Multiple sequence alignment - TraesCS3A01G435700

Loading Multiple Alignment...

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 TraesCS3A01G435700 chr3A 100.000 4156 0 0 1 4156 679503404 679507559 0.000000e+00 7675
1 TraesCS3A01G435700 chr3A 89.468 864 48 16 25 887 657118702 657119523 0.000000e+00 1051
2 TraesCS3A01G435700 chr3A 91.367 139 10 2 3723 3859 679506964 679507102 5.480000e-44 189
3 TraesCS3A01G435700 chr3A 91.367 139 10 2 3561 3699 679507126 679507262 5.480000e-44 189
4 TraesCS3A01G435700 chr3A 92.135 89 7 0 925 1013 657119518 657119606 4.360000e-25 126
5 TraesCS3A01G435700 chr3A 85.156 128 13 5 1845 1969 701670924 701671048 4.360000e-25 126
6 TraesCS3A01G435700 chr3B 97.885 2175 39 4 1983 4156 718687668 718689836 0.000000e+00 3755
7 TraesCS3A01G435700 chr3B 92.862 1569 73 17 325 1885 718686122 718687659 0.000000e+00 2241
8 TraesCS3A01G435700 chr3B 92.086 139 9 2 3723 3859 718689243 718689381 1.180000e-45 195
9 TraesCS3A01G435700 chr3B 92.086 139 9 2 3561 3699 718689405 718689541 1.180000e-45 195
10 TraesCS3A01G435700 chr3D 89.507 1887 114 36 25 1884 542821470 542823299 0.000000e+00 2311
11 TraesCS3A01G435700 chr3D 91.185 987 63 13 2595 3562 542823755 542824736 0.000000e+00 1319
12 TraesCS3A01G435700 chr3D 92.105 608 33 8 3561 4156 542824772 542825376 0.000000e+00 843
13 TraesCS3A01G435700 chr3D 91.549 142 11 1 3719 3859 542824768 542824909 1.180000e-45 195
14 TraesCS3A01G435700 chr3D 89.928 139 11 3 3561 3699 542824933 542825068 4.270000e-40 176
15 TraesCS3A01G435700 chr7B 90.258 1550 113 16 25 1572 598640495 598642008 0.000000e+00 1991
16 TraesCS3A01G435700 chr7B 90.129 1550 112 17 25 1572 598608252 598609762 0.000000e+00 1977
17 TraesCS3A01G435700 chr7B 90.044 1145 69 16 25 1167 644928193 644929294 0.000000e+00 1441
18 TraesCS3A01G435700 chr7B 89.867 977 63 14 25 990 643744914 643745865 0.000000e+00 1223
19 TraesCS3A01G435700 chr7B 88.682 751 55 9 25 773 598923166 598923888 0.000000e+00 889
20 TraesCS3A01G435700 chr7B 91.033 513 41 4 1323 1833 598930815 598931324 0.000000e+00 688
21 TraesCS3A01G435700 chr7B 90.485 515 44 5 1321 1833 643752636 643753147 0.000000e+00 675
22 TraesCS3A01G435700 chr7B 94.221 398 20 1 2114 2511 598649862 598650256 4.600000e-169 604
23 TraesCS3A01G435700 chr7B 93.719 398 22 1 2114 2511 598617636 598618030 9.950000e-166 593
24 TraesCS3A01G435700 chr7B 92.965 398 25 1 2114 2511 598931541 598931935 1.000000e-160 577
25 TraesCS3A01G435700 chr7B 92.965 398 24 2 2114 2511 644945970 644946363 1.000000e-160 577
26 TraesCS3A01G435700 chr7B 95.402 348 16 0 978 1325 598925025 598925372 4.690000e-154 555
27 TraesCS3A01G435700 chr7B 91.457 398 31 1 2114 2511 643753364 643753758 1.020000e-150 544
28 TraesCS3A01G435700 chr7B 93.966 348 20 1 978 1325 643746852 643747198 3.680000e-145 525
29 TraesCS3A01G435700 chr7B 90.339 383 36 1 25 406 599342405 599342787 6.200000e-138 501
30 TraesCS3A01G435700 chr7B 90.625 320 26 4 1253 1572 644938411 644938726 4.970000e-114 422
31 TraesCS3A01G435700 chr7B 92.593 270 19 1 1565 1833 598617161 598617430 1.810000e-103 387
