Multiple sequence alignment - TraesCS2D01G165700

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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 TraesCS2D01G165700 chr2D 100.000 2207 0 0 1 2207 109829908 109832114 0.000000e+00 4076.0
1 TraesCS2D01G165700 chr2D 92.802 653 41 2 1556 2207 109743434 109744081 0.000000e+00 941.0
2 TraesCS2D01G165700 chr2D 88.066 662 48 16 825 1475 109737494 109738135 0.000000e+00 756.0
3 TraesCS2D01G165700 chr2D 80.000 750 105 35 7 728 502112187 502112919 1.510000e-141 512.0
4 TraesCS2D01G165700 chr2D 90.881 329 30 0 1515 1843 109740868 109741196 2.010000e-120 442.0
5 TraesCS2D01G165700 chr2D 85.870 368 40 6 933 1292 109902020 109902383 4.450000e-102 381.0
6 TraesCS2D01G165700 chr2D 89.286 224 19 3 1847 2069 109782508 109782727 2.160000e-70 276.0
7 TraesCS2D01G165700 chr2D 78.571 308 47 13 1908 2207 643124533 643124829 3.740000e-43 185.0
8 TraesCS2D01G165700 chr2D 92.157 51 1 3 795 843 594656589 594656638 3.930000e-08 69.4
9 TraesCS2D01G165700 chr2D 97.436 39 0 1 795 833 545944813 545944850 5.090000e-07 65.8
10 TraesCS2D01G165700 chr2D 91.111 45 4 0 797 841 114515182 114515226 6.580000e-06 62.1
11 TraesCS2D01G165700 chr2A 91.373 1020 74 6 833 1846 105531692 105532703 0.000000e+00 1384.0
12 TraesCS2D01G165700 chr2A 85.552 616 70 15 825 1433 105522681 105523284 5.170000e-176 627.0
13 TraesCS2D01G165700 chr2A 89.583 48 4 1 795 842 695313940 695313894 2.370000e-05 60.2
14 TraesCS2D01G165700 chr2A 100.000 29 0 0 727 755 105522653 105522681 1.000000e-03 54.7
15 TraesCS2D01G165700 chr1D 92.483 745 39 6 1 728 44567914 44567170 0.000000e+00 1050.0
16 TraesCS2D01G165700 chr1D 90.464 755 37 15 1 728 315630563 315629817 0.000000e+00 963.0
17 TraesCS2D01G165700 chr1D 89.799 745 33 12 1 727 139135585 139136304 0.000000e+00 915.0
18 TraesCS2D01G165700 chr1D 86.912 787 38 13 1 728 126216999 126217779 0.000000e+00 822.0
19 TraesCS2D01G165700 chr1D 89.905 317 17 3 1 302 87829177 87829493 5.710000e-106 394.0
20 TraesCS2D01G165700 chr1D 80.068 296 41 13 1919 2206 25836559 25836274 1.030000e-48 204.0
21 TraesCS2D01G165700 chr1D 91.111 45 3 1 795 839 447530713 447530756 2.370000e-05 60.2
22 TraesCS2D01G165700 chr4D 92.049 742 43 6 1 728 22518051 22517312 0.000000e+00 1029.0
23 TraesCS2D01G165700 chr4D 93.023 43 2 1 795 837 134688637 134688596 6.580000e-06 62.1
24 TraesCS2D01G165700 chr4D 97.222 36 1 0 796 831 402528801 402528766 6.580000e-06 62.1
25 TraesCS2D01G165700 chr4D 97.297 37 0 1 795 831 445231260 445231225 6.580000e-06 62.1
26 TraesCS2D01G165700 chr4D 89.362 47 3 2 795 840 474502455 474502500 8.510000e-05 58.4
27 TraesCS2D01G165700 chrUn 90.464 755 37 15 1 728 455621836 455622582 0.000000e+00 963.0
28 TraesCS2D01G165700 chrUn 88.976 762 44 13 1 728 425480860 425481615 0.000000e+00 905.0
29 TraesCS2D01G165700 chrUn 84.848 297 36 7 4 293 304756669 304756375 7.710000e-75 291.0
30 TraesCS2D01G165700 chrUn 87.603 121 9 6 1938 2053 37392100 37391981 3.820000e-28 135.0
31 TraesCS2D01G165700 chr6D 90.331 755 43 13 1 728 152247320 152246569 0.000000e+00 963.0
32 TraesCS2D01G165700 chr6D 90.080 746 50 8 7 728 102978396 102977651 0.000000e+00 946.0
33 TraesCS2D01G165700 chr6D 88.742 755 45 19 1 728 102930982 102930241 0.000000e+00 887.0
