Multiple sequence alignment - TraesCS7A01G455700

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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 TraesCS7A01G455700 chr7A 100.000 2687 0 0 1 2687 652175756 652178442 0.000000e+00 4963.0
1 TraesCS7A01G455700 chr7A 83.025 1785 280 17 1 1768 652164176 652165954 0.000000e+00 1596.0
2 TraesCS7A01G455700 chr7A 79.952 1681 301 24 2 1663 652357655 652359318 0.000000e+00 1205.0
3 TraesCS7A01G455700 chr7A 79.448 1703 321 24 1 1681 652287186 652288881 0.000000e+00 1179.0
4 TraesCS7A01G455700 chr7A 97.416 658 16 1 2030 2687 204624830 204624174 0.000000e+00 1120.0
5 TraesCS7A01G455700 chr7A 96.866 670 14 2 2025 2687 722422852 722423521 0.000000e+00 1114.0
6 TraesCS7A01G455700 chr7D 84.323 1869 274 13 2 1856 565618130 565619993 0.000000e+00 1810.0
7 TraesCS7A01G455700 chr7D 82.209 1675 280 14 1 1663 566038202 566039870 0.000000e+00 1426.0
8 TraesCS7A01G455700 chr7D 80.164 1704 301 25 1 1681 565644390 565646079 0.000000e+00 1240.0
9 TraesCS7A01G455700 chr7D 80.047 1699 315 19 1 1681 566014720 566016412 0.000000e+00 1238.0
10 TraesCS7A01G455700 chr7D 89.781 685 42 12 2014 2687 545383062 545383729 0.000000e+00 852.0
11 TraesCS7A01G455700 chr7D 100.000 39 0 0 1874 1912 53277357 53277319 3.710000e-09 73.1
12 TraesCS7A01G455700 chr7B 83.151 1923 291 15 2 1912 616836985 616838886 0.000000e+00 1725.0
13 TraesCS7A01G455700 chr7B 81.824 1678 284 17 1 1663 617578467 617580138 0.000000e+00 1389.0
14 TraesCS7A01G455700 chr7B 80.129 1701 310 20 1 1681 617557197 617555505 0.000000e+00 1243.0
15 TraesCS7A01G455700 chr7B 89.167 120 12 1 1909 2027 663106161 663106280 5.990000e-32 148.0
16 TraesCS7A01G455700 chr7B 88.235 119 13 1 1909 2027 157803055 157803172 1.000000e-29 141.0
17 TraesCS7A01G455700 chr5A 97.717 657 14 1 2031 2687 536945147 536944492 0.000000e+00 1129.0
18 TraesCS7A01G455700 chr5A 97.561 656 16 0 2032 2687 523171179 523170524 0.000000e+00 1123.0
19 TraesCS7A01G455700 chr4A 97.428 661 16 1 2028 2687 99386563 99385903 0.000000e+00 1125.0
20 TraesCS7A01G455700 chr4A 85.755 695 64 21 2010 2687 304211055 304211731 0.000000e+00 702.0
21 TraesCS7A01G455700 chr4A 88.235 119 5 6 1909 2027 352481926 352481817 1.680000e-27 134.0
22 TraesCS7A01G455700 chr1A 97.568 658 15 1 2030 2687 544570675 544571331 0.000000e+00 1125.0
23 TraesCS7A01G455700 chr1A 95.252 674 28 3 2016 2687 548764920 548764249 0.000000e+00 1064.0
24 TraesCS7A01G455700 chr1A 86.555 119 16 0 1909 2027 52241495 52241377 6.040000e-27 132.0
25 TraesCS7A01G455700 chr1A 89.796 49 4 1 1865 1912 464856238 464856190 8.030000e-06 62.1
26 TraesCS7A01G455700 chr6A 97.561 656 16 0 2032 2687 23904949 23905604 0.000000e+00 1123.0
27 TraesCS7A01G455700 chr6A 97.269 659 18 0 2029 2687 103908346 103907688 0.000000e+00 1118.0
28 TraesCS7A01G455700 chr6A 94.364 692 24 5 2009 2687 46949778 46950467 0.000000e+00 1048.0
29 TraesCS7A01G455700 chr6A 82.400 250 36 7 2007 2254 121050472 121050229 7.540000e-51 211.0
30 TraesCS7A01G455700 chr6A 81.778 225 41 0 1438 1662 160476260 160476484 3.530000e-44 189.0
31 TraesCS7A01G455700 chr3A 97.561 656 16 0 2032 2687 599271084 599271739 0.000000e+00 1123.0
