Multiple sequence alignment - TraesCS6D01G121600

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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 TraesCS6D01G121600 chr6D 100.000 3945 0 0 1 3945 86597332 86601276 0.000000e+00 7286.0
1 TraesCS6D01G121600 chr6B 92.190 1575 86 26 810 2358 164030425 164031988 0.000000e+00 2193.0
2 TraesCS6D01G121600 chr6B 88.453 1429 108 19 2525 3945 164032337 164033716 0.000000e+00 1672.0
3 TraesCS6D01G121600 chr6B 90.526 190 9 4 2350 2538 164032139 164032320 3.940000e-60 243.0
4 TraesCS6D01G121600 chr6A 90.486 1440 96 13 2505 3936 104111363 104112769 0.000000e+00 1862.0
5 TraesCS6D01G121600 chr6A 90.408 1397 86 28 842 2202 104079293 104080677 0.000000e+00 1794.0
6 TraesCS6D01G121600 chr6A 93.059 389 23 2 2505 2893 104095195 104095579 2.060000e-157 566.0
7 TraesCS6D01G121600 chr6A 89.344 122 9 4 2275 2394 104080700 104080819 2.460000e-32 150.0
8 TraesCS6D01G121600 chr1D 89.386 782 71 8 1 777 287469432 287468658 0.000000e+00 974.0
9 TraesCS6D01G121600 chr1D 87.646 769 83 11 1 766 95444754 95443995 0.000000e+00 883.0
10 TraesCS6D01G121600 chr3B 88.525 793 79 10 1 790 244657721 244658504 0.000000e+00 950.0
11 TraesCS6D01G121600 chr7D 88.703 779 81 7 1 777 170284660 170283887 0.000000e+00 944.0
12 TraesCS6D01G121600 chr5D 90.443 722 59 7 1 721 480843199 480842487 0.000000e+00 942.0
13 TraesCS6D01G121600 chr7B 89.466 731 70 7 1 728 6084301 6083575 0.000000e+00 917.0
14 TraesCS6D01G121600 chr1B 88.296 769 74 12 1 766 619213135 619213890 0.000000e+00 907.0
15 TraesCS6D01G121600 chr2D 88.904 739 71 9 1 735 448633701 448634432 0.000000e+00 900.0
16 TraesCS6D01G121600 chr3D 88.042 761 83 7 6 764 464321826 464321072 0.000000e+00 894.0
17 TraesCS6D01G121600 chr3A 93.443 61 4 0 3868 3928 610045084 610045144 1.510000e-14 91.6
18 TraesCS6D01G121600 chr5A 89.706 68 6 1 3871 3937 683271028 683270961 7.020000e-13 86.1
19 TraesCS6D01G121600 chr4A 85.714 77 10 1 3868 3943 140988790 140988714 3.270000e-11 80.5
20 TraesCS6D01G121600 chr7A 87.143 70 8 1 3877 3945 126962358 126962289 1.180000e-10 78.7
21 TraesCS6D01G121600 chr1A 92.857 42 3 0 3868 3909 381313624 381313665 1.180000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G121600 chr6D 86597332 86601276 3944 False 7286.000000 7286 100.000000 1 3945 1 chr6D.!!$F1 3944
1 TraesCS6D01G121600 chr6B 164030425 164033716 3291 False 1369.333333 2193 90.389667 810 3945 3 chr6B.!!$F1 3135
2 TraesCS6D01G121600 chr6A 104111363 104112769 1406 False 1862.000000 1862 90.486000 2505 3936 1 chr6A.!!$F2 1431
3 TraesCS6D01G121600 chr6A 104079293 104080819 1526 False 972.000000 1794 89.876000 842 2394 2 chr6A.!!$F3 1552
4 TraesCS6D01G121600 chr1D 287468658 287469432 774 True 974.000000 974 89.386000 1 777 1 chr1D.!!$R2 776
5 TraesCS6D01G121600 chr1D 95443995 95444754 759 True 883.000000 883 87.646000 1 766 1 chr1D.!!$R1 765
6 TraesCS6D01G121600 chr3B 244657721 244658504 783 False 950.000000 950 88.525000 1 790 1 chr3B.!!$F1 789
7 TraesCS6D01G121600 chr7D 170283887 170284660 773 True 944.000000 944 88.703000 1 777 1 chr7D.!!$R1 776
8 TraesCS6D01G121600 chr5D 480842487 480843199 712 True 942.000000 942 90.443000 1 721 1 chr5D.!!$R1 720