34 TraesCS2D01G165700 chr6D 90.411 146 14 0 2062 2207 473348106 473347961 2.240000e-45 193.0
35 TraesCS2D01G165700 chr6D 97.297 37 0 1 795 831 29741031 29740996 6.580000e-06 62.1
36 TraesCS2D01G165700 chr6D 97.297 37 0 1 795 831 101445634 101445599 6.580000e-06 62.1
37 TraesCS2D01G165700 chr6D 97.297 37 0 1 795 831 142577078 142577113 6.580000e-06 62.1
38 TraesCS2D01G165700 chr6D 97.297 37 0 1 795 831 339469425 339469460 6.580000e-06 62.1
39 TraesCS2D01G165700 chr6D 97.297 37 0 1 795 831 378561687 378561722 6.580000e-06 62.1
40 TraesCS2D01G165700 chr6D 97.297 37 0 1 795 831 414526207 414526172 6.580000e-06 62.1
41 TraesCS2D01G165700 chr6D 97.222 36 0 1 795 830 462022607 462022573 2.370000e-05 60.2
42 TraesCS2D01G165700 chr6D 94.595 37 1 1 795 831 350632453 350632488 3.060000e-04 56.5
43 TraesCS2D01G165700 chr6D 97.059 34 0 1 797 830 473233585 473233617 3.060000e-04 56.5
44 TraesCS2D01G165700 chr5D 90.464 755 37 15 1 728 533649029 533649775 0.000000e+00 963.0
45 TraesCS2D01G165700 chr5D 88.381 766 41 23 1 728 80445412 80446167 0.000000e+00 878.0
46 TraesCS2D01G165700 chr5D 90.536 317 16 6 1 303 522202329 522202645 7.340000e-110 407.0
47 TraesCS2D01G165700 chr2B 93.851 618 32 4 727 1339 159299965 159300581 0.000000e+00 926.0
48 TraesCS2D01G165700 chr2B 85.714 357 39 6 942 1290 159319085 159319437 1.250000e-97 366.0
49 TraesCS2D01G165700 chr2B 92.029 138 11 0 1328 1465 159301140 159301277 6.220000e-46 195.0
50 TraesCS2D01G165700 chr6A 87.889 289 33 2 1919 2207 3484564 3484278 2.710000e-89 339.0
51 TraesCS2D01G165700 chr3B 85.811 296 35 7 4 293 449172627 449172333 7.650000e-80 307.0
52 TraesCS2D01G165700 chr3B 93.023 43 3 0 795 837 142956170 142956128 1.830000e-06 63.9
53 TraesCS2D01G165700 chr6B 87.681 276 16 8 1 270 49380257 49380520 2.750000e-79 305.0
54 TraesCS2D01G165700 chr6B 89.796 49 4 1 796 844 576199741 576199788 6.580000e-06 62.1
55 TraesCS2D01G165700 chr7D 79.448 326 44 17 1895 2206 106166223 106166539 2.220000e-50 209.0
56 TraesCS2D01G165700 chr7D 79.355 310 43 14 1908 2207 14651873 14651575 4.810000e-47 198.0
57 TraesCS2D01G165700 chr7B 79.801 302 43 14 1915 2207 652986093 652985801 1.030000e-48 204.0
58 TraesCS2D01G165700 chr7B 84.615 78 6 2 756 830 677422931 677422857 3.040000e-09 73.1
59 TraesCS2D01G165700 chr5B 80.669 269 40 11 1943 2207 74135519 74135259 4.810000e-47 198.0
60 TraesCS2D01G165700 chr5A 85.526 76 5 2 756 831 406535064 406534995 8.450000e-10 75.0
61 TraesCS2D01G165700 chr4B 93.478 46 2 1 795 840 660583491 660583447 1.410000e-07 67.6
62 TraesCS2D01G165700 chr3D 97.436 39 0 1 795 833 438805124 438805087 5.090000e-07 65.8
63 TraesCS2D01G165700 chr3D 97.368 38 0 1 795 832 517884784 517884820 1.830000e-06 63.9
64 TraesCS2D01G165700 chr4A 95.000 40 2 0 798 837 396758890 396758851 1.830000e-06 63.9


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 TraesCS2D01G165700 chr2D 109829908 109832114 2206 False 4076.00 4076 100.000 1 2207 1 chr2D.!!$F2 2206
1 TraesCS2D01G165700 chr2D 109737494 109744081 6587 False 713.00 941 90.583 825 2207 3 chr2D.!!$F9 1382
2 TraesCS2D01G165700 chr2D 502112187 502112919 732 False 512.00 512 80.000 7 728 1 chr2D.!!$F5 721
3 TraesCS2D01G165700 chr2A 105531692 105532703 1011 False 1384.00 1384 91.373 833 1846 1 chr2A.!!$F1 1013