32 TraesCS7A01G455700 chr3A 94.118 51 3 0 1874 1924 729609230 729609180 7.980000e-11 78.7
33 TraesCS7A01G455700 chr4D 90.351 684 49 7 2014 2687 503699073 503699749 0.000000e+00 881.0
34 TraesCS7A01G455700 chr3B 88.793 696 51 14 2006 2686 772957199 772956516 0.000000e+00 828.0
35 TraesCS7A01G455700 chr6B 88.012 684 59 11 2015 2686 592371514 592372186 0.000000e+00 787.0
36 TraesCS7A01G455700 chr6B 81.778 225 41 0 1438 1662 216356807 216357031 3.530000e-44 189.0
37 TraesCS7A01G455700 chr6B 94.872 39 2 0 1874 1912 194591405 194591367 8.030000e-06 62.1
38 TraesCS7A01G455700 chr3D 86.938 689 59 17 2013 2687 523532143 523532814 0.000000e+00 745.0
39 TraesCS7A01G455700 chr3D 88.235 119 13 1 1909 2027 17531781 17531898 1.000000e-29 141.0
40 TraesCS7A01G455700 chr3D 92.105 38 3 0 1874 1911 597734666 597734703 1.000000e-03 54.7
41 TraesCS7A01G455700 chr6D 82.222 225 40 0 1438 1662 122519807 122520031 7.590000e-46 195.0
42 TraesCS7A01G455700 chr6D 97.436 39 1 0 1874 1912 42152483 42152521 1.730000e-07 67.6
43 TraesCS7A01G455700 chr2B 90.756 119 11 0 1909 2027 438744102 438743984 2.770000e-35 159.0
44 TraesCS7A01G455700 chr2B 91.837 49 4 0 1863 1911 654706517 654706565 4.800000e-08 69.4
45 TraesCS7A01G455700 chr2B 95.122 41 2 0 1871 1911 654656419 654656459 6.210000e-07 65.8
46 TraesCS7A01G455700 chr2B 95.122 41 2 0 1871 1911 654735451 654735491 6.210000e-07 65.8
47 TraesCS7A01G455700 chr2A 90.000 120 11 1 1909 2027 69311034 69311153 1.290000e-33 154.0
48 TraesCS7A01G455700 chr2A 89.167 120 8 3 1909 2027 1304384 1304499 7.750000e-31 145.0
49 TraesCS7A01G455700 chr1B 89.076 119 9 3 1909 2027 633139900 633139786 7.750000e-31 145.0
50 TraesCS7A01G455700 chr2D 100.000 39 0 0 1874 1912 547807108 547807146 3.710000e-09 73.1
51 TraesCS7A01G455700 chr1D 82.022 89 10 6 1839 1927 468969214 468969132 1.330000e-08 71.3
52 TraesCS7A01G455700 chr1D 94.872 39 2 0 1874 1912 86862215 86862253 8.030000e-06 62.1
53 TraesCS7A01G455700 chr1D 90.476 42 4 0 1871 1912 338915907 338915948 3.740000e-04 56.5
54 TraesCS7A01G455700 chrUn 95.122 41 2 0 1871 1911 248129854 248129894 6.210000e-07 65.8
55 TraesCS7A01G455700 chr4B 94.872 39 2 0 1874 1912 56718303 56718265 8.030000e-06 62.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G455700 chr7A 652175756 652178442 2686 False 4963 4963 100.000 1 2687 1 chr7A.!!$F2 2686
1 TraesCS7A01G455700 chr7A 652164176 652165954 1778 False 1596 1596 83.025 1 1768 1 chr7A.!!$F1 1767
2 TraesCS7A01G455700 chr7A 652357655 652359318 1663 False 1205 1205 79.952 2 1663 1 chr7A.!!$F4 1661
3 TraesCS7A01G455700 chr7A 652287186 652288881 1695 False 1179 1179 79.448 1 1681 1 chr7A.!!$F3 1680
4 TraesCS7A01G455700 chr7A 204624174 204624830 656 True 1120 1120 97.416 2030 2687 1 chr7A.!!$R1 657
5 TraesCS7A01G455700 chr7A 722422852 722423521 669 False 1114 1114 96.866 2025 2687 1 chr7A.!!$F5 662
6 TraesCS7A01G455700 chr7D 565618130 565619993 1863 False 1810 1810 84.323 2 1856 1 chr7D.!!$F2 1854
7 TraesCS7A01G455700 chr7D 566038202 566039870 1668 False 1426 1426 82.209 1 1663 1 chr7D.!!$F5 1662
