Multiple sequence alignment - TraesCS7A01G129100

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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 TraesCS7A01G129100 chr7A 100.000 2504 0 0 1 2504 83128128 83130631 0.000000e+00 4625.0
1 TraesCS7A01G129100 chr7A 93.333 270 14 3 2013 2279 556745059 556744791 1.800000e-106 396.0
2 TraesCS7A01G129100 chr7A 81.994 311 37 11 1669 1964 488305427 488305121 1.920000e-61 246.0
3 TraesCS7A01G129100 chr7A 81.272 283 34 9 1652 1916 65814813 65815094 7.020000e-51 211.0
4 TraesCS7A01G129100 chr7A 96.341 82 3 0 1 82 49305068 49305149 4.340000e-28 135.0
5 TraesCS7A01G129100 chr7A 100.000 56 0 0 1986 2041 83130050 83130105 1.230000e-18 104.0
6 TraesCS7A01G129100 chr7A 100.000 56 0 0 1923 1978 83130113 83130168 1.230000e-18 104.0
7 TraesCS7A01G129100 chr7D 90.580 966 56 16 627 1571 80321995 80322946 0.000000e+00 1247.0
8 TraesCS7A01G129100 chr7D 89.368 997 54 24 622 1580 80466588 80467570 0.000000e+00 1206.0
9 TraesCS7A01G129100 chr7D 86.647 1041 76 28 645 1643 80389145 80390164 0.000000e+00 1094.0
10 TraesCS7A01G129100 chr7D 89.969 648 54 7 966 1606 80459924 80460567 0.000000e+00 826.0
11 TraesCS7A01G129100 chr7D 90.714 280 23 2 155 433 80456690 80456967 1.090000e-98 370.0
12 TraesCS7A01G129100 chr7D 87.248 298 31 4 83 374 80321132 80321428 1.440000e-87 333.0
13 TraesCS7A01G129100 chr7D 86.577 298 31 6 83 374 80465727 80466021 1.120000e-83 320.0
14 TraesCS7A01G129100 chr7D 90.385 208 12 5 636 836 80456991 80457197 1.480000e-67 267.0
15 TraesCS7A01G129100 chr7D 80.392 306 33 13 83 363 80388648 80388951 9.080000e-50 207.0
16 TraesCS7A01G129100 chr7D 83.264 239 18 14 1652 1877 27422989 27422760 1.520000e-47 200.0
17 TraesCS7A01G129100 chr7D 85.455 165 18 4 473 634 29568805 29568644 1.540000e-37 167.0
18 TraesCS7A01G129100 chr7D 76.590 346 55 19 816 1149 85932040 85931709 1.540000e-37 167.0
19 TraesCS7A01G129100 chr7D 94.949 99 5 0 883 981 80457818 80457916 3.330000e-34 156.0
20 TraesCS7A01G129100 chr7D 92.632 95 7 0 1 95 25361302 25361396 1.210000e-28 137.0
21 TraesCS7A01G129100 chr7B 87.413 858 64 19 657 1485 27493543 27494385 0.000000e+00 946.0
22 TraesCS7A01G129100 chr7B 80.769 338 46 13 1642 1964 679786755 679786422 1.920000e-61 246.0
23 TraesCS7A01G129100 chr7B 77.814 311 47 18 864 1169 35101460 35101167 3.310000e-39 172.0
24 TraesCS7A01G129100 chr7B 83.333 174 28 1 462 634 213468111 213467938 2.580000e-35 159.0
25 TraesCS7A01G129100 chr7B 91.011 89 6 1 1520 1606 27494522 27494610 4.380000e-23 119.0
26 TraesCS7A01G129100 chr2B 87.093 891 36 25 1652 2504 150879071 150879920 0.000000e+00 935.0
27 TraesCS7A01G129100 chr2B 89.759 498 13 5 2018 2504 712365875 712365405 9.910000e-169 603.0
28 TraesCS7A01G129100 chr2B 92.647 272 18 2 2057 2326 795736485 795736214 8.400000e-105 390.0
