Multiple sequence alignment - TraesCS4D01G129500

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 TraesCS4D01G129500 chr4D 100.000 5214 0 0 1 5214 115120081 115125294 0.000000e+00 9629.0
1 TraesCS4D01G129500 chr4D 96.911 874 27 0 1 874 301309383 301310256 0.000000e+00 1465.0
2 TraesCS4D01G129500 chr4D 94.737 874 44 2 1 873 503682668 503681796 0.000000e+00 1358.0
3 TraesCS4D01G129500 chr4D 90.136 882 42 20 1944 2822 447979465 447980304 0.000000e+00 1105.0
4 TraesCS4D01G129500 chr4D 94.096 542 31 1 2809 3350 472132307 472131767 0.000000e+00 822.0
5 TraesCS4D01G129500 chr4D 89.277 429 23 7 3351 3778 447980288 447980694 2.780000e-142 516.0
6 TraesCS4D01G129500 chr4A 94.283 1959 71 19 875 2822 462205519 462203591 0.000000e+00 2959.0
7 TraesCS4D01G129500 chr4A 94.281 1871 86 12 3354 5214 462203604 462201745 0.000000e+00 2843.0
8 TraesCS4D01G129500 chr4A 92.752 883 38 11 1943 2822 611199247 611200106 0.000000e+00 1253.0
9 TraesCS4D01G129500 chr4A 88.167 431 26 8 3351 3778 611200090 611200498 1.690000e-134 490.0
10 TraesCS4D01G129500 chr4A 91.026 78 7 0 1847 1924 27665579 27665656 7.140000e-19 106.0
11 TraesCS4D01G129500 chr4B 93.384 1451 49 20 875 2315 175560708 175562121 0.000000e+00 2104.0
12 TraesCS4D01G129500 chr4B 95.366 1079 42 6 3354 4428 175562588 175563662 0.000000e+00 1709.0
13 TraesCS4D01G129500 chr4B 92.906 874 60 2 1 873 81112359 81111487 0.000000e+00 1269.0
14 TraesCS4D01G129500 chr4B 94.318 792 38 7 4427 5214 175563775 175564563 0.000000e+00 1206.0
15 TraesCS4D01G129500 chr4B 91.974 461 21 4 2373 2822 175562146 175562601 2.650000e-177 632.0
16 TraesCS4D01G129500 chr2D 96.682 874 22 2 1 874 627335882 627335016 0.000000e+00 1447.0
17 TraesCS4D01G129500 chr6D 93.167 922 42 9 1894 2812 163352695 163353598 0.000000e+00 1334.0
18 TraesCS4D01G129500 chr5D 94.273 873 49 1 1 873 384426501 384425630 0.000000e+00 1334.0
19 TraesCS4D01G129500 chr5D 93.566 544 34 1 2809 3351 500322187 500322730 0.000000e+00 809.0
20 TraesCS4D01G129500 chr5D 93.554 543 32 3 2809 3350 266688718 266689258 0.000000e+00 806.0
21 TraesCS4D01G129500 chr5D 80.592 608 77 24 1668 2267 218569369 218568795 1.040000e-116 431.0
22 TraesCS4D01G129500 chr2B 93.998 883 33 11 1943 2822 654362864 654361999 0.000000e+00 1319.0
23 TraesCS4D01G129500 chr2B 92.000 875 66 4 1 874 171784202 171785073 0.000000e+00 1225.0
24 TraesCS4D01G129500 chr2B 88.967 426 24 7 3354 3778 654362012 654361609 6.030000e-139 505.0
25 TraesCS4D01G129500 chr2B 88.889 54 6 0 1707 1760 66199483 66199430 3.370000e-07 67.6
26 TraesCS4D01G129500 chr7B 92.375 918 61 6 1894 2811 109172678 109171770 0.000000e+00 1299.0
27 TraesCS4D01G129500 chr7B 92.986 884 38 12 1943 2822 686929072 686929935 0.000000e+00 1267.0
28 TraesCS4D01G129500 chr7B 88.578 429 26 8 3351 3778 686929919 686930325 2.800000e-137 499.0
29 TraesCS4D01G129500 chr7B 90.432 324 24 5 3542 3864 109180132 109180449 2.250000e-113 420.0
30 TraesCS4D01G129500 chr7B 92.810 153 11 0 3354 3506 109171627 109171475 6.800000e-54 222.0
31 TraesCS4D01G129500 chr6B 93.052 878 57 3 1 875 586037807 586038683 0.000000e+00 1280.0
32 TraesCS4D01G129500 chr5B 92.865 883 39 9 1943 2822 614981710 614980849 0.000000e+00 1260.0
33 TraesCS4D01G129500 chr5B 93.325 764 27 12 2059 2822 629973564 629972825 0.000000e+00 1107.0
34 TraesCS4D01G129500 chr5B 88.732 426 25 7 3354 3778 629972838 629972435 2.800000e-137 499.0
35 TraesCS4D01G129500 chr3A 92.352 876 63 3 1 873 749433589 749432715 0.000000e+00 1243.0
36 TraesCS4D01G129500 chr1B 91.876 874 69 2 1 873 474753487 474754359 0.000000e+00 1219.0
37 TraesCS4D01G129500 chr1B 95.176 539 21 2 2812 3350 348101112 348100579 0.000000e+00 846.0