8 TraesCS7A01G455700 chr7D 565644390 565646079 1689 False 1240 1240 80.164 1 1681 1 chr7D.!!$F3 1680
9 TraesCS7A01G455700 chr7D 566014720 566016412 1692 False 1238 1238 80.047 1 1681 1 chr7D.!!$F4 1680
10 TraesCS7A01G455700 chr7D 545383062 545383729 667 False 852 852 89.781 2014 2687 1 chr7D.!!$F1 673
11 TraesCS7A01G455700 chr7B 616836985 616838886 1901 False 1725 1725 83.151 2 1912 1 chr7B.!!$F2 1910
12 TraesCS7A01G455700 chr7B 617578467 617580138 1671 False 1389 1389 81.824 1 1663 1 chr7B.!!$F3 1662
13 TraesCS7A01G455700 chr7B 617555505 617557197 1692 True 1243 1243 80.129 1 1681 1 chr7B.!!$R1 1680
14 TraesCS7A01G455700 chr5A 536944492 536945147 655 True 1129 1129 97.717 2031 2687 1 chr5A.!!$R2 656
15 TraesCS7A01G455700 chr5A 523170524 523171179 655 True 1123 1123 97.561 2032 2687 1 chr5A.!!$R1 655
16 TraesCS7A01G455700 chr4A 99385903 99386563 660 True 1125 1125 97.428 2028 2687 1 chr4A.!!$R1 659
17 TraesCS7A01G455700 chr4A 304211055 304211731 676 False 702 702 85.755 2010 2687 1 chr4A.!!$F1 677
18 TraesCS7A01G455700 chr1A 544570675 544571331 656 False 1125 1125 97.568 2030 2687 1 chr1A.!!$F1 657
19 TraesCS7A01G455700 chr1A 548764249 548764920 671 True 1064 1064 95.252 2016 2687 1 chr1A.!!$R3 671
20 TraesCS7A01G455700 chr6A 23904949 23905604 655 False 1123 1123 97.561 2032 2687 1 chr6A.!!$F1 655
21 TraesCS7A01G455700 chr6A 103907688 103908346 658 True 1118 1118 97.269 2029 2687 1 chr6A.!!$R1 658
22 TraesCS7A01G455700 chr6A 46949778 46950467 689 False 1048 1048 94.364 2009 2687 1 chr6A.!!$F2 678
23 TraesCS7A01G455700 chr3A 599271084 599271739 655 False 1123 1123 97.561 2032 2687 1 chr3A.!!$F1 655
24 TraesCS7A01G455700 chr4D 503699073 503699749 676 False 881 881 90.351 2014 2687 1 chr4D.!!$F1 673
25 TraesCS7A01G455700 chr3B 772956516 772957199 683 True 828 828 88.793 2006 2686 1 chr3B.!!$R1 680
26 TraesCS7A01G455700 chr6B 592371514 592372186 672 False 787 787 88.012 2015 2686 1 chr6B.!!$F2 671
27 TraesCS7A01G455700 chr3D 523532143 523532814 671 False 745 745 86.938 2013 2687 1 chr3D.!!$F2 674

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
197 198 0.170561 GGCGTCTGCGACTAGAAGAA 59.829 55.0 0.00 0.0 44.12 2.52 F
499 506 0.177604 AGAGCTCCGCAATCTTCAGG 59.822 55.0 10.93 0.0 0.00 3.86 F
980 1018 0.246910 GTCCGACTCCTTGGGTTCTC 59.753 60.0 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1363 0.465097 CTGCCTTGGCACTGATAGGG 60.465 60.000 10.65 0.0 0.0 3.53 R
1372 1421 1.443872 CAGAGTTTCGTCGTCCCGG 60.444 63.158 0.00 0.0 0.0 5.73 R
2337 2415 1.557371 GGGGAAAGAACAGAGAGGAGG 59.443 57.143 0.00 0.0 0.0 4.30 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 2.869503 CTTACCGGCGCCTCACCAAT 62.870 60.000 26.68 4.01 0.00 3.16
33 34 1.414181 CGCCTCACCAATGTCCTCTAT 59.586 52.381 0.00 0.00 0.00 1.98
55 56 1.066656 CAATGCAACCATCACACGCG 61.067 55.000 3.53 3.53 0.00 6.01
70 71 4.057428 GCGTGGTGCTCGAGGTCT 62.057 66.667 15.58 0.00 41.73 3.85
72 73 2.336478 CGTGGTGCTCGAGGTCTCT 61.336 63.158 15.58 0.00 0.00 3.10
84 85 0.616111 AGGTCTCTGGCCAGACGAAT 60.616 55.000 32.00 19.37 43.43 3.34
87 88 2.891580 GGTCTCTGGCCAGACGAATATA 59.108 50.000 32.00 8.94 43.43 0.86
197 198 0.170561 GGCGTCTGCGACTAGAAGAA 59.829 55.000 0.00 0.00 44.12 2.52