32 TraesCS3A01G435700 chr7B 92.222 270 20 1 1565 1833 598649387 598649656 8.430000e-102 381
33 TraesCS3A01G435700 chr7B 89.259 270 28 1 1565 1833 644945484 644945753 1.850000e-88 337
34 TraesCS3A01G435700 chr7B 89.552 134 6 4 1983 2108 598617468 598617601 3.320000e-36 163
35 TraesCS3A01G435700 chr7B 88.889 135 7 4 1983 2109 598649694 598649828 4.300000e-35 159
36 TraesCS3A01G435700 chr7B 94.000 100 6 0 1983 2082 598931362 598931461 7.200000e-33 152
37 TraesCS3A01G435700 chr7B 94.000 100 6 0 1983 2082 643753185 643753284 7.200000e-33 152
38 TraesCS3A01G435700 chr7B 94.059 101 5 1 1983 2082 644945791 644945891 7.200000e-33 152
39 TraesCS3A01G435700 chr1D 89.273 867 55 8 25 890 402721950 402721121 0.000000e+00 1051
40 TraesCS3A01G435700 chr1A 84.703 961 89 19 25 974 497962392 497961479 0.000000e+00 907
41 TraesCS3A01G435700 chr7D 93.137 102 3 3 1881 1978 514661125 514661024 3.350000e-31 147
42 TraesCS3A01G435700 chr2A 93.137 102 3 4 1866 1964 82350896 82350996 3.350000e-31 147
43 TraesCS3A01G435700 chr2A 92.000 100 4 3 1869 1965 362046351 362046449 2.010000e-28 137
44 TraesCS3A01G435700 chr5D 92.157 102 4 3 1871 1969 107238565 107238665 1.560000e-29 141
45 TraesCS3A01G435700 chr4A 92.929 99 3 3 1882 1977 4152056 4151959 1.560000e-29 141
46 TraesCS3A01G435700 chr1B 90.476 105 7 2 1879 1980 668678440 668678544 7.250000e-28 135
47 TraesCS3A01G435700 chr4D 89.286 112 4 7 1861 1967 164649437 164649545 2.610000e-27 134
48 TraesCS3A01G435700 chr5B 87.826 115 10 3 1871 1981 92002688 92002574 9.370000e-27 132


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 TraesCS3A01G435700 chr3A 679503404 679507559 4155 False 2684.333333 7675 94.244667 1 4156 3 chr3A.!!$F3 4155
1 TraesCS3A01G435700 chr3A 657118702 657119606 904 False 588.500000 1051 90.801500 25 1013 2 chr3A.!!$F2 988
2 TraesCS3A01G435700 chr3B 718686122 718689836 3714 False 1596.500000 3755 93.729750 325 4156 4 chr3B.!!$F1 3831
3 TraesCS3A01G435700 chr3D 542821470 542825376 3906 False 968.800000 2311 90.854800 25 4156 5 chr3D.!!$F1 4131
4 TraesCS3A01G435700 chr7B 598640495 598642008 1513 False 1991.000000 1991 90.258000 25 1572 1 chr7B.!!$F2 1547
5 TraesCS3A01G435700 chr7B 598608252 598609762 1510 False 1977.000000 1977 90.129000 25 1572 1 chr7B.!!$F1 1547
6 TraesCS3A01G435700 chr7B 644928193 644929294 1101 False 1441.000000 1441 90.044000 25 1167 1 chr7B.!!$F4 1142
7 TraesCS3A01G435700 chr7B 643744914 643747198 2284 False 874.000000 1223 91.916500 25 1325 2 chr7B.!!$F10 1300
8 TraesCS3A01G435700 chr7B 598923166 598925372 2206 False 722.000000 889 92.042000 25 1325 2 chr7B.!!$F8 1300
9 TraesCS3A01G435700 chr7B 598930815 598931935 1120 False 472.333333 688 92.666000 1323 2511 3 chr7B.!!$F9 1188
10 TraesCS3A01G435700 chr7B 643752636 643753758 1122 False 457.000000 675 91.980667 1321 2511 3 chr7B.!!$F11 1190
11 TraesCS3A01G435700 chr7B 598649387 598650256 869 False 381.333333 604 91.777333 1565 2511 3 chr7B.!!$F7 946
12 TraesCS3A01G435700 chr7B 598617161 598618030 869 False 381.000000 593 91.954667 1565 2511 3 chr7B.!!$F6 946
13 TraesCS3A01G435700 chr7B 644945484 644946363 879 False 355.333333 577 92.094333 1565 2511 3 chr7B.!!$F12 946
