Multiple sequence alignment - TraesCS2D01G504800

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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 TraesCS2D01G504800 chr2D 100.000 3609 0 0 1 3609 598939254 598935646 0.000000e+00 6665.0
1 TraesCS2D01G504800 chr2D 94.975 199 10 0 1 199 598945273 598945075 2.710000e-81 313.0
2 TraesCS2D01G504800 chr2D 97.727 44 1 0 681 724 598938319 598938362 3.860000e-10 76.8
3 TraesCS2D01G504800 chr2D 97.727 44 1 0 893 936 598938531 598938574 3.860000e-10 76.8
4 TraesCS2D01G504800 chr2B 94.703 2454 92 19 992 3425 728312777 728310342 0.000000e+00 3777.0
5 TraesCS2D01G504800 chr2B 90.023 1303 76 17 2325 3609 725161970 725160704 0.000000e+00 1637.0
6 TraesCS2D01G504800 chr2B 87.613 775 63 19 1032 1799 725194500 725193752 0.000000e+00 869.0
7 TraesCS2D01G504800 chr2B 89.174 702 46 10 3 678 725212826 725212129 0.000000e+00 848.0
8 TraesCS2D01G504800 chr2B 91.388 627 39 11 1 619 728323201 728322582 0.000000e+00 845.0
9 TraesCS2D01G504800 chr2B 87.126 334 25 3 1876 2209 725162287 725161972 2.650000e-96 363.0
10 TraesCS2D01G504800 chr2B 94.975 199 10 0 1 199 728326288 728326090 2.710000e-81 313.0
11 TraesCS2D01G504800 chr2B 96.403 139 4 1 3472 3609 728310339 728310201 1.010000e-55 228.0
12 TraesCS2D01G504800 chr2B 83.500 200 11 3 681 880 728313817 728313640 2.230000e-37 167.0
13 TraesCS2D01G504800 chr2A 94.775 2335 92 15 992 3310 733178348 733176028 0.000000e+00 3609.0
14 TraesCS2D01G504800 chr2A 93.235 680 40 6 1 678 733180226 733179551 0.000000e+00 996.0
15 TraesCS2D01G504800 chr2A 94.203 138 6 1 3472 3609 733175946 733175811 3.650000e-50 209.0
16 TraesCS2D01G504800 chr2A 85.000 200 11 1 681 880 733179493 733179313 6.150000e-43 185.0
17 TraesCS2D01G504800 chr2A 93.069 101 7 0 893 993 733179450 733179550 8.070000e-32 148.0
18 TraesCS2D01G504800 chr7D 88.178 1328 81 23 2323 3609 82621553 82620261 0.000000e+00 1513.0
19 TraesCS2D01G504800 chr7D 92.628 624 33 9 1213 1830 594011013 594011629 0.000000e+00 885.0
20 TraesCS2D01G504800 chr7D 91.923 520 28 8 992 1508 82622746 82622238 0.000000e+00 715.0
21 TraesCS2D01G504800 chr7D 84.818 685 41 29 2463 3112 579915530 579914874 6.580000e-177 630.0
22 TraesCS2D01G504800 chr7D 84.818 685 41 29 2463 3112 599176809 599177465 6.580000e-177 630.0
23 TraesCS2D01G504800 chr7D 86.348 586 35 13 121 680 594009195 594009761 6.670000e-167 597.0
24 TraesCS2D01G504800 chr7D 84.615 663 33 33 2463 3112 598907297 598907903 2.400000e-166 595.0
25 TraesCS2D01G504800 chr7D 92.566 417 18 4 2323 2730 594012030 594012442 1.440000e-163 586.0
26 TraesCS2D01G504800 chr7D 94.030 335 20 0 1876 2210 82621886 82621552 3.210000e-140 508.0