4 TraesCS2D01G165700 chr2A 105522653 105523284 631 False 340.85 627 92.776 727 1433 2 chr2A.!!$F2 706
5 TraesCS2D01G165700 chr1D 44567170 44567914 744 True 1050.00 1050 92.483 1 728 1 chr1D.!!$R2 727
6 TraesCS2D01G165700 chr1D 315629817 315630563 746 True 963.00 963 90.464 1 728 1 chr1D.!!$R3 727
7 TraesCS2D01G165700 chr1D 139135585 139136304 719 False 915.00 915 89.799 1 727 1 chr1D.!!$F3 726
8 TraesCS2D01G165700 chr1D 126216999 126217779 780 False 822.00 822 86.912 1 728 1 chr1D.!!$F2 727
9 TraesCS2D01G165700 chr4D 22517312 22518051 739 True 1029.00 1029 92.049 1 728 1 chr4D.!!$R1 727
10 TraesCS2D01G165700 chrUn 455621836 455622582 746 False 963.00 963 90.464 1 728 1 chrUn.!!$F2 727
11 TraesCS2D01G165700 chrUn 425480860 425481615 755 False 905.00 905 88.976 1 728 1 chrUn.!!$F1 727
12 TraesCS2D01G165700 chr6D 152246569 152247320 751 True 963.00 963 90.331 1 728 1 chr6D.!!$R5 727
13 TraesCS2D01G165700 chr6D 102977651 102978396 745 True 946.00 946 90.080 7 728 1 chr6D.!!$R4 721
14 TraesCS2D01G165700 chr6D 102930241 102930982 741 True 887.00 887 88.742 1 728 1 chr6D.!!$R3 727
15 TraesCS2D01G165700 chr5D 533649029 533649775 746 False 963.00 963 90.464 1 728 1 chr5D.!!$F3 727
16 TraesCS2D01G165700 chr5D 80445412 80446167 755 False 878.00 878 88.381 1 728 1 chr5D.!!$F1 727
17 TraesCS2D01G165700 chr2B 159299965 159301277 1312 False 560.50 926 92.940 727 1465 2 chr2B.!!$F2 738

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
325 365 0.101759 TACGAGAGGCGGTATTGTGC 59.898 55.0 0.0 0.0 46.49 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 7904 1.073284 ACAACCTTGCCCGATACAACT 59.927 47.619 0.0 0.0 0.0 3.16 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
51 52 1.134401 ACGGTGATGAAGGCGATGATT 60.134 47.619 0.00 0.00 0.00 2.57
169 173 0.389817 CAGGATCGCAAGGACGAACA 60.390 55.000 0.00 0.00 46.59 3.18
175 179 1.566018 CGCAAGGACGAACAGTTCCC 61.566 60.000 7.76 4.22 34.06 3.97
309 349 8.226448 GCCGGTAGCTGTATATATATTAGTACG 58.774 40.741 1.90 4.76 38.99 3.67
325 365 0.101759 TACGAGAGGCGGTATTGTGC 59.898 55.000 0.00 0.00 46.49 4.57
368 409 7.941795 CCGACTTGGTTTCTAATTCGTATAT 57.058 36.000 0.00 0.00 31.04 0.86
448 513 2.357034 TGCAAGGAGACGAACCGC 60.357 61.111 0.00 0.00 0.00 5.68
563 690 3.580731 GTCTTCCCTTTCTCTTCTCACG 58.419 50.000 0.00 0.00 0.00 4.35
568 695 1.433534 CTTTCTCTTCTCACGCACCC 58.566 55.000 0.00 0.00 0.00 4.61
754 882 7.591426 GTGTTTCTTTTACATGCTCCAAACTAG 59.409 37.037 0.00 0.00 0.00 2.57
755 883 7.284489 TGTTTCTTTTACATGCTCCAAACTAGT 59.716 33.333 0.00 0.00 0.00 2.57
756 884 8.780249 GTTTCTTTTACATGCTCCAAACTAGTA 58.220 33.333 0.00 0.00 0.00 1.82
757 885 7.900782 TCTTTTACATGCTCCAAACTAGTAC 57.099 36.000 0.00 0.00 0.00 2.73
758 886 7.676947 TCTTTTACATGCTCCAAACTAGTACT 58.323 34.615 0.00 0.00 0.00 2.73
759 887 7.817962 TCTTTTACATGCTCCAAACTAGTACTC 59.182 37.037 0.00 0.00 0.00 2.59
760 888 4.473477 ACATGCTCCAAACTAGTACTCC 57.527 45.455 0.00 0.00 0.00 3.85
761 889 3.197983 ACATGCTCCAAACTAGTACTCCC 59.802 47.826 0.00 0.00 0.00 4.30
762 890 3.185880 TGCTCCAAACTAGTACTCCCT 57.814 47.619 0.00 0.00 0.00 4.20
763 891 3.097614 TGCTCCAAACTAGTACTCCCTC 58.902 50.000 0.00 0.00 0.00 4.30
764 892 3.245658 TGCTCCAAACTAGTACTCCCTCT 60.246 47.826 0.00 0.00 0.00 3.69
765 893 3.131400 GCTCCAAACTAGTACTCCCTCTG 59.869 52.174 0.00 0.00 0.00 3.35