29 TraesCS7A01G129100 chr2B 85.619 299 18 7 1640 1914 712366888 712366591 8.760000e-75 291.0
30 TraesCS7A01G129100 chr2B 75.862 435 45 46 1652 2042 773438419 773438001 1.540000e-37 167.0
31 TraesCS7A01G129100 chr2B 96.386 83 3 0 1 83 426416205 426416123 1.210000e-28 137.0
32 TraesCS7A01G129100 chr5B 87.119 590 32 18 1916 2504 692853899 692853353 1.630000e-176 628.0
33 TraesCS7A01G129100 chr5B 91.912 272 20 2 2057 2326 558558562 558558291 1.820000e-101 379.0
34 TraesCS7A01G129100 chr5B 83.051 413 36 15 1654 2043 692854277 692853876 6.630000e-91 344.0
35 TraesCS7A01G129100 chr1B 90.000 490 11 4 2026 2504 676924122 676924584 1.280000e-167 599.0
36 TraesCS7A01G129100 chr1B 87.129 303 15 9 1652 1931 676923074 676923375 3.110000e-84 322.0
37 TraesCS7A01G129100 chr1B 81.928 332 34 19 1652 1958 662457269 662456939 8.890000e-65 257.0
38 TraesCS7A01G129100 chrUn 90.821 414 11 2 2050 2463 480388756 480388370 1.710000e-146 529.0
39 TraesCS7A01G129100 chr5A 83.415 410 36 22 1654 2042 589028375 589028773 3.960000e-93 351.0
40 TraesCS7A01G129100 chr5A 83.626 171 28 0 473 643 475595258 475595088 7.170000e-36 161.0
41 TraesCS7A01G129100 chr4B 80.183 328 44 16 1652 1964 593369679 593369358 2.510000e-55 226.0
42 TraesCS7A01G129100 chr4B 77.995 409 43 32 1652 2042 111986414 111986793 1.950000e-51 213.0
43 TraesCS7A01G129100 chr4B 80.364 275 23 22 1652 1908 666621450 666621711 1.980000e-41 180.0
44 TraesCS7A01G129100 chr4B 97.531 81 2 0 1 81 111701857 111701777 3.360000e-29 139.0
45 TraesCS7A01G129100 chr4B 94.444 90 3 2 1 90 613032521 613032608 1.210000e-28 137.0
46 TraesCS7A01G129100 chr4B 85.593 118 10 6 1926 2042 111986740 111986851 1.570000e-22 117.0
47 TraesCS7A01G129100 chr4B 83.871 124 13 6 1920 2042 666621752 666621869 7.320000e-21 111.0
48 TraesCS7A01G129100 chr6A 87.037 162 21 0 473 634 153367035 153366874 1.530000e-42 183.0
49 TraesCS7A01G129100 chr6A 87.342 79 5 2 1959 2032 564512244 564512322 4.440000e-13 86.1
50 TraesCS7A01G129100 chr2A 85.714 161 23 0 473 633 504326782 504326622 1.190000e-38 171.0
51 TraesCS7A01G129100 chr2A 97.561 82 2 0 1 82 688426318 688426399 9.340000e-30 141.0
52 TraesCS7A01G129100 chr4D 85.455 165 18 4 473 634 403011916 403012077 1.540000e-37 167.0
53 TraesCS7A01G129100 chr2D 85.455 165 18 4 473 634 644820683 644820844 1.540000e-37 167.0
54 TraesCS7A01G129100 chr1D 85.455 165 18 4 473 634 187811387 187811548 1.540000e-37 167.0
55 TraesCS7A01G129100 chr1D 97.619 84 2 0 1 84 438038509 438038592 7.220000e-31 145.0
56 TraesCS7A01G129100 chr4A 82.902 193 21 7 1652 1836 295132798 295132986 1.990000e-36 163.0
57 TraesCS7A01G129100 chr3D 83.333 180 23 5 459 634 107216732 107216908 2.580000e-35 159.0
58 TraesCS7A01G129100 chr3D 97.561 82 2 0 1 82 279734323 279734404 9.340000e-30 141.0