27 TraesCS2D01G504800 chr7D 92.537 335 25 0 1876 2210 594011697 594012031 7.010000e-132 481.0
28 TraesCS2D01G504800 chr7D 92.568 296 13 7 1571 1865 82622250 82621963 2.000000e-112 416.0
29 TraesCS2D01G504800 chr7D 83.740 246 15 8 3369 3609 579914770 579914545 3.650000e-50 209.0
30 TraesCS2D01G504800 chr7D 83.673 245 16 8 3369 3609 598908007 598908231 3.650000e-50 209.0
31 TraesCS2D01G504800 chr7D 91.549 142 9 3 681 820 594009817 594009957 3.680000e-45 193.0
32 TraesCS2D01G504800 chr7D 94.565 92 5 0 2208 2299 203567771 203567680 3.760000e-30 143.0
33 TraesCS2D01G504800 chr7D 94.565 92 5 0 2208 2299 382035863 382035954 3.760000e-30 143.0
34 TraesCS2D01G504800 chr7A 86.888 1327 101 26 2323 3609 84319291 84317998 0.000000e+00 1419.0
35 TraesCS2D01G504800 chr7A 92.269 802 46 11 1069 1864 84320493 84319702 0.000000e+00 1123.0
36 TraesCS2D01G504800 chr7A 87.607 702 58 9 1 678 112587376 112588072 0.000000e+00 787.0
37 TraesCS2D01G504800 chr7A 81.890 635 87 19 1248 1868 8239531 8238911 8.940000e-141 510.0
38 TraesCS2D01G504800 chr7A 93.134 335 22 1 1876 2210 84319623 84319290 1.160000e-134 490.0
39 TraesCS2D01G504800 chr7A 86.520 319 30 5 1 314 55584191 55584501 4.460000e-89 339.0
40 TraesCS2D01G504800 chr7A 87.879 198 23 1 683 879 112588145 112588342 7.790000e-57 231.0
41 TraesCS2D01G504800 chr7A 95.652 92 4 0 2208 2299 60335101 60335192 8.070000e-32 148.0
42 TraesCS2D01G504800 chr6B 85.250 1139 121 26 2323 3421 32012602 32013733 0.000000e+00 1129.0
43 TraesCS2D01G504800 chr6B 87.291 299 27 7 1569 1860 32011866 32012160 7.470000e-87 331.0
44 TraesCS2D01G504800 chr6B 83.959 293 33 4 1918 2210 32012325 32012603 5.940000e-68 268.0
45 TraesCS2D01G504800 chr6B 95.652 92 4 0 2208 2299 596663398 596663489 8.070000e-32 148.0
46 TraesCS2D01G504800 chr1B 92.593 702 28 6 2 680 132288569 132289269 0.000000e+00 987.0
47 TraesCS2D01G504800 chr1B 92.841 433 23 6 989 1415 132290386 132290816 3.960000e-174 621.0
48 TraesCS2D01G504800 chr1B 86.912 489 40 12 3135 3609 562072328 562071850 8.880000e-146 527.0
49 TraesCS2D01G504800 chr1B 90.955 199 16 2 682 879 132289326 132289523 2.140000e-67 267.0
50 TraesCS2D01G504800 chr1A 86.415 714 58 24 2927 3609 513266194 513265489 0.000000e+00 745.0
51 TraesCS2D01G504800 chr1D 90.278 576 30 7 1 553 80296249 80296821 0.000000e+00 730.0
52 TraesCS2D01G504800 chr1D 93.478 414 21 4 989 1400 80303223 80303632 8.570000e-171 610.0
53 TraesCS2D01G504800 chr1D 84.565 460 36 19 3031 3459 415463390 415462935 1.200000e-114 424.0
54 TraesCS2D01G504800 chr1D 82.741 394 40 9 2454 2839 491931490 491931117 3.470000e-85 326.0
55 TraesCS2D01G504800 chr1D 93.500 200 12 1 681 879 80302125 80302324 2.720000e-76 296.0
56 TraesCS2D01G504800 chr1D 93.939 132 8 0 549 680 80301940 80302071 2.200000e-47 200.0