9 TraesCS6D01G121600 chr7B 6083575 6084301 726 True 917.000000 917 89.466000 1 728 1 chr7B.!!$R1 727
10 TraesCS6D01G121600 chr1B 619213135 619213890 755 False 907.000000 907 88.296000 1 766 1 chr1B.!!$F1 765
11 TraesCS6D01G121600 chr2D 448633701 448634432 731 False 900.000000 900 88.904000 1 735 1 chr2D.!!$F1 734
12 TraesCS6D01G121600 chr3D 464321072 464321826 754 True 894.000000 894 88.042000 6 764 1 chr3D.!!$R1 758

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
613 623 0.038021 ATTTGGTGCAATTTGGGGCC 59.962 50.0 0.00 0.00 0.0 5.80 F
2036 2078 0.036388 ATAATCCGGCGGCCATACAG 60.036 55.0 23.83 1.43 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2152 0.247736 GATGAGGAAGTGCTCACCGT 59.752 55.0 4.51 0.0 31.95 4.83 R
3442 3717 0.246635 CATGTCGACCCCGAGTTCTT 59.753 55.0 14.12 0.0 46.52 2.52 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
104 106 0.247736 CAGTAGCTTTGCTCCGGACT 59.752 55.000 0.00 0.00 40.44 3.85
144 146 5.245751 TCACTCTTCTCTCTTTGATTGAGCT 59.754 40.000 0.00 0.00 0.00 4.09
159 161 5.468072 TGATTGAGCTCTTGAAGTTGAGAAC 59.532 40.000 16.19 0.00 32.44 3.01
195 197 1.135721 GTCCATTTCCTCTTGCATGCC 59.864 52.381 16.68 0.00 0.00 4.40
222 224 4.597004 AGCATGATCATGTCCACTTCTTT 58.403 39.130 31.09 7.66 40.80 2.52
277 280 4.263639 TGAATCATTTGGTCAAGCTCCTCT 60.264 41.667 0.00 0.00 0.00 3.69
410 417 3.293714 TTGCCGGACGTACCACGA 61.294 61.111 5.05 0.00 46.05 4.35
582 591 1.971505 AAATGGATCCGGCAGCTCGA 61.972 55.000 7.39 0.00 0.00 4.04
612 622 1.452110 GATTTGGTGCAATTTGGGGC 58.548 50.000 0.00 0.00 0.00 5.80
613 623 0.038021 ATTTGGTGCAATTTGGGGCC 59.962 50.000 0.00 0.00 0.00 5.80
618 628 2.363147 GCAATTTGGGGCCGGGTA 60.363 61.111 2.18 0.00 0.00 3.69
690 702 4.568380 GCCTCATATTTGGGCTGGATATGA 60.568 45.833 12.87 12.87 42.31 2.15
725 737 3.056328 GGGCGTTTGAGGGCTGTC 61.056 66.667 0.00 0.00 0.00 3.51
750 763 0.961753 GGCCTGTCTGGGTCAAAAAG 59.038 55.000 0.00 0.00 36.00 2.27
766 779 2.457366 AAAGTCATGACCGGACAGTC 57.543 50.000 22.21 2.92 37.74 3.51
767 780 1.633774 AAGTCATGACCGGACAGTCT 58.366 50.000 22.21 5.44 37.74 3.24
768 781 2.509166 AGTCATGACCGGACAGTCTA 57.491 50.000 22.21 0.00 37.74 2.59
769 782 3.019799 AGTCATGACCGGACAGTCTAT 57.980 47.619 22.21 0.00 37.74 1.98
782 795 0.899720 AGTCTATCCGGGCGTTTGAA 59.100 50.000 0.00 0.00 0.00 2.69
795 808 1.830086 GTTTGAAACGGGTTTGTCGG 58.170 50.000 0.82 0.00 32.11 4.79
796 809 0.739561 TTTGAAACGGGTTTGTCGGG 59.260 50.000 0.82 0.00 32.11 5.14
797 810 0.394080 TTGAAACGGGTTTGTCGGGT 60.394 50.000 0.82 0.00 32.11 5.28
798 811 0.814812 TGAAACGGGTTTGTCGGGTC 60.815 55.000 0.82 0.00 32.11 4.46
799 812 0.533531 GAAACGGGTTTGTCGGGTCT 60.534 55.000 0.82 0.00 32.11 3.85
800 813 0.816421 AAACGGGTTTGTCGGGTCTG 60.816 55.000 0.00 0.00 0.00 3.51
801 814 2.358247 CGGGTTTGTCGGGTCTGG 60.358 66.667 0.00 0.00 0.00 3.86
802 815 2.833957 GGGTTTGTCGGGTCTGGT 59.166 61.111 0.00 0.00 0.00 4.00
803 816 1.149854 GGGTTTGTCGGGTCTGGTT 59.850 57.895 0.00 0.00 0.00 3.67
804 817 1.170290 GGGTTTGTCGGGTCTGGTTG 61.170 60.000 0.00 0.00 0.00 3.77
805 818 0.464916 GGTTTGTCGGGTCTGGTTGT 60.465 55.000 0.00 0.00 0.00 3.32
806 819 1.202675 GGTTTGTCGGGTCTGGTTGTA 60.203 52.381 0.00 0.00 0.00 2.41