59 TraesCS7A01G129100 chr3D 97.561 82 2 0 1 82 477341946 477342027 9.340000e-30 141.0
60 TraesCS7A01G129100 chr3A 75.457 383 61 27 1673 2042 745941721 745942083 3.330000e-34 156.0


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 TraesCS7A01G129100 chr7A 83128128 83130631 2503 False 1611.00 4625 100.00000 1 2504 3 chr7A.!!$F3 2503
1 TraesCS7A01G129100 chr7D 80321132 80322946 1814 False 790.00 1247 88.91400 83 1571 2 chr7D.!!$F2 1488
2 TraesCS7A01G129100 chr7D 80465727 80467570 1843 False 763.00 1206 87.97250 83 1580 2 chr7D.!!$F5 1497
3 TraesCS7A01G129100 chr7D 80388648 80390164 1516 False 650.50 1094 83.51950 83 1643 2 chr7D.!!$F3 1560
4 TraesCS7A01G129100 chr7D 80456690 80460567 3877 False 404.75 826 91.50425 155 1606 4 chr7D.!!$F4 1451
5 TraesCS7A01G129100 chr7B 27493543 27494610 1067 False 532.50 946 89.21200 657 1606 2 chr7B.!!$F1 949
6 TraesCS7A01G129100 chr2B 150879071 150879920 849 False 935.00 935 87.09300 1652 2504 1 chr2B.!!$F1 852
7 TraesCS7A01G129100 chr2B 712365405 712366888 1483 True 447.00 603 87.68900 1640 2504 2 chr2B.!!$R4 864
8 TraesCS7A01G129100 chr5B 692853353 692854277 924 True 486.00 628 85.08500 1654 2504 2 chr5B.!!$R2 850
9 TraesCS7A01G129100 chr1B 676923074 676924584 1510 False 460.50 599 88.56450 1652 2504 2 chr1B.!!$F1 852

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
536 875 0.106335 TGGTCTACCCGCGAAACAAA 59.894 50.0 8.23 0.0 35.15 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 4576 0.179015 ACACGGTGGGCATACAACAA 60.179 50.0 13.48 0.0 0.0 2.83 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
21 22 4.705110 TTCATCTTTGTCTCCCACAAGA 57.295 40.909 0.00 0.00 45.98 3.02
22 23 4.916041 TCATCTTTGTCTCCCACAAGAT 57.084 40.909 0.00 0.00 45.98 2.40
23 24 6.373005 TTCATCTTTGTCTCCCACAAGATA 57.627 37.500 0.00 0.00 45.98 1.98
24 25 6.373005 TCATCTTTGTCTCCCACAAGATAA 57.627 37.500 0.00 0.00 45.98 1.75
25 26 6.778821 TCATCTTTGTCTCCCACAAGATAAA 58.221 36.000 0.00 0.00 45.98 1.40
26 27 6.655003 TCATCTTTGTCTCCCACAAGATAAAC 59.345 38.462 0.00 0.00 45.98 2.01
27 28 5.935945 TCTTTGTCTCCCACAAGATAAACA 58.064 37.500 0.00 0.00 45.98 2.83
28 29 6.361433 TCTTTGTCTCCCACAAGATAAACAA 58.639 36.000 0.00 0.00 45.98 2.83
29 30 7.004086 TCTTTGTCTCCCACAAGATAAACAAT 58.996 34.615 0.00 0.00 45.98 2.71
30 31 7.505585 TCTTTGTCTCCCACAAGATAAACAATT 59.494 33.333 0.00 0.00 45.98 2.32
31 32 7.595819 TTGTCTCCCACAAGATAAACAATTT 57.404 32.000 0.00 0.00 40.29 1.82
32 33 6.980593 TGTCTCCCACAAGATAAACAATTTG 58.019 36.000 0.00 0.00 29.30 2.32
33 34 6.549364 TGTCTCCCACAAGATAAACAATTTGT 59.451 34.615 0.00 0.00 34.31 2.83
34 35 7.721842 TGTCTCCCACAAGATAAACAATTTGTA 59.278 33.333 1.76 0.00 32.86 2.41
35 36 8.739972 GTCTCCCACAAGATAAACAATTTGTAT 58.260 33.333 1.76 0.00 32.86 2.29
36 37 9.967451 TCTCCCACAAGATAAACAATTTGTATA 57.033 29.630 1.76 0.00 32.86 1.47