57 TraesCS2D01G504800 chr3A 82.921 849 94 26 1050 1876 653976518 653975699 0.000000e+00 717.0
58 TraesCS2D01G504800 chr7B 85.651 676 58 18 2964 3609 31566824 31566158 0.000000e+00 675.0
59 TraesCS2D01G504800 chr7B 85.070 355 28 8 1 333 46029660 46030011 4.460000e-89 339.0
60 TraesCS2D01G504800 chr7B 90.431 209 19 1 1876 2084 709480132 709479925 1.280000e-69 274.0
61 TraesCS2D01G504800 chr7B 82.890 263 21 7 3353 3609 678550183 678550427 7.850000e-52 215.0
62 TraesCS2D01G504800 chr7B 95.652 92 4 0 2208 2299 716824130 716824039 8.070000e-32 148.0
63 TraesCS2D01G504800 chr5D 84.649 684 44 27 2463 3112 445815316 445814660 3.060000e-175 625.0
64 TraesCS2D01G504800 chr5D 82.212 208 13 8 3369 3572 445953973 445953786 1.340000e-34 158.0
65 TraesCS2D01G504800 chr4D 84.689 627 57 17 87 681 485783568 485782949 1.120000e-164 590.0
66 TraesCS2D01G504800 chr4B 83.758 628 57 18 87 681 619981161 619980546 1.460000e-153 553.0
67 TraesCS2D01G504800 chr5B 80.923 650 86 25 1253 1876 67682400 67683037 2.520000e-131 479.0
68 TraesCS2D01G504800 chr3D 83.601 311 36 8 1896 2197 534157082 534157386 9.870000e-71 278.0
69 TraesCS2D01G504800 chrUn 89.474 209 21 1 1876 2084 480659964 480660171 2.760000e-66 263.0
70 TraesCS2D01G504800 chrUn 95.652 92 4 0 2208 2299 182421100 182421191 8.070000e-32 148.0
71 TraesCS2D01G504800 chrUn 95.652 92 4 0 2208 2299 433174181 433174090 8.070000e-32 148.0


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 TraesCS2D01G504800 chr2D 598935646 598939254 3608 True 6665.000000 6665 100.000000 1 3609 1 chr2D.!!$R1 3608
1 TraesCS2D01G504800 chr2B 728310201 728313817 3616 True 1390.666667 3777 91.535333 681 3609 3 chr2B.!!$R4 2928
2 TraesCS2D01G504800 chr2B 725160704 725162287 1583 True 1000.000000 1637 88.574500 1876 3609 2 chr2B.!!$R3 1733
3 TraesCS2D01G504800 chr2B 725193752 725194500 748 True 869.000000 869 87.613000 1032 1799 1 chr2B.!!$R1 767
4 TraesCS2D01G504800 chr2B 725212129 725212826 697 True 848.000000 848 89.174000 3 678 1 chr2B.!!$R2 675
5 TraesCS2D01G504800 chr2B 728322582 728326288 3706 True 579.000000 845 93.181500 1 619 2 chr2B.!!$R5 618
6 TraesCS2D01G504800 chr2A 733175811 733180226 4415 True 1249.750000 3609 91.803250 1 3609 4 chr2A.!!$R1 3608
7 TraesCS2D01G504800 chr7D 82620261 82622746 2485 True 788.000000 1513 91.674750 992 3609 4 chr7D.!!$R2 2617
8 TraesCS2D01G504800 chr7D 599176809 599177465 656 False 630.000000 630 84.818000 2463 3112 1 chr7D.!!$F2 649
9 TraesCS2D01G504800 chr7D 594009195 594012442 3247 False 548.400000 885 91.125600 121 2730 5 chr7D.!!$F3 2609
10 TraesCS2D01G504800 chr7D 579914545 579915530 985 True 419.500000 630 84.279000 2463 3609 2 chr7D.!!$R3 1146