200 201 1.790838 CGTCTGCGACTAGAAGAACCG 60.791 57.143 0.00 0.00 35.96 4.44
237 238 3.072468 CCTGGGTTCGCTCCGGTA 61.072 66.667 0.00 0.00 0.00 4.02
241 242 2.484062 GGGTTCGCTCCGGTATCGA 61.484 63.158 0.00 6.34 39.00 3.59
255 256 2.492196 GGTATCGAAGGGGGACTGGATA 60.492 54.545 0.00 0.00 0.00 2.59
334 335 2.195567 TCGACAACGGACGGGTTCT 61.196 57.895 0.00 0.00 40.21 3.01
336 337 0.877213 CGACAACGGACGGGTTCTTT 60.877 55.000 0.00 0.00 35.72 2.52
346 347 2.727544 GGTTCTTTGCGCTGCCAA 59.272 55.556 9.73 0.00 0.00 4.52
349 350 0.527385 GTTCTTTGCGCTGCCAAACA 60.527 50.000 9.73 1.35 31.85 2.83
354 355 0.317799 TTGCGCTGCCAAACATGAAT 59.682 45.000 9.73 0.00 0.00 2.57
366 367 3.931907 AACATGAATCTCCCCGATGAA 57.068 42.857 0.00 0.00 31.20 2.57
370 371 4.141413 ACATGAATCTCCCCGATGAATCAA 60.141 41.667 0.00 0.00 31.20 2.57
374 375 3.931907 TCTCCCCGATGAATCAATTGT 57.068 42.857 5.13 0.00 0.00 2.71
376 377 2.880890 CTCCCCGATGAATCAATTGTCC 59.119 50.000 5.13 0.00 0.00 4.02
378 379 3.714280 TCCCCGATGAATCAATTGTCCTA 59.286 43.478 5.13 0.00 0.00 2.94
407 408 2.613977 CCCAGAGCAAAGTAGAGTGTGG 60.614 54.545 0.00 0.00 0.00 4.17
410 411 4.564406 CCAGAGCAAAGTAGAGTGTGGATT 60.564 45.833 0.00 0.00 0.00 3.01
436 437 2.224621 TGCCTAAAGAACTGCTCTTGCT 60.225 45.455 0.00 0.00 44.00 3.91
456 457 3.839432 GCCTACGCCTTCTCCGCT 61.839 66.667 0.00 0.00 0.00 5.52
477 484 1.077212 GGAGTGCACCATCTGGCAT 60.077 57.895 14.63 0.00 42.75 4.40
499 506 0.177604 AGAGCTCCGCAATCTTCAGG 59.822 55.000 10.93 0.00 0.00 3.86
510 517 3.432749 GCAATCTTCAGGGACTCTATGCA 60.433 47.826 0.00 0.00 34.60 3.96
519 526 2.383855 GGACTCTATGCAGACTCTGGT 58.616 52.381 8.17 0.00 31.21 4.00
534 541 2.686106 GGTAGCCCCGGGTCAGAA 60.686 66.667 21.85 0.00 0.00 3.02
587 603 2.025155 AGATCTCCGCAACGTAGACAT 58.975 47.619 0.00 0.00 0.00 3.06
617 633 2.963101 GGGGGAATAAGTTATGGGTTGC 59.037 50.000 0.00 0.00 0.00 4.17
644 660 3.753272 GGCATCACATTGTCTAGTGTTGT 59.247 43.478 0.00 0.00 37.62 3.32
688 707 4.107820 ACTAGCCTGGAGGATTCTTCTTT 58.892 43.478 0.00 0.00 37.39 2.52
693 712 1.065418 TGGAGGATTCTTCTTTCCCGC 60.065 52.381 0.00 0.00 32.05 6.13
722 750 2.162681 GGCCAGTACAGCAAACAAGAT 58.837 47.619 0.00 0.00 0.00 2.40
723 751 2.162408 GGCCAGTACAGCAAACAAGATC 59.838 50.000 0.00 0.00 0.00 2.75
751 779 1.270412 CCTTGGCCGTGTACAGTTACA 60.270 52.381 0.00 0.00 35.75 2.41
756 784 2.546373 GGCCGTGTACAGTTACAGTGAA 60.546 50.000 0.00 0.00 38.95 3.18
766 794 2.889045 AGTTACAGTGAACTCCGTGCTA 59.111 45.455 0.00 0.00 34.48 3.49
821 849 0.824759 GGCTTCGGATCAGTGTACCT 59.175 55.000 0.00 0.00 0.00 3.08
822 850 1.207329 GGCTTCGGATCAGTGTACCTT 59.793 52.381 0.00 0.00 0.00 3.50
826 854 3.090210 TCGGATCAGTGTACCTTGGTA 57.910 47.619 0.00 0.00 0.00 3.25
829 857 3.383505 CGGATCAGTGTACCTTGGTATCA 59.616 47.826 2.59 1.26 0.00 2.15
831 859 5.243060 CGGATCAGTGTACCTTGGTATCATA 59.757 44.000 2.59 0.00 0.00 2.15
834 862 7.990886 GGATCAGTGTACCTTGGTATCATAAAA 59.009 37.037 2.59 0.00 0.00 1.52
835 863 9.391006 GATCAGTGTACCTTGGTATCATAAAAA 57.609 33.333 2.59 0.00 0.00 1.94
858 886 3.811083 ACAAAAGGGACACAATACGACA 58.189 40.909 0.00 0.00 0.00 4.35