38 TraesCS4D01G129500 chr3D 90.870 931 48 20 1894 2822 554391669 554392564 0.000000e+00 1214.0
39 TraesCS4D01G129500 chr3D 87.354 514 42 7 3351 3864 554392548 554393038 7.580000e-158 568.0
40 TraesCS4D01G129500 chr7A 93.586 764 25 12 2059 2822 284784500 284785239 0.000000e+00 1118.0
41 TraesCS4D01G129500 chr7A 88.578 429 26 7 3351 3778 284785223 284785629 2.800000e-137 499.0
42 TraesCS4D01G129500 chr2A 92.948 709 30 11 1943 2648 711070376 711071067 0.000000e+00 1014.0
43 TraesCS4D01G129500 chr2A 88.578 429 26 7 3351 3778 711071318 711071724 2.800000e-137 499.0
44 TraesCS4D01G129500 chr7D 93.773 546 33 1 2809 3353 417992842 417992297 0.000000e+00 819.0
45 TraesCS4D01G129500 chr1D 93.923 543 31 2 2809 3350 171331783 171332324 0.000000e+00 819.0
46 TraesCS4D01G129500 chr5A 93.911 542 32 1 2809 3350 662225162 662224622 0.000000e+00 817.0
47 TraesCS4D01G129500 chr1A 93.566 544 33 2 2809 3351 563165987 563166529 0.000000e+00 809.0
48 TraesCS4D01G129500 chr1A 92.922 551 37 2 2809 3359 260954891 260954343 0.000000e+00 800.0


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 TraesCS4D01G129500 chr4D 115120081 115125294 5213 False 9629.00 9629 100.0000 1 5214 1 chr4D.!!$F1 5213
1 TraesCS4D01G129500 chr4D 301309383 301310256 873 False 1465.00 1465 96.9110 1 874 1 chr4D.!!$F2 873
2 TraesCS4D01G129500 chr4D 503681796 503682668 872 True 1358.00 1358 94.7370 1 873 1 chr4D.!!$R2 872
3 TraesCS4D01G129500 chr4D 472131767 472132307 540 True 822.00 822 94.0960 2809 3350 1 chr4D.!!$R1 541
4 TraesCS4D01G129500 chr4D 447979465 447980694 1229 False 810.50 1105 89.7065 1944 3778 2 chr4D.!!$F3 1834
5 TraesCS4D01G129500 chr4A 462201745 462205519 3774 True 2901.00 2959 94.2820 875 5214 2 chr4A.!!$R1 4339
6 TraesCS4D01G129500 chr4A 611199247 611200498 1251 False 871.50 1253 90.4595 1943 3778 2 chr4A.!!$F2 1835
7 TraesCS4D01G129500 chr4B 175560708 175564563 3855 False 1412.75 2104 93.7605 875 5214 4 chr4B.!!$F1 4339
8 TraesCS4D01G129500 chr4B 81111487 81112359 872 True 1269.00 1269 92.9060 1 873 1 chr4B.!!$R1 872
9 TraesCS4D01G129500 chr2D 627335016 627335882 866 True 1447.00 1447 96.6820 1 874 1 chr2D.!!$R1 873
10 TraesCS4D01G129500 chr6D 163352695 163353598 903 False 1334.00 1334 93.1670 1894 2812 1 chr6D.!!$F1 918
11 TraesCS4D01G129500 chr5D 384425630 384426501 871 True 1334.00 1334 94.2730 1 873 1 chr5D.!!$R2 872
12 TraesCS4D01G129500 chr5D 500322187 500322730 543 False 809.00 809 93.5660 2809 3351 1 chr5D.!!$F2 542
13 TraesCS4D01G129500 chr5D 266688718 266689258 540 False 806.00 806 93.5540 2809 3350 1 chr5D.!!$F1 541
14 TraesCS4D01G129500 chr5D 218568795 218569369 574 True 431.00 431 80.5920 1668 2267 1 chr5D.!!$R1 599
15 TraesCS4D01G129500 chr2B 171784202 171785073 871 False 1225.00 1225 92.0000 1 874 1 chr2B.!!$F1 873
16 TraesCS4D01G129500 chr2B 654361609 654362864 1255 True 912.00 1319 91.4825 1943 3778 2 chr2B.!!$R2 1835
17 TraesCS4D01G129500 chr7B 686929072 686930325 1253 False 883.00 1267 90.7820 1943 3778 2 chr7B.!!$F2 1835
18 TraesCS4D01G129500 chr7B 109171475 109172678 1203 True 760.50 1299 92.5925 1894 3506 2 chr7B.!!$R1 1612
19 TraesCS4D01G129500 chr6B 586037807 586038683 876 False 1280.00 1280 93.0520 1 875 1 chr6B.!!$F1 874
20 TraesCS4D01G129500 chr5B 614980849 614981710 861 True 1260.00 1260 92.8650 1943 2822 1 chr5B.!!$R1 879
21 TraesCS4D01G129500 chr5B 629972435 629973564 1129 True 803.00 1107 91.0285 2059 3778 2 chr5B.!!$R2 1719
22 TraesCS4D01G129500 chr3A 749432715 749433589 874 True 1243.00 1243 92.3520 1 873 1 chr3A.!!$R1 872
23 TraesCS4D01G129500 chr1B 474753487 474754359 872 False 1219.00 1219 91.8760 1 873 1 chr1B.!!$F1 872