14 TraesCS3A01G435700 chr1D 402721121 402721950 829 True 1051.000000 1051 89.273000 25 890 1 chr1D.!!$R1 865
15 TraesCS3A01G435700 chr1A 497961479 497962392 913 True 907.000000 907 84.703000 25 974 1 chr1A.!!$R1 949

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
22 23 0.106015 GGCTTTCCATGGCCAGGTAT 60.106 55.0 17.55 0.0 46.84 2.73 F
505 517 0.762418 TTCCGTTGCTCTCCTTGGAA 59.238 50.0 0.00 0.0 33.34 3.53 F
1426 2474 0.247736 AGTAAGGCGCTTCTGACTGG 59.752 55.0 7.64 0.0 27.61 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 2474 0.173255 CGGAATTCCCCATTGTGCAC 59.827 55.0 19.01 10.75 0.0 4.57 R
1608 2664 0.451135 GCAACGACGATGACAAGCAC 60.451 55.0 9.52 0.00 0.0 4.40 R
3322 4525 0.178891 AGGGAGCCTCTGGAAAGTCA 60.179 55.0 0.00 0.00 0.0 3.41 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
20 21 2.037847 GGCTTTCCATGGCCAGGT 59.962 61.111 17.55 0.00 46.84 4.00
21 22 1.306296 GGCTTTCCATGGCCAGGTA 59.694 57.895 17.55 6.56 46.84 3.08
22 23 0.106015 GGCTTTCCATGGCCAGGTAT 60.106 55.000 17.55 0.00 46.84 2.73
23 24 1.144913 GGCTTTCCATGGCCAGGTATA 59.855 52.381 17.55 0.00 46.84 1.47
50 51 7.421530 TGTGACAAGAAACTTATTCTACAGC 57.578 36.000 0.00 0.00 0.00 4.40
100 101 1.890625 TTGCAATGTGGGGAGCATGC 61.891 55.000 10.51 10.51 0.00 4.06
109 110 2.202987 GGAGCATGCCGGTCTCAG 60.203 66.667 15.66 0.00 42.06 3.35
143 144 5.782893 TTTCCAACATACAACTTCCTTGG 57.217 39.130 0.00 0.00 33.66 3.61
166 167 2.417924 CCACCTGAAGCTGCTACACTAG 60.418 54.545 0.90 0.00 0.00 2.57
208 209 4.156739 GGTTGACCAAGAAGCAGGATTTAG 59.843 45.833 0.00 0.00 35.64 1.85
439 450 4.549516 GGCGCCGACGAGTACTCC 62.550 72.222 12.58 3.24 43.93 3.85
440 451 3.807538 GCGCCGACGAGTACTCCA 61.808 66.667 17.23 0.00 43.93 3.86
441 452 2.403987 CGCCGACGAGTACTCCAG 59.596 66.667 17.23 6.76 43.93 3.86
442 453 2.102553 GCCGACGAGTACTCCAGC 59.897 66.667 17.23 10.70 0.00 4.85
443 454 2.408241 GCCGACGAGTACTCCAGCT 61.408 63.158 17.23 0.00 0.00 4.24
444 455 1.722677 CCGACGAGTACTCCAGCTC 59.277 63.158 17.23 5.98 0.00 4.09
480 491 1.446272 CGAGAGGTTCGGCTTGACC 60.446 63.158 0.00 0.00 45.54 4.02
505 517 0.762418 TTCCGTTGCTCTCCTTGGAA 59.238 50.000 0.00 0.00 33.34 3.53
518 530 0.817634 CTTGGAAACGGCAGTGGTGA 60.818 55.000 0.00 0.00 0.00 4.02
601 625 2.691409 AATTGGAGCTCGGATTCGAA 57.309 45.000 7.83 0.00 45.47 3.71
753 784 3.161450 CGGGGTCGGGGATGACAT 61.161 66.667 0.00 0.00 40.72 3.06
924 970 1.296715 CCAGGCTCAAACCTAGCGT 59.703 57.895 0.00 0.00 41.03 5.07
1426 2474 0.247736 AGTAAGGCGCTTCTGACTGG 59.752 55.000 7.64 0.00 27.61 4.00
1437 2488 0.250858 TCTGACTGGTGCACAATGGG 60.251 55.000 20.43 5.75 0.00 4.00
1443 2494 1.205417 CTGGTGCACAATGGGGAATTC 59.795 52.381 20.43 0.00 0.00 2.17
1493 2546 9.357652 CTAAAAACTAAATACTGTGCGGTACTA 57.642 33.333 0.00 0.00 0.00 1.82
1494 2547 7.823149 AAAACTAAATACTGTGCGGTACTAG 57.177 36.000 0.00 0.00 0.00 2.57
1503 2556 1.064654 GTGCGGTACTAGTACTTCGGG 59.935 57.143 27.71 15.19 36.36 5.14
1558 2614 2.025981 TGGAGATTGGATTGTGGTGAGG 60.026 50.000 0.00 0.00 0.00 3.86
1563 2619 0.770499 TGGATTGTGGTGAGGCAAGA 59.230 50.000 0.00 0.00 0.00 3.02
1608 2664 4.696479 ATGACAGGGCTTAGATTAGGTG 57.304 45.455 0.00 0.00 0.00 4.00