807 820 2.140717 GTTTGTCGGGTCTGGTTGTAG 58.859 52.381 0.00 0.00 0.00 2.74
808 821 1.707106 TTGTCGGGTCTGGTTGTAGA 58.293 50.000 0.00 0.00 0.00 2.59
824 837 5.800438 GGTTGTAGATTTCGAATTTCTTGCC 59.200 40.000 14.21 9.17 0.00 4.52
826 839 4.693566 TGTAGATTTCGAATTTCTTGCCGT 59.306 37.500 14.21 0.00 0.00 5.68
827 840 4.083581 AGATTTCGAATTTCTTGCCGTG 57.916 40.909 0.00 0.00 0.00 4.94
828 841 2.697431 TTTCGAATTTCTTGCCGTGG 57.303 45.000 0.00 0.00 0.00 4.94
829 842 0.239879 TTCGAATTTCTTGCCGTGGC 59.760 50.000 3.30 3.30 42.35 5.01
830 843 1.154035 CGAATTTCTTGCCGTGGCC 60.154 57.895 8.69 0.00 41.09 5.36
831 844 1.861542 CGAATTTCTTGCCGTGGCCA 61.862 55.000 0.00 0.00 41.09 5.36
911 924 4.911514 TTTTCCCTCAAAAGAACGAAGG 57.088 40.909 0.00 0.00 30.07 3.46
916 929 4.951094 TCCCTCAAAAGAACGAAGGAAAAA 59.049 37.500 0.00 0.00 0.00 1.94
927 940 7.677892 AGAACGAAGGAAAAATTAGTACCTCT 58.322 34.615 0.00 0.00 0.00 3.69
928 941 8.155510 AGAACGAAGGAAAAATTAGTACCTCTT 58.844 33.333 0.00 0.00 0.00 2.85
1025 1046 4.554363 CCGTCGCCGAGATCGCTT 62.554 66.667 0.00 0.00 38.18 4.68
1036 1057 1.884926 GATCGCTTGCGGAAGAGGG 60.885 63.158 21.87 8.57 30.40 4.30
1042 1063 3.171828 TTGCGGAAGAGGGCGAACA 62.172 57.895 0.00 0.00 0.00 3.18
1093 1114 1.289380 GCGACGTCCTTCTCCAAGT 59.711 57.895 10.58 0.00 0.00 3.16
1132 1153 1.627550 GAAGACGGCGCAGTTCTTCC 61.628 60.000 26.31 12.67 32.91 3.46
1533 1554 4.508128 TACTACGCTGCCGCTGCC 62.508 66.667 15.72 0.00 38.22 4.85
1755 1776 1.323412 CGGAGAGGGAGGAGTACATG 58.677 60.000 0.00 0.00 0.00 3.21
1757 1778 2.489985 CGGAGAGGGAGGAGTACATGAT 60.490 54.545 0.00 0.00 0.00 2.45
1779 1800 2.577059 GGGCAACGATGGAGACGA 59.423 61.111 0.00 0.00 37.60 4.20
1806 1827 1.605710 GCTAACATGGCGATTCAGCAT 59.394 47.619 0.00 0.00 39.27 3.79
1850 1884 5.869344 TCAGTCTCTTTATCCAACAATCACG 59.131 40.000 0.00 0.00 0.00 4.35
1874 1908 7.001922 CGTCTTCATACGCCTATTTTATTTCG 58.998 38.462 0.00 0.00 35.87 3.46
1907 1949 5.639506 GGTGCTAATCGTCATTGCTATGTAT 59.360 40.000 8.01 0.00 33.34 2.29
1908 1950 6.811665 GGTGCTAATCGTCATTGCTATGTATA 59.188 38.462 8.01 0.00 33.34 1.47
1909 1951 7.201444 GGTGCTAATCGTCATTGCTATGTATAC 60.201 40.741 8.01 0.00 33.34 1.47
2036 2078 0.036388 ATAATCCGGCGGCCATACAG 60.036 55.000 23.83 1.43 0.00 2.74
2052 2094 1.230324 ACAGCTCTTCTTTGCGGAAC 58.770 50.000 0.00 0.00 0.00 3.62
2109 2152 5.386060 TGTCCAAGACTCTGTCTCTCTAAA 58.614 41.667 0.42 0.00 42.59 1.85
2126 2169 0.468226 AAACGGTGAGCACTTCCTCA 59.532 50.000 0.16 0.00 39.42 3.86
2197 2260 4.561105 AGCTTTCTTTGGTAGAGAACGAG 58.439 43.478 0.00 0.00 33.15 4.18
2209 2272 1.325943 GAGAACGAGTAATGCTGCTGC 59.674 52.381 8.89 8.89 40.20 5.25
2216 2286 2.606725 GAGTAATGCTGCTGCTGTACTG 59.393 50.000 25.23 0.00 38.57 2.74
2222 2292 1.664659 GCTGCTGCTGTACTGAATCAG 59.335 52.381 8.98 8.98 35.34 2.90
2229 2299 2.092838 GCTGTACTGAATCAGCGTCAAC 59.907 50.000 10.62 2.22 45.42 3.18
2231 2301 4.733850 CTGTACTGAATCAGCGTCAACTA 58.266 43.478 10.62 0.00 34.37 2.24
2232 2302 5.128992 TGTACTGAATCAGCGTCAACTAA 57.871 39.130 10.62 0.00 34.37 2.24
2233 2303 5.720202 TGTACTGAATCAGCGTCAACTAAT 58.280 37.500 10.62 0.00 34.37 1.73
2234 2304 6.859017 TGTACTGAATCAGCGTCAACTAATA 58.141 36.000 10.62 0.00 34.37 0.98