11 TraesCS2D01G504800 chr7D 598907297 598908231 934 False 402.000000 595 84.144000 2463 3609 2 chr7D.!!$F4 1146
12 TraesCS2D01G504800 chr7A 84317998 84320493 2495 True 1010.666667 1419 90.763667 1069 3609 3 chr7A.!!$R2 2540
13 TraesCS2D01G504800 chr7A 8238911 8239531 620 True 510.000000 510 81.890000 1248 1868 1 chr7A.!!$R1 620
14 TraesCS2D01G504800 chr7A 112587376 112588342 966 False 509.000000 787 87.743000 1 879 2 chr7A.!!$F3 878
15 TraesCS2D01G504800 chr6B 32011866 32013733 1867 False 576.000000 1129 85.500000 1569 3421 3 chr6B.!!$F2 1852
16 TraesCS2D01G504800 chr1B 132288569 132290816 2247 False 625.000000 987 92.129667 2 1415 3 chr1B.!!$F1 1413
17 TraesCS2D01G504800 chr1A 513265489 513266194 705 True 745.000000 745 86.415000 2927 3609 1 chr1A.!!$R1 682
18 TraesCS2D01G504800 chr1D 80296249 80296821 572 False 730.000000 730 90.278000 1 553 1 chr1D.!!$F1 552
19 TraesCS2D01G504800 chr1D 80301940 80303632 1692 False 368.666667 610 93.639000 549 1400 3 chr1D.!!$F2 851
20 TraesCS2D01G504800 chr3A 653975699 653976518 819 True 717.000000 717 82.921000 1050 1876 1 chr3A.!!$R1 826
21 TraesCS2D01G504800 chr7B 31566158 31566824 666 True 675.000000 675 85.651000 2964 3609 1 chr7B.!!$R1 645
22 TraesCS2D01G504800 chr5D 445814660 445815316 656 True 625.000000 625 84.649000 2463 3112 1 chr5D.!!$R1 649
23 TraesCS2D01G504800 chr4D 485782949 485783568 619 True 590.000000 590 84.689000 87 681 1 chr4D.!!$R1 594
24 TraesCS2D01G504800 chr4B 619980546 619981161 615 True 553.000000 553 83.758000 87 681 1 chr4B.!!$R1 594
25 TraesCS2D01G504800 chr5B 67682400 67683037 637 False 479.000000 479 80.923000 1253 1876 1 chr5B.!!$F1 623

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
904 4097 0.253894 TGGTCCTATCACCGAGACGA 59.746 55.000 0.00 0.0 39.62 4.20 F
938 4131 0.258774 AAGCCGCATAATCCCCAGTT 59.741 50.000 0.00 0.0 0.00 3.16 F
940 4133 0.668535 GCCGCATAATCCCCAGTTTC 59.331 55.000 0.00 0.0 0.00 2.78 F
1042 5093 1.671742 CTCGCAGGTACCCACAGTT 59.328 57.895 8.74 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 6256 0.251916 CTCGCTGGTCCCCAACATTA 59.748 55.000 0.00 0.00 30.80 1.90 R
2250 6486 0.909610 TTGGAAGAGGAGCCGTGGAT 60.910 55.000 0.00 0.00 0.00 3.41 R
2538 6799 1.527433 GACCCCTTTGAAGGCAGTGC 61.527 60.000 6.55 6.55 45.10 4.40 R
2606 6873 1.895798 ACTCGAGCATCCAGAGTTTCA 59.104 47.619 13.61 0.00 41.93 2.69 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
24 25 5.707298 GGTATTGGTGGACTATTGGATCATG 59.293 44.000 0.00 0.00 0.00 3.07
39 40 8.798859 ATTGGATCATGTTGGATATTACTAGC 57.201 34.615 0.00 0.00 0.00 3.42
180 181 8.999431 GTAGTTGGTAGACTTTGATGATTTTGA 58.001 33.333 0.00 0.00 0.00 2.69
690 3882 1.143684 CCTCTCCACATGGGGGTTATG 59.856 57.143 15.76 0.28 38.77 1.90