766 894 4.345854 CTCCAAACTAGTACTCCCTCTGT 58.654 47.826 0.00 0.00 0.00 3.41
767 895 4.342359 TCCAAACTAGTACTCCCTCTGTC 58.658 47.826 0.00 0.00 0.00 3.51
768 896 4.044317 TCCAAACTAGTACTCCCTCTGTCT 59.956 45.833 0.00 0.00 0.00 3.41
769 897 4.399934 CCAAACTAGTACTCCCTCTGTCTC 59.600 50.000 0.00 0.00 0.00 3.36
770 898 4.931027 AACTAGTACTCCCTCTGTCTCA 57.069 45.455 0.00 0.00 0.00 3.27
771 899 4.224991 ACTAGTACTCCCTCTGTCTCAC 57.775 50.000 0.00 0.00 0.00 3.51
772 900 2.116827 AGTACTCCCTCTGTCTCACG 57.883 55.000 0.00 0.00 0.00 4.35
773 901 1.629353 AGTACTCCCTCTGTCTCACGA 59.371 52.381 0.00 0.00 0.00 4.35
774 902 2.240160 AGTACTCCCTCTGTCTCACGAT 59.760 50.000 0.00 0.00 0.00 3.73
775 903 1.468985 ACTCCCTCTGTCTCACGATG 58.531 55.000 0.00 0.00 0.00 3.84
776 904 1.272203 ACTCCCTCTGTCTCACGATGT 60.272 52.381 0.00 0.00 0.00 3.06
777 905 2.026169 ACTCCCTCTGTCTCACGATGTA 60.026 50.000 0.00 0.00 0.00 2.29
778 906 2.356382 CTCCCTCTGTCTCACGATGTAC 59.644 54.545 0.00 0.00 0.00 2.90
779 907 2.026169 TCCCTCTGTCTCACGATGTACT 60.026 50.000 0.00 0.00 0.00 2.73
780 908 3.199289 TCCCTCTGTCTCACGATGTACTA 59.801 47.826 0.00 0.00 0.00 1.82
781 909 3.945921 CCCTCTGTCTCACGATGTACTAA 59.054 47.826 0.00 0.00 0.00 2.24
782 910 4.035792 CCCTCTGTCTCACGATGTACTAAG 59.964 50.000 0.00 0.00 0.00 2.18
783 911 4.876679 CCTCTGTCTCACGATGTACTAAGA 59.123 45.833 0.00 0.00 0.00 2.10
784 912 5.220700 CCTCTGTCTCACGATGTACTAAGAC 60.221 48.000 0.00 0.00 34.98 3.01
785 913 4.329256 TCTGTCTCACGATGTACTAAGACG 59.671 45.833 0.00 0.00 36.73 4.18
786 914 3.999001 TGTCTCACGATGTACTAAGACGT 59.001 43.478 0.00 0.00 36.73 4.34
787 915 4.453478 TGTCTCACGATGTACTAAGACGTT 59.547 41.667 0.00 0.00 36.73 3.99
788 916 5.049198 TGTCTCACGATGTACTAAGACGTTT 60.049 40.000 0.00 0.00 36.73 3.60
789 917 5.855395 GTCTCACGATGTACTAAGACGTTTT 59.145 40.000 0.00 0.00 35.05 2.43
790 918 6.361748 GTCTCACGATGTACTAAGACGTTTTT 59.638 38.462 0.00 0.00 35.05 1.94
791 919 6.361481 TCTCACGATGTACTAAGACGTTTTTG 59.639 38.462 0.00 0.00 35.05 2.44
792 920 5.070862 CACGATGTACTAAGACGTTTTTGC 58.929 41.667 0.00 0.00 35.05 3.68
793 921 4.746115 ACGATGTACTAAGACGTTTTTGCA 59.254 37.500 0.00 0.00 33.48 4.08
794 922 5.107607 ACGATGTACTAAGACGTTTTTGCAG 60.108 40.000 0.00 0.00 33.48 4.41
795 923 4.461992 TGTACTAAGACGTTTTTGCAGC 57.538 40.909 0.00 0.00 0.00 5.25
796 924 3.872182 TGTACTAAGACGTTTTTGCAGCA 59.128 39.130 0.00 0.00 0.00 4.41
797 925 4.333095 TGTACTAAGACGTTTTTGCAGCAA 59.667 37.500 2.83 2.83 0.00 3.91
798 926 4.364415 ACTAAGACGTTTTTGCAGCAAA 57.636 36.364 16.93 16.93 0.00 3.68
799 927 4.102649 ACTAAGACGTTTTTGCAGCAAAC 58.897 39.130 20.49 9.89 32.79 2.93
800 928 2.645730 AGACGTTTTTGCAGCAAACA 57.354 40.000 20.49 11.53 34.33 2.83
801 929 2.953020 AGACGTTTTTGCAGCAAACAA 58.047 38.095 20.49 14.14 34.33 2.83
802 930 2.666022 AGACGTTTTTGCAGCAAACAAC 59.334 40.909 20.49 21.99 34.33 3.32
803 931 1.388431 ACGTTTTTGCAGCAAACAACG 59.612 42.857 35.44 35.44 43.77 4.10
804 932 1.388431 CGTTTTTGCAGCAAACAACGT 59.612 42.857 32.70 0.00 39.61 3.99
805 933 2.531998 CGTTTTTGCAGCAAACAACGTC 60.532 45.455 32.70 15.74 39.61 4.34
806 934 2.645730 TTTTGCAGCAAACAACGTCT 57.354 40.000 20.49 0.00 32.79 4.18
807 935 2.645730 TTTGCAGCAAACAACGTCTT 57.354 40.000 16.93 0.00 0.00 3.01
808 936 3.766676 TTTGCAGCAAACAACGTCTTA 57.233 38.095 16.93 0.00 0.00 2.10
