Multiple sequence alignment - TraesCS3D01G265200

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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 TraesCS3D01G265200 chr3D 100.000 3339 0 0 1480 4818 367307507 367310845 0.000000e+00 6167.0
1 TraesCS3D01G265200 chr3D 100.000 513 0 0 564 1076 367306591 367307103 0.000000e+00 948.0
2 TraesCS3D01G265200 chr3D 100.000 266 0 0 1 266 367306028 367306293 4.330000e-135 492.0
3 TraesCS3D01G265200 chr3A 94.008 3121 121 23 1480 4577 489458672 489461749 0.000000e+00 4667.0
4 TraesCS3D01G265200 chr3A 89.286 476 21 7 564 1035 489457863 489458312 1.950000e-158 569.0
5 TraesCS3D01G265200 chr3A 92.430 251 16 3 1 249 489457505 489457754 5.930000e-94 355.0
6 TraesCS3D01G265200 chr3A 85.774 239 28 4 9 243 606745423 606745659 1.040000e-61 248.0
7 TraesCS3D01G265200 chr3A 89.595 173 8 1 4643 4805 489461733 489461905 1.360000e-50 211.0
8 TraesCS3D01G265200 chr3B 93.268 1931 67 26 2497 4417 479298474 479300351 0.000000e+00 2787.0
9 TraesCS3D01G265200 chr3B 94.812 983 44 3 1516 2498 479297405 479298380 0.000000e+00 1526.0
10 TraesCS3D01G265200 chr3B 93.361 241 7 5 841 1076 479296593 479296829 9.920000e-92 348.0
11 TraesCS3D01G265200 chr3B 92.391 184 8 3 4400 4577 479300374 479300557 1.720000e-64 257.0
12 TraesCS3D01G265200 chr3B 94.444 108 6 0 4643 4750 479300541 479300648 2.980000e-37 167.0
13 TraesCS3D01G265200 chr3B 92.537 67 4 1 4752 4817 479300676 479300742 1.430000e-15 95.3
14 TraesCS3D01G265200 chr1B 94.205 604 31 3 2839 3438 372996778 372996175 0.000000e+00 918.0
15 TraesCS3D01G265200 chr1B 89.683 126 13 0 3174 3299 632718977 632719102 1.390000e-35 161.0
16 TraesCS3D01G265200 chr1B 91.111 90 8 0 987 1076 632715715 632715804 6.550000e-24 122.0
17 TraesCS3D01G265200 chr2B 93.377 604 36 3 2839 3438 380731261 380731864 0.000000e+00 891.0
18 TraesCS3D01G265200 chr2B 84.861 251 25 4 3128 3365 73788586 73788836 1.730000e-59 241.0
19 TraesCS3D01G265200 chr6B 92.715 604 40 3 2839 3438 298649191 298649794 0.000000e+00 869.0
20 TraesCS3D01G265200 chr6A 86.400 250 30 4 4 251 263726 263479 2.210000e-68 270.0
21 TraesCS3D01G265200 chr1A 86.475 244 31 2 1 243 353654760 353654518 2.860000e-67 267.0
22 TraesCS3D01G265200 chr1A 84.800 250 29 8 1 245 353654655 353654410 4.820000e-60 243.0
23 TraesCS3D01G265200 chr1A 83.673 245 34 6 609 850 568069780 568070021 4.850000e-55 226.0
24 TraesCS3D01G265200 chr1A 80.408 245 35 7 608 843 449464945 449465185 1.780000e-39 174.0
25 TraesCS3D01G265200 chr1A 89.216 102 11 0 975 1076 551744318 551744419 1.410000e-25 128.0
26 TraesCS3D01G265200 chr7A 86.345 249 27 7 1 244 666969951 666969705 1.030000e-66 265.0
27 TraesCS3D01G265200 chr7A 79.791 287 36 20 564 842 195481960 195482232 6.370000e-44 189.0
28 TraesCS3D01G265200 chr6D 85.433 254 29 8 1 251 801164 800916 1.720000e-64 257.0
29 TraesCS3D01G265200 chr1D 84.706 255 28 10 1 249 244622307 244622556 1.340000e-60 244.0
30 TraesCS3D01G265200 chr1D 85.340 191 20 7 661 846 25677145 25676958 1.770000e-44 191.0
31 TraesCS3D01G265200 chr1D 92.222 90 7 0 987 1076 460190921 460191010 1.410000e-25 128.0
32 TraesCS3D01G265200 chr7D 84.190 253 33 7 1 251 188554043 188553796 6.230000e-59 239.0
33 TraesCS3D01G265200 chr7D 80.272 294 36 14 565 849 450006964 450006684 8.180000e-48 202.0
34 TraesCS3D01G265200 chr4A 82.095 296 34 13 564 844 56511591 56511300 8.060000e-58 235.0
35 TraesCS3D01G265200 chr4B 81.229 293 39 13 566 844 492225704 492225414 6.280000e-54 222.0
36 TraesCS3D01G265200 chr4D 81.356 295 33 15 566 844 84606853 84607141 2.260000e-53 220.0