2236 2306 6.834959 ACTGAATCAGCGTCAACTAATATG 57.165 37.500 10.62 0.00 34.37 1.78
2237 2307 6.573434 ACTGAATCAGCGTCAACTAATATGA 58.427 36.000 10.62 0.00 34.37 2.15
2238 2308 7.041721 ACTGAATCAGCGTCAACTAATATGAA 58.958 34.615 10.62 0.00 34.37 2.57
2239 2309 7.712639 ACTGAATCAGCGTCAACTAATATGAAT 59.287 33.333 10.62 0.00 34.37 2.57
2240 2310 8.437360 TGAATCAGCGTCAACTAATATGAATT 57.563 30.769 0.00 0.00 0.00 2.17
2241 2311 8.337532 TGAATCAGCGTCAACTAATATGAATTG 58.662 33.333 0.00 0.00 0.00 2.32
2242 2312 6.603237 TCAGCGTCAACTAATATGAATTGG 57.397 37.500 0.00 0.00 0.00 3.16
2243 2313 6.112734 TCAGCGTCAACTAATATGAATTGGT 58.887 36.000 0.00 0.00 38.33 3.67
2253 2324 5.725551 AATATGAATTGGTGGGGAGTACA 57.274 39.130 0.00 0.00 0.00 2.90
2295 2371 5.736951 ATCAGGAGTGTATGAGGATTAGC 57.263 43.478 0.00 0.00 0.00 3.09
2336 2413 3.947910 ACTCATTGGTGCTTTTGATGG 57.052 42.857 0.00 0.00 0.00 3.51
2480 2717 5.026121 TGCTAGTCAGGGCTATATATGCTT 58.974 41.667 0.00 0.00 0.00 3.91
2481 2718 5.127845 TGCTAGTCAGGGCTATATATGCTTC 59.872 44.000 0.00 0.00 0.00 3.86
2482 2719 5.452636 GCTAGTCAGGGCTATATATGCTTCC 60.453 48.000 0.00 0.00 0.00 3.46
2483 2720 3.449018 AGTCAGGGCTATATATGCTTCCG 59.551 47.826 0.00 0.00 0.00 4.30
2485 2722 4.100189 GTCAGGGCTATATATGCTTCCGAT 59.900 45.833 0.00 0.00 0.00 4.18
2488 2725 7.176865 GTCAGGGCTATATATGCTTCCGATATA 59.823 40.741 0.00 0.00 0.00 0.86
2489 2726 7.728532 TCAGGGCTATATATGCTTCCGATATAA 59.271 37.037 0.00 0.00 0.00 0.98
2490 2727 7.815068 CAGGGCTATATATGCTTCCGATATAAC 59.185 40.741 0.00 0.00 0.00 1.89
2491 2728 7.038941 AGGGCTATATATGCTTCCGATATAACC 60.039 40.741 0.00 0.00 0.00 2.85
2492 2729 7.256190 GGGCTATATATGCTTCCGATATAACCA 60.256 40.741 0.00 0.00 30.63 3.67
2493 2730 7.599245 GGCTATATATGCTTCCGATATAACCAC 59.401 40.741 0.00 0.00 29.96 4.16
2494 2731 8.141909 GCTATATATGCTTCCGATATAACCACA 58.858 37.037 0.00 0.00 0.00 4.17
2495 2732 9.464714 CTATATATGCTTCCGATATAACCACAC 57.535 37.037 0.00 0.00 0.00 3.82
2574 2841 1.122632 TGCCCGTGTCCTAAGTTGGA 61.123 55.000 0.00 0.00 0.00 3.53
2577 2844 2.483188 GCCCGTGTCCTAAGTTGGATAG 60.483 54.545 0.00 0.00 38.52 2.08
2578 2845 2.764572 CCCGTGTCCTAAGTTGGATAGT 59.235 50.000 0.00 0.00 38.52 2.12
2579 2846 3.956199 CCCGTGTCCTAAGTTGGATAGTA 59.044 47.826 0.00 0.00 38.52 1.82
2590 2857 5.941948 AGTTGGATAGTAACTGTTTGTGC 57.058 39.130 0.00 0.00 37.03 4.57
2950 3217 6.730960 TTCATGGTAATTCGGTAGTTCAAC 57.269 37.500 0.00 0.00 0.00 3.18
2977 3244 7.083858 GCAATGAGAAGTTGCTTTTATGTACA 58.916 34.615 0.00 0.00 46.34 2.90
3012 3279 2.626780 CGAGTGCACGGAGACCTCA 61.627 63.158 12.01 0.00 0.00 3.86
3051 3318 1.210234 TGAGACCATCGTGGAATGCAT 59.790 47.619 10.46 0.00 40.96 3.96
3053 3320 1.065199 AGACCATCGTGGAATGCATGT 60.065 47.619 0.00 0.00 40.96 3.21
3054 3321 1.064505 GACCATCGTGGAATGCATGTG 59.935 52.381 0.00 0.00 40.96 3.21
3068 3335 2.483877 TGCATGTGAAAAAGTAGGAGCG 59.516 45.455 0.00 0.00 0.00 5.03
3072 3339 5.757886 CATGTGAAAAAGTAGGAGCGAAAA 58.242 37.500 0.00 0.00 0.00 2.29
3081 3348 7.642082 AAAGTAGGAGCGAAAAGTAGATAGA 57.358 36.000 0.00 0.00 0.00 1.98
3086 3353 5.652891 AGGAGCGAAAAGTAGATAGAAGACA 59.347 40.000 0.00 0.00 0.00 3.41
3107 3374 3.379372 CACAAGATGTAGGATTGCAAGGG 59.621 47.826 4.94 0.00 0.00 3.95