24 TraesCS4D01G129500 chr1B 348100579 348101112 533 True 846.00 846 95.1760 2812 3350 1 chr1B.!!$R1 538
25 TraesCS4D01G129500 chr3D 554391669 554393038 1369 False 891.00 1214 89.1120 1894 3864 2 chr3D.!!$F1 1970
26 TraesCS4D01G129500 chr7A 284784500 284785629 1129 False 808.50 1118 91.0820 2059 3778 2 chr7A.!!$F1 1719
27 TraesCS4D01G129500 chr2A 711070376 711071724 1348 False 756.50 1014 90.7630 1943 3778 2 chr2A.!!$F1 1835
28 TraesCS4D01G129500 chr7D 417992297 417992842 545 True 819.00 819 93.7730 2809 3353 1 chr7D.!!$R1 544
29 TraesCS4D01G129500 chr1D 171331783 171332324 541 False 819.00 819 93.9230 2809 3350 1 chr1D.!!$F1 541
30 TraesCS4D01G129500 chr5A 662224622 662225162 540 True 817.00 817 93.9110 2809 3350 1 chr5A.!!$R1 541
31 TraesCS4D01G129500 chr1A 563165987 563166529 542 False 809.00 809 93.5660 2809 3351 1 chr1A.!!$F1 542
32 TraesCS4D01G129500 chr1A 260954343 260954891 548 True 800.00 800 92.9220 2809 3359 1 chr1A.!!$R1 550

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
925 941 0.513820 TTTTCTTTTACCGCGAGCCG 59.486 50.000 8.23 0.00 0.00 5.52 F
1008 1030 0.389817 CACGGACAGAAATGGCTCGA 60.390 55.000 0.00 0.00 0.00 4.04 F
1009 1031 0.537188 ACGGACAGAAATGGCTCGAT 59.463 50.000 0.00 0.00 0.00 3.59 F
1184 1207 0.737715 AAGTCGAATGCGCCTCTCAC 60.738 55.000 4.18 1.39 37.46 3.51 F
2378 2431 1.876156 CTGCCTGTTTCACTGAAGTCC 59.124 52.381 0.00 0.00 0.00 3.85 F
3527 3713 2.217393 CGCGATGTCTGATTAAGCACTC 59.783 50.000 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2679 2860 0.034089 AAGCAGACACTATTGCCCCC 60.034 55.000 0.00 0.0 41.17 5.40 R
2807 2988 3.040477 CCCATGGGTAAAATTGCCATCT 58.960 45.455 23.93 0.0 34.27 2.90 R
2919 3100 3.309121 GCTATACCCGTACCCTACCCATA 60.309 52.174 0.00 0.0 0.00 2.74 R
3093 3275 4.011023 TCTCAGCTCAGTAACAGGTAGAC 58.989 47.826 0.00 0.0 0.00 2.59 R
3884 4070 0.773644 ACACCATCTGAGGTTGGCTT 59.226 50.000 2.81 0.0 40.77 4.35 R
4404 4593 0.323302 TCAAATGCTACCCGTGCTCA 59.677 50.000 0.00 0.0 0.00 4.26 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
364 365 1.905637 AGCCAAAACTAGGGTTTCCG 58.094 50.000 0.00 0.00 43.90 4.30
597 607 1.999002 GGTGGGGCCAGCCTAAGTA 60.999 63.158 4.39 0.00 38.38 2.24
705 716 2.671070 CCGCAACTGGACCAGGAT 59.329 61.111 25.34 11.15 35.51 3.24
828 841 2.341846 TTTTCCGAAAGCAGGTCAGT 57.658 45.000 0.00 0.00 0.00 3.41
829 842 2.341846 TTTCCGAAAGCAGGTCAGTT 57.658 45.000 0.00 0.00 0.00 3.16
830 843 2.341846 TTCCGAAAGCAGGTCAGTTT 57.658 45.000 0.00 0.00 0.00 2.66
831 844 1.593196 TCCGAAAGCAGGTCAGTTTG 58.407 50.000 0.00 0.00 0.00 2.93
832 845 1.134220 TCCGAAAGCAGGTCAGTTTGT 60.134 47.619 0.00 0.00 0.00 2.83
833 846 1.002468 CCGAAAGCAGGTCAGTTTGTG 60.002 52.381 0.00 0.00 0.00 3.33
834 847 1.939934 CGAAAGCAGGTCAGTTTGTGA 59.060 47.619 0.00 0.00 0.00 3.58
835 848 2.549754 CGAAAGCAGGTCAGTTTGTGAT 59.450 45.455 0.00 0.00 37.56 3.06
836 849 3.003689 CGAAAGCAGGTCAGTTTGTGATT 59.996 43.478 0.00 0.00 37.56 2.57
837 850 4.498009 CGAAAGCAGGTCAGTTTGTGATTT 60.498 41.667 0.00 0.00 37.56 2.17
838 851 3.996150 AGCAGGTCAGTTTGTGATTTG 57.004 42.857 0.00 0.00 37.56 2.32
839 852 3.554934 AGCAGGTCAGTTTGTGATTTGA 58.445 40.909 0.00 0.00 37.56 2.69
840 853 4.147321 AGCAGGTCAGTTTGTGATTTGAT 58.853 39.130 0.00 0.00 37.56 2.57
841 854 4.586001 AGCAGGTCAGTTTGTGATTTGATT 59.414 37.500 0.00 0.00 37.56 2.57
842 855 5.069516 AGCAGGTCAGTTTGTGATTTGATTT 59.930 36.000 0.00 0.00 37.56 2.17
843 856 5.403466 GCAGGTCAGTTTGTGATTTGATTTC 59.597 40.000 0.00 0.00 37.56 2.17
844 857 6.736794 GCAGGTCAGTTTGTGATTTGATTTCT 60.737 38.462 0.00 0.00 37.56 2.52
845 858 6.860023 CAGGTCAGTTTGTGATTTGATTTCTC 59.140 38.462 0.00 0.00 37.56 2.87