865 893 3.322369 GGACACAATACGACACATGTCA 58.678 45.455 12.32 0.00 44.99 3.58
867 895 4.391830 GGACACAATACGACACATGTCAAT 59.608 41.667 12.32 2.47 44.99 2.57
885 913 3.076621 CAATGTGGCAGTCAAGAAGCTA 58.923 45.455 0.00 0.00 0.00 3.32
902 933 3.243724 AGCTAGAAAGTCTTGGACAGGT 58.756 45.455 0.00 0.00 34.60 4.00
903 934 4.417437 AGCTAGAAAGTCTTGGACAGGTA 58.583 43.478 0.00 0.00 34.60 3.08
916 947 2.300437 GGACAGGTAGACAAGCAGTTCT 59.700 50.000 0.00 0.00 0.00 3.01
936 974 1.595993 GGACAGAGGTGAGCACGCTA 61.596 60.000 0.00 0.00 0.00 4.26
980 1018 0.246910 GTCCGACTCCTTGGGTTCTC 59.753 60.000 0.00 0.00 0.00 2.87
983 1021 1.618888 CCGACTCCTTGGGTTCTCCTA 60.619 57.143 0.00 0.00 36.20 2.94
991 1029 0.619255 TGGGTTCTCCTAATCCGGCA 60.619 55.000 0.00 0.00 36.20 5.69
1025 1063 2.384828 TGTCTACGAGTACATGCCCAT 58.615 47.619 0.00 0.00 0.00 4.00
1132 1181 1.741770 CTGGCGTACCTGCACCTTC 60.742 63.158 0.00 0.00 36.63 3.46
1314 1363 0.548031 TGGAATGGATCTCTGGGCAC 59.452 55.000 0.00 0.00 0.00 5.01
1350 1399 1.605712 GCAGACGTCTACAGCTTTGGT 60.606 52.381 19.57 0.00 0.00 3.67
1413 1466 1.676678 GATACAGCGAGGTGGAGGCA 61.677 60.000 7.23 0.00 0.00 4.75
1480 1539 4.522789 GGGCTACAGGAAAGATTGTTGAAA 59.477 41.667 0.00 0.00 0.00 2.69
1483 1542 5.473504 GCTACAGGAAAGATTGTTGAAAGGA 59.526 40.000 0.00 0.00 0.00 3.36
1493 1552 0.536460 GTTGAAAGGAAGGTGGGCGA 60.536 55.000 0.00 0.00 0.00 5.54
1494 1553 0.250727 TTGAAAGGAAGGTGGGCGAG 60.251 55.000 0.00 0.00 0.00 5.03
1495 1554 1.375326 GAAAGGAAGGTGGGCGAGT 59.625 57.895 0.00 0.00 0.00 4.18
1701 1760 4.502282 GTCTCATGAGCTCACGTAATTCAG 59.498 45.833 20.97 2.81 0.00 3.02
1728 1792 1.873591 GGACGCGCCAATATTCTCATT 59.126 47.619 5.73 0.00 36.34 2.57
1729 1793 2.349817 GGACGCGCCAATATTCTCATTG 60.350 50.000 5.73 0.00 35.97 2.82
1780 1844 3.605634 ACAAGCGTAGATGGCAATACAA 58.394 40.909 12.11 0.00 0.00 2.41
1802 1866 7.322664 ACAAAAGAATTTATCGTGCCATTCAT 58.677 30.769 0.00 0.00 37.28 2.57
1821 1885 9.256477 CCATTCATGAATACAGATCAAATTTGG 57.744 33.333 20.32 10.13 0.00 3.28
1827 1891 6.550854 TGAATACAGATCAAATTTGGGGATCC 59.449 38.462 17.90 1.92 38.52 3.36
1868 1932 9.642343 AAGAATTGTTTTAGTACTTCCTTCCTT 57.358 29.630 0.00 0.00 0.00 3.36
1870 1934 9.678941 GAATTGTTTTAGTACTTCCTTCCTTTG 57.321 33.333 0.00 0.00 0.00 2.77
1872 1936 7.797038 TGTTTTAGTACTTCCTTCCTTTGTC 57.203 36.000 0.00 0.00 0.00 3.18
1873 1937 7.571025 TGTTTTAGTACTTCCTTCCTTTGTCT 58.429 34.615 0.00 0.00 0.00 3.41
1874 1938 8.050930 TGTTTTAGTACTTCCTTCCTTTGTCTT 58.949 33.333 0.00 0.00 0.00 3.01
1875 1939 8.900781 GTTTTAGTACTTCCTTCCTTTGTCTTT 58.099 33.333 0.00 0.00 0.00 2.52
1887 1951 5.553123 TCCTTTGTCTTTATTTACTCCGCA 58.447 37.500 0.00 0.00 0.00 5.69
1890 1954 7.990886 TCCTTTGTCTTTATTTACTCCGCATAT 59.009 33.333 0.00 0.00 0.00 1.78
1901 1965 6.913873 TTACTCCGCATATTAGTTTTGACC 57.086 37.500 0.00 0.00 0.00 4.02
1922 1986 7.674471 GACCTAAGTCAAACAATCTAAGCTT 57.326 36.000 3.48 3.48 42.99 3.74
1923 1987 8.100508 GACCTAAGTCAAACAATCTAAGCTTT 57.899 34.615 3.20 0.00 42.99 3.51
1924 1988 8.100508 ACCTAAGTCAAACAATCTAAGCTTTC 57.899 34.615 3.20 0.00 0.00 2.62
1925 1989 7.719633 ACCTAAGTCAAACAATCTAAGCTTTCA 59.280 33.333 3.20 0.00 0.00 2.69