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 TraesCS3D01G265200 chr3D 367306028 367310845 4817 False 2535.666667 6167 100.000000 1 4818 3 chr3D.!!$F1 4817
1 TraesCS3D01G265200 chr3A 489457505 489461905 4400 False 1450.500000 4667 91.329750 1 4805 4 chr3A.!!$F2 4804
2 TraesCS3D01G265200 chr3B 479296593 479300742 4149 False 863.383333 2787 93.468833 841 4817 6 chr3B.!!$F1 3976
3 TraesCS3D01G265200 chr1B 372996175 372996778 603 True 918.000000 918 94.205000 2839 3438 1 chr1B.!!$R1 599
4 TraesCS3D01G265200 chr2B 380731261 380731864 603 False 891.000000 891 93.377000 2839 3438 1 chr2B.!!$F2 599
5 TraesCS3D01G265200 chr6B 298649191 298649794 603 False 869.000000 869 92.715000 2839 3438 1 chr6B.!!$F1 599

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
821 826 0.252103 ACTTCCCCCTGTCTCGCTTA 60.252 55.0 0.00 0.00 0.0 3.09 F
1059 1069 0.108019 ACCCCACCTCTTTCGTCAAC 59.892 55.0 0.00 0.00 0.0 3.18 F
2087 2235 0.528466 TGTAGATGCTACGCTGCTGC 60.528 55.0 5.34 5.34 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1958 2.012673 CAGGCAGCTTATCAGACCAAC 58.987 52.381 0.00 0.00 0.00 3.77 R
2937 3184 0.670162 GCCCTCACATGCGCATAAAT 59.330 50.000 24.84 8.98 0.00 1.40 R
3998 4254 0.178068 ACGCAGTGTGTCAGAACCTT 59.822 50.000 2.75 0.00 42.51 3.50 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
65 67 8.564574 TGCTCAATATTTTTCAAGTACTCGTTT 58.435 29.630 0.00 0.00 0.00 3.60
160 163 9.658799 TCCAAATACTTGTTCAACATTTTTGAA 57.341 25.926 12.81 0.00 36.21 2.69
167 170 9.019764 ACTTGTTCAACATTTTTGAAATACTCG 57.980 29.630 0.00 0.00 39.76 4.18
763 768 4.115199 GGTCATGGCCTCCCGCTT 62.115 66.667 9.76 0.00 37.74 4.68
811 816 3.069318 GACGCGAGACTTCCCCCT 61.069 66.667 15.93 0.00 0.00 4.79
812 817 3.358076 GACGCGAGACTTCCCCCTG 62.358 68.421 15.93 0.00 0.00 4.45
813 818 3.382832 CGCGAGACTTCCCCCTGT 61.383 66.667 0.00 0.00 0.00 4.00
814 819 2.579738 GCGAGACTTCCCCCTGTC 59.420 66.667 0.00 0.00 0.00 3.51
815 820 1.985116 GCGAGACTTCCCCCTGTCT 60.985 63.158 0.00 0.00 45.06 3.41
819 824 1.985116 GACTTCCCCCTGTCTCGCT 60.985 63.158 0.00 0.00 0.00 4.93
820 825 1.536662 ACTTCCCCCTGTCTCGCTT 60.537 57.895 0.00 0.00 0.00 4.68
821 826 0.252103 ACTTCCCCCTGTCTCGCTTA 60.252 55.000 0.00 0.00 0.00 3.09
822 827 0.902531 CTTCCCCCTGTCTCGCTTAA 59.097 55.000 0.00 0.00 0.00 1.85
823 828 1.278127 CTTCCCCCTGTCTCGCTTAAA 59.722 52.381 0.00 0.00 0.00 1.52
824 829 0.902531 TCCCCCTGTCTCGCTTAAAG 59.097 55.000 0.00 0.00 0.00 1.85
825 830 0.744771 CCCCCTGTCTCGCTTAAAGC 60.745 60.000 0.00 0.00 38.02 3.51
837 842 2.484889 GCTTAAAGCGAGACATAGGGG 58.515 52.381 0.00 0.00 0.00 4.79
838 843 2.484889 CTTAAAGCGAGACATAGGGGC 58.515 52.381 0.00 0.00 0.00 5.80
839 844 0.387929 TAAAGCGAGACATAGGGGCG 59.612 55.000 0.00 0.00 0.00 6.13
841 846 4.971125 GCGAGACATAGGGGCGCC 62.971 72.222 21.18 21.18 41.65 6.53
842 847 4.301027 CGAGACATAGGGGCGCCC 62.301 72.222 38.57 38.57 45.90 6.13
930 935 1.113788 CTTCTCTCTCCTCTGGGCTG 58.886 60.000 0.00 0.00 0.00 4.85
1044 1054 3.670377 GCGGTGCTGAACAACCCC 61.670 66.667 0.00 0.00 29.21 4.95
1059 1069 0.108019 ACCCCACCTCTTTCGTCAAC 59.892 55.000 0.00 0.00 0.00 3.18
1508 1518 3.186047 CGGGCGCTCGTTTCGATT 61.186 61.111 24.35 0.00 34.61 3.34
1556 1702 2.238942 TTCGATTGCTGGATATGCGT 57.761 45.000 0.00 0.00 0.00 5.24
1619 1765 6.762187 GGCTTGTATTCTAGGGTTTTAGAGTC 59.238 42.308 0.00 0.00 31.68 3.36
1762 1908 5.771666 AGATCATTTCCTTCTGCTTTGACAA 59.228 36.000 0.00 0.00 0.00 3.18
1778 1924 4.341366 TGACAATGAAACAGAGCTCTGA 57.659 40.909 42.76 25.20 46.59 3.27