846 859 6.015940 AGGTCAGTTTGTGATTTGATTTCTCC 60.016 38.462 0.00 0.00 37.56 3.71
847 860 6.152379 GTCAGTTTGTGATTTGATTTCTCCC 58.848 40.000 0.00 0.00 37.56 4.30
848 861 6.015940 GTCAGTTTGTGATTTGATTTCTCCCT 60.016 38.462 0.00 0.00 37.56 4.20
849 862 6.207417 TCAGTTTGTGATTTGATTTCTCCCTC 59.793 38.462 0.00 0.00 0.00 4.30
850 863 5.182001 AGTTTGTGATTTGATTTCTCCCTCG 59.818 40.000 0.00 0.00 0.00 4.63
851 864 3.609853 TGTGATTTGATTTCTCCCTCGG 58.390 45.455 0.00 0.00 0.00 4.63
852 865 2.945668 GTGATTTGATTTCTCCCTCGGG 59.054 50.000 0.00 0.00 0.00 5.14
853 866 2.576191 TGATTTGATTTCTCCCTCGGGT 59.424 45.455 1.18 0.00 36.47 5.28
854 867 2.781681 TTTGATTTCTCCCTCGGGTC 57.218 50.000 1.18 0.00 36.47 4.46
855 868 1.651737 TTGATTTCTCCCTCGGGTCA 58.348 50.000 1.18 0.00 36.47 4.02
856 869 1.651737 TGATTTCTCCCTCGGGTCAA 58.348 50.000 1.18 0.00 36.47 3.18
857 870 1.982226 TGATTTCTCCCTCGGGTCAAA 59.018 47.619 1.18 3.12 36.47 2.69
858 871 2.576191 TGATTTCTCCCTCGGGTCAAAT 59.424 45.455 11.33 11.33 36.47 2.32
859 872 3.778075 TGATTTCTCCCTCGGGTCAAATA 59.222 43.478 1.18 0.00 36.47 1.40
860 873 4.412199 TGATTTCTCCCTCGGGTCAAATAT 59.588 41.667 1.18 0.00 36.47 1.28
861 874 3.838244 TTCTCCCTCGGGTCAAATATG 57.162 47.619 1.18 0.00 36.47 1.78
862 875 2.759355 TCTCCCTCGGGTCAAATATGT 58.241 47.619 1.18 0.00 36.47 2.29
863 876 2.434336 TCTCCCTCGGGTCAAATATGTG 59.566 50.000 1.18 0.00 36.47 3.21
864 877 2.434336 CTCCCTCGGGTCAAATATGTGA 59.566 50.000 1.18 0.00 36.47 3.58
865 878 3.045634 TCCCTCGGGTCAAATATGTGAT 58.954 45.455 0.00 0.00 36.47 3.06
866 879 3.458118 TCCCTCGGGTCAAATATGTGATT 59.542 43.478 0.00 0.00 36.47 2.57
867 880 4.080015 TCCCTCGGGTCAAATATGTGATTT 60.080 41.667 0.00 0.00 36.47 2.17
868 881 4.275936 CCCTCGGGTCAAATATGTGATTTC 59.724 45.833 0.00 0.00 0.00 2.17
869 882 5.126067 CCTCGGGTCAAATATGTGATTTCT 58.874 41.667 0.00 0.00 0.00 2.52
870 883 5.008019 CCTCGGGTCAAATATGTGATTTCTG 59.992 44.000 0.00 0.00 0.00 3.02
871 884 4.335315 TCGGGTCAAATATGTGATTTCTGC 59.665 41.667 0.00 0.00 0.00 4.26
872 885 4.498009 CGGGTCAAATATGTGATTTCTGCC 60.498 45.833 0.00 0.00 0.00 4.85
873 886 4.498009 GGGTCAAATATGTGATTTCTGCCG 60.498 45.833 0.00 0.00 0.00 5.69
905 918 5.279758 GGGCAGTCTACTTCTTTTCTTCTCT 60.280 44.000 0.00 0.00 0.00 3.10
923 939 3.185797 TCTCTTTTTCTTTTACCGCGAGC 59.814 43.478 8.23 0.00 0.00 5.03
924 940 2.224784 TCTTTTTCTTTTACCGCGAGCC 59.775 45.455 8.23 0.00 0.00 4.70
925 941 0.513820 TTTTCTTTTACCGCGAGCCG 59.486 50.000 8.23 0.00 0.00 5.52
970 989 7.858382 TGTCATAAACATTTGGTTACGACAAAG 59.142 33.333 13.17 0.00 40.70 2.77
1008 1030 0.389817 CACGGACAGAAATGGCTCGA 60.390 55.000 0.00 0.00 0.00 4.04
1009 1031 0.537188 ACGGACAGAAATGGCTCGAT 59.463 50.000 0.00 0.00 0.00 3.59
1031 1053 1.103398 GGTCATGGATTGCCCTTCCG 61.103 60.000 0.00 0.00 35.94 4.30
1062 1085 4.025040 TCAGATGACTTGGCACTTCATT 57.975 40.909 10.53 0.91 29.93 2.57
1064 1087 4.828939 TCAGATGACTTGGCACTTCATTTT 59.171 37.500 10.53 2.05 29.93 1.82
1066 1089 3.096489 TGACTTGGCACTTCATTTTGC 57.904 42.857 0.00 0.00 38.06 3.68
1184 1207 0.737715 AAGTCGAATGCGCCTCTCAC 60.738 55.000 4.18 1.39 37.46 3.51
1224 1247 3.060615 GCAGTTGCCAGCTGGGAG 61.061 66.667 33.46 20.22 40.01 4.30
1225 1248 2.433446 CAGTTGCCAGCTGGGAGT 59.567 61.111 33.46 19.28 40.01 3.85
1226 1249 1.970114 CAGTTGCCAGCTGGGAGTG 60.970 63.158 33.46 25.83 40.01 3.51
1227 1250 2.674380 GTTGCCAGCTGGGAGTGG 60.674 66.667 33.46 9.13 40.01 4.00
1228 1251 3.970410 TTGCCAGCTGGGAGTGGG 61.970 66.667 33.46 7.31 40.01 4.61
1229 1252 4.980592 TGCCAGCTGGGAGTGGGA 62.981 66.667 33.46 6.16 40.01 4.37
1296 1319 2.522198 AAAACCACTGGCCACCACCA 62.522 55.000 0.00 0.00 38.29 4.17
1303 1326 4.035102 GGCCACCACCACCTCCTC 62.035 72.222 0.00 0.00 0.00 3.71