1772 2851 4.689071 TGCAAGCATCATCCATTCATTTC 58.311 39.130 0.00 0.00 0.00 2.17
1783 2862 7.605449 TCATCCATTCATTTCAAAAGGAACTC 58.395 34.615 4.86 0.00 40.85 3.01
1884 2963 7.168219 TCTTGGTTGAATGCTTACTTCATACT 58.832 34.615 0.00 0.00 32.94 2.12
1885 2964 6.985188 TGGTTGAATGCTTACTTCATACTC 57.015 37.500 0.00 0.00 32.94 2.59
1886 2965 5.880332 TGGTTGAATGCTTACTTCATACTCC 59.120 40.000 0.00 0.00 32.94 3.85
1887 2966 5.297029 GGTTGAATGCTTACTTCATACTCCC 59.703 44.000 0.00 0.00 32.94 4.30
1888 2967 5.957771 TGAATGCTTACTTCATACTCCCT 57.042 39.130 0.00 0.00 0.00 4.20
1889 2968 5.918608 TGAATGCTTACTTCATACTCCCTC 58.081 41.667 0.00 0.00 0.00 4.30
1890 2969 4.965200 ATGCTTACTTCATACTCCCTCC 57.035 45.455 0.00 0.00 0.00 4.30
1891 2970 2.693591 TGCTTACTTCATACTCCCTCCG 59.306 50.000 0.00 0.00 0.00 4.63
1892 2971 2.694109 GCTTACTTCATACTCCCTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
1893 2972 3.132467 GCTTACTTCATACTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
1894 2973 4.737055 GCTTACTTCATACTCCCTCCGTTC 60.737 50.000 0.00 0.00 0.00 3.95
1895 2974 2.108970 ACTTCATACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
1896 2975 2.108168 CTTCATACTCCCTCCGTTCCA 58.892 52.381 0.00 0.00 0.00 3.53
1897 2976 2.241281 TCATACTCCCTCCGTTCCAA 57.759 50.000 0.00 0.00 0.00 3.53
1898 2977 2.542550 TCATACTCCCTCCGTTCCAAA 58.457 47.619 0.00 0.00 0.00 3.28
1899 2978 2.907696 TCATACTCCCTCCGTTCCAAAA 59.092 45.455 0.00 0.00 0.00 2.44
1900 2979 3.521937 TCATACTCCCTCCGTTCCAAAAT 59.478 43.478 0.00 0.00 0.00 1.82
1901 2980 4.717778 TCATACTCCCTCCGTTCCAAAATA 59.282 41.667 0.00 0.00 0.00 1.40
1902 2981 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1903 2982 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1904 2983 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1905 2984 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1906 2985 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1907 2986 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1908 2987 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1909 2988 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1910 2989 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1911 2990 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1912 2991 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1913 2992 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1914 2993 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1915 2994 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1916 2995 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1917 2996 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1918 2997 8.463930 TCCAAAATAGATGACTCAACTTTGTT 57.536 30.769 0.00 0.00 0.00 2.83
1919 2998 9.567776 TCCAAAATAGATGACTCAACTTTGTTA 57.432 29.630 0.00 0.00 0.00 2.41
1938 3017 9.434559 CTTTGTTAAGTTAGTACAAAGTTGAGC 57.565 33.333 21.71 0.00 46.82 4.26
1939 3018 7.486802 TGTTAAGTTAGTACAAAGTTGAGCC 57.513 36.000 0.00 0.00 0.00 4.70
1940 3019 7.049133 TGTTAAGTTAGTACAAAGTTGAGCCA 58.951 34.615 0.00 0.00 0.00 4.75
1941 3020 7.717875 TGTTAAGTTAGTACAAAGTTGAGCCAT 59.282 33.333 0.00 0.00 0.00 4.40