809 937 2.748461 TGCAGCAAACAACGTCTTAC 57.252 45.000 0.00 0.00 0.00 2.34
810 938 2.010497 TGCAGCAAACAACGTCTTACA 58.990 42.857 0.00 0.00 0.00 2.41
811 939 2.616376 TGCAGCAAACAACGTCTTACAT 59.384 40.909 0.00 0.00 0.00 2.29
812 940 3.066064 TGCAGCAAACAACGTCTTACATT 59.934 39.130 0.00 0.00 0.00 2.71
813 941 3.421888 GCAGCAAACAACGTCTTACATTG 59.578 43.478 0.00 0.00 0.00 2.82
814 942 4.597079 CAGCAAACAACGTCTTACATTGT 58.403 39.130 0.00 0.00 38.18 2.71
815 943 4.437495 CAGCAAACAACGTCTTACATTGTG 59.563 41.667 0.00 0.00 36.69 3.33
816 944 3.728718 GCAAACAACGTCTTACATTGTGG 59.271 43.478 0.00 0.00 36.69 4.17
817 945 4.286910 CAAACAACGTCTTACATTGTGGG 58.713 43.478 0.00 0.00 36.69 4.61
818 946 3.478857 ACAACGTCTTACATTGTGGGA 57.521 42.857 0.00 0.00 35.28 4.37
819 947 3.135994 ACAACGTCTTACATTGTGGGAC 58.864 45.455 0.00 6.72 35.28 4.46
821 949 1.355971 CGTCTTACATTGTGGGACGG 58.644 55.000 24.96 14.26 43.69 4.79
822 950 1.067425 CGTCTTACATTGTGGGACGGA 60.067 52.381 24.96 5.37 43.69 4.69
823 951 2.618053 GTCTTACATTGTGGGACGGAG 58.382 52.381 0.00 0.00 0.00 4.63
839 1036 3.819902 GACGGAGGGAGTACCACTTATAG 59.180 52.174 0.00 0.00 43.89 1.31
973 1173 3.646637 ACCAGGAAGCACTACTACTTGTT 59.353 43.478 0.00 0.00 0.00 2.83
1015 1215 1.228644 AACATGAGCAAGCCAGGCA 60.229 52.632 15.80 0.00 0.00 4.75
1077 1277 3.267812 TGATCAAGGAGGCAAAGGAGAAT 59.732 43.478 0.00 0.00 0.00 2.40
1083 1283 5.456921 AGGAGGCAAAGGAGAATATCAAA 57.543 39.130 0.00 0.00 0.00 2.69
1113 1313 2.416893 GCCGAACCTCAAAGTCAGAATC 59.583 50.000 0.00 0.00 0.00 2.52
1179 1382 4.039357 CGCGTCTGGGTCGACACT 62.039 66.667 20.37 0.00 33.54 3.55
1258 1462 1.076485 GGCCCATGCAAGTCTCCAT 60.076 57.895 0.00 0.00 40.13 3.41
1259 1463 1.105759 GGCCCATGCAAGTCTCCATC 61.106 60.000 0.00 0.00 40.13 3.51
1357 2138 4.222114 GTTTGTGAGTTGTAAGCATCAGC 58.778 43.478 0.00 0.00 42.56 4.26
1364 2145 7.094248 TGTGAGTTGTAAGCATCAGCAATATTT 60.094 33.333 0.00 0.00 45.49 1.40
1366 2147 8.306038 TGAGTTGTAAGCATCAGCAATATTTTT 58.694 29.630 0.00 0.00 45.49 1.94
1391 2172 8.177119 TGAGCCACTGTTTATTGTTTAAGAAT 57.823 30.769 0.00 0.00 0.00 2.40
1393 2174 8.816640 AGCCACTGTTTATTGTTTAAGAATTG 57.183 30.769 0.00 0.00 0.00 2.32
1445 2226 4.037923 TGTGAATTCTTCTTGAAGGCCAAC 59.962 41.667 5.01 0.00 38.18 3.77
1453 2234 2.092968 TCTTGAAGGCCAACGATATGCT 60.093 45.455 5.01 0.00 0.00 3.79
1613 5087 5.010213 GCCTCCAGATTAGAAGTCGAGTAAT 59.990 44.000 0.00 0.00 0.00 1.89
1629 7628 6.144402 GTCGAGTAATCACAACGGTTCTTTTA 59.856 38.462 0.00 0.00 0.00 1.52
1638 7637 9.886132 ATCACAACGGTTCTTTTAGTATAAGAT 57.114 29.630 4.18 0.00 32.09 2.40
1641 7640 8.932791 ACAACGGTTCTTTTAGTATAAGATGTG 58.067 33.333 4.18 1.09 32.09 3.21
1685 7684 8.190784 ACAAGAGTAAAAGGTTGTTCATTCTTG 58.809 33.333 0.00 0.00 41.94 3.02
1718 7718 5.567037 TTTCTTCAGAAGAGACCCAATGA 57.433 39.130 12.74 0.00 39.03 2.57
1725 7725 7.601705 TCAGAAGAGACCCAATGAAAATTTT 57.398 32.000 2.28 2.28 0.00 1.82
1891 7891 6.790350 GTGTGTCGACTTGTATGTACAAAATG 59.210 38.462 17.92 0.00 44.67 2.32
1904 7904 6.927294 TGTACAAAATGTGTGTATGTGTGA 57.073 33.333 0.00 0.00 41.89 3.58
1905 7905 6.953843 TGTACAAAATGTGTGTATGTGTGAG 58.046 36.000 0.00 0.00 41.89 3.51
1906 7906 6.540551 TGTACAAAATGTGTGTATGTGTGAGT 59.459 34.615 0.00 0.00 41.89 3.41
1907 7907 6.449635 ACAAAATGTGTGTATGTGTGAGTT 57.550 33.333 0.00 0.00 39.72 3.01