1926 1990 8.017946 CCTAAGTCAAACAATCTAAGCTTTCAC 58.982 37.037 3.20 0.00 0.00 3.18
1927 1991 6.942532 AGTCAAACAATCTAAGCTTTCACA 57.057 33.333 3.20 0.00 0.00 3.58
1928 1992 7.333528 AGTCAAACAATCTAAGCTTTCACAA 57.666 32.000 3.20 0.00 0.00 3.33
1929 1993 7.945134 AGTCAAACAATCTAAGCTTTCACAAT 58.055 30.769 3.20 0.00 0.00 2.71
1930 1994 9.066892 AGTCAAACAATCTAAGCTTTCACAATA 57.933 29.630 3.20 0.00 0.00 1.90
1931 1995 9.677567 GTCAAACAATCTAAGCTTTCACAATAA 57.322 29.630 3.20 0.00 0.00 1.40
1932 1996 9.677567 TCAAACAATCTAAGCTTTCACAATAAC 57.322 29.630 3.20 0.00 0.00 1.89
1933 1997 9.462174 CAAACAATCTAAGCTTTCACAATAACA 57.538 29.630 3.20 0.00 0.00 2.41
1934 1998 9.463443 AAACAATCTAAGCTTTCACAATAACAC 57.537 29.630 3.20 0.00 0.00 3.32
1935 1999 8.165239 ACAATCTAAGCTTTCACAATAACACA 57.835 30.769 3.20 0.00 0.00 3.72
1936 2000 8.796475 ACAATCTAAGCTTTCACAATAACACAT 58.204 29.630 3.20 0.00 0.00 3.21
1940 2004 9.448438 TCTAAGCTTTCACAATAACACATATGT 57.552 29.630 3.20 1.41 42.46 2.29
1945 2009 9.599322 GCTTTCACAATAACACATATGTATAGC 57.401 33.333 8.32 2.48 38.45 2.97
1949 2013 9.995003 TCACAATAACACATATGTATAGCATGA 57.005 29.630 8.32 5.05 38.45 3.07
1995 2059 9.130661 TCTAATGGTATTGATTTGGTATTGTGG 57.869 33.333 0.00 0.00 0.00 4.17
1996 2060 7.969690 AATGGTATTGATTTGGTATTGTGGA 57.030 32.000 0.00 0.00 0.00 4.02
1997 2061 8.551682 AATGGTATTGATTTGGTATTGTGGAT 57.448 30.769 0.00 0.00 0.00 3.41
1998 2062 7.345422 TGGTATTGATTTGGTATTGTGGATG 57.655 36.000 0.00 0.00 0.00 3.51
1999 2063 6.894654 TGGTATTGATTTGGTATTGTGGATGT 59.105 34.615 0.00 0.00 0.00 3.06
2000 2064 7.398618 TGGTATTGATTTGGTATTGTGGATGTT 59.601 33.333 0.00 0.00 0.00 2.71
2001 2065 8.908903 GGTATTGATTTGGTATTGTGGATGTTA 58.091 33.333 0.00 0.00 0.00 2.41
2224 2300 1.312815 GGTGGCAGGATGTTATCAGC 58.687 55.000 0.00 0.00 39.31 4.26
2337 2415 0.039764 CTGTTCTTCCCCTTTCCCCC 59.960 60.000 0.00 0.00 0.00 5.40
2421 2512 1.413812 GCCCCCATCCATTCAAATGAC 59.586 52.381 4.30 0.00 38.70 3.06
2638 2738 5.389859 TTCTAAATCTCCGTCGTAACCAA 57.610 39.130 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.961893 ATTGGTGAGGCGCCGGTAA 61.962 57.895 23.20 13.57 36.72 2.85
24 25 3.008923 TGGTTGCATTGTCATAGAGGACA 59.991 43.478 0.00 0.00 45.54 4.02
33 34 1.266446 CGTGTGATGGTTGCATTGTCA 59.734 47.619 0.00 0.00 0.00 3.58
55 56 1.214062 CAGAGACCTCGAGCACCAC 59.786 63.158 6.99 0.00 34.09 4.16
66 67 1.112113 TATTCGTCTGGCCAGAGACC 58.888 55.000 35.92 22.48 39.47 3.85
67 68 4.792521 ATATATTCGTCTGGCCAGAGAC 57.207 45.455 35.92 23.95 38.27 3.36
70 71 5.952347 AGATGTATATATTCGTCTGGCCAGA 59.048 40.000 32.00 32.00 34.56 3.86
72 73 5.965922 CAGATGTATATATTCGTCTGGCCA 58.034 41.667 23.89 4.71 41.34 5.36
84 85 2.100749 CGCGGGCATCCAGATGTATATA 59.899 50.000 9.29 0.00 40.80 0.86
87 88 1.004560 CGCGGGCATCCAGATGTAT 60.005 57.895 9.29 0.00 40.80 2.29
190 191 2.577059 CGGCAGCCGGTTCTTCTA 59.423 61.111 27.32 0.00 44.15 2.10
222 223 2.777972 CGATACCGGAGCGAACCCA 61.778 63.158 9.46 0.00 40.14 4.51
237 238 1.220750 AGTATCCAGTCCCCCTTCGAT 59.779 52.381 0.00 0.00 0.00 3.59
241 242 2.661176 TTGAGTATCCAGTCCCCCTT 57.339 50.000 0.00 0.00 0.00 3.95
255 256 1.349026 CCACCACTCCAGTCATTGAGT 59.651 52.381 0.00 0.00 42.41 3.41