1967 2005 4.468689 GTAGGGTGCTCCGGTGGC 62.469 72.222 13.57 13.57 41.52 5.01
2325 2378 9.060347 CATACATGTAGCTACTCCATTCAAATT 57.940 33.333 23.84 1.67 0.00 1.82
2340 2393 2.997986 TCAAATTAGAAGACGGCGAACC 59.002 45.455 16.62 1.74 0.00 3.62
2342 2395 3.329929 AATTAGAAGACGGCGAACCTT 57.670 42.857 16.62 13.64 0.00 3.50
2378 2431 1.876156 CTGCCTGTTTCACTGAAGTCC 59.124 52.381 0.00 0.00 0.00 3.85
2397 2454 6.051179 AGTCCAAGGGATCAGTAAGTTTAC 57.949 41.667 0.00 0.00 32.73 2.01
2398 2455 5.546499 AGTCCAAGGGATCAGTAAGTTTACA 59.454 40.000 4.97 0.00 33.23 2.41
2399 2456 6.043938 AGTCCAAGGGATCAGTAAGTTTACAA 59.956 38.462 4.97 0.00 33.23 2.41
2400 2457 6.371825 GTCCAAGGGATCAGTAAGTTTACAAG 59.628 42.308 4.97 0.00 33.23 3.16
2460 2532 6.015434 ACATTGATGTGAGTGTGTAGTGTAGA 60.015 38.462 0.00 0.00 40.03 2.59
2492 2564 7.402054 TCATCTCCCTTGCTAGTTGATTTTAA 58.598 34.615 0.00 0.00 0.00 1.52
2662 2841 5.573219 TGGATCCTTCTGTGTTGAATGATT 58.427 37.500 14.23 0.00 33.58 2.57
2679 2860 7.679783 TGAATGATTAGGTGGTGTAGATATGG 58.320 38.462 0.00 0.00 0.00 2.74
2774 2955 5.989777 AGTGGTACAGTTACAAGTGATTGTC 59.010 40.000 3.84 0.00 40.27 3.18
2797 2978 6.950428 GTCGCAGCATAAATAATCTATCAACG 59.050 38.462 0.00 0.00 0.00 4.10
2919 3100 2.773661 CCCATACCCTACCCGTTAAGTT 59.226 50.000 0.00 0.00 0.00 2.66
3105 3287 6.032717 GGTCATTTACTCGTCTACCTGTTAC 58.967 44.000 0.00 0.00 0.00 2.50
3275 3459 3.007290 GGGTACGGGTATGGGTAGAATTC 59.993 52.174 0.00 0.00 0.00 2.17
3367 3551 7.389053 CCATCCTTAAGCAGATGTAATTCTACC 59.611 40.741 16.05 0.00 38.57 3.18
3409 3593 3.053693 AGCCTACTGTTTGATGGCCATTA 60.054 43.478 21.84 14.01 44.19 1.90
3433 3617 4.943705 ACATTCACATGTTATCCTGGTGAC 59.056 41.667 0.00 0.00 41.16 3.67
3435 3619 4.842531 TCACATGTTATCCTGGTGACAT 57.157 40.909 0.00 0.30 41.51 3.06
3484 3670 9.492973 AAAAGAAAAGAATAAATGGACACATGG 57.507 29.630 0.00 0.00 37.40 3.66
3506 3692 3.614616 GTGCTTCACTAGACATACACTGC 59.385 47.826 0.00 0.00 0.00 4.40
3527 3713 2.217393 CGCGATGTCTGATTAAGCACTC 59.783 50.000 0.00 0.00 0.00 3.51
3884 4070 4.349636 TCTGGTTGTTATTCTCACCAGGAA 59.650 41.667 15.49 0.00 43.43 3.36
3901 4087 1.272147 GGAAAGCCAACCTCAGATGGT 60.272 52.381 0.00 0.00 43.11 3.55
3926 4112 2.621407 GCATTGTTTCCCTGATCCTCCA 60.621 50.000 0.00 0.00 0.00 3.86
4057 4244 1.550524 TCGGATCTTGACACTTCAGGG 59.449 52.381 0.00 0.00 31.71 4.45
4375 4562 2.098607 ACGGCAATTCAGAATGCATCAG 59.901 45.455 0.00 0.00 44.32 2.90
4404 4593 0.998145 AGCCCTGCTTCCTTCTCATT 59.002 50.000 0.00 0.00 33.89 2.57
4432 4736 3.945285 CGGGTAGCATTTGACCTATTTGT 59.055 43.478 0.00 0.00 35.91 2.83
4433 4737 5.120399 CGGGTAGCATTTGACCTATTTGTA 58.880 41.667 0.00 0.00 35.91 2.41
4434 4738 5.763204 CGGGTAGCATTTGACCTATTTGTAT 59.237 40.000 0.00 0.00 35.91 2.29
4473 4777 4.379652 TCATATTCGTGTGATGTCCCATG 58.620 43.478 0.00 0.00 0.00 3.66
4572 4878 7.697946 AGAACACCTAGTAGTAGAACTAAGGT 58.302 38.462 6.14 5.12 35.58 3.50
4580 4886 5.642919 AGTAGTAGAACTAAGGTGACAGACG 59.357 44.000 0.00 0.00 31.62 4.18
4630 4936 8.632679 CCCATTATATTCAGTAACAATGCAAGT 58.367 33.333 0.00 0.00 0.00 3.16
4644 4950 1.142667 TGCAAGTTCAGTCACCCATGA 59.857 47.619 0.00 0.00 0.00 3.07
4708 5015 3.192633 GGTACTAAAGTGGCATGGTTTGG 59.807 47.826 0.00 0.00 0.00 3.28
4831 5145 6.824305 ATATATACTTGTTCCTTGGCATGC 57.176 37.500 9.90 9.90 0.00 4.06
4859 5173 2.507992 CGAGAGCACGCCAAGAGG 60.508 66.667 0.00 0.00 38.23 3.69
4863 5177 0.108585 AGAGCACGCCAAGAGGAAAA 59.891 50.000 0.00 0.00 36.89 2.29
4908 5222 0.546122 CCCCCAATCACCGATCTGAA 59.454 55.000 0.00 0.00 0.00 3.02
4943 5257 2.182030 GATCGATCGATCCCCGCC 59.818 66.667 36.97 18.96 43.71 6.13
4948 5262 2.443952 ATCGATCCCCGCCACAGA 60.444 61.111 0.00 0.00 38.37 3.41
5037 5351 1.695114 CCGAGGGGCACATACATGGA 61.695 60.000 0.00 0.00 0.00 3.41