54 55 9.754382 ATTTGTATAAATGCATCTTGATGTTCC 57.246 29.630 0.00 0.00 35.26 3.62
55 56 6.958255 TGTATAAATGCATCTTGATGTTCCG 58.042 36.000 0.00 0.00 0.00 4.30
56 57 6.542005 TGTATAAATGCATCTTGATGTTCCGT 59.458 34.615 0.00 0.00 0.00 4.69
57 58 3.770263 AATGCATCTTGATGTTCCGTG 57.230 42.857 0.00 0.00 0.00 4.94
58 59 0.804364 TGCATCTTGATGTTCCGTGC 59.196 50.000 11.61 0.00 0.00 5.34
59 60 0.804364 GCATCTTGATGTTCCGTGCA 59.196 50.000 11.61 0.00 0.00 4.57
60 61 1.199789 GCATCTTGATGTTCCGTGCAA 59.800 47.619 11.61 0.00 0.00 4.08
61 62 2.855180 CATCTTGATGTTCCGTGCAAC 58.145 47.619 0.00 0.00 0.00 4.17
72 73 4.120331 GTGCAACGCATGGGCCTC 62.120 66.667 10.10 0.00 41.91 4.70
73 74 4.349503 TGCAACGCATGGGCCTCT 62.350 61.111 10.10 0.00 36.38 3.69
74 75 3.064324 GCAACGCATGGGCCTCTT 61.064 61.111 10.10 0.00 36.38 2.85
75 76 2.879907 CAACGCATGGGCCTCTTG 59.120 61.111 10.10 3.13 36.38 3.02
76 77 3.064324 AACGCATGGGCCTCTTGC 61.064 61.111 10.10 17.00 41.47 4.01
77 78 3.574074 AACGCATGGGCCTCTTGCT 62.574 57.895 21.46 11.42 42.35 3.91
78 79 2.190313 CGCATGGGCCTCTTGCTA 59.810 61.111 21.46 0.00 42.35 3.49
79 80 1.890979 CGCATGGGCCTCTTGCTAG 60.891 63.158 21.46 9.83 42.35 3.42
80 81 1.225704 GCATGGGCCTCTTGCTAGT 59.774 57.895 18.69 0.00 41.60 2.57
81 82 0.469917 GCATGGGCCTCTTGCTAGTA 59.530 55.000 18.69 0.00 41.60 1.82
84 85 1.040646 TGGGCCTCTTGCTAGTATCG 58.959 55.000 4.53 0.00 40.92 2.92
87 88 2.158943 GGGCCTCTTGCTAGTATCGTTT 60.159 50.000 0.84 0.00 40.92 3.60
117 119 5.903010 TGTCAGTTATAAGATGCCCTAAGGA 59.097 40.000 0.00 0.00 33.47 3.36
131 133 5.243730 TGCCCTAAGGATGTCTTTTCAAAAG 59.756 40.000 3.20 3.20 36.93 2.27
133 135 6.349694 GCCCTAAGGATGTCTTTTCAAAAGAG 60.350 42.308 13.09 0.00 36.93 2.85
134 136 6.151817 CCCTAAGGATGTCTTTTCAAAAGAGG 59.848 42.308 13.09 7.99 36.93 3.69
180 182 7.868415 GTGACTCAGTACACTCTCAAGTAATTT 59.132 37.037 0.00 0.00 33.25 1.82
193 195 8.758633 TCTCAAGTAATTTAGTTTTCTCTCCG 57.241 34.615 0.00 0.00 0.00 4.63
245 251 3.427233 CGGTTAAGGTGAGTTCTAGACCG 60.427 52.174 0.00 0.00 36.89 4.79
247 273 4.380339 GGTTAAGGTGAGTTCTAGACCGTC 60.380 50.000 0.00 0.00 34.72 4.79
269 295 6.798315 TCGTATTTTGGGTTAAATTCGACA 57.202 33.333 0.00 0.00 40.17 4.35
342 368 7.247728 TGATTTGTATTCGCATGAAGTTTACC 58.752 34.615 0.00 0.00 37.57 2.85
363 389 3.865745 CCGCAATACCACTCTTTCTACAG 59.134 47.826 0.00 0.00 0.00 2.74
436 702 2.556144 GGGGGCTAATAAACCCTACG 57.444 55.000 0.00 0.00 46.19 3.51
437 703 1.544093 GGGGGCTAATAAACCCTACGC 60.544 57.143 0.00 0.00 46.19 4.42
438 704 1.141455 GGGGCTAATAAACCCTACGCA 59.859 52.381 0.00 0.00 46.19 5.24
440 706 3.281158 GGGCTAATAAACCCTACGCAAA 58.719 45.455 0.00 0.00 43.36 3.68
441 707 3.887110 GGGCTAATAAACCCTACGCAAAT 59.113 43.478 0.00 0.00 43.36 2.32
442 708 4.261447 GGGCTAATAAACCCTACGCAAATG 60.261 45.833 0.00 0.00 43.36 2.32