1779 1925 4.707105 TGACAATGAAACAGAGCTCTGAA 58.293 39.130 42.76 26.68 46.59 3.02
1812 1958 5.241662 AGTTTTAGCAGAAAGTAGCAGAGG 58.758 41.667 0.00 0.00 0.00 3.69
1827 1973 2.093235 GCAGAGGTTGGTCTGATAAGCT 60.093 50.000 5.05 8.43 46.02 3.74
1903 2049 5.140454 GGGAAATGTATTGGCCTCTTACAT 58.860 41.667 15.65 15.65 37.99 2.29
1965 2111 7.506599 TGCAACTGATTATATGAACATGGGATT 59.493 33.333 0.00 0.00 0.00 3.01
2001 2149 9.110502 CAATTTAAGTGGTCTAGGGAGAAATAC 57.889 37.037 0.00 0.00 31.96 1.89
2016 2164 6.921307 GGGAGAAATACGTGTGTTTTTCATTT 59.079 34.615 12.47 0.00 43.94 2.32
2079 2227 8.818141 ACATGTATATTGTGTGTAGATGCTAC 57.182 34.615 0.00 0.00 31.09 3.58
2087 2235 0.528466 TGTAGATGCTACGCTGCTGC 60.528 55.000 5.34 5.34 0.00 5.25
2112 2260 4.406648 TCTACTATGCAAGTGTGATGGG 57.593 45.455 10.59 0.00 39.39 4.00
2254 2402 7.069578 AGTCTACAGGTTCTTTCAGTTGAGTTA 59.930 37.037 0.00 0.00 0.00 2.24
2274 2422 7.990886 TGAGTTATCTAAAATTAAGGCGGTGAT 59.009 33.333 0.00 0.00 0.00 3.06
2346 2494 9.562583 TTTTGTTTATGATACTTGCCGATAAAC 57.437 29.630 0.00 0.00 38.84 2.01
2429 2577 6.594788 ATGCACAGGTTCTTGTATGAAATT 57.405 33.333 0.00 0.00 0.00 1.82
2493 2641 4.843728 CCACTTTCCTGGTCTAGCAAATA 58.156 43.478 0.00 0.00 0.00 1.40
2614 2857 4.096382 AGTTACGGGAATTCATGTTCATGC 59.904 41.667 7.93 0.00 0.00 4.06
2908 3155 8.600449 ATTACTGCTATTGTAGAATGAGCTTC 57.400 34.615 0.00 0.00 34.19 3.86
2912 3159 6.643388 TGCTATTGTAGAATGAGCTTCTTGA 58.357 36.000 12.12 0.00 41.60 3.02
2937 3184 7.867305 TGTTTCTGTTTCTGTTTGGTATGTA 57.133 32.000 0.00 0.00 0.00 2.29
3017 3270 0.999712 CCCACACCTCCCCTTAATGT 59.000 55.000 0.00 0.00 0.00 2.71
3448 3704 7.175104 TGCTCCTACCTCAGATTAAAATTTGT 58.825 34.615 0.00 0.00 0.00 2.83
3532 3788 0.038159 GCGAGGAGGACATAATCGGG 60.038 60.000 0.00 0.00 34.11 5.14
3538 3794 2.701951 GGAGGACATAATCGGGGTTACA 59.298 50.000 0.00 0.00 0.00 2.41
3700 3956 2.932234 CGACAAGCCCCGAGTCACT 61.932 63.158 0.00 0.00 32.68 3.41
3724 3980 2.700371 GTTCCCCATCAATTTCCATCCC 59.300 50.000 0.00 0.00 0.00 3.85
3781 4037 3.126001 TCAGCTGTACCTGAAAACCAG 57.874 47.619 14.67 0.00 38.81 4.00
3820 4076 1.612726 GCCAGCACAGATCTTTGACCT 60.613 52.381 13.11 0.00 0.00 3.85
3953 4209 5.213675 GTGCGCCACTAAACTAGACTATAG 58.786 45.833 4.18 0.00 0.00 1.31
3987 4243 0.608856 TGGTTAGCCATGTGCCTGTG 60.609 55.000 0.00 0.00 40.46 3.66
3994 4250 1.378378 CATGTGCCTGTGGTGGGTA 59.622 57.895 0.00 0.00 0.00 3.69
3995 4251 0.677731 CATGTGCCTGTGGTGGGTAG 60.678 60.000 0.00 0.00 0.00 3.18
3996 4252 1.852157 ATGTGCCTGTGGTGGGTAGG 61.852 60.000 0.00 0.00 34.67 3.18
3997 4253 2.122144 TGCCTGTGGTGGGTAGGT 60.122 61.111 0.00 0.00 34.06 3.08
3998 4254 1.158944 TGCCTGTGGTGGGTAGGTA 59.841 57.895 0.00 0.00 34.06 3.08
4106 4365 4.763073 TGTCTCTTGGATTATGTCTGCAG 58.237 43.478 7.63 7.63 0.00 4.41
4135 4394 3.683340 GGGTTCGTTAGATGACTTTGGTC 59.317 47.826 0.00 0.00 42.42 4.02
4204 4463 2.361567 GCTGCCCCCTTTCCATTGG 61.362 63.158 0.00 0.00 0.00 3.16
4215 4474 4.013728 CCTTTCCATTGGTCACGGAAATA 58.986 43.478 1.86 0.00 45.31 1.40
4224 4483 3.930229 TGGTCACGGAAATATTCAGTTCG 59.070 43.478 0.00 0.00 35.91 3.95
4232 4491 5.231568 CGGAAATATTCAGTTCGTACAGACC 59.768 44.000 0.00 0.00 29.38 3.85
4300 4559 2.818274 GGTAAGGGCTCGCCGTTG 60.818 66.667 22.14 0.00 43.12 4.10
4301 4560 2.263540 GTAAGGGCTCGCCGTTGA 59.736 61.111 22.14 7.13 43.12 3.18
4302 4561 1.810030 GTAAGGGCTCGCCGTTGAG 60.810 63.158 22.14 0.00 43.12 3.02
4303 4562 1.980232 TAAGGGCTCGCCGTTGAGA 60.980 57.895 22.14 3.61 43.12 3.27
4304 4563 1.945354 TAAGGGCTCGCCGTTGAGAG 61.945 60.000 22.14 0.00 43.12 3.20