1942 3021 6.803154 AAGTTAGTACAAAGTTGAGCCATC 57.197 37.500 0.00 0.00 0.00 3.51
1943 3022 6.115448 AGTTAGTACAAAGTTGAGCCATCT 57.885 37.500 0.00 0.00 0.00 2.90
1944 3023 7.241042 AGTTAGTACAAAGTTGAGCCATCTA 57.759 36.000 0.00 0.00 0.00 1.98
1945 3024 7.852263 AGTTAGTACAAAGTTGAGCCATCTAT 58.148 34.615 0.00 0.00 0.00 1.98
1946 3025 8.322091 AGTTAGTACAAAGTTGAGCCATCTATT 58.678 33.333 0.00 0.00 0.00 1.73
1947 3026 8.947115 GTTAGTACAAAGTTGAGCCATCTATTT 58.053 33.333 0.00 0.00 0.00 1.40
1948 3027 9.515226 TTAGTACAAAGTTGAGCCATCTATTTT 57.485 29.630 0.00 0.00 0.00 1.82
1949 3028 7.820648 AGTACAAAGTTGAGCCATCTATTTTG 58.179 34.615 0.00 6.27 40.82 2.44
1950 3029 6.029346 ACAAAGTTGAGCCATCTATTTTGG 57.971 37.500 10.53 0.00 40.00 3.28
1951 3030 5.774690 ACAAAGTTGAGCCATCTATTTTGGA 59.225 36.000 10.53 0.00 40.00 3.53
1952 3031 6.267471 ACAAAGTTGAGCCATCTATTTTGGAA 59.733 34.615 10.53 0.00 40.00 3.53
1953 3032 5.904362 AGTTGAGCCATCTATTTTGGAAC 57.096 39.130 0.00 0.00 36.26 3.62
1954 3033 4.396166 AGTTGAGCCATCTATTTTGGAACG 59.604 41.667 0.00 0.00 36.26 3.95
1955 3034 3.278574 TGAGCCATCTATTTTGGAACGG 58.721 45.455 0.00 0.00 36.26 4.44
1956 3035 3.054728 TGAGCCATCTATTTTGGAACGGA 60.055 43.478 0.00 0.00 36.26 4.69
1957 3036 3.545703 AGCCATCTATTTTGGAACGGAG 58.454 45.455 0.00 0.00 36.26 4.63
1958 3037 2.618709 GCCATCTATTTTGGAACGGAGG 59.381 50.000 0.00 0.00 36.26 4.30
1959 3038 3.214328 CCATCTATTTTGGAACGGAGGG 58.786 50.000 0.00 0.00 36.26 4.30
1960 3039 3.118038 CCATCTATTTTGGAACGGAGGGA 60.118 47.826 0.00 0.00 36.26 4.20
1961 3040 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1962 3041 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1963 3042 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1964 3043 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1974 3053 2.418746 CGGAGGGAGTACTTGTGAATGG 60.419 54.545 0.00 0.00 0.00 3.16
1975 3054 2.633488 GAGGGAGTACTTGTGAATGGC 58.367 52.381 0.00 0.00 0.00 4.40
1976 3055 1.985159 AGGGAGTACTTGTGAATGGCA 59.015 47.619 0.00 0.00 0.00 4.92
1977 3056 2.578021 AGGGAGTACTTGTGAATGGCAT 59.422 45.455 0.00 0.00 0.00 4.40
1978 3057 2.684881 GGGAGTACTTGTGAATGGCATG 59.315 50.000 0.00 0.00 0.00 4.06
1979 3058 3.609853 GGAGTACTTGTGAATGGCATGA 58.390 45.455 0.00 0.00 0.00 3.07
1980 3059 3.624861 GGAGTACTTGTGAATGGCATGAG 59.375 47.826 0.00 0.00 0.00 2.90
1981 3060 4.256920 GAGTACTTGTGAATGGCATGAGT 58.743 43.478 0.00 3.58 0.00 3.41
2122 3250 0.877743 GCTCAAGCTGGGACACTTTC 59.122 55.000 0.00 0.00 38.21 2.62
2200 3328 4.202367 GCAAGTATGGTGGCCTCTAGTTAT 60.202 45.833 3.32 0.00 0.00 1.89
2366 3495 9.862149 TTCCACTTTCTAGAAAAAGGAATTACT 57.138 29.630 29.43 0.00 39.96 2.24
2485 3635 5.735285 TCTGTTCTGAGTGATCATTCAGT 57.265 39.130 34.18 4.69 43.21 3.41
2563 3714 5.424121 AACATGACTTTCGGTCTTTTGAG 57.576 39.130 0.00 0.00 44.74 3.02
2591 3742 7.498900 CCATGCACTATTCATAAAGTAGGTTCA 59.501 37.037 0.00 0.00 0.00 3.18
2665 3864 7.168972 TCTCCATGTTTTGCGTTTTCTTATTTG 59.831 33.333 0.00 0.00 0.00 2.32
3306 4509 3.253220 ACTGGGGTGTGTTATCTGGTTA 58.747 45.455 0.00 0.00 0.00 2.85
3322 4525 5.513233 TCTGGTTAAGGTCGTATTAGGAGT 58.487 41.667 0.00 0.00 0.00 3.85