443 709 4.337274 GGCTAATAAACCCTACGCAAATGT 59.663 41.667 0.00 0.00 0.00 2.71
444 710 5.528320 GGCTAATAAACCCTACGCAAATGTA 59.472 40.000 0.00 0.00 0.00 2.29
445 711 6.206048 GGCTAATAAACCCTACGCAAATGTAT 59.794 38.462 0.00 0.00 0.00 2.29
446 712 7.388500 GGCTAATAAACCCTACGCAAATGTATA 59.612 37.037 0.00 0.00 0.00 1.47
447 713 8.440833 GCTAATAAACCCTACGCAAATGTATAG 58.559 37.037 0.00 0.00 0.00 1.31
448 714 7.739498 AATAAACCCTACGCAAATGTATAGG 57.261 36.000 5.57 5.57 34.99 2.57
449 715 5.362105 AAACCCTACGCAAATGTATAGGA 57.638 39.130 11.49 0.00 37.02 2.94
450 716 5.362105 AACCCTACGCAAATGTATAGGAA 57.638 39.130 11.49 0.00 37.02 3.36
451 717 4.700700 ACCCTACGCAAATGTATAGGAAC 58.299 43.478 11.49 0.00 37.02 3.62
452 718 4.407945 ACCCTACGCAAATGTATAGGAACT 59.592 41.667 11.49 0.00 46.37 3.01
453 719 5.104652 ACCCTACGCAAATGTATAGGAACTT 60.105 40.000 11.49 0.00 41.75 2.66
454 720 5.465724 CCCTACGCAAATGTATAGGAACTTC 59.534 44.000 11.49 0.00 41.75 3.01
455 721 6.046593 CCTACGCAAATGTATAGGAACTTCA 58.953 40.000 6.36 0.00 41.75 3.02
456 722 6.706270 CCTACGCAAATGTATAGGAACTTCAT 59.294 38.462 6.36 0.00 41.75 2.57
457 723 7.226720 CCTACGCAAATGTATAGGAACTTCATT 59.773 37.037 6.36 0.00 41.75 2.57
458 724 7.391148 ACGCAAATGTATAGGAACTTCATTT 57.609 32.000 0.00 0.00 40.50 2.32
459 725 8.500753 ACGCAAATGTATAGGAACTTCATTTA 57.499 30.769 0.00 0.00 39.17 1.40
460 726 9.120538 ACGCAAATGTATAGGAACTTCATTTAT 57.879 29.630 0.00 0.00 39.17 1.40
461 727 9.950680 CGCAAATGTATAGGAACTTCATTTATT 57.049 29.630 0.00 0.00 39.17 1.40
498 837 8.191534 ACTCCGTATGTTCCTAAATATAAGCT 57.808 34.615 0.00 0.00 0.00 3.74
525 864 8.575649 TTTTAGAGATTCCAAAATGGTCTACC 57.424 34.615 0.00 0.00 39.03 3.18
528 867 1.828979 TTCCAAAATGGTCTACCCGC 58.171 50.000 0.00 0.00 39.03 6.13
529 868 0.391927 TCCAAAATGGTCTACCCGCG 60.392 55.000 0.00 0.00 39.03 6.46
530 869 0.391927 CCAAAATGGTCTACCCGCGA 60.392 55.000 8.23 0.00 35.15 5.87
534 873 0.322322 AATGGTCTACCCGCGAAACA 59.678 50.000 8.23 0.00 35.15 2.83
536 875 0.106335 TGGTCTACCCGCGAAACAAA 59.894 50.000 8.23 0.00 35.15 2.83
537 876 1.228533 GGTCTACCCGCGAAACAAAA 58.771 50.000 8.23 0.00 0.00 2.44
538 877 1.808343 GGTCTACCCGCGAAACAAAAT 59.192 47.619 8.23 0.00 0.00 1.82
539 878 2.413634 GGTCTACCCGCGAAACAAAATG 60.414 50.000 8.23 0.00 0.00 2.32
540 879 2.481185 GTCTACCCGCGAAACAAAATGA 59.519 45.455 8.23 0.00 0.00 2.57
541 880 2.739913 TCTACCCGCGAAACAAAATGAG 59.260 45.455 8.23 0.00 0.00 2.90
542 881 1.314730 ACCCGCGAAACAAAATGAGT 58.685 45.000 8.23 0.00 0.00 3.41
543 882 1.001815 ACCCGCGAAACAAAATGAGTG 60.002 47.619 8.23 0.00 0.00 3.51
545 884 2.287308 CCCGCGAAACAAAATGAGTGAA 60.287 45.455 8.23 0.00 0.00 3.18
546 885 3.564511 CCGCGAAACAAAATGAGTGAAT 58.435 40.909 8.23 0.00 0.00 2.57
547 886 3.603770 CCGCGAAACAAAATGAGTGAATC 59.396 43.478 8.23 0.00 0.00 2.52