782 3974 6.729100 TCTCCTCCTCTCCACTGTTTAATTTA 59.271 38.462 0.00 0.00 0.00 1.40
783 3975 7.403231 TCTCCTCCTCTCCACTGTTTAATTTAT 59.597 37.037 0.00 0.00 0.00 1.40
847 4040 4.881850 CAGAAGTTGGAATTATACGGCCTT 59.118 41.667 0.00 0.00 0.00 4.35
848 4041 5.357032 CAGAAGTTGGAATTATACGGCCTTT 59.643 40.000 0.00 0.00 0.00 3.11
867 4060 3.806949 TTCAGGTGGTCCTATTTTGCT 57.193 42.857 0.00 0.00 43.07 3.91
880 4073 1.674359 TTTTGCTTCTGCGGTTCTCA 58.326 45.000 0.00 0.00 43.34 3.27
881 4074 1.229428 TTTGCTTCTGCGGTTCTCAG 58.771 50.000 0.00 0.00 43.34 3.35
882 4075 1.230635 TTGCTTCTGCGGTTCTCAGC 61.231 55.000 0.00 0.00 43.34 4.26
883 4076 1.375268 GCTTCTGCGGTTCTCAGCT 60.375 57.895 0.00 0.00 35.86 4.24
884 4077 0.952984 GCTTCTGCGGTTCTCAGCTT 60.953 55.000 0.00 0.00 35.86 3.74
885 4078 1.517242 CTTCTGCGGTTCTCAGCTTT 58.483 50.000 0.00 0.00 35.86 3.51
886 4079 1.196354 CTTCTGCGGTTCTCAGCTTTG 59.804 52.381 0.00 0.00 35.86 2.77
887 4080 0.603707 TCTGCGGTTCTCAGCTTTGG 60.604 55.000 0.00 0.00 35.86 3.28
888 4081 0.886490 CTGCGGTTCTCAGCTTTGGT 60.886 55.000 0.00 0.00 35.86 3.67
890 4083 1.578206 GCGGTTCTCAGCTTTGGTCC 61.578 60.000 0.00 0.00 0.00 4.46
892 4085 1.275291 CGGTTCTCAGCTTTGGTCCTA 59.725 52.381 0.00 0.00 0.00 2.94
893 4086 2.093447 CGGTTCTCAGCTTTGGTCCTAT 60.093 50.000 0.00 0.00 0.00 2.57
895 4088 3.055094 GGTTCTCAGCTTTGGTCCTATCA 60.055 47.826 0.00 0.00 0.00 2.15
896 4089 3.895232 TCTCAGCTTTGGTCCTATCAC 57.105 47.619 0.00 0.00 0.00 3.06
897 4090 2.501723 TCTCAGCTTTGGTCCTATCACC 59.498 50.000 0.00 0.00 36.90 4.02
898 4091 1.207089 TCAGCTTTGGTCCTATCACCG 59.793 52.381 0.00 0.00 39.62 4.94
899 4092 1.207089 CAGCTTTGGTCCTATCACCGA 59.793 52.381 0.00 0.00 39.62 4.69
900 4093 1.482593 AGCTTTGGTCCTATCACCGAG 59.517 52.381 0.00 0.00 39.62 4.63
901 4094 1.480954 GCTTTGGTCCTATCACCGAGA 59.519 52.381 0.00 0.00 39.62 4.04
902 4095 2.738964 GCTTTGGTCCTATCACCGAGAC 60.739 54.545 0.00 0.00 39.62 3.36
903 4096 1.100510 TTGGTCCTATCACCGAGACG 58.899 55.000 0.00 0.00 39.62 4.18
904 4097 0.253894 TGGTCCTATCACCGAGACGA 59.746 55.000 0.00 0.00 39.62 4.20
906 4099 2.105306 TGGTCCTATCACCGAGACGATA 59.895 50.000 0.00 0.00 39.62 2.92
907 4100 2.743126 GGTCCTATCACCGAGACGATAG 59.257 54.545 0.00 0.00 40.46 2.08
911 4104 4.711980 CACCGAGACGATAGGTGC 57.288 61.111 10.51 0.00 46.06 5.01
912 4105 1.065928 CACCGAGACGATAGGTGCC 59.934 63.158 10.51 0.00 46.06 5.01
913 4106 2.125961 ACCGAGACGATAGGTGCCC 61.126 63.158 0.00 0.00 35.26 5.36
915 4108 2.857744 CGAGACGATAGGTGCCCCC 61.858 68.421 0.00 0.00 43.77 5.40
916 4109 2.838225 AGACGATAGGTGCCCCCG 60.838 66.667 0.00 0.00 43.77 5.73
920 4113 2.504274 CGATAGGTGCCCCCGCTAA 61.504 63.158 0.00 0.00 38.74 3.09
921 4114 1.371558 GATAGGTGCCCCCGCTAAG 59.628 63.158 0.00 0.00 38.74 2.18