3624 4878 5.994416 ATGGAACCTTATGGATTAGGTGT 57.006 39.130 0.81 0.00 43.88 4.16
3626 4880 6.894735 TGGAACCTTATGGATTAGGTGTTA 57.105 37.500 0.81 0.00 43.88 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.656947 TATACCTGGCCATGGAAAGC 57.343 50.000 23.24 0.00 0.00 3.51
5 6 4.895297 ACAAATATACCTGGCCATGGAAAG 59.105 41.667 23.24 11.61 0.00 2.62
6 7 4.648762 CACAAATATACCTGGCCATGGAAA 59.351 41.667 23.24 13.28 0.00 3.13
7 8 4.079500 TCACAAATATACCTGGCCATGGAA 60.080 41.667 23.24 7.83 0.00 3.53
8 9 3.461458 TCACAAATATACCTGGCCATGGA 59.539 43.478 23.24 11.74 0.00 3.41
9 10 3.569701 GTCACAAATATACCTGGCCATGG 59.430 47.826 5.51 13.05 0.00 3.66
10 11 4.206375 TGTCACAAATATACCTGGCCATG 58.794 43.478 5.51 6.06 0.00 3.66
11 12 4.518278 TGTCACAAATATACCTGGCCAT 57.482 40.909 5.51 0.00 0.00 4.40
12 13 4.018870 TCTTGTCACAAATATACCTGGCCA 60.019 41.667 4.71 4.71 0.00 5.36
13 14 4.523083 TCTTGTCACAAATATACCTGGCC 58.477 43.478 0.00 0.00 0.00 5.36
14 15 6.151144 AGTTTCTTGTCACAAATATACCTGGC 59.849 38.462 0.00 0.00 0.00 4.85
15 16 7.687941 AGTTTCTTGTCACAAATATACCTGG 57.312 36.000 0.00 0.00 0.00 4.45
100 101 1.079543 CAGCTCCAACTGAGACCGG 60.080 63.158 0.00 0.00 44.42 5.28
143 144 1.746991 GTAGCAGCTTCAGGTGGGC 60.747 63.158 0.00 0.00 43.24 5.36
166 167 1.869690 GGTGGCGCTTCTTCAAGTC 59.130 57.895 7.64 0.00 31.45 3.01
208 209 4.851179 GGACCGCCCGATCCAACC 62.851 72.222 0.00 0.00 34.87 3.77
366 376 2.522436 ACCACCGACGTCTCCCAA 60.522 61.111 14.70 0.00 0.00 4.12
442 453 2.131183 GAATCCGAGCTCCAAATCGAG 58.869 52.381 8.47 0.00 41.40 4.04
443 454 1.536072 CGAATCCGAGCTCCAAATCGA 60.536 52.381 16.96 0.00 41.40 3.59
444 455 0.855349 CGAATCCGAGCTCCAAATCG 59.145 55.000 8.47 9.92 38.22 3.34
445 456 2.225068 TCGAATCCGAGCTCCAAATC 57.775 50.000 8.47 1.22 40.30 2.17
505 517 0.036952 CAGAGATCACCACTGCCGTT 60.037 55.000 0.00 0.00 0.00 4.44
518 530 3.842923 CCAGCCGACGCCAGAGAT 61.843 66.667 0.00 0.00 34.57 2.75
601 625 4.394712 CGCAGCCCTCGAAACCCT 62.395 66.667 0.00 0.00 0.00 4.34
845 876 2.659610 GCCAGCAAGACCGAGTCT 59.340 61.111 1.23 1.23 45.64 3.24
847 878 3.241530 TGGCCAGCAAGACCGAGT 61.242 61.111 0.00 0.00 0.00 4.18
924 970 0.677731 GCTGAATGTACTGGGCTGCA 60.678 55.000 0.50 0.00 0.00 4.41
1426 2474 0.173255 CGGAATTCCCCATTGTGCAC 59.827 55.000 19.01 10.75 0.00 4.57
1437 2488 3.065371 CACTAGCATTTCACCGGAATTCC 59.935 47.826 15.01 15.01 31.93 3.01
1443 2494 2.967362 TGTACACTAGCATTTCACCGG 58.033 47.619 0.00 0.00 0.00 5.28
1487 2540 4.632153 TCGTATCCCGAAGTACTAGTACC 58.368 47.826 25.97 13.05 44.03 3.34
1558 2614 5.105877 TGACCTGTAGTATACACAGTCTTGC 60.106 44.000 22.67 13.29 46.14 4.01
1563 2619 4.017775 TCCCTGACCTGTAGTATACACAGT 60.018 45.833 22.67 15.57 46.14 3.55
1608 2664 0.451135 GCAACGACGATGACAAGCAC 60.451 55.000 9.52 0.00 0.00 4.40
1636 2692 4.400961 AGAGCCAGCAGGAACCGC 62.401 66.667 0.00 0.00 36.89 5.68
1638 2694 2.045536 CCAGAGCCAGCAGGAACC 60.046 66.667 0.00 0.00 36.89 3.62
1772 2851 1.002468 CACAGGTGCGAGTTCCTTTTG 60.002 52.381 0.00 0.00 30.91 2.44
1783 2862 1.202348 TGACTACAGATCACAGGTGCG 59.798 52.381 0.00 0.00 0.00 5.34