550 889 5.504755 CGCGAAACAAAATGAGTGAATCTAC 59.495 40.000 0.00 0.00 0.00 2.59
551 890 6.370593 GCGAAACAAAATGAGTGAATCTACA 58.629 36.000 0.00 0.00 0.00 2.74
552 891 6.303259 GCGAAACAAAATGAGTGAATCTACAC 59.697 38.462 0.00 0.00 40.60 2.90
587 926 8.631480 TGTCTATATACATTCGTATGTGGTCT 57.369 34.615 16.91 3.06 44.56 3.85
601 971 9.692749 TCGTATGTGGTCTATATTGAAATCTTC 57.307 33.333 0.00 0.00 0.00 2.87
651 1040 7.048512 AGGGAGTACTACAATTTGTAAGATGC 58.951 38.462 7.57 3.70 31.67 3.91
660 1056 5.703592 ACAATTTGTAAGATGCCGACTTGTA 59.296 36.000 0.00 0.00 0.00 2.41
761 1158 0.459237 CAACGCGGATCTCAGCTTCT 60.459 55.000 12.47 0.00 34.89 2.85
772 1169 2.079925 CTCAGCTTCTAACTTGGTGCC 58.920 52.381 0.00 0.00 0.00 5.01
773 1173 0.798776 CAGCTTCTAACTTGGTGCCG 59.201 55.000 0.00 0.00 0.00 5.69
810 1213 2.353505 CCGGATCAGCACTCCATCTATG 60.354 54.545 0.00 0.00 32.72 2.23
868 1833 4.991153 TCAGATCTACAGTGCCTACAAG 57.009 45.455 0.00 0.00 0.00 3.16
952 1936 1.410517 TGTGCAGATCGATCTTCCTCC 59.589 52.381 25.25 11.47 34.22 4.30
976 3983 4.730949 AACTATAGTTAGCCTTGCGTGA 57.269 40.909 16.60 0.00 36.32 4.35
982 3989 0.250295 TTAGCCTTGCGTGAACAGCT 60.250 50.000 0.00 0.00 35.28 4.24
984 3991 2.856032 CCTTGCGTGAACAGCTCG 59.144 61.111 0.00 0.00 36.63 5.03
985 3992 1.664649 CCTTGCGTGAACAGCTCGA 60.665 57.895 0.00 0.00 35.64 4.04
992 3999 1.795768 GTGAACAGCTCGATCCACAA 58.204 50.000 0.00 0.00 0.00 3.33
1147 4192 2.520458 CACCACCACCACCACCAT 59.480 61.111 0.00 0.00 0.00 3.55
1149 4194 1.774217 ACCACCACCACCACCATCT 60.774 57.895 0.00 0.00 0.00 2.90
1473 4531 3.308014 GAAGGAGTGCTCTGCGCCT 62.308 63.158 4.18 0.00 40.23 5.52
1504 4562 2.392662 CATGGAGCCCTCAGAACTAGA 58.607 52.381 0.00 0.00 0.00 2.43
1518 4576 8.855110 CCTCAGAACTAGATAGTATCATGTGTT 58.145 37.037 12.66 10.28 34.99 3.32
1556 4719 3.908189 TGCCGGTGCATTCATCTG 58.092 55.556 1.90 0.00 44.23 2.90
1592 4761 5.714047 CAGTGTGTACTATGATGTGACACT 58.286 41.667 7.20 0.00 41.45 3.55
1599 4768 8.171196 GTGTACTATGATGTGACACTGAATTTG 58.829 37.037 7.20 0.00 37.89 2.32
1647 4817 5.741388 AAAGCTCACGTATCATTTCATCC 57.259 39.130 0.00 0.00 0.00 3.51
1649 4819 4.965814 AGCTCACGTATCATTTCATCCAT 58.034 39.130 0.00 0.00 0.00 3.41
1650 4820 4.993584 AGCTCACGTATCATTTCATCCATC 59.006 41.667 0.00 0.00 0.00 3.51
1696 4868 5.735354 GCAGATCCAAACAATCACATCCATC 60.735 44.000 0.00 0.00 0.00 3.51
1705 4877 5.641155 ACAATCACATCCATCCATCATCAT 58.359 37.500 0.00 0.00 0.00 2.45
1716 4888 8.166479 TCCATCCATCATCATAATCTAATGGT 57.834 34.615 0.00 0.00 36.04 3.55
1739 4911 9.575868 TGGTCCTTAATTATTCTGTGTTTAACA 57.424 29.630 0.00 0.00 37.22 2.41
1751 4923 4.199840 GTGTTTAACACTACCAACCACG 57.800 45.455 19.64 0.00 45.27 4.94
1758 4930 3.478509 ACACTACCAACCACGCAATAAA 58.521 40.909 0.00 0.00 0.00 1.40
1759 4931 3.500680 ACACTACCAACCACGCAATAAAG 59.499 43.478 0.00 0.00 0.00 1.85