3159 3427 5.221986 GGTGGGTTTAGTTTAAGAAGGGAGA 60.222 44.000 0.00 0.00 0.00 3.71
3211 3479 7.774134 TGTACAGATAGCCTCGTTAAAACATA 58.226 34.615 0.00 0.00 0.00 2.29
3213 3481 7.948278 ACAGATAGCCTCGTTAAAACATATC 57.052 36.000 0.00 0.00 0.00 1.63
3236 3504 5.949354 TCTGGAGAAACTTTGGAAAAACTCA 59.051 36.000 0.00 0.00 0.00 3.41
3279 3548 7.756395 ATAATCCTATCTTTTGGCAGATGTG 57.244 36.000 0.00 0.00 35.08 3.21
3298 3570 4.735369 TGTGCTTTCTCCCCTTAATTCAA 58.265 39.130 0.00 0.00 0.00 2.69
3344 3616 7.769272 TCAAAATTTTGAAGCTTCGATTGTT 57.231 28.000 27.22 11.36 43.62 2.83
3353 3625 6.460781 TGAAGCTTCGATTGTTAACTAGGAA 58.539 36.000 21.11 6.65 0.00 3.36
3362 3637 8.258007 TCGATTGTTAACTAGGAATGACTTCAT 58.742 33.333 7.22 0.00 38.41 2.57
3454 3729 3.917300 AGATCATAGAAGAACTCGGGGT 58.083 45.455 0.00 0.00 0.00 4.95
3499 3774 4.823989 AGTCAATTTCACATAGCCTATGCC 59.176 41.667 11.65 0.00 39.79 4.40
3528 3803 7.835634 TGTGCAACGTATTCTTGATTACATA 57.164 32.000 0.00 0.00 42.39 2.29
3529 3804 8.432110 TGTGCAACGTATTCTTGATTACATAT 57.568 30.769 0.00 0.00 42.39 1.78
3530 3805 8.888716 TGTGCAACGTATTCTTGATTACATATT 58.111 29.630 0.00 0.00 42.39 1.28
3533 3808 7.740346 GCAACGTATTCTTGATTACATATTCCG 59.260 37.037 0.00 0.00 0.00 4.30
3580 3855 1.097232 CGAACACACATGATGCCCAT 58.903 50.000 0.00 0.00 35.44 4.00
3582 3857 2.880268 CGAACACACATGATGCCCATAT 59.120 45.455 0.00 0.00 33.31 1.78
3607 3882 6.014584 TGTGGTACTTCATTCTCTTGAGCTAA 60.015 38.462 0.00 0.00 0.00 3.09
3856 4134 8.006590 GTGAGCGCTAAATATGTCATTCTAAAG 58.993 37.037 11.50 0.00 0.00 1.85
3865 4143 5.786401 ATGTCATTCTAAAGTTGCTCGTC 57.214 39.130 0.00 0.00 0.00 4.20
3875 4153 1.203523 AGTTGCTCGTCACAGAGGATC 59.796 52.381 0.00 0.00 38.37 3.36
3886 4164 4.223032 GTCACAGAGGATCCTTTGGTCTTA 59.777 45.833 30.19 12.07 33.66 2.10
3927 4205 5.406649 TGGTTAGTGTTTCTTTGTGCAAAG 58.593 37.500 16.16 16.16 46.82 2.77
3928 4206 5.047660 TGGTTAGTGTTTCTTTGTGCAAAGT 60.048 36.000 20.02 6.53 45.88 2.66
3937 4215 3.375610 TCTTTGTGCAAAGTTAGCGTTCA 59.624 39.130 20.02 0.20 45.88 3.18
3939 4217 5.821375 CTTTGTGCAAAGTTAGCGTTCAGC 61.821 45.833 14.55 0.00 43.26 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 2.054799 TGCTCCCACACCTACTTTTCT 58.945 47.619 0.00 0.00 0.00 2.52
104 106 0.895530 GTGATCAACCGGGACAGAGA 59.104 55.000 6.32 0.00 0.00 3.10
144 146 4.067896 GGAGCATGTTCTCAACTTCAAGA 58.932 43.478 9.57 0.00 34.84 3.02
159 161 2.360350 ACCGGCAAGTGGAGCATG 60.360 61.111 0.00 0.00 0.00 4.06
222 224 0.248336 CGATTCGTCGGATTCGGACA 60.248 55.000 20.26 6.14 40.52 4.02
249 251 6.205101 AGCTTGACCAAATGATTCAAGATC 57.795 37.500 20.16 9.61 46.16 2.75
277 280 1.121407 CGGATGAGGAGTATGGCCCA 61.121 60.000 0.00 0.00 0.00 5.36
420 428 3.041940 GGGACGTTGTCACTGGCG 61.042 66.667 0.00 0.00 32.50 5.69
613 623 3.456105 GATCCGCCAACCCTACCCG 62.456 68.421 0.00 0.00 0.00 5.28
618 628 3.782443 GTCGGATCCGCCAACCCT 61.782 66.667 29.62 0.00 39.59 4.34
660 671 3.780294 AGCCCAAATATGAGGCGGATATA 59.220 43.478 5.52 0.00 43.56 0.86
670 682 5.045359 CCTCTCATATCCAGCCCAAATATGA 60.045 44.000 0.00 0.00 39.09 2.15
725 737 1.611851 ACCCAGACAGGCCTCTCAG 60.612 63.158 10.95 1.85 35.39 3.35
750 763 2.034812 GGATAGACTGTCCGGTCATGAC 59.965 54.545 17.91 17.91 38.57 3.06