1884 2963 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1885 2964 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1886 2965 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1887 2966 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1888 2967 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1889 2968 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1890 2969 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1891 2970 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1892 2971 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1893 2972 8.463930 AACAAAGTTGAGTCATCTATTTTGGA 57.536 30.769 14.35 0.00 40.00 3.53
1903 2982 9.826574 TGTACTAACTTAACAAAGTTGAGTCAT 57.173 29.630 12.54 0.00 42.47 3.06
1904 2983 9.656040 TTGTACTAACTTAACAAAGTTGAGTCA 57.344 29.630 12.54 0.00 42.47 3.41
1913 2992 8.400186 GGCTCAACTTTGTACTAACTTAACAAA 58.600 33.333 0.00 0.00 39.95 2.83
1914 2993 7.553402 TGGCTCAACTTTGTACTAACTTAACAA 59.447 33.333 0.00 0.00 0.00 2.83
1915 2994 7.049133 TGGCTCAACTTTGTACTAACTTAACA 58.951 34.615 0.00 0.00 0.00 2.41
1916 2995 7.486802 TGGCTCAACTTTGTACTAACTTAAC 57.513 36.000 0.00 0.00 0.00 2.01
1917 2996 8.154856 AGATGGCTCAACTTTGTACTAACTTAA 58.845 33.333 0.00 0.00 0.00 1.85
1918 2997 7.676947 AGATGGCTCAACTTTGTACTAACTTA 58.323 34.615 0.00 0.00 0.00 2.24
1919 2998 6.534634 AGATGGCTCAACTTTGTACTAACTT 58.465 36.000 0.00 0.00 0.00 2.66
1920 2999 6.115448 AGATGGCTCAACTTTGTACTAACT 57.885 37.500 0.00 0.00 0.00 2.24
1921 3000 8.494016 AATAGATGGCTCAACTTTGTACTAAC 57.506 34.615 0.00 0.00 0.00 2.34
1922 3001 9.515226 AAAATAGATGGCTCAACTTTGTACTAA 57.485 29.630 0.00 0.00 0.00 2.24
1923 3002 8.946085 CAAAATAGATGGCTCAACTTTGTACTA 58.054 33.333 0.00 0.00 0.00 1.82
1924 3003 7.094205 CCAAAATAGATGGCTCAACTTTGTACT 60.094 37.037 0.00 0.00 0.00 2.73
1925 3004 7.029563 CCAAAATAGATGGCTCAACTTTGTAC 58.970 38.462 0.00 0.00 0.00 2.90
1926 3005 6.945435 TCCAAAATAGATGGCTCAACTTTGTA 59.055 34.615 0.00 0.00 37.88 2.41
1927 3006 5.774690 TCCAAAATAGATGGCTCAACTTTGT 59.225 36.000 0.00 0.00 37.88 2.83
1928 3007 6.271488 TCCAAAATAGATGGCTCAACTTTG 57.729 37.500 0.00 0.00 37.88 2.77
1929 3008 6.570378 CGTTCCAAAATAGATGGCTCAACTTT 60.570 38.462 0.00 0.00 37.88 2.66
1930 3009 5.106157 CGTTCCAAAATAGATGGCTCAACTT 60.106 40.000 0.00 0.00 37.88 2.66
1931 3010 4.396166 CGTTCCAAAATAGATGGCTCAACT 59.604 41.667 0.00 0.00 37.88 3.16
1932 3011 4.438744 CCGTTCCAAAATAGATGGCTCAAC 60.439 45.833 0.00 0.00 37.88 3.18
1933 3012 3.694072 CCGTTCCAAAATAGATGGCTCAA 59.306 43.478 0.00 0.00 37.88 3.02
1934 3013 3.054728 TCCGTTCCAAAATAGATGGCTCA 60.055 43.478 0.00 0.00 37.88 4.26
1935 3014 3.541632 TCCGTTCCAAAATAGATGGCTC 58.458 45.455 0.00 0.00 37.88 4.70
1936 3015 3.545703 CTCCGTTCCAAAATAGATGGCT 58.454 45.455 0.00 0.00 37.88 4.75
1937 3016 2.618709 CCTCCGTTCCAAAATAGATGGC 59.381 50.000 0.00 0.00 37.88 4.40
1938 3017 3.118038 TCCCTCCGTTCCAAAATAGATGG 60.118 47.826 0.00 0.00 39.41 3.51
1939 3018 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1940 3019 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1941 3020 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1942 3021 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1943 3022 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