1760 4932 3.749088 CACTACCAACCACGCAATAAAGA 59.251 43.478 0.00 0.00 0.00 2.52
1772 4944 4.870426 ACGCAATAAAGACACAATCGATCT 59.130 37.500 0.00 0.00 0.00 2.75
1804 4976 2.223852 TGCCCCGCAGTAAAAAGAAAAC 60.224 45.455 0.00 0.00 33.32 2.43
1805 4977 2.035449 GCCCCGCAGTAAAAAGAAAACT 59.965 45.455 0.00 0.00 0.00 2.66
1806 4978 3.638484 CCCCGCAGTAAAAAGAAAACTG 58.362 45.455 0.00 0.00 42.80 3.16
1845 5023 4.135153 CTCCCGCACGACCTCCTG 62.135 72.222 0.00 0.00 0.00 3.86
2095 5979 7.786178 TCTACATTGGCTTGATACAACATAC 57.214 36.000 0.00 0.00 0.00 2.39
2097 5981 5.182487 ACATTGGCTTGATACAACATACGA 58.818 37.500 0.00 0.00 0.00 3.43
2106 5990 7.201609 GCTTGATACAACATACGAATTCAGGAA 60.202 37.037 6.22 0.00 0.00 3.36
2119 6003 6.096282 ACGAATTCAGGAAAAGGTCAAAAGAA 59.904 34.615 6.22 0.00 0.00 2.52
2250 6134 1.408702 GCTCCAGGTGCTTTTGTTTCA 59.591 47.619 6.23 0.00 0.00 2.69
2251 6135 2.544486 GCTCCAGGTGCTTTTGTTTCAG 60.544 50.000 6.23 0.00 0.00 3.02
2252 6136 2.031120 TCCAGGTGCTTTTGTTTCAGG 58.969 47.619 0.00 0.00 0.00 3.86
2253 6137 2.031120 CCAGGTGCTTTTGTTTCAGGA 58.969 47.619 0.00 0.00 0.00 3.86
2254 6138 2.629617 CCAGGTGCTTTTGTTTCAGGAT 59.370 45.455 0.00 0.00 0.00 3.24
2255 6139 3.305608 CCAGGTGCTTTTGTTTCAGGATC 60.306 47.826 0.00 0.00 0.00 3.36
2256 6140 3.318839 CAGGTGCTTTTGTTTCAGGATCA 59.681 43.478 0.00 0.00 0.00 2.92
2257 6141 4.021719 CAGGTGCTTTTGTTTCAGGATCAT 60.022 41.667 0.00 0.00 0.00 2.45
2258 6142 4.021719 AGGTGCTTTTGTTTCAGGATCATG 60.022 41.667 0.00 0.00 0.00 3.07
2259 6143 3.676646 GTGCTTTTGTTTCAGGATCATGC 59.323 43.478 1.57 0.00 0.00 4.06
2260 6144 3.575256 TGCTTTTGTTTCAGGATCATGCT 59.425 39.130 1.57 0.00 0.00 3.79
2261 6145 4.766373 TGCTTTTGTTTCAGGATCATGCTA 59.234 37.500 1.57 0.00 0.00 3.49
2262 6146 5.419788 TGCTTTTGTTTCAGGATCATGCTAT 59.580 36.000 1.57 0.00 0.00 2.97
2263 6147 6.602803 TGCTTTTGTTTCAGGATCATGCTATA 59.397 34.615 1.57 0.00 0.00 1.31
2264 6148 7.122501 TGCTTTTGTTTCAGGATCATGCTATAA 59.877 33.333 1.57 0.00 0.00 0.98
2265 6149 8.139989 GCTTTTGTTTCAGGATCATGCTATAAT 58.860 33.333 1.57 0.00 0.00 1.28
2338 6222 3.853355 GGAATGACTCCATGTCTCCAT 57.147 47.619 0.00 0.00 44.67 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.705110 TCTTGTGGGAGACAAAGATGAA 57.295 40.909 0.00 0.00 44.14 2.57
1 2 4.916041 ATCTTGTGGGAGACAAAGATGA 57.084 40.909 0.00 0.00 44.14 2.92
2 3 6.430925 TGTTTATCTTGTGGGAGACAAAGATG 59.569 38.462 6.95 0.00 44.14 2.90
3 4 6.542821 TGTTTATCTTGTGGGAGACAAAGAT 58.457 36.000 0.00 0.00 44.14 2.40
4 5 5.935945 TGTTTATCTTGTGGGAGACAAAGA 58.064 37.500 0.00 0.00 44.14 2.52
5 6 6.633500 TTGTTTATCTTGTGGGAGACAAAG 57.367 37.500 0.00 0.00 44.14 2.77
6 7 7.595819 AATTGTTTATCTTGTGGGAGACAAA 57.404 32.000 0.00 0.00 44.14 2.83
7 8 7.069331 ACAAATTGTTTATCTTGTGGGAGACAA 59.931 33.333 0.00 0.00 42.55 3.18