922 4115 2.733319 GATAGGTGCCCCCGCTAAGC 62.733 65.000 0.00 0.00 38.74 3.09
928 4121 3.936203 CCCCCGCTAAGCCGCATA 61.936 66.667 0.00 0.00 0.00 3.14
929 4122 2.110213 CCCCGCTAAGCCGCATAA 59.890 61.111 0.00 0.00 0.00 1.90
930 4123 1.302511 CCCCGCTAAGCCGCATAAT 60.303 57.895 0.00 0.00 0.00 1.28
931 4124 1.298859 CCCCGCTAAGCCGCATAATC 61.299 60.000 0.00 0.00 0.00 1.75
932 4125 1.298859 CCCGCTAAGCCGCATAATCC 61.299 60.000 0.00 0.00 0.00 3.01
933 4126 1.298859 CCGCTAAGCCGCATAATCCC 61.299 60.000 0.00 0.00 0.00 3.85
936 4129 1.813513 CTAAGCCGCATAATCCCCAG 58.186 55.000 0.00 0.00 0.00 4.45
938 4131 0.258774 AAGCCGCATAATCCCCAGTT 59.741 50.000 0.00 0.00 0.00 3.16
939 4132 0.258774 AGCCGCATAATCCCCAGTTT 59.741 50.000 0.00 0.00 0.00 2.66
940 4133 0.668535 GCCGCATAATCCCCAGTTTC 59.331 55.000 0.00 0.00 0.00 2.78
942 4135 1.949525 CCGCATAATCCCCAGTTTCTG 59.050 52.381 0.00 0.00 0.00 3.02
955 4148 4.670896 CAGTTTCTGGAAAACCACCAAT 57.329 40.909 0.00 0.00 36.95 3.16
956 4149 5.782893 CAGTTTCTGGAAAACCACCAATA 57.217 39.130 0.00 0.00 36.95 1.90
957 4150 6.155475 CAGTTTCTGGAAAACCACCAATAA 57.845 37.500 0.00 0.00 36.95 1.40
958 4151 6.578023 CAGTTTCTGGAAAACCACCAATAAA 58.422 36.000 0.00 0.00 36.95 1.40
959 4152 7.216494 CAGTTTCTGGAAAACCACCAATAAAT 58.784 34.615 0.00 0.00 36.95 1.40
961 4154 5.146010 TCTGGAAAACCACCAATAAATGC 57.854 39.130 0.00 0.00 36.95 3.56
964 4157 5.684704 TGGAAAACCACCAATAAATGCAAA 58.315 33.333 0.00 0.00 34.25 3.68
966 4159 6.774656 TGGAAAACCACCAATAAATGCAAATT 59.225 30.769 0.00 0.00 34.25 1.82
967 4160 7.939039 TGGAAAACCACCAATAAATGCAAATTA 59.061 29.630 0.00 0.00 34.25 1.40
968 4161 8.955388 GGAAAACCACCAATAAATGCAAATTAT 58.045 29.630 0.00 0.00 0.00 1.28
1042 5093 1.671742 CTCGCAGGTACCCACAGTT 59.328 57.895 8.74 0.00 0.00 3.16
1073 5130 5.012239 TCTCTTTTGATTTGATCCCCACAG 58.988 41.667 0.00 0.00 0.00 3.66
1224 5283 8.767478 AAATTTAGCTCCAATGAACTGAATTG 57.233 30.769 0.00 0.00 34.79 2.32
1225 5284 6.899393 TTTAGCTCCAATGAACTGAATTGT 57.101 33.333 0.00 0.00 33.93 2.71
1246 5307 2.414250 TTTGGGCATCCCTTTTTCCT 57.586 45.000 3.27 0.00 45.70 3.36
1324 5387 7.215789 AGCTCATTCCTTACTCATTCTATGTG 58.784 38.462 0.00 0.00 0.00 3.21
1390 5455 2.630158 CAGTTAGATGCTGCTTGCTCT 58.370 47.619 0.00 0.87 43.37 4.09
1564 5660 6.533723 TCTTTGCCATACGATGTGTTAGTAAG 59.466 38.462 0.00 0.00 0.00 2.34
2087 6323 5.767665 TGAAATAAAGCTGAAGTAAGCCACA 59.232 36.000 0.00 0.00 44.68 4.17
2161 6397 9.745323 GAACATGTTTGTTTTCTTTCTTTCAAG 57.255 29.630 13.36 0.00 46.01 3.02
2222 6458 4.944962 TGTCATCCTGCATTCTTTAACG 57.055 40.909 0.00 0.00 0.00 3.18
2250 6486 3.318275 GGACATAGGAACGATGAGCTGTA 59.682 47.826 0.00 0.00 44.26 2.74