4305 4564 4.070552 GGGCTCGCCGTTGAGAGT 62.071 66.667 1.24 0.00 40.22 3.24
4306 4565 2.048127 GGCTCGCCGTTGAGAGTT 60.048 61.111 5.42 0.00 40.22 3.01
4320 4579 3.008330 TGAGAGTTGAGACGCCTACTAC 58.992 50.000 0.00 0.00 0.00 2.73
4338 4597 6.601613 CCTACTACAGGGCAAAATGTCATTAA 59.398 38.462 0.00 0.00 41.26 1.40
4343 4602 4.925054 CAGGGCAAAATGTCATTAACACTG 59.075 41.667 0.00 4.63 41.75 3.66
4344 4603 3.679502 GGGCAAAATGTCATTAACACTGC 59.320 43.478 0.00 3.77 41.75 4.40
4345 4604 4.559153 GGCAAAATGTCATTAACACTGCT 58.441 39.130 0.00 0.00 41.75 4.24
4346 4605 4.386652 GGCAAAATGTCATTAACACTGCTG 59.613 41.667 0.00 0.00 41.75 4.41
4347 4606 4.386652 GCAAAATGTCATTAACACTGCTGG 59.613 41.667 0.00 0.00 41.75 4.85
4348 4607 5.531634 CAAAATGTCATTAACACTGCTGGT 58.468 37.500 0.00 0.00 41.75 4.00
4375 4634 6.455647 CTGTGTACAGAGAAAAGATGGTACA 58.544 40.000 14.69 0.00 46.59 2.90
4376 4635 7.099764 CTGTGTACAGAGAAAAGATGGTACAT 58.900 38.462 14.69 0.00 45.47 2.29
4377 4636 7.063898 CTGTGTACAGAGAAAAGATGGTACATG 59.936 40.741 14.69 0.00 45.47 3.21
4447 4756 6.578023 AGCTAGAGCACCAAAGTAGAAATAG 58.422 40.000 4.01 0.00 45.16 1.73
4481 4790 0.323816 AGTCCAGCTGATCTCCACGA 60.324 55.000 17.39 0.00 0.00 4.35
4536 4848 2.210711 CGAGGGGGCTACTCCATCC 61.211 68.421 0.00 0.00 36.21 3.51
4544 4856 1.689273 GGCTACTCCATCCAAGACGAT 59.311 52.381 0.00 0.00 34.01 3.73
4577 4889 3.867857 GCTTCTATAGCTCCCATAAGGC 58.132 50.000 0.00 0.00 46.77 4.35
4578 4890 3.677424 GCTTCTATAGCTCCCATAAGGCG 60.677 52.174 0.00 0.00 46.77 5.52
4579 4891 3.170991 TCTATAGCTCCCATAAGGCGT 57.829 47.619 0.00 0.00 34.51 5.68
4580 4892 4.311520 TCTATAGCTCCCATAAGGCGTA 57.688 45.455 0.00 0.00 34.51 4.42
4608 4920 6.607004 TTCTATAGCTCCCATAAGGTTAGC 57.393 41.667 0.00 1.38 40.52 3.09
4624 4936 4.750460 GCGTAATGATCGCCCTCA 57.250 55.556 0.00 0.00 46.61 3.86
4625 4937 2.986311 GCGTAATGATCGCCCTCAA 58.014 52.632 0.00 0.00 46.61 3.02
4626 4938 0.582005 GCGTAATGATCGCCCTCAAC 59.418 55.000 0.00 0.00 46.61 3.18
4627 4939 1.806623 GCGTAATGATCGCCCTCAACT 60.807 52.381 0.00 0.00 46.61 3.16
4628 4940 2.128035 CGTAATGATCGCCCTCAACTC 58.872 52.381 0.00 0.00 0.00 3.01
4629 4941 2.484889 GTAATGATCGCCCTCAACTCC 58.515 52.381 0.00 0.00 0.00 3.85
4630 4942 1.207791 AATGATCGCCCTCAACTCCT 58.792 50.000 0.00 0.00 0.00 3.69
4631 4943 1.207791 ATGATCGCCCTCAACTCCTT 58.792 50.000 0.00 0.00 0.00 3.36
4632 4944 0.984230 TGATCGCCCTCAACTCCTTT 59.016 50.000 0.00 0.00 0.00 3.11
4633 4945 1.351017 TGATCGCCCTCAACTCCTTTT 59.649 47.619 0.00 0.00 0.00 2.27
4634 4946 1.740025 GATCGCCCTCAACTCCTTTTG 59.260 52.381 0.00 0.00 0.00 2.44
4635 4947 0.472471 TCGCCCTCAACTCCTTTTGT 59.528 50.000 0.00 0.00 0.00 2.83
4636 4948 0.593128 CGCCCTCAACTCCTTTTGTG 59.407 55.000 0.00 0.00 0.00 3.33
4637 4949 0.961753 GCCCTCAACTCCTTTTGTGG 59.038 55.000 0.00 0.00 39.07 4.17
4639 4951 0.961753 CCTCAACTCCTTTTGTGGGC 59.038 55.000 0.00 0.00 36.76 5.36
4640 4952 1.691196 CTCAACTCCTTTTGTGGGCA 58.309 50.000 0.00 0.00 0.00 5.36
4641 4953 1.338020 CTCAACTCCTTTTGTGGGCAC 59.662 52.381 0.00 0.00 0.00 5.01
4658 4970 3.944087 GGCACCTATAGCTTCCATAAGG 58.056 50.000 0.00 0.00 32.98 2.69
4659 4971 3.328050 GGCACCTATAGCTTCCATAAGGT 59.672 47.826 0.00 0.00 45.22 3.50
4660 4972 4.202472 GGCACCTATAGCTTCCATAAGGTT 60.202 45.833 0.00 0.00 40.51 3.50
4661 4973 5.012768 GGCACCTATAGCTTCCATAAGGTTA 59.987 44.000 0.00 0.00 40.51 2.85
4662 4974 6.166982 GCACCTATAGCTTCCATAAGGTTAG 58.833 44.000 0.00 0.00 40.51 2.34
4663 4975 6.166982 CACCTATAGCTTCCATAAGGTTAGC 58.833 44.000 0.00 5.96 40.51 3.09