5159 5473 3.692406 GTCCCTGGCGGTCGAACT 61.692 66.667 0.00 0.00 0.00 3.01
5162 5476 2.125912 CCTGGCGGTCGAACTGAG 60.126 66.667 0.00 0.00 0.00 3.35
5164 5478 3.573772 CTGGCGGTCGAACTGAGCA 62.574 63.158 0.00 0.00 45.52 4.26
5166 5480 1.741770 GGCGGTCGAACTGAGCATT 60.742 57.895 0.00 0.00 45.52 3.56
5171 5485 2.688507 GGTCGAACTGAGCATTGAAGA 58.311 47.619 0.00 0.00 44.60 2.87
5181 5495 1.072331 AGCATTGAAGAAGTGACCGGT 59.928 47.619 6.92 6.92 0.00 5.28
5196 5510 2.993264 GGTTCTGACCCCGACGGA 60.993 66.667 17.49 0.00 40.25 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
303 304 9.248291 GTGTTGAATCATGTTATGTTTCTTTGT 57.752 29.630 11.63 0.00 38.91 2.83
364 365 4.164822 TGCTCAAATCTTGCTACTTTGC 57.835 40.909 0.00 0.00 31.50 3.68
513 517 1.074850 CCCTCCTCTCTTCCCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
632 642 2.159448 GCGCCACACTTGTAATATGCAA 60.159 45.455 0.00 0.00 0.00 4.08
782 793 0.033504 TCTGCTGACCCTTTCGTGTC 59.966 55.000 0.00 0.00 0.00 3.67
813 826 1.002468 CACAAACTGACCTGCTTTCGG 60.002 52.381 0.00 0.00 0.00 4.30
823 836 6.015940 AGGGAGAAATCAAATCACAAACTGAC 60.016 38.462 0.00 0.00 0.00 3.51
824 837 6.070656 AGGGAGAAATCAAATCACAAACTGA 58.929 36.000 0.00 0.00 0.00 3.41
825 838 6.336842 AGGGAGAAATCAAATCACAAACTG 57.663 37.500 0.00 0.00 0.00 3.16
826 839 5.182001 CGAGGGAGAAATCAAATCACAAACT 59.818 40.000 0.00 0.00 0.00 2.66
827 840 5.393962 CGAGGGAGAAATCAAATCACAAAC 58.606 41.667 0.00 0.00 0.00 2.93
828 841 4.458989 CCGAGGGAGAAATCAAATCACAAA 59.541 41.667 0.00 0.00 0.00 2.83
829 842 4.009675 CCGAGGGAGAAATCAAATCACAA 58.990 43.478 0.00 0.00 0.00 3.33
830 843 3.609853 CCGAGGGAGAAATCAAATCACA 58.390 45.455 0.00 0.00 0.00 3.58
831 844 2.945668 CCCGAGGGAGAAATCAAATCAC 59.054 50.000 0.84 0.00 37.50 3.06
832 845 2.576191 ACCCGAGGGAGAAATCAAATCA 59.424 45.455 16.26 0.00 38.96 2.57
833 846 3.206964 GACCCGAGGGAGAAATCAAATC 58.793 50.000 16.26 0.00 38.96 2.17
834 847 2.576191 TGACCCGAGGGAGAAATCAAAT 59.424 45.455 16.26 0.00 38.96 2.32
835 848 1.982226 TGACCCGAGGGAGAAATCAAA 59.018 47.619 16.26 0.00 38.96 2.69
836 849 1.651737 TGACCCGAGGGAGAAATCAA 58.348 50.000 16.26 0.00 38.96 2.57
837 850 1.651737 TTGACCCGAGGGAGAAATCA 58.348 50.000 16.26 4.71 38.96 2.57
838 851 2.781681 TTTGACCCGAGGGAGAAATC 57.218 50.000 16.26 1.84 38.96 2.17
839 852 4.166144 ACATATTTGACCCGAGGGAGAAAT 59.834 41.667 16.26 17.93 38.96 2.17
840 853 3.521937 ACATATTTGACCCGAGGGAGAAA 59.478 43.478 16.26 12.58 38.96 2.52
841 854 3.112263 ACATATTTGACCCGAGGGAGAA 58.888 45.455 16.26 6.63 38.96 2.87
842 855 2.434336 CACATATTTGACCCGAGGGAGA 59.566 50.000 16.26 0.00 38.96 3.71
843 856 2.434336 TCACATATTTGACCCGAGGGAG 59.566 50.000 16.26 0.00 38.96 4.30
844 857 2.473070 TCACATATTTGACCCGAGGGA 58.527 47.619 16.26 0.00 38.96 4.20
845 858 3.492102 ATCACATATTTGACCCGAGGG 57.508 47.619 6.63 6.63 42.03 4.30
846 859 5.008019 CAGAAATCACATATTTGACCCGAGG 59.992 44.000 0.00 0.00 0.00 4.63
847 860 5.504665 GCAGAAATCACATATTTGACCCGAG 60.505 44.000 0.00 0.00 0.00 4.63
848 861 4.335315 GCAGAAATCACATATTTGACCCGA 59.665 41.667 0.00 0.00 0.00 5.14
849 862 4.498009 GGCAGAAATCACATATTTGACCCG 60.498 45.833 0.00 0.00 0.00 5.28
850 863 4.498009 CGGCAGAAATCACATATTTGACCC 60.498 45.833 0.00 0.00 0.00 4.46
851 864 4.096382 ACGGCAGAAATCACATATTTGACC 59.904 41.667 0.00 0.00 0.00 4.02
852 865 5.235305 ACGGCAGAAATCACATATTTGAC 57.765 39.130 0.00 0.00 0.00 3.18
853 866 5.895636 AACGGCAGAAATCACATATTTGA 57.104 34.783 0.00 0.00 0.00 2.69
854 867 5.516339 GGAAACGGCAGAAATCACATATTTG 59.484 40.000 0.00 0.00 0.00 2.32
855 868 5.418840 AGGAAACGGCAGAAATCACATATTT 59.581 36.000 0.00 0.00 0.00 1.40
856 869 4.949856 AGGAAACGGCAGAAATCACATATT 59.050 37.500 0.00 0.00 0.00 1.28