782 795 1.227734 CAGACCCGACAAACCCGTT 60.228 57.895 0.00 0.00 0.00 4.44
790 803 1.933021 ATCTACAACCAGACCCGACA 58.067 50.000 0.00 0.00 0.00 4.35
791 804 3.259902 GAAATCTACAACCAGACCCGAC 58.740 50.000 0.00 0.00 0.00 4.79
792 805 2.094390 CGAAATCTACAACCAGACCCGA 60.094 50.000 0.00 0.00 0.00 5.14
793 806 2.094390 TCGAAATCTACAACCAGACCCG 60.094 50.000 0.00 0.00 0.00 5.28
794 807 3.604875 TCGAAATCTACAACCAGACCC 57.395 47.619 0.00 0.00 0.00 4.46
795 808 6.371825 AGAAATTCGAAATCTACAACCAGACC 59.628 38.462 13.40 0.00 0.00 3.85
796 809 7.365840 AGAAATTCGAAATCTACAACCAGAC 57.634 36.000 13.40 0.00 0.00 3.51
797 810 7.573096 GCAAGAAATTCGAAATCTACAACCAGA 60.573 37.037 14.88 0.00 0.00 3.86
798 811 6.524586 GCAAGAAATTCGAAATCTACAACCAG 59.475 38.462 14.88 4.19 0.00 4.00
799 812 6.378582 GCAAGAAATTCGAAATCTACAACCA 58.621 36.000 14.88 0.00 0.00 3.67
800 813 5.800438 GGCAAGAAATTCGAAATCTACAACC 59.200 40.000 14.88 10.97 0.00 3.77
801 814 5.508224 CGGCAAGAAATTCGAAATCTACAAC 59.492 40.000 14.88 7.05 0.00 3.32
802 815 5.180492 ACGGCAAGAAATTCGAAATCTACAA 59.820 36.000 14.88 0.00 0.00 2.41
803 816 4.693566 ACGGCAAGAAATTCGAAATCTACA 59.306 37.500 14.88 0.00 0.00 2.74
804 817 5.022021 CACGGCAAGAAATTCGAAATCTAC 58.978 41.667 14.88 11.03 0.00 2.59
805 818 4.094294 CCACGGCAAGAAATTCGAAATCTA 59.906 41.667 14.88 0.00 0.00 1.98
806 819 3.119849 CCACGGCAAGAAATTCGAAATCT 60.120 43.478 0.00 6.47 0.00 2.40
807 820 3.171277 CCACGGCAAGAAATTCGAAATC 58.829 45.455 0.00 3.93 0.00 2.17
808 821 2.671070 GCCACGGCAAGAAATTCGAAAT 60.671 45.455 0.00 0.00 41.49 2.17
824 837 1.544691 AGTAGTTCAGTACTGGCCACG 59.455 52.381 22.48 0.00 37.73 4.94
826 839 2.884320 TCAGTAGTTCAGTACTGGCCA 58.116 47.619 22.48 4.71 46.81 5.36
827 840 4.434520 GAATCAGTAGTTCAGTACTGGCC 58.565 47.826 22.48 12.95 46.81 5.36
828 841 4.081642 TGGAATCAGTAGTTCAGTACTGGC 60.082 45.833 22.48 15.19 46.81 4.85
829 842 5.661056 TGGAATCAGTAGTTCAGTACTGG 57.339 43.478 22.48 4.94 46.81 4.00
831 844 7.397476 TCAGATTGGAATCAGTAGTTCAGTACT 59.603 37.037 2.32 0.00 38.11 2.73
911 924 5.446875 CGGGCGAAAGAGGTACTAATTTTTC 60.447 44.000 0.00 0.00 41.55 2.29
916 929 1.202498 GCGGGCGAAAGAGGTACTAAT 60.202 52.381 0.00 0.00 41.55 1.73
927 940 2.126657 GCGATTTTGCGGGCGAAA 60.127 55.556 8.41 8.41 34.26 3.46
973 986 3.814268 CCGCTTCGCCCATTGTGG 61.814 66.667 0.00 0.00 37.25 4.17
974 987 4.481112 GCCGCTTCGCCCATTGTG 62.481 66.667 0.00 0.00 0.00 3.33
1024 1045 2.358247 GTTCGCCCTCTTCCGCAA 60.358 61.111 0.00 0.00 0.00 4.85
1025 1046 3.621805 TGTTCGCCCTCTTCCGCA 61.622 61.111 0.00 0.00 0.00 5.69
1036 1057 1.970917 CTCGCCTCCATTGTGTTCGC 61.971 60.000 0.00 0.00 0.00 4.70
1038 1059 1.026718 CCCTCGCCTCCATTGTGTTC 61.027 60.000 0.00 0.00 0.00 3.18
1042 1063 3.329889 TGCCCTCGCCTCCATTGT 61.330 61.111 0.00 0.00 0.00 2.71
1184 1205 0.836400 GGTCTTCCTCACCCACTCCA 60.836 60.000 0.00 0.00 0.00 3.86
1335 1356 3.889044 GATGCGCCGTCGGAGAGA 61.889 66.667 20.01 4.36 39.97 3.10
1654 1675 4.194720 GACGGCCAGTCGCTCGAT 62.195 66.667 2.24 0.00 40.43 3.59
1755 1776 1.961277 CCATCGTTGCCCGGCTATC 60.961 63.158 11.61 0.13 37.11 2.08
1757 1778 3.078196 TCCATCGTTGCCCGGCTA 61.078 61.111 11.61 0.00 37.11 3.93
1779 1800 4.941263 TGAATCGCCATGTTAGCTAACTTT 59.059 37.500 31.14 18.97 37.12 2.66
