
637 656 7.336475 AGAAAAGAAAGAGAGGTTAGGGAAT 57.664 36.000 0.00 0.00 0.00 3.01
850 930 0.340208 AGGAAACGAGGGAGAGGGAT 59.660 55.000 0.00 0.00 0.00 3.85
924 1805 0.966920 GTTTGAGGAGAGGGACGACA 59.033 55.000 0.00 0.00 0.00 4.35
1032 2051 2.435586 GAGGTCGACGTCTCCGGA 60.436 66.667 26.59 2.93 38.78 5.14
1247 2266 1.004918 GGTGCTGTAGCTTGACGGT 60.005 57.895 5.38 0.00 42.66 4.83
1258 2277 2.930562 GGAGGGTCCTGGTGCTGT 60.931 66.667 0.00 0.00 32.53 4.40
1332 2351 4.442893 CGCAAGGTGTTTCTATGGATCCTA 60.443 45.833 14.23 0.00 0.00 2.94
1398 2417 3.706373 GCACGGAAGAGGGCCTCA 61.706 66.667 33.86 0.00 32.06 3.86
1408 2427 3.950794 GACCAGCGATGGCACGGAA 62.951 63.158 21.97 0.00 43.41 4.30
1425 2444 1.483004 TCTTGACAACGACAACAGGGA 59.517 47.619 0.00 0.00 0.00 4.20
1533 2552 2.652530 GTGTTCGGAGCGGTGGTA 59.347 61.111 0.00 0.00 0.00 3.25
1549 2568 4.151883 TCGGGTTTGTAGTAGTACTTGGT 58.848 43.478 8.40 0.00 0.00 3.67
1584 2603 1.760029 GGTCTCCTCAGGGACTTGATC 59.240 57.143 11.00 0.00 34.60 2.92
1670 2689 3.130516 TGATAGCTCGAAGGTGTACTTGG 59.869 47.826 0.00 0.00 40.21 3.61
1678 2697 2.288273 GCGGTATTGATAGCTCGAAGGT 60.288 50.000 0.00 0.00 0.00 3.50
1733 2752 5.526506 ACAGTAGAGGTACAAACGTTCTT 57.473 39.130 0.00 0.00 0.00 2.52
1758 2777 0.813184 GGTACTTGTCGGATCCACGA 59.187 55.000 13.41 8.16 41.13 4.35
1803 2822 3.508762 GTTCTTAGCGATTCCGAAGACA 58.491 45.455 0.00 0.00 38.22 3.41
2009 3063 0.252197 GATGCGGTGTAGGGGAAGTT 59.748 55.000 0.00 0.00 0.00 2.66
2044 3100 8.783093 GTTATACCTTTGTAGCATGCATTATCA 58.217 33.333 21.98 8.21 0.00 2.15
2054 3111 5.027460 TCTCAGGGTTATACCTTTGTAGCA 58.973 41.667 0.00 0.00 39.34 3.49
2217 3314 4.282195 TGCCGGTACAAAAGGAAAAATGAT 59.718 37.500 1.90 0.00 0.00 2.45
2233 3330 1.399714 ACTCGATTGAGATGCCGGTA 58.600 50.000 17.27 0.00 45.57 4.02
2325 3425 4.381825 GGCAATATGAAGCATTTGTCACCA 60.382 41.667 0.00 0.00 0.00 4.17
2554 3669 9.369672 TGTTTAGGTACCCAACAAGATTAAATT 57.630 29.630 20.18 0.00 0.00 1.82
2809 3941 3.139077 AGTTGAACGGATCCTCACAAAC 58.861 45.455 10.75 7.96 0.00 2.93
2814 3946 2.933495 CGTAGTTGAACGGATCCTCA 57.067 50.000 10.75 4.76 39.19 3.86
2938 4085 4.447290 TCGTAGCATAGGCATAGCAAAAA 58.553 39.130 0.67 0.00 44.61 1.94


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

AutoCloner maintained by Alex Coulton.