4664 4976 5.047235 ACCTATAGCTTCCATAAGGTTAGCG 60.047 44.000 0.00 0.00 40.51 4.26
4665 4977 4.957684 ATAGCTTCCATAAGGTTAGCGT 57.042 40.909 0.00 1.04 40.51 5.07
4666 4978 6.152323 CCTATAGCTTCCATAAGGTTAGCGTA 59.848 42.308 0.00 5.62 40.51 4.42
4667 4979 4.323553 AGCTTCCATAAGGTTAGCGTAG 57.676 45.455 7.76 0.00 40.51 3.51
4668 4980 3.705072 AGCTTCCATAAGGTTAGCGTAGT 59.295 43.478 7.76 0.00 40.51 2.73
4669 4981 3.802685 GCTTCCATAAGGTTAGCGTAGTG 59.197 47.826 0.00 0.00 35.26 2.74
4670 4982 4.441079 GCTTCCATAAGGTTAGCGTAGTGA 60.441 45.833 0.00 0.00 35.26 3.41
4671 4983 5.739358 GCTTCCATAAGGTTAGCGTAGTGAT 60.739 44.000 0.00 0.00 35.26 3.06
4672 4984 5.864418 TCCATAAGGTTAGCGTAGTGATT 57.136 39.130 0.00 0.00 35.89 2.57
4673 4985 5.597806 TCCATAAGGTTAGCGTAGTGATTG 58.402 41.667 0.00 0.00 35.89 2.67
4674 4986 4.211374 CCATAAGGTTAGCGTAGTGATTGC 59.789 45.833 0.00 0.00 0.00 3.56
4675 4987 2.311124 AGGTTAGCGTAGTGATTGCC 57.689 50.000 0.00 0.00 0.00 4.52
4791 5129 0.322546 GCCAGAACCAAATCGTCCCT 60.323 55.000 0.00 0.00 0.00 4.20
4812 5151 1.400242 GCAAAGACGCAAGCAAGTAGG 60.400 52.381 0.00 0.00 45.62 3.18
4817 5156 1.394917 GACGCAAGCAAGTAGGATGTG 59.605 52.381 0.00 0.00 45.62 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
743 748 4.864334 CGGGAGGCCATGACCTGC 62.864 72.222 11.30 11.30 46.82 4.85
819 824 1.202486 CGCCCCTATGTCTCGCTTTAA 60.202 52.381 0.00 0.00 0.00 1.52
820 825 0.387929 CGCCCCTATGTCTCGCTTTA 59.612 55.000 0.00 0.00 0.00 1.85
821 826 1.144057 CGCCCCTATGTCTCGCTTT 59.856 57.895 0.00 0.00 0.00 3.51
822 827 2.815308 CGCCCCTATGTCTCGCTT 59.185 61.111 0.00 0.00 0.00 4.68
823 828 3.917760 GCGCCCCTATGTCTCGCT 61.918 66.667 0.00 0.00 42.19 4.93
824 829 4.971125 GGCGCCCCTATGTCTCGC 62.971 72.222 18.11 0.00 44.39 5.03
825 830 4.301027 GGGCGCCCCTATGTCTCG 62.301 72.222 36.64 0.00 41.34 4.04
836 841 4.467084 TCGATGTTGAGGGGCGCC 62.467 66.667 21.18 21.18 0.00 6.53
837 842 3.195698 GTCGATGTTGAGGGGCGC 61.196 66.667 0.00 0.00 0.00 6.53
838 843 1.811266 CTGTCGATGTTGAGGGGCG 60.811 63.158 0.00 0.00 0.00 6.13
839 844 0.741221 GACTGTCGATGTTGAGGGGC 60.741 60.000 0.00 0.00 0.00 5.80
840 845 0.608130 TGACTGTCGATGTTGAGGGG 59.392 55.000 2.98 0.00 0.00 4.79
841 846 1.673033 GGTGACTGTCGATGTTGAGGG 60.673 57.143 2.98 0.00 0.00 4.30
842 847 1.714794 GGTGACTGTCGATGTTGAGG 58.285 55.000 2.98 0.00 0.00 3.86
843 848 1.340658 CGGTGACTGTCGATGTTGAG 58.659 55.000 2.98 0.00 0.00 3.02
844 849 0.666274 GCGGTGACTGTCGATGTTGA 60.666 55.000 2.98 0.00 0.00 3.18
1044 1054 0.396811 AGGGGTTGACGAAAGAGGTG 59.603 55.000 0.00 0.00 0.00 4.00
1505 1515 7.816031 AGAACAACCATGAATCATGACAAAATC 59.184 33.333 23.55 13.62 43.81 2.17
1508 1518 6.653526 AGAACAACCATGAATCATGACAAA 57.346 33.333 23.55 0.00 43.81 2.83
1556 1702 0.704076 AACCCCTATTTCAGCAGCCA 59.296 50.000 0.00 0.00 0.00 4.75
1619 1765 0.033504 ACAGTAACTGCTCCACCACG 59.966 55.000 0.00 0.00 34.37 4.94
1778 1924 9.067986 ACTTTCTGCTAAAACTTGTATAGCTTT 57.932 29.630 14.93 0.00 41.97 3.51
1779 1925 8.622948 ACTTTCTGCTAAAACTTGTATAGCTT 57.377 30.769 14.93 0.00 41.97 3.74
1812 1958 2.012673 CAGGCAGCTTATCAGACCAAC 58.987 52.381 0.00 0.00 0.00 3.77
1827 1973 4.444733 CCCTACACATCATGATAACAGGCA 60.445 45.833 8.15 0.00 0.00 4.75
1874 2020 2.091885 GGCCAATACATTTCCCAGAGGA 60.092 50.000 0.00 0.00 41.88 3.71
1903 2049 9.996554 TCTGAATCTAACACTAGACAAATTCAA 57.003 29.630 0.00 0.00 36.98 2.69
2001 2149 9.352163 GCAAATAAAGTAAATGAAAAACACACG 57.648 29.630 0.00 0.00 0.00 4.49
2024 2172 6.096141 TGGTGAAGAAGACATTTACTTTGCAA 59.904 34.615 0.00 0.00 0.00 4.08