334 335 0.103755 TTCATGTTTGGCAGCGCAAA 59.896 45.000 11.47 0.00 0.00 3.68
336 337 0.109179 GATTCATGTTTGGCAGCGCA 60.109 50.000 11.47 0.00 0.00 6.09
346 347 3.931907 TTCATCGGGGAGATTCATGTT 57.068 42.857 0.00 0.00 37.52 2.71
349 350 4.712051 TTGATTCATCGGGGAGATTCAT 57.288 40.909 0.00 0.00 37.52 2.57
354 355 3.433598 GGACAATTGATTCATCGGGGAGA 60.434 47.826 13.59 0.00 0.00 3.71
366 367 1.959042 CAGCGCCTAGGACAATTGAT 58.041 50.000 14.75 0.02 0.00 2.57
370 371 2.190578 GGCAGCGCCTAGGACAAT 59.809 61.111 14.75 0.00 46.69 2.71
407 408 3.674410 GCAGTTCTTTAGGCAAGCCAATC 60.674 47.826 14.40 0.00 38.92 2.67
410 411 1.202927 AGCAGTTCTTTAGGCAAGCCA 60.203 47.619 14.40 0.00 38.92 4.75
456 457 2.605607 CCAGATGGTGCACTCCCCA 61.606 63.158 17.98 6.51 34.66 4.96
510 517 2.042843 CCGGGGCTACCAGAGTCT 60.043 66.667 0.00 0.00 40.22 3.24
519 526 1.987855 CAGTTCTGACCCGGGGCTA 60.988 63.158 30.93 13.79 0.00 3.93
534 541 2.457598 TCTGAAAGCCGGAGATACAGT 58.542 47.619 5.05 0.00 0.00 3.55
578 591 2.236395 CCCCCTTTCTTCATGTCTACGT 59.764 50.000 0.00 0.00 0.00 3.57
617 633 1.843368 AGACAATGTGATGCCAAGGG 58.157 50.000 0.00 0.00 0.00 3.95
634 650 3.937814 CACCCAATGCTACAACACTAGA 58.062 45.455 0.00 0.00 0.00 2.43
661 677 3.142977 AGAATCCTCCAGGCTAGTATGGA 59.857 47.826 14.89 14.89 43.34 3.41
688 707 4.344865 GGCCACTTTCCTGCGGGA 62.345 66.667 11.27 11.27 40.36 5.14
693 712 1.813513 CTGTACTGGCCACTTTCCTG 58.186 55.000 0.00 0.00 0.00 3.86
698 720 1.318576 GTTTGCTGTACTGGCCACTT 58.681 50.000 0.00 0.00 0.00 3.16
700 722 1.001378 CTTGTTTGCTGTACTGGCCAC 60.001 52.381 0.00 0.00 0.00 5.01
751 779 0.317479 GTGGTAGCACGGAGTTCACT 59.683 55.000 9.66 0.00 41.61 3.41
756 784 1.585006 CTTCGTGGTAGCACGGAGT 59.415 57.895 36.37 0.00 46.12 3.85
766 794 1.269998 CTCCGAGAAGTTCTTCGTGGT 59.730 52.381 6.88 0.75 0.00 4.16
834 862 5.125739 TGTCGTATTGTGTCCCTTTTGTTTT 59.874 36.000 0.00 0.00 0.00 2.43
835 863 4.641094 TGTCGTATTGTGTCCCTTTTGTTT 59.359 37.500 0.00 0.00 0.00 2.83
837 865 3.562557 GTGTCGTATTGTGTCCCTTTTGT 59.437 43.478 0.00 0.00 0.00 2.83
858 886 2.275134 TGACTGCCACATTGACATGT 57.725 45.000 0.00 0.00 45.18 3.21
865 893 2.283145 AGCTTCTTGACTGCCACATT 57.717 45.000 0.00 0.00 0.00 2.71
867 895 1.970640 TCTAGCTTCTTGACTGCCACA 59.029 47.619 0.00 0.00 0.00 4.17
885 913 4.223953 TGTCTACCTGTCCAAGACTTTCT 58.776 43.478 3.65 0.00 40.25 2.52
902 933 3.230976 TCTGTCCAGAACTGCTTGTCTA 58.769 45.455 0.00 0.00 33.91 2.59
903 934 2.036992 CTCTGTCCAGAACTGCTTGTCT 59.963 50.000 0.00 0.00 36.94 3.41
916 947 3.051210 CGTGCTCACCTCTGTCCA 58.949 61.111 0.00 0.00 0.00 4.02
980 1018 1.136305 TCTTCTCGTTGCCGGATTAGG 59.864 52.381 5.05 0.00 33.95 2.69
983 1021 1.656652 CATCTTCTCGTTGCCGGATT 58.343 50.000 5.05 0.00 33.95 3.01
991 1029 3.190744 TCGTAGACAAGCATCTTCTCGTT 59.809 43.478 0.00 0.00 0.00 3.85
1005 1043 1.842052 TGGGCATGTACTCGTAGACA 58.158 50.000 0.00 0.00 0.00 3.41
1054 1092 3.058160 GCTCAGGCATGCACCGTT 61.058 61.111 21.36 0.00 38.54 4.44
1132 1181 3.857854 GATGCACTCGTGGCAGCG 61.858 66.667 0.00 0.00 45.68 5.18
1295 1344 0.548031 GTGCCCAGAGATCCATTCCA 59.452 55.000 0.00 0.00 0.00 3.53
1314 1363 0.465097 CTGCCTTGGCACTGATAGGG 60.465 60.000 10.65 0.00 0.00 3.53