1908 7908 6.264832 ACAAAATGTGTGTATGTGTGAGTTG 58.735 36.000 0.00 0.00 39.72 3.16
1913 7913 4.920927 TGTGTGTATGTGTGAGTTGTATCG 59.079 41.667 0.00 0.00 0.00 2.92
1928 7928 2.568062 TGTATCGGGCAAGGTTGTTAGA 59.432 45.455 0.00 0.00 0.00 2.10
1936 7936 5.254115 GGGCAAGGTTGTTAGAAAGTCTAT 58.746 41.667 0.00 0.00 0.00 1.98
1983 7983 3.288092 GGGTCAAGACTTCAACAACCTT 58.712 45.455 0.00 0.00 0.00 3.50
2057 8057 4.064388 TGAGATCATCAAACGCTTCACAA 58.936 39.130 0.00 0.00 34.02 3.33
2104 8104 0.109153 CCTCCGATTCATCCATGGCA 59.891 55.000 6.96 0.00 0.00 4.92
2121 8121 2.297033 TGGCAAGTTCCTCTGCAAATTC 59.703 45.455 0.00 0.00 0.00 2.17
2137 8137 4.603131 CAAATTCTTTCCCCTCATCTCCA 58.397 43.478 0.00 0.00 0.00 3.86
2145 8145 1.341285 CCCCTCATCTCCATTTGCACA 60.341 52.381 0.00 0.00 0.00 4.57
2146 8146 2.449464 CCCTCATCTCCATTTGCACAA 58.551 47.619 0.00 0.00 0.00 3.33
2149 8149 4.441079 CCCTCATCTCCATTTGCACAAATC 60.441 45.833 5.64 0.00 38.84 2.17
2176 8176 3.500014 CGAGAAACTTACGAGAGGGAAC 58.500 50.000 0.00 0.00 0.00 3.62
2182 8182 0.169672 TTACGAGAGGGAACGAAGCG 59.830 55.000 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.509463 CAAGTCGGCGGTGCTACTA 59.491 57.895 7.21 0.00 0.00 1.82
169 173 0.968393 GAGAGCAGGTCTCGGGAACT 60.968 60.000 13.82 0.00 46.44 3.01
198 234 5.983720 CGTCGTAATCTACTTCATCCCAAAT 59.016 40.000 0.00 0.00 0.00 2.32
306 346 0.101759 GCACAATACCGCCTCTCGTA 59.898 55.000 0.00 0.00 36.19 3.43
309 349 1.883084 CGGCACAATACCGCCTCTC 60.883 63.158 0.00 0.00 46.62 3.20
325 365 0.098728 GTTTGGGATTGTGATCGCGG 59.901 55.000 6.13 0.00 45.44 6.46
448 513 2.073056 TGTGAATGGTCCGTCGAAATG 58.927 47.619 0.00 0.00 0.00 2.32
455 520 1.003839 ATGCGTGTGAATGGTCCGT 60.004 52.632 0.00 0.00 0.00 4.69
568 695 2.498078 GGTTCTCTCCACCACTCTAAGG 59.502 54.545 0.00 0.00 34.04 2.69
754 882 2.110901 TCGTGAGACAGAGGGAGTAC 57.889 55.000 0.00 0.00 33.31 2.73
755 883 2.026169 ACATCGTGAGACAGAGGGAGTA 60.026 50.000 0.00 0.00 46.97 2.59
756 884 1.272203 ACATCGTGAGACAGAGGGAGT 60.272 52.381 0.00 0.00 46.97 3.85
757 885 1.468985 ACATCGTGAGACAGAGGGAG 58.531 55.000 0.00 0.00 46.97 4.30
758 886 2.026169 AGTACATCGTGAGACAGAGGGA 60.026 50.000 0.00 0.00 46.97 4.20
759 887 2.370349 AGTACATCGTGAGACAGAGGG 58.630 52.381 0.00 0.00 46.97 4.30
760 888 4.876679 TCTTAGTACATCGTGAGACAGAGG 59.123 45.833 0.00 0.00 46.97 3.69
761 889 5.501092 CGTCTTAGTACATCGTGAGACAGAG 60.501 48.000 0.00 0.00 46.97 3.35
762 890 4.329256 CGTCTTAGTACATCGTGAGACAGA 59.671 45.833 0.00 0.00 46.97 3.41
763 891 4.093115 ACGTCTTAGTACATCGTGAGACAG 59.907 45.833 0.00 0.00 46.97 3.51
764 892 3.999001 ACGTCTTAGTACATCGTGAGACA 59.001 43.478 0.00 0.00 46.97 3.41
765 893 4.596801 ACGTCTTAGTACATCGTGAGAC 57.403 45.455 0.00 0.00 46.97 3.36
767 895 6.514171 CAAAAACGTCTTAGTACATCGTGAG 58.486 40.000 0.00 0.00 35.00 3.51
768 896 5.107760 GCAAAAACGTCTTAGTACATCGTGA 60.108 40.000 0.00 0.00 35.00 4.35
769 897 5.070862 GCAAAAACGTCTTAGTACATCGTG 58.929 41.667 0.00 0.00 35.00 4.35
770 898 4.746115 TGCAAAAACGTCTTAGTACATCGT 59.254 37.500 0.00 0.00 36.31 3.73
771 899 5.258685 TGCAAAAACGTCTTAGTACATCG 57.741 39.130 0.00 0.00 0.00 3.84
772 900 5.080068 GCTGCAAAAACGTCTTAGTACATC 58.920 41.667 0.00 0.00 0.00 3.06
773 901 4.513692 TGCTGCAAAAACGTCTTAGTACAT 59.486 37.500 0.00 0.00 0.00 2.29
774 902 3.872182 TGCTGCAAAAACGTCTTAGTACA 59.128 39.130 0.00 0.00 0.00 2.90