2087 2235 6.648310 CCCATCACACTTGCATAGTAGAATAG 59.352 42.308 0.00 0.00 34.56 1.73
2112 2260 6.259550 AGATTAACATTCACAAACCAGAGC 57.740 37.500 0.00 0.00 0.00 4.09
2152 2300 7.977293 CAGCCTAACAATCATCAATCAAAATCA 59.023 33.333 0.00 0.00 0.00 2.57
2159 2307 5.357878 TCCAACAGCCTAACAATCATCAATC 59.642 40.000 0.00 0.00 0.00 2.67
2254 2402 6.998074 TCATCATCACCGCCTTAATTTTAGAT 59.002 34.615 0.00 0.00 0.00 1.98
2274 2422 4.284490 AGCTCCAGAAAACTGTACTCATCA 59.716 41.667 0.00 0.00 0.00 3.07
2429 2577 9.653287 CCTTATTTTGTTCAGTCTGTAGTATCA 57.347 33.333 0.00 0.00 0.00 2.15
2614 2857 7.484140 TCACTACACTAATGTAAGCAGAGATG 58.516 38.462 0.00 0.00 40.84 2.90
2791 3037 8.586879 TTGATGTGACACCCAATTAATATTGA 57.413 30.769 2.45 0.00 43.12 2.57
2881 3127 8.600449 AGCTCATTCTACAATAGCAGTAATTC 57.400 34.615 0.00 0.00 35.63 2.17
2901 3148 5.824624 AGAAACAGAAACATCAAGAAGCTCA 59.175 36.000 0.00 0.00 0.00 4.26
2908 3155 6.332630 ACCAAACAGAAACAGAAACATCAAG 58.667 36.000 0.00 0.00 0.00 3.02
2912 3159 7.346751 ACATACCAAACAGAAACAGAAACAT 57.653 32.000 0.00 0.00 0.00 2.71
2937 3184 0.670162 GCCCTCACATGCGCATAAAT 59.330 50.000 24.84 8.98 0.00 1.40
2998 3251 0.999712 ACATTAAGGGGAGGTGTGGG 59.000 55.000 0.00 0.00 0.00 4.61
2999 3252 1.633432 TCACATTAAGGGGAGGTGTGG 59.367 52.381 0.00 0.00 40.29 4.17
3017 3270 4.998671 TGGAAAGTTTTGCACATCTTCA 57.001 36.364 0.00 0.00 33.44 3.02
3373 3629 2.284263 CAGATCTCTGCGCAGTTGTA 57.716 50.000 34.70 19.43 37.15 2.41
3396 3652 4.581824 CAGCTGCCCAACTGTAATATGAAT 59.418 41.667 0.00 0.00 0.00 2.57
3532 3788 3.380320 AGGTCAACAAAAGCACTGTAACC 59.620 43.478 8.24 8.24 0.00 2.85
3538 3794 3.088532 TGAACAGGTCAACAAAAGCACT 58.911 40.909 0.00 0.00 31.51 4.40
3700 3956 5.208121 GGATGGAAATTGATGGGGAACTTA 58.792 41.667 0.00 0.00 0.00 2.24
3724 3980 1.738099 CTGTCCTCCGCTGGTTTCG 60.738 63.158 0.00 0.00 0.00 3.46
3781 4037 1.301677 CCTTGCTCCCTTCGCTTGTC 61.302 60.000 0.00 0.00 0.00 3.18
3820 4076 2.875296 CATTCCCAAGTTTCCAGACCA 58.125 47.619 0.00 0.00 0.00 4.02
3953 4209 3.740832 GCTAACCAATGTGAGTTTTTGGC 59.259 43.478 0.98 0.00 42.98 4.52
3987 4243 2.235650 GTCAGAACCTTACCTACCCACC 59.764 54.545 0.00 0.00 0.00 4.61
3994 4250 2.224305 GCAGTGTGTCAGAACCTTACCT 60.224 50.000 0.00 0.00 0.00 3.08
3995 4251 2.143925 GCAGTGTGTCAGAACCTTACC 58.856 52.381 0.00 0.00 0.00 2.85
3996 4252 1.792949 CGCAGTGTGTCAGAACCTTAC 59.207 52.381 0.00 0.00 0.00 2.34
3997 4253 1.411246 ACGCAGTGTGTCAGAACCTTA 59.589 47.619 2.75 0.00 42.51 2.69
3998 4254 0.178068 ACGCAGTGTGTCAGAACCTT 59.822 50.000 2.75 0.00 42.51 3.50
4106 4365 1.659098 CATCTAACGAACCCTTGCGAC 59.341 52.381 0.00 0.00 0.00 5.19
4135 4394 3.490761 GGACCAAAACATGATTATGGGCG 60.491 47.826 15.87 0.00 40.24 6.13
4204 4463 5.574055 TGTACGAACTGAATATTTCCGTGAC 59.426 40.000 0.00 0.00 0.00 3.67
4215 4474 3.079578 TCTCGGTCTGTACGAACTGAAT 58.920 45.455 9.48 0.00 40.16 2.57
4224 4483 5.221087 CCTTTTCCTATCTCTCGGTCTGTAC 60.221 48.000 0.00 0.00 0.00 2.90
4232 4491 3.070302 CCTTCCCCTTTTCCTATCTCTCG 59.930 52.174 0.00 0.00 0.00 4.04
4300 4559 3.008330 TGTAGTAGGCGTCTCAACTCTC 58.992 50.000 0.00 0.00 0.00 3.20
4301 4560 3.011119 CTGTAGTAGGCGTCTCAACTCT 58.989 50.000 0.00 0.00 0.00 3.24
4302 4561 2.097791 CCTGTAGTAGGCGTCTCAACTC 59.902 54.545 0.00 0.00 40.38 3.01
4303 4562 2.093106 CCTGTAGTAGGCGTCTCAACT 58.907 52.381 0.00 0.00 40.38 3.16
4304 4563 1.134560 CCCTGTAGTAGGCGTCTCAAC 59.865 57.143 0.00 0.00 45.89 3.18
4305 4564 1.471119 CCCTGTAGTAGGCGTCTCAA 58.529 55.000 0.00 0.00 45.89 3.02
4306 4565 1.035932 GCCCTGTAGTAGGCGTCTCA 61.036 60.000 0.00 0.00 45.89 3.27