857 870 4.526970 AGGAAACGGCAGAAATCACATAT 58.473 39.130 0.00 0.00 0.00 1.78
858 871 3.938963 GAGGAAACGGCAGAAATCACATA 59.061 43.478 0.00 0.00 0.00 2.29
859 872 2.749621 GAGGAAACGGCAGAAATCACAT 59.250 45.455 0.00 0.00 0.00 3.21
860 873 2.151202 GAGGAAACGGCAGAAATCACA 58.849 47.619 0.00 0.00 0.00 3.58
861 874 1.128692 CGAGGAAACGGCAGAAATCAC 59.871 52.381 0.00 0.00 0.00 3.06
862 875 1.438651 CGAGGAAACGGCAGAAATCA 58.561 50.000 0.00 0.00 0.00 2.57
863 876 0.727398 CCGAGGAAACGGCAGAAATC 59.273 55.000 0.00 0.00 46.20 2.17
864 877 2.854522 CCGAGGAAACGGCAGAAAT 58.145 52.632 0.00 0.00 46.20 2.17
865 878 4.371975 CCGAGGAAACGGCAGAAA 57.628 55.556 0.00 0.00 46.20 2.52
872 885 0.458025 GTAGACTGCCCGAGGAAACG 60.458 60.000 0.00 0.00 0.00 3.60
873 886 0.896226 AGTAGACTGCCCGAGGAAAC 59.104 55.000 0.00 0.00 0.00 2.78
905 918 1.069771 CGGCTCGCGGTAAAAGAAAAA 60.070 47.619 6.13 0.00 0.00 1.94
923 939 1.934589 TTCTATGGACACGAATGCGG 58.065 50.000 0.00 0.00 43.17 5.69
924 940 3.309682 ACATTTCTATGGACACGAATGCG 59.690 43.478 0.00 0.00 38.66 4.73
925 941 4.332543 TGACATTTCTATGGACACGAATGC 59.667 41.667 0.00 0.00 36.01 3.56
926 942 6.609237 ATGACATTTCTATGGACACGAATG 57.391 37.500 0.00 1.00 36.01 2.67
927 943 8.612619 GTTTATGACATTTCTATGGACACGAAT 58.387 33.333 0.00 0.00 36.01 3.34
928 944 7.604545 TGTTTATGACATTTCTATGGACACGAA 59.395 33.333 0.00 0.00 36.01 3.85
929 945 7.100409 TGTTTATGACATTTCTATGGACACGA 58.900 34.615 0.00 0.00 36.01 4.35
930 946 7.302350 TGTTTATGACATTTCTATGGACACG 57.698 36.000 0.00 0.00 36.01 4.49
958 974 5.684550 AATTCTTCACCTTTGTCGTAACC 57.315 39.130 0.00 0.00 0.00 2.85
1031 1053 5.157067 GCCAAGTCATCTGAAAAGCTAAAC 58.843 41.667 0.00 0.00 0.00 2.01
1066 1089 4.514577 CGCACTGGCCGAGTAGGG 62.515 72.222 7.41 0.00 41.48 3.53
1102 1125 3.451793 CGTTGGATGATGAACGGGA 57.548 52.632 0.00 0.00 40.96 5.14
1173 1196 4.704103 AGAGGGGTGAGAGGCGCA 62.704 66.667 10.83 0.00 0.00 6.09
1219 1242 2.122729 CTCCCACTCCCACTCCCA 59.877 66.667 0.00 0.00 0.00 4.37
1227 1250 4.779733 TCCTCCCGCTCCCACTCC 62.780 72.222 0.00 0.00 0.00 3.85
1228 1251 3.151022 CTCCTCCCGCTCCCACTC 61.151 72.222 0.00 0.00 0.00 3.51
1229 1252 3.670629 CTCTCCTCCCGCTCCCACT 62.671 68.421 0.00 0.00 0.00 4.00
1296 1319 0.254107 AGAGAGGAGGAGGAGGAGGT 60.254 60.000 0.00 0.00 0.00 3.85
1303 1326 2.495669 GTGTCAAGAAGAGAGGAGGAGG 59.504 54.545 0.00 0.00 0.00 4.30
1934 1969 1.333881 CCTACGCTTACCTCGTGATCG 60.334 57.143 0.00 0.00 40.69 3.69
1984 2025 3.397482 CTCACCCACAACTCTTCTTCTG 58.603 50.000 0.00 0.00 0.00 3.02
2325 2378 0.963962 ACAAGGTTCGCCGTCTTCTA 59.036 50.000 0.00 0.00 43.66 2.10
2340 2393 3.989817 GGCAGTTTGCTTAATTCCACAAG 59.010 43.478 0.67 0.00 44.28 3.16
2342 2395 3.005684 CAGGCAGTTTGCTTAATTCCACA 59.994 43.478 0.67 0.00 44.28 4.17
2378 2431 5.705441 TGCTTGTAAACTTACTGATCCCTTG 59.295 40.000 1.58 0.00 34.77 3.61
2397 2454 4.104696 TCATGATCATGTTGCTTGCTTG 57.895 40.909 30.01 6.86 39.72 4.01
2398 2455 4.021807 TGTTCATGATCATGTTGCTTGCTT 60.022 37.500 30.01 0.00 39.72 3.91
2399 2456 3.508402 TGTTCATGATCATGTTGCTTGCT 59.492 39.130 30.01 0.00 39.72 3.91
2400 2457 3.840468 TGTTCATGATCATGTTGCTTGC 58.160 40.909 30.01 15.71 39.72 4.01
2460 2532 5.574188 ACTAGCAAGGGAGATGAAATTTGT 58.426 37.500 0.00 0.00 0.00 2.83
2492 2564 6.878317 TCACAAGTTATGATTCGGAGAAGAT 58.122 36.000 0.00 0.00 45.90 2.40
2662 2841 3.269592 CCCCCATATCTACACCACCTA 57.730 52.381 0.00 0.00 0.00 3.08
2679 2860 0.034089 AAGCAGACACTATTGCCCCC 60.034 55.000 0.00 0.00 41.17 5.40
2774 2955 6.243551 CCGTTGATAGATTATTTATGCTGCG 58.756 40.000 0.00 0.00 0.00 5.18
2797 2978 5.535753 AAAATTGCCATCTGCTATTACCC 57.464 39.130 0.00 0.00 43.23 3.69