1944 3023 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
1945 3024 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1946 3025 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1947 3026 1.621814 CAAGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
1948 3027 1.263356 CAAGTACTCCCTCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
1949 3028 1.067071 CACAAGTACTCCCTCCGTTCC 60.067 57.143 0.00 0.00 0.00 3.62
1950 3029 1.891150 TCACAAGTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
1951 3030 2.005370 TCACAAGTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
1952 3031 2.005370 TTCACAAGTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
1953 3032 2.418746 CCATTCACAAGTACTCCCTCCG 60.419 54.545 0.00 0.00 0.00 4.63
1954 3033 2.681097 GCCATTCACAAGTACTCCCTCC 60.681 54.545 0.00 0.00 0.00 4.30
1955 3034 2.027192 TGCCATTCACAAGTACTCCCTC 60.027 50.000 0.00 0.00 0.00 4.30
1956 3035 1.985159 TGCCATTCACAAGTACTCCCT 59.015 47.619 0.00 0.00 0.00 4.20
1957 3036 2.489938 TGCCATTCACAAGTACTCCC 57.510 50.000 0.00 0.00 0.00 4.30
1958 3037 3.609853 TCATGCCATTCACAAGTACTCC 58.390 45.455 0.00 0.00 0.00 3.85
1959 3038 4.093998 CACTCATGCCATTCACAAGTACTC 59.906 45.833 0.00 0.00 0.00 2.59
1960 3039 4.005650 CACTCATGCCATTCACAAGTACT 58.994 43.478 0.00 0.00 0.00 2.73
1961 3040 3.426695 GCACTCATGCCATTCACAAGTAC 60.427 47.826 0.00 0.00 46.97 2.73
1962 3041 2.749076 GCACTCATGCCATTCACAAGTA 59.251 45.455 0.00 0.00 46.97 2.24
1963 3042 1.542915 GCACTCATGCCATTCACAAGT 59.457 47.619 0.00 0.00 46.97 3.16
1964 3043 2.273370 GCACTCATGCCATTCACAAG 57.727 50.000 0.00 0.00 46.97 3.16
1976 3055 3.538591 CACCACATAGTCATGCACTCAT 58.461 45.455 0.00 0.00 36.43 2.90
1977 3056 2.355007 CCACCACATAGTCATGCACTCA 60.355 50.000 0.00 0.00 36.43 3.41
1978 3057 2.283298 CCACCACATAGTCATGCACTC 58.717 52.381 0.00 0.00 36.43 3.51
1979 3058 1.630369 ACCACCACATAGTCATGCACT 59.370 47.619 0.00 0.00 39.41 4.40
1980 3059 2.113860 ACCACCACATAGTCATGCAC 57.886 50.000 0.00 0.00 35.39 4.57
1981 3060 3.990959 TTACCACCACATAGTCATGCA 57.009 42.857 0.00 0.00 35.39 3.96
1994 3073 2.564947 TGGTCATTGCCAATTTACCACC 59.435 45.455 14.54 5.27 35.25 4.61
2122 3250 1.542030 CATACTCCCTCCGATCGGAAG 59.458 57.143 34.77 29.83 44.66 3.46
2331 3459 9.965824 TTTTTCTAGAAAGTGGAAGCTTTATTG 57.034 29.630 17.05 0.00 38.64 1.90
2366 3495 3.869912 GCCCATTGCTTCTGAAGAGTGTA 60.870 47.826 21.06 1.37 36.87 2.90
2367 3496 2.787994 CCCATTGCTTCTGAAGAGTGT 58.212 47.619 21.06 0.90 0.00 3.55
2368 3497 1.471684 GCCCATTGCTTCTGAAGAGTG 59.528 52.381 21.06 13.95 36.87 3.51
2429 3558 8.603304 ACTATGTACACAGAAAGTATTCCCTTT 58.397 33.333 8.45 0.00 37.37 3.11
2470 3620 3.405823 TGCACACTGAATGATCACTCA 57.594 42.857 6.69 6.69 35.41 3.41
2563 3714 6.992715 ACCTACTTTATGAATAGTGCATGGTC 59.007 38.462 0.00 0.00 0.00 4.02
2591 3742 2.946329 TGCACTTTTCGTACACCAATGT 59.054 40.909 0.00 0.00 43.30 2.71
3001 4202 3.207354 GCATCTGCAGCTGCCAAT 58.793 55.556 34.64 24.16 41.18 3.16
3306 4509 5.105432 GGAAAGTCACTCCTAATACGACCTT 60.105 44.000 0.00 0.00 0.00 3.50
3322 4525 0.178891 AGGGAGCCTCTGGAAAGTCA 60.179 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.