4320 4579 4.925054 CAGTGTTAATGACATTTTGCCCTG 59.075 41.667 5.89 3.61 41.10 4.45
4343 4602 1.151668 CTCTGTACACAGCAACCAGC 58.848 55.000 4.43 0.00 43.46 4.85
4344 4603 2.820059 TCTCTGTACACAGCAACCAG 57.180 50.000 4.43 0.00 43.46 4.00
4345 4604 3.552132 TTTCTCTGTACACAGCAACCA 57.448 42.857 4.43 0.00 43.46 3.67
4346 4605 4.127171 TCTTTTCTCTGTACACAGCAACC 58.873 43.478 4.43 0.00 43.46 3.77
4347 4606 5.334414 CCATCTTTTCTCTGTACACAGCAAC 60.334 44.000 4.43 0.00 43.46 4.17
4348 4607 4.756642 CCATCTTTTCTCTGTACACAGCAA 59.243 41.667 4.43 0.00 43.46 3.91
4354 4613 7.239763 TCATGTACCATCTTTTCTCTGTACA 57.760 36.000 0.00 0.00 41.68 2.90
4375 4634 5.363580 AGTGGATGTTTTGTTTCACCTTCAT 59.636 36.000 0.00 0.00 0.00 2.57
4376 4635 4.709397 AGTGGATGTTTTGTTTCACCTTCA 59.291 37.500 0.00 0.00 0.00 3.02
4377 4636 5.262588 AGTGGATGTTTTGTTTCACCTTC 57.737 39.130 0.00 0.00 0.00 3.46
4447 4756 3.685272 GCTGGACTACTTAAAGCAGAACC 59.315 47.826 0.00 0.00 34.01 3.62
4481 4790 1.170919 ATATAGAGCGTGACGGGCGT 61.171 55.000 7.25 0.00 35.00 5.68
4554 4866 4.080638 GCCTTATGGGAGCTATAGAAGCAT 60.081 45.833 3.21 0.00 44.25 3.79
4555 4867 3.261897 GCCTTATGGGAGCTATAGAAGCA 59.738 47.826 3.21 0.00 44.25 3.91
4556 4868 3.677424 CGCCTTATGGGAGCTATAGAAGC 60.677 52.174 3.21 0.00 43.04 3.86
4557 4869 3.511934 ACGCCTTATGGGAGCTATAGAAG 59.488 47.826 3.21 0.00 38.52 2.85
4558 4870 3.507411 ACGCCTTATGGGAGCTATAGAA 58.493 45.455 3.21 0.00 38.52 2.10
4559 4871 3.170991 ACGCCTTATGGGAGCTATAGA 57.829 47.619 3.21 0.00 38.52 1.98
4560 4872 5.352284 CATTACGCCTTATGGGAGCTATAG 58.648 45.833 0.00 0.00 38.52 1.31
4561 4873 4.382685 GCATTACGCCTTATGGGAGCTATA 60.383 45.833 0.00 0.00 38.52 1.31
4562 4874 3.619979 GCATTACGCCTTATGGGAGCTAT 60.620 47.826 0.00 0.00 38.52 2.97
4563 4875 2.289444 GCATTACGCCTTATGGGAGCTA 60.289 50.000 0.00 0.00 38.52 3.32
4564 4876 1.543429 GCATTACGCCTTATGGGAGCT 60.543 52.381 0.00 0.00 38.52 4.09
4565 4877 0.875059 GCATTACGCCTTATGGGAGC 59.125 55.000 0.00 0.00 38.52 4.70
4566 4878 2.550830 AGCATTACGCCTTATGGGAG 57.449 50.000 0.00 0.00 44.04 4.30
4567 4879 2.438021 AGAAGCATTACGCCTTATGGGA 59.562 45.455 0.00 0.00 44.04 4.37
4568 4880 2.851195 AGAAGCATTACGCCTTATGGG 58.149 47.619 0.00 0.00 44.04 4.00
4569 4881 6.893958 CTATAGAAGCATTACGCCTTATGG 57.106 41.667 0.00 0.00 44.04 2.74
4578 4890 7.310734 ACCTTATGGGAGCTATAGAAGCATTAC 60.311 40.741 3.21 0.00 45.77 1.89
4579 4891 6.730977 ACCTTATGGGAGCTATAGAAGCATTA 59.269 38.462 3.21 0.00 45.77 1.90
4580 4892 5.549619 ACCTTATGGGAGCTATAGAAGCATT 59.450 40.000 3.21 0.00 45.77 3.56
4608 4920 2.128035 GAGTTGAGGGCGATCATTACG 58.872 52.381 0.00 0.00 0.00 3.18
4621 4933 1.338020 GTGCCCACAAAAGGAGTTGAG 59.662 52.381 0.00 0.00 32.59 3.02
4622 4934 1.398692 GTGCCCACAAAAGGAGTTGA 58.601 50.000 0.00 0.00 32.59 3.18
4623 4935 0.389025 GGTGCCCACAAAAGGAGTTG 59.611 55.000 0.40 0.00 34.52 3.16
4624 4936 0.261696 AGGTGCCCACAAAAGGAGTT 59.738 50.000 0.40 0.00 0.00 3.01
4625 4937 1.145571 TAGGTGCCCACAAAAGGAGT 58.854 50.000 0.40 0.00 0.00 3.85
4626 4938 2.514458 ATAGGTGCCCACAAAAGGAG 57.486 50.000 0.40 0.00 0.00 3.69
4627 4939 2.356741 GCTATAGGTGCCCACAAAAGGA 60.357 50.000 1.04 0.00 0.00 3.36
4628 4940 2.024414 GCTATAGGTGCCCACAAAAGG 58.976 52.381 1.04 0.00 0.00 3.11
4629 4941 3.004752 AGCTATAGGTGCCCACAAAAG 57.995 47.619 3.03 0.00 0.00 2.27
4630 4942 3.352648 GAAGCTATAGGTGCCCACAAAA 58.647 45.455 4.96 0.00 0.00 2.44
4631 4943 2.356741 GGAAGCTATAGGTGCCCACAAA 60.357 50.000 17.22 0.00 35.14 2.83
4632 4944 1.211949 GGAAGCTATAGGTGCCCACAA 59.788 52.381 17.22 0.00 35.14 3.33