2806 2987 3.181463 CCCATGGGTAAAATTGCCATCTG 60.181 47.826 23.93 0.00 34.27 2.90
2807 2988 3.040477 CCCATGGGTAAAATTGCCATCT 58.960 45.455 23.93 0.00 34.27 2.90
2919 3100 3.309121 GCTATACCCGTACCCTACCCATA 60.309 52.174 0.00 0.00 0.00 2.74
3093 3275 4.011023 TCTCAGCTCAGTAACAGGTAGAC 58.989 47.826 0.00 0.00 0.00 2.59
3275 3459 2.621998 CCCGTATAGTCAGTGGGTACAG 59.378 54.545 0.00 0.00 35.05 2.74
3367 3551 3.000925 GCTGATAATACCCGTCAACGTTG 59.999 47.826 22.35 22.35 37.74 4.10
3409 3593 5.415701 GTCACCAGGATAACATGTGAATGTT 59.584 40.000 0.00 8.92 45.64 2.71
3470 3654 3.505680 GTGAAGCACCATGTGTCCATTTA 59.494 43.478 0.00 0.00 35.75 1.40
3484 3670 3.614616 GCAGTGTATGTCTAGTGAAGCAC 59.385 47.826 0.00 0.00 34.10 4.40
3506 3692 2.196749 AGTGCTTAATCAGACATCGCG 58.803 47.619 0.00 0.00 0.00 5.87
3527 3713 1.281867 TGCATCTACTTGGAACTGGGG 59.718 52.381 0.00 0.00 0.00 4.96
3562 3748 2.416547 CAGGTATGCACAGTTTCTTCCG 59.583 50.000 0.00 0.00 0.00 4.30
3789 3975 8.821894 CATGATGTAAAGCCTAGTTAGAAGTTC 58.178 37.037 0.00 0.00 0.00 3.01
3791 3977 7.275920 CCATGATGTAAAGCCTAGTTAGAAGT 58.724 38.462 0.00 0.00 0.00 3.01
3798 3984 3.813443 CTGCCATGATGTAAAGCCTAGT 58.187 45.455 0.00 0.00 0.00 2.57
3831 4017 3.006112 TGAACATAGAGAGTCCTCGCT 57.994 47.619 5.86 5.86 44.08 4.93
3884 4070 0.773644 ACACCATCTGAGGTTGGCTT 59.226 50.000 2.81 0.00 40.77 4.35
3901 4087 2.083774 GATCAGGGAAACAATGCGACA 58.916 47.619 0.00 0.00 0.00 4.35
3926 4112 5.311649 AGATTCAGGTAGTATGCCATCCATT 59.688 40.000 0.00 0.00 46.86 3.16
4015 4201 2.964310 ATGCCGCTGCCTGTTCTCT 61.964 57.895 0.00 0.00 36.33 3.10
4057 4244 3.330701 TGATAGTAATTCCCCCATGCTCC 59.669 47.826 0.00 0.00 0.00 4.70
4180 4367 0.899717 ATTTCCACGTGGCCTGCATT 60.900 50.000 30.25 6.93 34.44 3.56
4355 4542 2.727777 CTGATGCATTCTGAATTGCCG 58.272 47.619 0.00 2.86 0.00 5.69
4375 4562 2.488952 GAAGCAGGGCTGAGTAATAGC 58.511 52.381 0.00 0.00 39.62 2.97
4404 4593 0.323302 TCAAATGCTACCCGTGCTCA 59.677 50.000 0.00 0.00 0.00 4.26
4432 4736 7.888514 ATATGAAAGATGGGGGAACTGTATA 57.111 36.000 0.00 0.00 0.00 1.47
4433 4737 6.786843 ATATGAAAGATGGGGGAACTGTAT 57.213 37.500 0.00 0.00 0.00 2.29
4434 4738 6.590656 AATATGAAAGATGGGGGAACTGTA 57.409 37.500 0.00 0.00 0.00 2.74
4473 4777 2.610727 GGGCGTGCCTCTATGTTCTATC 60.611 54.545 11.25 0.00 36.10 2.08
4495 4799 2.198827 ATGTCATTTTGGCGTCTGGA 57.801 45.000 0.00 0.00 0.00 3.86
4553 4858 7.280652 GTCTGTCACCTTAGTTCTACTACTAGG 59.719 44.444 0.00 0.00 32.54 3.02
4572 4878 4.700365 CGAGCGTGCCGTCTGTCA 62.700 66.667 0.00 0.00 0.00 3.58
4580 4886 0.666577 AACACTAGTTCGAGCGTGCC 60.667 55.000 7.10 0.00 30.46 5.01
4585 4891 2.202566 GGGCATAACACTAGTTCGAGC 58.797 52.381 0.00 0.00 39.15 5.03
4586 4892 2.167693 TGGGGCATAACACTAGTTCGAG 59.832 50.000 0.00 0.00 39.15 4.04
4630 4936 4.623886 GCTACTGAATCATGGGTGACTGAA 60.624 45.833 0.00 0.00 37.14 3.02
4708 5015 0.811281 GTGGATGTTGGTGCCTAAGC 59.189 55.000 0.00 0.00 40.48 3.09
4831 5145 1.923204 CGTGCTCTCGGAAGATTCTTG 59.077 52.381 3.03 0.00 40.84 3.02
4908 5222 0.530744 TCGCGCACTCTTTGGTAGAT 59.469 50.000 8.75 0.00 30.92 1.98
4943 5257 8.131100 ACTAATCGCATTTTGGAATTATCTGTG 58.869 33.333 0.00 0.00 0.00 3.66
5089 5403 3.712907 GTAGCCGCCTTCCCCACA 61.713 66.667 0.00 0.00 0.00 4.17
5159 5473 2.416747 CGGTCACTTCTTCAATGCTCA 58.583 47.619 0.00 0.00 0.00 4.26
5162 5476 1.523758 ACCGGTCACTTCTTCAATGC 58.476 50.000 0.00 0.00 0.00 3.56
5164 5478 3.071023 TCAGAACCGGTCACTTCTTCAAT 59.929 43.478 8.04 0.00 0.00 2.57
5166 5480 2.036387 TCAGAACCGGTCACTTCTTCA 58.964 47.619 8.04 0.00 0.00 3.02
5181 5495 2.678934 CCTCCGTCGGGGTCAGAA 60.679 66.667 10.99 0.00 37.00 3.02
5196 5510 4.806339 CTCTCCCCCGCTTCCCCT 62.806 72.222 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.