2297 6533 7.011202 CCAATATCGCAATGGATCTATCTTCAG 59.989 40.741 0.00 0.00 36.27 3.02
2313 6549 8.677300 TCTATCTTCAGCGCTTTTATTCAATTT 58.323 29.630 7.50 0.00 0.00 1.82
2461 6697 4.264460 TGTTTGACCAAAAGTTTGCTGT 57.736 36.364 0.00 0.00 36.86 4.40
2538 6799 1.133025 GAATGCCATGGTTGTCTTCGG 59.867 52.381 14.67 0.00 0.00 4.30
2606 6873 1.685820 GCTGCCAGGGAAACTAGGT 59.314 57.895 0.00 0.00 0.00 3.08
2714 7006 4.439153 CCTCAAATTTGGTCCATGACATCG 60.439 45.833 17.90 0.00 33.68 3.84
2791 7083 6.719829 AGTACTGTTTAGGCAAGGCTTTTTAT 59.280 34.615 0.00 0.00 0.00 1.40
2972 7268 8.367156 AGCAACTGAATTTTTGTACATACCATT 58.633 29.630 0.00 0.00 0.00 3.16
3283 7612 7.706179 GCCTTTAGAATACATGCAAGCAAATTA 59.294 33.333 0.00 0.00 0.00 1.40
3284 7613 9.754382 CCTTTAGAATACATGCAAGCAAATTAT 57.246 29.630 0.00 0.35 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.613153 AGGATCCAGCTAGTAATATCCAAC 57.387 41.667 15.82 0.00 36.22 3.77
39 40 5.151454 AGTTATCTCCAACCTAGGATCCAG 58.849 45.833 17.98 9.25 36.99 3.86
107 108 5.618236 CTCATATCCATATGGGGCACATAG 58.382 45.833 21.78 7.32 44.79 2.23
658 3782 5.358160 CCATGTGGAGAGGAGGAAATTAAAC 59.642 44.000 0.00 0.00 37.39 2.01
668 3792 0.916358 AACCCCCATGTGGAGAGGAG 60.916 60.000 0.00 0.00 37.39 3.69
758 3950 5.428184 AATTAAACAGTGGAGAGGAGGAG 57.572 43.478 0.00 0.00 0.00 3.69
782 3974 5.508153 CCGAATCAGAATTGTCGAGGACTAT 60.508 44.000 0.00 0.00 33.15 2.12
783 3975 4.202020 CCGAATCAGAATTGTCGAGGACTA 60.202 45.833 0.00 0.00 33.15 2.59
867 4060 1.229428 CAAAGCTGAGAACCGCAGAA 58.771 50.000 1.96 0.00 33.20 3.02
880 4073 1.482593 CTCGGTGATAGGACCAAAGCT 59.517 52.381 0.00 0.00 35.50 3.74
881 4074 1.480954 TCTCGGTGATAGGACCAAAGC 59.519 52.381 0.00 0.00 35.50 3.51
882 4075 2.479730 CGTCTCGGTGATAGGACCAAAG 60.480 54.545 0.00 0.00 35.50 2.77
883 4076 1.475280 CGTCTCGGTGATAGGACCAAA 59.525 52.381 0.00 0.00 35.50 3.28
884 4077 1.100510 CGTCTCGGTGATAGGACCAA 58.899 55.000 0.00 0.00 35.50 3.67
885 4078 0.253894 TCGTCTCGGTGATAGGACCA 59.746 55.000 0.00 0.00 35.50 4.02
886 4079 1.606903 ATCGTCTCGGTGATAGGACC 58.393 55.000 0.00 0.00 0.00 4.46
895 4088 3.522808 GGCACCTATCGTCTCGGT 58.477 61.111 0.00 0.00 0.00 4.69
911 4104 2.748058 ATTATGCGGCTTAGCGGGGG 62.748 60.000 13.45 0.00 40.67 5.40
912 4105 1.298859 GATTATGCGGCTTAGCGGGG 61.299 60.000 13.45 0.00 40.67 5.73
913 4106 1.298859 GGATTATGCGGCTTAGCGGG 61.299 60.000 13.45 1.81 40.67 6.13
915 4108 1.298859 GGGGATTATGCGGCTTAGCG 61.299 60.000 0.00 0.00 40.67 4.26
916 4109 0.250727 TGGGGATTATGCGGCTTAGC 60.251 55.000 0.00 0.00 37.71 3.09
918 4111 1.136828 ACTGGGGATTATGCGGCTTA 58.863 50.000 0.00 0.00 0.00 3.09
920 4113 0.258774 AAACTGGGGATTATGCGGCT 59.741 50.000 0.00 0.00 0.00 5.52
921 4114 0.668535 GAAACTGGGGATTATGCGGC 59.331 55.000 0.00 0.00 0.00 6.53