4633 4945 0.837272 GGAAGCTATAGGTGCCCACA 59.163 55.000 17.22 0.00 35.14 4.17
4634 4946 0.837272 TGGAAGCTATAGGTGCCCAC 59.163 55.000 23.73 2.47 40.59 4.61
4635 4947 1.819753 ATGGAAGCTATAGGTGCCCA 58.180 50.000 23.73 22.40 40.59 5.36
4636 4948 3.307762 CCTTATGGAAGCTATAGGTGCCC 60.308 52.174 23.73 18.24 40.59 5.36
4637 4949 3.328050 ACCTTATGGAAGCTATAGGTGCC 59.672 47.826 20.62 20.62 41.69 5.01
4638 4950 4.625607 ACCTTATGGAAGCTATAGGTGC 57.374 45.455 4.96 2.81 37.04 5.01
4639 4951 6.166982 GCTAACCTTATGGAAGCTATAGGTG 58.833 44.000 4.96 0.00 40.30 4.00
4640 4952 5.047235 CGCTAACCTTATGGAAGCTATAGGT 60.047 44.000 17.91 0.00 40.84 3.08
4641 4953 5.047235 ACGCTAACCTTATGGAAGCTATAGG 60.047 44.000 17.91 0.00 40.84 2.57
4642 4954 6.026947 ACGCTAACCTTATGGAAGCTATAG 57.973 41.667 17.91 0.00 40.84 1.31
4643 4955 6.718454 ACTACGCTAACCTTATGGAAGCTATA 59.282 38.462 17.91 12.12 40.84 1.31
4644 4956 4.957684 ACGCTAACCTTATGGAAGCTAT 57.042 40.909 17.91 8.64 40.84 2.97
4645 4957 4.891756 ACTACGCTAACCTTATGGAAGCTA 59.108 41.667 17.91 11.55 40.84 3.32
4646 4958 3.705072 ACTACGCTAACCTTATGGAAGCT 59.295 43.478 17.91 11.21 40.84 3.74
4647 4959 3.802685 CACTACGCTAACCTTATGGAAGC 59.197 47.826 13.25 13.25 40.17 3.86
4648 4960 5.258456 TCACTACGCTAACCTTATGGAAG 57.742 43.478 0.81 0.11 37.04 3.46
4649 4961 5.864418 ATCACTACGCTAACCTTATGGAA 57.136 39.130 0.81 0.00 37.04 3.53
4650 4962 5.597806 CAATCACTACGCTAACCTTATGGA 58.402 41.667 0.81 0.00 37.04 3.41
4651 4963 4.211374 GCAATCACTACGCTAACCTTATGG 59.789 45.833 0.00 0.00 39.83 2.74
4652 4964 4.211374 GGCAATCACTACGCTAACCTTATG 59.789 45.833 0.00 0.00 0.00 1.90
4653 4965 4.377897 GGCAATCACTACGCTAACCTTAT 58.622 43.478 0.00 0.00 0.00 1.73
4654 4966 3.431207 GGGCAATCACTACGCTAACCTTA 60.431 47.826 0.00 0.00 0.00 2.69
4655 4967 2.629051 GGCAATCACTACGCTAACCTT 58.371 47.619 0.00 0.00 0.00 3.50
4656 4968 1.134491 GGGCAATCACTACGCTAACCT 60.134 52.381 0.00 0.00 0.00 3.50
4657 4969 1.134491 AGGGCAATCACTACGCTAACC 60.134 52.381 0.00 0.00 0.00 2.85
4658 4970 2.202566 GAGGGCAATCACTACGCTAAC 58.797 52.381 0.00 0.00 0.00 2.34
4659 4971 1.828595 TGAGGGCAATCACTACGCTAA 59.171 47.619 0.00 0.00 0.00 3.09
4660 4972 1.480789 TGAGGGCAATCACTACGCTA 58.519 50.000 0.00 0.00 0.00 4.26
4661 4973 0.613260 TTGAGGGCAATCACTACGCT 59.387 50.000 0.00 0.00 0.00 5.07
4662 4974 0.727398 GTTGAGGGCAATCACTACGC 59.273 55.000 0.00 0.00 36.22 4.42
4663 4975 2.271800 GAGTTGAGGGCAATCACTACG 58.728 52.381 0.00 0.00 36.22 3.51
4664 4976 2.237392 AGGAGTTGAGGGCAATCACTAC 59.763 50.000 0.00 0.00 36.22 2.73
4665 4977 2.551270 AGGAGTTGAGGGCAATCACTA 58.449 47.619 0.00 0.00 36.22 2.74
4666 4978 1.366319 AGGAGTTGAGGGCAATCACT 58.634 50.000 0.00 0.00 36.22 3.41
4667 4979 2.206576 AAGGAGTTGAGGGCAATCAC 57.793 50.000 0.00 0.00 36.22 3.06
4668 4980 2.892852 CAAAAGGAGTTGAGGGCAATCA 59.107 45.455 0.00 0.00 36.22 2.57
4669 4981 2.353109 GCAAAAGGAGTTGAGGGCAATC 60.353 50.000 0.00 0.00 36.22 2.67
4670 4982 1.620323 GCAAAAGGAGTTGAGGGCAAT 59.380 47.619 0.00 0.00 36.22 3.56
4671 4983 1.039856 GCAAAAGGAGTTGAGGGCAA 58.960 50.000 0.00 0.00 0.00 4.52
4672 4984 1.172180 CGCAAAAGGAGTTGAGGGCA 61.172 55.000 0.00 0.00 0.00 5.36
4673 4985 1.581447 CGCAAAAGGAGTTGAGGGC 59.419 57.895 0.00 0.00 0.00 5.19
4674 4986 2.257353 CCGCAAAAGGAGTTGAGGG 58.743 57.895 0.28 0.00 42.78 4.30
4675 4987 1.866853 GCCCGCAAAAGGAGTTGAGG 61.867 60.000 1.19 1.19 45.19 3.86
4791 5129 1.264020 CTACTTGCTTGCGTCTTTGCA 59.736 47.619 0.00 0.00 44.61 4.08


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

AutoCloner maintained by Alex Coulton.