1372 1421 1.443872 CAGAGTTTCGTCGTCCCGG 60.444 63.158 0.00 0.00 0.00 5.73
1413 1466 2.443016 CTACTCCCGCTCCCTGCT 60.443 66.667 0.00 0.00 40.11 4.24
1480 1539 2.750350 CAACTCGCCCACCTTCCT 59.250 61.111 0.00 0.00 0.00 3.36
1483 1542 3.570212 AGCCAACTCGCCCACCTT 61.570 61.111 0.00 0.00 0.00 3.50
1529 1588 2.123683 CCCGCTCCAGCTCCTCTA 60.124 66.667 0.00 0.00 39.32 2.43
1720 1780 7.898918 TGTCAAATTGATTCACCAATGAGAAT 58.101 30.769 0.00 1.57 36.90 2.40
1728 1792 5.241506 GTCCTCTTGTCAAATTGATTCACCA 59.758 40.000 0.00 0.00 0.00 4.17
1729 1793 5.241506 TGTCCTCTTGTCAAATTGATTCACC 59.758 40.000 0.00 0.00 0.00 4.02
1742 1806 4.377431 CGCTTGTACAATTGTCCTCTTGTC 60.377 45.833 15.85 0.00 36.92 3.18
1780 1844 7.099266 TCATGAATGGCACGATAAATTCTTT 57.901 32.000 0.00 0.00 31.66 2.52
1802 1866 6.550854 GGATCCCCAAATTTGATCTGTATTCA 59.449 38.462 19.86 0.00 36.12 2.57
1837 1901 8.515414 AGGAAGTACTAAAACAATTCTTGATGC 58.485 33.333 0.00 0.00 0.00 3.91
1840 1904 9.063615 GGAAGGAAGTACTAAAACAATTCTTGA 57.936 33.333 0.00 0.00 0.00 3.02
1841 1905 9.067986 AGGAAGGAAGTACTAAAACAATTCTTG 57.932 33.333 0.00 0.00 0.00 3.02
1864 1928 5.553123 TGCGGAGTAAATAAAGACAAAGGA 58.447 37.500 0.00 0.00 0.00 3.36
1868 1932 9.826574 ACTAATATGCGGAGTAAATAAAGACAA 57.173 29.630 0.00 0.00 0.00 3.18
1875 1939 9.048446 GGTCAAAACTAATATGCGGAGTAAATA 57.952 33.333 0.00 0.00 0.00 1.40
1876 1940 7.773690 AGGTCAAAACTAATATGCGGAGTAAAT 59.226 33.333 0.00 0.00 0.00 1.40
1877 1941 7.107542 AGGTCAAAACTAATATGCGGAGTAAA 58.892 34.615 0.00 0.00 0.00 2.01
1901 1965 8.559536 TGTGAAAGCTTAGATTGTTTGACTTAG 58.440 33.333 0.00 0.00 0.00 2.18
1914 1978 9.448438 ACATATGTGTTATTGTGAAAGCTTAGA 57.552 29.630 7.78 0.00 34.01 2.10
1919 1983 9.599322 GCTATACATATGTGTTATTGTGAAAGC 57.401 33.333 18.81 10.01 39.77 3.51
1923 1987 9.995003 TCATGCTATACATATGTGTTATTGTGA 57.005 29.630 18.81 10.97 39.77 3.58
1969 2033 9.130661 CCACAATACCAAATCAATACCATTAGA 57.869 33.333 0.00 0.00 0.00 2.10
1970 2034 9.130661 TCCACAATACCAAATCAATACCATTAG 57.869 33.333 0.00 0.00 0.00 1.73
1971 2035 9.653516 ATCCACAATACCAAATCAATACCATTA 57.346 29.630 0.00 0.00 0.00 1.90
1972 2036 7.969690 TCCACAATACCAAATCAATACCATT 57.030 32.000 0.00 0.00 0.00 3.16
1973 2037 7.564660 ACATCCACAATACCAAATCAATACCAT 59.435 33.333 0.00 0.00 0.00 3.55
1974 2038 6.894654 ACATCCACAATACCAAATCAATACCA 59.105 34.615 0.00 0.00 0.00 3.25
1975 2039 7.346751 ACATCCACAATACCAAATCAATACC 57.653 36.000 0.00 0.00 0.00 2.73
1979 2043 9.029368 TGATTAACATCCACAATACCAAATCAA 57.971 29.630 0.00 0.00 29.42 2.57
1980 2044 8.586879 TGATTAACATCCACAATACCAAATCA 57.413 30.769 0.00 0.00 0.00 2.57
2025 2095 6.934645 TGACCCTTTTTCTACTAGTGATTGTG 59.065 38.462 5.39 0.00 0.00 3.33
2027 2097 7.979444 TTGACCCTTTTTCTACTAGTGATTG 57.021 36.000 5.39 0.00 0.00 2.67
2271 2347 7.674772 GGGTCTATGTAGGATGACCTTTAGTAT 59.325 40.741 10.28 0.00 45.36 2.12
2337 2415 1.557371 GGGGAAAGAACAGAGAGGAGG 59.443 57.143 0.00 0.00 0.00 4.30
2421 2512 4.261614 GGAAAGAGTTGCTAACCTTTGTGG 60.262 45.833 14.09 0.00 42.93 4.17
2638 2738 2.874780 GTTGCGAGCGATCGACGT 60.875 61.111 29.29 1.32 44.60 4.34


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

AutoCloner maintained by Alex Coulton.