775 903 4.461992 TGCTGCAAAAACGTCTTAGTAC 57.538 40.909 0.00 0.00 0.00 2.73
776 904 5.163744 TGTTTGCTGCAAAAACGTCTTAGTA 60.164 36.000 27.49 0.00 39.81 1.82
777 905 4.102649 GTTTGCTGCAAAAACGTCTTAGT 58.897 39.130 27.49 0.00 35.03 2.24
778 906 4.101942 TGTTTGCTGCAAAAACGTCTTAG 58.898 39.130 27.49 0.00 39.81 2.18
779 907 4.098055 TGTTTGCTGCAAAAACGTCTTA 57.902 36.364 27.49 1.32 39.81 2.10
780 908 2.953020 TGTTTGCTGCAAAAACGTCTT 58.047 38.095 27.49 0.00 39.81 3.01
781 909 2.645730 TGTTTGCTGCAAAAACGTCT 57.354 40.000 27.49 0.00 39.81 4.18
782 910 2.531998 CGTTGTTTGCTGCAAAAACGTC 60.532 45.455 34.87 24.14 39.61 4.34
783 911 1.388431 CGTTGTTTGCTGCAAAAACGT 59.612 42.857 34.87 0.00 39.61 3.99
784 912 1.388431 ACGTTGTTTGCTGCAAAAACG 59.612 42.857 37.46 37.46 43.77 3.60
785 913 2.666022 AGACGTTGTTTGCTGCAAAAAC 59.334 40.909 27.49 26.39 35.03 2.43
786 914 2.953020 AGACGTTGTTTGCTGCAAAAA 58.047 38.095 27.49 20.87 35.03 1.94
787 915 2.645730 AGACGTTGTTTGCTGCAAAA 57.354 40.000 27.49 15.62 35.03 2.44
788 916 2.645730 AAGACGTTGTTTGCTGCAAA 57.354 40.000 22.84 22.84 0.00 3.68
789 917 2.420372 TGTAAGACGTTGTTTGCTGCAA 59.580 40.909 11.69 11.69 0.00 4.08
790 918 2.010497 TGTAAGACGTTGTTTGCTGCA 58.990 42.857 0.00 0.00 0.00 4.41
791 919 2.748461 TGTAAGACGTTGTTTGCTGC 57.252 45.000 0.00 0.00 0.00 5.25
800 928 2.409975 CGTCCCACAATGTAAGACGTT 58.590 47.619 21.67 0.00 43.89 3.99
801 929 1.337447 CCGTCCCACAATGTAAGACGT 60.337 52.381 25.28 0.00 46.62 4.34
803 931 2.618053 CTCCGTCCCACAATGTAAGAC 58.382 52.381 5.24 5.24 0.00 3.01
804 932 1.553248 CCTCCGTCCCACAATGTAAGA 59.447 52.381 0.00 0.00 0.00 2.10
805 933 1.406887 CCCTCCGTCCCACAATGTAAG 60.407 57.143 0.00 0.00 0.00 2.34
806 934 0.616371 CCCTCCGTCCCACAATGTAA 59.384 55.000 0.00 0.00 0.00 2.41
807 935 0.252330 TCCCTCCGTCCCACAATGTA 60.252 55.000 0.00 0.00 0.00 2.29
808 936 1.537889 TCCCTCCGTCCCACAATGT 60.538 57.895 0.00 0.00 0.00 2.71
809 937 1.221840 CTCCCTCCGTCCCACAATG 59.778 63.158 0.00 0.00 0.00 2.82
810 938 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
811 939 0.901580 GTACTCCCTCCGTCCCACAA 60.902 60.000 0.00 0.00 0.00 3.33
812 940 1.304713 GTACTCCCTCCGTCCCACA 60.305 63.158 0.00 0.00 0.00 4.17
813 941 2.056815 GGTACTCCCTCCGTCCCAC 61.057 68.421 0.00 0.00 0.00 4.61
814 942 2.361771 GGTACTCCCTCCGTCCCA 59.638 66.667 0.00 0.00 0.00 4.37
815 943 2.056815 GTGGTACTCCCTCCGTCCC 61.057 68.421 0.00 0.00 0.00 4.46
816 944 0.614134 AAGTGGTACTCCCTCCGTCC 60.614 60.000 0.00 0.00 0.00 4.79
817 945 2.134789 TAAGTGGTACTCCCTCCGTC 57.865 55.000 0.00 0.00 0.00 4.79
818 946 2.842645 ATAAGTGGTACTCCCTCCGT 57.157 50.000 0.00 0.00 0.00 4.69
819 947 4.096190 TCTATAAGTGGTACTCCCTCCG 57.904 50.000 0.00 0.00 0.00 4.63
820 948 5.898397 AGTTTCTATAAGTGGTACTCCCTCC 59.102 44.000 0.00 0.00 0.00 4.30
821 949 7.421087 AAGTTTCTATAAGTGGTACTCCCTC 57.579 40.000 0.00 0.00 0.00 4.30
839 1036 9.967346 AGCTGAACTTTTTCCTTTATAAGTTTC 57.033 29.630 0.00 0.00 40.00 2.78
878 1076 1.619654 CCAGCCACAACTCAATCCAA 58.380 50.000 0.00 0.00 0.00 3.53
973 1173 3.742433 AACGAAATTGGACAAATGCCA 57.258 38.095 0.00 0.00 0.00 4.92
1015 1215 1.835712 ACTCCGTCTTGGGACCGTT 60.836 57.895 0.00 0.00 39.15 4.44
1055 1255 2.269023 TCTCCTTTGCCTCCTTGATCA 58.731 47.619 0.00 0.00 0.00 2.92
1077 1277 2.188469 GGCCGGTCCGCTTTGATA 59.812 61.111 5.50 0.00 0.00 2.15