1783 1804 2.872245 GCTGAATCGCCATGTTAGCTAA 59.128 45.455 0.86 0.86 0.00 3.09
1785 1806 1.303309 GCTGAATCGCCATGTTAGCT 58.697 50.000 0.00 0.00 0.00 3.32
1806 1827 1.905843 CCCAATGGTGCGGTTCCAA 60.906 57.895 0.00 0.00 38.52 3.53
1850 1884 7.792508 CACGAAATAAAATAGGCGTATGAAGAC 59.207 37.037 0.00 0.00 0.00 3.01
1874 1908 0.381801 CGATTAGCACCAATGGCCAC 59.618 55.000 8.16 0.00 0.00 5.01
1907 1949 4.510205 CCCTTGGGAGGAAGAAATTTGGTA 60.510 45.833 0.00 0.00 46.74 3.25
1908 1950 3.510459 CCTTGGGAGGAAGAAATTTGGT 58.490 45.455 0.00 0.00 46.74 3.67
1909 1951 2.833943 CCCTTGGGAGGAAGAAATTTGG 59.166 50.000 0.00 0.00 46.74 3.28
2036 2078 1.730446 GCATGTTCCGCAAAGAAGAGC 60.730 52.381 0.00 0.00 0.00 4.09
2052 2094 1.741528 GCCCCCATTTTTCTTGCATG 58.258 50.000 0.00 0.00 0.00 4.06
2109 2152 0.247736 GATGAGGAAGTGCTCACCGT 59.752 55.000 4.51 0.00 31.95 4.83
2197 2260 2.621338 TCAGTACAGCAGCAGCATTAC 58.379 47.619 3.17 4.00 45.49 1.89
2209 2272 3.579709 AGTTGACGCTGATTCAGTACAG 58.420 45.455 14.90 7.16 37.22 2.74
2216 2286 7.800380 CCAATTCATATTAGTTGACGCTGATTC 59.200 37.037 0.00 0.00 0.00 2.52
2222 2292 5.505654 CCCACCAATTCATATTAGTTGACGC 60.506 44.000 0.00 0.00 0.00 5.19
2226 2296 6.129179 ACTCCCCACCAATTCATATTAGTTG 58.871 40.000 0.00 0.00 0.00 3.16
2229 2299 6.837312 TGTACTCCCCACCAATTCATATTAG 58.163 40.000 0.00 0.00 0.00 1.73
2231 2301 5.725551 TGTACTCCCCACCAATTCATATT 57.274 39.130 0.00 0.00 0.00 1.28
2232 2302 5.725551 TTGTACTCCCCACCAATTCATAT 57.274 39.130 0.00 0.00 0.00 1.78
2233 2303 5.725551 ATTGTACTCCCCACCAATTCATA 57.274 39.130 0.00 0.00 0.00 2.15
2234 2304 4.608170 ATTGTACTCCCCACCAATTCAT 57.392 40.909 0.00 0.00 0.00 2.57
2236 2306 7.287810 ACTATTATTGTACTCCCCACCAATTC 58.712 38.462 0.00 0.00 0.00 2.17
2237 2307 7.220890 ACTATTATTGTACTCCCCACCAATT 57.779 36.000 0.00 0.00 0.00 2.32
2238 2308 6.841781 ACTATTATTGTACTCCCCACCAAT 57.158 37.500 0.00 0.00 0.00 3.16
2239 2309 7.792736 AGATACTATTATTGTACTCCCCACCAA 59.207 37.037 0.00 0.00 0.00 3.67
2240 2310 7.310634 AGATACTATTATTGTACTCCCCACCA 58.689 38.462 0.00 0.00 0.00 4.17
2241 2311 7.793948 AGATACTATTATTGTACTCCCCACC 57.206 40.000 0.00 0.00 0.00 4.61
2295 2371 7.681125 GAGTATAGTTGTACTCATCGTTTGG 57.319 40.000 10.14 0.00 46.28 3.28
2323 2399 7.547227 ACTTAAATATCACCATCAAAAGCACC 58.453 34.615 0.00 0.00 0.00 5.01
2414 2650 9.471702 AAATCATTGTCTTGTCAAGGAATAGAT 57.528 29.630 12.66 12.07 40.51 1.98
2415 2651 8.868522 AAATCATTGTCTTGTCAAGGAATAGA 57.131 30.769 12.66 10.76 40.51 1.98
2450 2687 3.618690 AGCCCTGACTAGCAACTAAAG 57.381 47.619 0.00 0.00 0.00 1.85
2455 2692 5.105146 AGCATATATAGCCCTGACTAGCAAC 60.105 44.000 0.00 0.00 0.00 4.17
2480 2717 2.754465 ACCCAGTGTGGTTATATCGGA 58.246 47.619 0.00 0.00 33.91 4.55
2481 2718 4.566004 CATACCCAGTGTGGTTATATCGG 58.434 47.826 8.37 0.00 39.91 4.18
2482 2719 3.994392 GCATACCCAGTGTGGTTATATCG 59.006 47.826 8.37 0.00 39.91 2.92
2483 2720 4.324267 GGCATACCCAGTGTGGTTATATC 58.676 47.826 8.37 0.00 39.91 1.63
2485 2722 3.849563 GGCATACCCAGTGTGGTTATA 57.150 47.619 8.37 0.00 39.91 0.98
2549 2816 2.285977 CTTAGGACACGGGCATTAACC 58.714 52.381 0.00 0.00 0.00 2.85
2574 2841 8.712285 ATGTATTACGCACAAACAGTTACTAT 57.288 30.769 0.00 0.00 0.00 2.12