922 4115 1.949525 CAGAAACTGGGGATTATGCGG 59.050 52.381 0.00 0.00 0.00 5.69
942 4135 6.816134 ATTTGCATTTATTGGTGGTTTTCC 57.184 33.333 0.00 0.00 41.14 3.13
971 4164 9.155975 GAGCTTAACTCATCTTTAATCTCACAA 57.844 33.333 0.00 0.00 45.49 3.33
987 4180 3.326747 ACGTTCCATGTGAGCTTAACTC 58.673 45.455 0.00 0.00 46.45 3.01
990 5040 3.621268 GCATACGTTCCATGTGAGCTTAA 59.379 43.478 0.00 0.00 0.00 1.85
1042 5093 7.102346 GGATCAAATCAAAAGAGAGAGAGACA 58.898 38.462 0.00 0.00 0.00 3.41
1073 5130 6.992063 TCCACAGAAATAAAGCTGAGAATC 57.008 37.500 0.00 0.00 36.07 2.52
1246 5307 5.543020 AGATGAGATGATAATGACCTGCAGA 59.457 40.000 17.39 0.00 0.00 4.26
1324 5387 5.858581 CAGTGAATAAAGCTACAAAACTGGC 59.141 40.000 0.00 0.00 31.17 4.85
1390 5455 5.973899 TTGCAGCCAACATAGTCAAAATA 57.026 34.783 0.00 0.00 0.00 1.40
1564 5660 8.885494 AAGATTATCTAACATTCTCAGTCAGC 57.115 34.615 0.00 0.00 0.00 4.26
1645 5742 5.484715 TGGTATTACTGCACAGAAGTAACC 58.515 41.667 4.31 5.96 41.59 2.85
1646 5743 7.611213 AATGGTATTACTGCACAGAAGTAAC 57.389 36.000 4.31 0.00 41.59 2.50
1648 5745 7.120579 CCAAAATGGTATTACTGCACAGAAGTA 59.879 37.037 4.31 0.00 31.35 2.24
1649 5746 6.071952 CCAAAATGGTATTACTGCACAGAAGT 60.072 38.462 4.31 0.00 31.35 3.01
2020 6256 0.251916 CTCGCTGGTCCCCAACATTA 59.748 55.000 0.00 0.00 30.80 1.90
2087 6323 2.761208 AGTATGCGAAGTAGGCTCAGTT 59.239 45.455 0.00 0.00 0.00 3.16
2161 6397 3.068024 TGCCACTGATTGTTGGAAAGAAC 59.932 43.478 0.00 0.00 29.22 3.01
2222 6458 3.005472 TCATCGTTCCTATGTCCGGAATC 59.995 47.826 5.23 0.00 42.12 2.52
2250 6486 0.909610 TTGGAAGAGGAGCCGTGGAT 60.910 55.000 0.00 0.00 0.00 3.41
2260 6496 3.278574 TGCGATATTGGTTTGGAAGAGG 58.721 45.455 0.00 0.00 0.00 3.69
2297 6533 3.791353 CCTCGGAAATTGAATAAAAGCGC 59.209 43.478 0.00 0.00 0.00 5.92
2313 6549 2.203938 AAAGGGGAGTGCCTCGGA 60.204 61.111 0.00 0.00 40.72 4.55
2347 6583 2.202987 CGCTGGCCTGCTTCCTAG 60.203 66.667 29.18 11.29 0.00 3.02
2538 6799 1.527433 GACCCCTTTGAAGGCAGTGC 61.527 60.000 6.55 6.55 45.10 4.40
2606 6873 1.895798 ACTCGAGCATCCAGAGTTTCA 59.104 47.619 13.61 0.00 41.93 2.69
2714 7006 2.639327 GGGACCACATGGCAAGCAC 61.639 63.158 0.00 0.00 39.32 4.40
2757 7049 7.439655 CCTTGCCTAAACAGTACTTCATAGATC 59.560 40.741 0.00 0.00 0.00 2.75
2972 7268 7.993101 CATCAAATAGAGGCAGAAAGAAATCA 58.007 34.615 0.00 0.00 0.00 2.57
3283 7612 5.012561 GCATCCTAATAAGTCACCTGGAGAT 59.987 44.000 0.00 0.00 0.00 2.75
3284 7613 4.345257 GCATCCTAATAAGTCACCTGGAGA 59.655 45.833 0.00 0.00 0.00 3.71
3285 7614 4.101585 TGCATCCTAATAAGTCACCTGGAG 59.898 45.833 0.00 0.00 0.00 3.86
3415 7769 9.025041 TCATAAGTCACCTATCGTATCATCATT 57.975 33.333 0.00 0.00 0.00 2.57
3416 7770 8.581253 TCATAAGTCACCTATCGTATCATCAT 57.419 34.615 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.