1096 1296 3.557264 GGGACGATTCTGACTTTGAGGTT 60.557 47.826 0.00 0.00 0.00 3.50
1258 1462 3.823281 TTATTCGGCCGATTAACTGGA 57.177 42.857 31.56 12.14 0.00 3.86
1259 1463 6.548441 TTATTTATTCGGCCGATTAACTGG 57.452 37.500 31.67 2.25 0.00 4.00
1317 1528 7.766283 TCACAAACAAAACAACATCACATAGA 58.234 30.769 0.00 0.00 0.00 1.98
1324 1535 6.704512 ACAACTCACAAACAAAACAACATC 57.295 33.333 0.00 0.00 0.00 3.06
1357 2138 9.206870 ACAATAAACAGTGGCTCAAAAATATTG 57.793 29.630 0.00 0.00 34.71 1.90
1364 2145 8.001881 TCTTAAACAATAAACAGTGGCTCAAA 57.998 30.769 0.00 0.00 0.00 2.69
1366 2147 7.575414 TTCTTAAACAATAAACAGTGGCTCA 57.425 32.000 0.00 0.00 0.00 4.26
1391 2172 7.847096 TGTCCTAATGCTGAAGTAGATTACAA 58.153 34.615 0.00 0.00 0.00 2.41
1393 2174 8.304202 CATGTCCTAATGCTGAAGTAGATTAC 57.696 38.462 0.00 0.00 0.00 1.89
1445 2226 9.599866 TTATTAGAAATCATACCCAGCATATCG 57.400 33.333 0.00 0.00 0.00 2.92
1453 2234 7.441157 CGCTGAACTTATTAGAAATCATACCCA 59.559 37.037 0.00 0.00 0.00 4.51
1590 5064 6.263392 TGATTACTCGACTTCTAATCTGGAGG 59.737 42.308 0.00 0.00 31.00 4.30
1595 5069 6.967767 CGTTGTGATTACTCGACTTCTAATCT 59.032 38.462 0.00 0.00 31.00 2.40
1597 5071 6.034591 CCGTTGTGATTACTCGACTTCTAAT 58.965 40.000 7.18 0.00 0.00 1.73
1613 5087 9.146984 CATCTTATACTAAAAGAACCGTTGTGA 57.853 33.333 0.00 0.00 36.60 3.58
1638 7637 5.620206 TGTTGATCTAGGAAAAAGAGCACA 58.380 37.500 0.00 0.00 38.98 4.57
1641 7640 6.652900 ACTCTTGTTGATCTAGGAAAAAGAGC 59.347 38.462 17.40 0.00 41.88 4.09
1685 7684 6.652481 TCTCTTCTGAAGAAAATGATGACACC 59.348 38.462 19.73 0.00 37.02 4.16
1790 7790 5.016173 TGGGATGTGCTAGCTGTTAAAATT 58.984 37.500 17.23 0.00 0.00 1.82
1797 7797 1.279496 TCTTGGGATGTGCTAGCTGT 58.721 50.000 17.23 1.20 0.00 4.40
1835 7835 6.015180 ACCTATCGTTTAACACTGTGGAGTAA 60.015 38.462 13.09 4.94 0.00 2.24
1867 7867 6.480651 ACATTTTGTACATACAAGTCGACACA 59.519 34.615 19.50 7.67 45.77 3.72
1891 7891 4.326278 CCGATACAACTCACACATACACAC 59.674 45.833 0.00 0.00 0.00 3.82
1904 7904 1.073284 ACAACCTTGCCCGATACAACT 59.927 47.619 0.00 0.00 0.00 3.16
1905 7905 1.530323 ACAACCTTGCCCGATACAAC 58.470 50.000 0.00 0.00 0.00 3.32
1906 7906 2.279935 AACAACCTTGCCCGATACAA 57.720 45.000 0.00 0.00 0.00 2.41
1907 7907 2.568062 TCTAACAACCTTGCCCGATACA 59.432 45.455 0.00 0.00 0.00 2.29
1908 7908 3.255969 TCTAACAACCTTGCCCGATAC 57.744 47.619 0.00 0.00 0.00 2.24
1913 7913 3.487372 AGACTTTCTAACAACCTTGCCC 58.513 45.455 0.00 0.00 0.00 5.36
1946 7946 7.288158 AGTCTTGACCCCTAGTTCAAGATATAC 59.712 40.741 22.08 14.36 46.51 1.47
1951 7951 3.858135 AGTCTTGACCCCTAGTTCAAGA 58.142 45.455 18.14 18.14 44.04 3.02
1983 7983 2.082140 AGGTACATGCGGTGATAGGA 57.918 50.000 0.00 0.00 0.00 2.94
2049 8049 5.351458 ACCATGAAAGAAAAGTTGTGAAGC 58.649 37.500 0.00 0.00 0.00 3.86
2057 8057 6.151817 GGCTCTCATTACCATGAAAGAAAAGT 59.848 38.462 0.00 0.00 39.04 2.66
2104 8104 5.459536 GGAAAGAATTTGCAGAGGAACTT 57.540 39.130 0.00 0.00 46.44 2.66
2121 8121 2.692041 GCAAATGGAGATGAGGGGAAAG 59.308 50.000 0.00 0.00 0.00 2.62
2145 8145 3.120786 CGTAAGTTTCTCGGTTGCGATTT 60.121 43.478 0.00 0.00 31.87 2.17
2146 8146 2.410730 CGTAAGTTTCTCGGTTGCGATT 59.589 45.455 0.00 0.00 31.87 3.34
2149 8149 1.385743 CTCGTAAGTTTCTCGGTTGCG 59.614 52.381 0.00 0.00 39.48 4.85


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

AutoCloner maintained by Alex Coulton.