2577 2844 6.823531 TGATGTATTACGCACAAACAGTTAC 58.176 36.000 0.00 0.00 0.00 2.50
2578 2845 7.118535 ACATGATGTATTACGCACAAACAGTTA 59.881 33.333 0.00 0.00 0.00 2.24
2579 2846 5.933187 TGATGTATTACGCACAAACAGTT 57.067 34.783 0.00 0.00 0.00 3.16
2666 2933 6.365970 AAACATGTCCAATCTGAGACTAGT 57.634 37.500 0.00 0.00 34.02 2.57
2857 3124 2.202797 CGGTCCATGTGCCTCGAG 60.203 66.667 5.13 5.13 0.00 4.04
2977 3244 2.884639 ACTCGCCTTTTTGTGCTTACAT 59.115 40.909 0.00 0.00 0.00 2.29
3012 3279 6.428159 GGTCTCAACACATACAACAATCTTCT 59.572 38.462 0.00 0.00 0.00 2.85
3051 3318 4.879545 ACTTTTCGCTCCTACTTTTTCACA 59.120 37.500 0.00 0.00 0.00 3.58
3053 3320 6.518493 TCTACTTTTCGCTCCTACTTTTTCA 58.482 36.000 0.00 0.00 0.00 2.69
3054 3321 7.598189 ATCTACTTTTCGCTCCTACTTTTTC 57.402 36.000 0.00 0.00 0.00 2.29
3068 3335 9.646427 ACATCTTGTGTCTTCTATCTACTTTTC 57.354 33.333 0.00 0.00 35.77 2.29
3072 3339 8.275758 TCCTACATCTTGTGTCTTCTATCTACT 58.724 37.037 0.00 0.00 42.29 2.57
3081 3348 4.910195 TGCAATCCTACATCTTGTGTCTT 58.090 39.130 0.00 0.00 42.29 3.01
3086 3353 3.624777 CCCTTGCAATCCTACATCTTGT 58.375 45.455 0.00 0.00 0.00 3.16
3107 3374 2.289506 GGTAGACTCCAACTCCAACACC 60.290 54.545 0.00 0.00 0.00 4.16
3190 3458 7.116948 CCAGATATGTTTTAACGAGGCTATCTG 59.883 40.741 8.00 8.00 40.03 2.90
3191 3459 7.015292 TCCAGATATGTTTTAACGAGGCTATCT 59.985 37.037 0.00 0.00 0.00 1.98
3211 3479 6.607198 TGAGTTTTTCCAAAGTTTCTCCAGAT 59.393 34.615 0.00 0.00 0.00 2.90
3213 3481 6.207691 TGAGTTTTTCCAAAGTTTCTCCAG 57.792 37.500 0.00 0.00 0.00 3.86
3249 3517 8.938883 TCTGCCAAAAGATAGGATTATACTCTT 58.061 33.333 0.00 0.00 0.00 2.85
3250 3518 8.497910 TCTGCCAAAAGATAGGATTATACTCT 57.502 34.615 0.00 0.00 0.00 3.24
3279 3548 5.921962 ATGTTGAATTAAGGGGAGAAAGC 57.078 39.130 0.00 0.00 0.00 3.51
3400 3675 8.393366 GCAAATGCATGAACGATATACAGATAT 58.607 33.333 0.00 0.00 41.59 1.63
3401 3676 7.742151 GCAAATGCATGAACGATATACAGATA 58.258 34.615 0.00 0.00 41.59 1.98
3402 3677 6.605849 GCAAATGCATGAACGATATACAGAT 58.394 36.000 0.00 0.00 41.59 2.90
3403 3678 5.989249 GCAAATGCATGAACGATATACAGA 58.011 37.500 0.00 0.00 41.59 3.41
3439 3714 1.271543 TGTCGACCCCGAGTTCTTCTA 60.272 52.381 14.12 0.00 46.52 2.10
3442 3717 0.246635 CATGTCGACCCCGAGTTCTT 59.753 55.000 14.12 0.00 46.52 2.52
3499 3774 5.635549 TCAAGAATACGTTGCACATATCG 57.364 39.130 0.00 0.00 0.00 2.92
3528 3803 4.156455 ACACCAGCAATTATCTCGGAAT 57.844 40.909 0.00 0.00 0.00 3.01
3529 3804 3.627395 ACACCAGCAATTATCTCGGAA 57.373 42.857 0.00 0.00 0.00 4.30
3530 3805 3.627395 AACACCAGCAATTATCTCGGA 57.373 42.857 0.00 0.00 0.00 4.55
3533 3808 5.357878 TCCATCAAACACCAGCAATTATCTC 59.642 40.000 0.00 0.00 0.00 2.75
3580 3855 6.155221 AGCTCAAGAGAATGAAGTACCACATA 59.845 38.462 0.32 0.00 0.00 2.29
3582 3857 4.284490 AGCTCAAGAGAATGAAGTACCACA 59.716 41.667 0.32 0.00 0.00 4.17
3679 3955 8.209917 AGAAAAGAGTCGTTGTGTTCTAATTT 57.790 30.769 0.00 0.00 0.00 1.82
3829 4107 4.445718 AGAATGACATATTTAGCGCTCACG 59.554 41.667 16.34 0.00 44.07 4.35
3856 4134 1.634702 GATCCTCTGTGACGAGCAAC 58.365 55.000 0.00 0.00 0.00 4.17
3865 4143 3.710209 AAGACCAAAGGATCCTCTGTG 57.290 47.619 16.52 13.36 0.00 3.66


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

AutoCloner maintained by Alex Coulton.