8 9 6.549364 ACAAATTGTTTATCTTGTGGGAGACA 59.451 34.615 0.00 0.00 31.00 3.41
9 10 6.981722 ACAAATTGTTTATCTTGTGGGAGAC 58.018 36.000 0.00 0.00 31.00 3.36
10 11 8.877864 ATACAAATTGTTTATCTTGTGGGAGA 57.122 30.769 3.17 0.00 34.08 3.71
28 29 9.754382 GGAACATCAAGATGCATTTATACAAAT 57.246 29.630 9.85 0.00 42.39 2.32
29 30 7.914871 CGGAACATCAAGATGCATTTATACAAA 59.085 33.333 9.85 0.00 42.39 2.83
30 31 7.066887 ACGGAACATCAAGATGCATTTATACAA 59.933 33.333 9.85 0.00 42.39 2.41
31 32 6.542005 ACGGAACATCAAGATGCATTTATACA 59.458 34.615 9.85 0.00 42.39 2.29
32 33 6.852853 CACGGAACATCAAGATGCATTTATAC 59.147 38.462 9.85 0.00 42.39 1.47
33 34 6.513230 GCACGGAACATCAAGATGCATTTATA 60.513 38.462 9.85 0.00 42.39 0.98
34 35 5.734220 GCACGGAACATCAAGATGCATTTAT 60.734 40.000 9.85 0.00 42.39 1.40
35 36 4.438608 GCACGGAACATCAAGATGCATTTA 60.439 41.667 9.85 0.00 42.39 1.40
36 37 3.674138 GCACGGAACATCAAGATGCATTT 60.674 43.478 9.85 0.00 42.39 2.32
37 38 2.159338 GCACGGAACATCAAGATGCATT 60.159 45.455 9.85 0.00 42.39 3.56
38 39 1.402968 GCACGGAACATCAAGATGCAT 59.597 47.619 9.85 0.00 42.39 3.96
39 40 0.804364 GCACGGAACATCAAGATGCA 59.196 50.000 9.85 0.00 42.39 3.96
40 41 0.804364 TGCACGGAACATCAAGATGC 59.196 50.000 9.85 0.00 42.39 3.91
41 42 2.725759 CGTTGCACGGAACATCAAGATG 60.726 50.000 8.45 8.45 40.19 2.90
42 43 1.464608 CGTTGCACGGAACATCAAGAT 59.535 47.619 2.31 0.00 38.08 2.40
43 44 0.865111 CGTTGCACGGAACATCAAGA 59.135 50.000 2.31 0.00 38.08 3.02
44 45 0.725784 GCGTTGCACGGAACATCAAG 60.726 55.000 10.02 0.00 42.82 3.02
45 46 1.281353 GCGTTGCACGGAACATCAA 59.719 52.632 10.02 0.00 42.82 2.57
46 47 1.233950 ATGCGTTGCACGGAACATCA 61.234 50.000 6.93 0.00 46.78 3.07
47 48 0.794229 CATGCGTTGCACGGAACATC 60.794 55.000 6.93 0.00 46.78 3.06
48 49 1.209898 CATGCGTTGCACGGAACAT 59.790 52.632 6.93 2.04 46.78 2.71
49 50 2.636462 CATGCGTTGCACGGAACA 59.364 55.556 6.93 0.00 46.78 3.18
50 51 2.126888 CCATGCGTTGCACGGAAC 60.127 61.111 0.00 0.00 45.44 3.62
51 52 3.361158 CCCATGCGTTGCACGGAA 61.361 61.111 5.32 0.00 45.44 4.30
55 56 4.120331 GAGGCCCATGCGTTGCAC 62.120 66.667 0.00 0.00 43.04 4.57
56 57 3.866379 AAGAGGCCCATGCGTTGCA 62.866 57.895 0.00 0.00 44.86 4.08
57 58 3.064324 AAGAGGCCCATGCGTTGC 61.064 61.111 0.00 0.00 38.85 4.17
58 59 2.879907 CAAGAGGCCCATGCGTTG 59.120 61.111 0.00 0.00 38.85 4.10
59 60 2.196997 TAGCAAGAGGCCCATGCGTT 62.197 55.000 16.56 5.87 46.50 4.84
60 61 2.599645 CTAGCAAGAGGCCCATGCGT 62.600 60.000 16.56 9.60 46.50 5.24
61 62 1.890979 CTAGCAAGAGGCCCATGCG 60.891 63.158 16.56 3.24 46.50 4.73
62 63 0.469917 TACTAGCAAGAGGCCCATGC 59.530 55.000 15.24 15.24 46.50 4.06
63 64 2.611473 CGATACTAGCAAGAGGCCCATG 60.611 54.545 0.00 0.00 46.50 3.66
64 65 1.620819 CGATACTAGCAAGAGGCCCAT 59.379 52.381 0.00 0.00 46.50 4.00
65 66 1.040646 CGATACTAGCAAGAGGCCCA 58.959 55.000 0.00 0.00 46.50 5.36
66 67 1.041437 ACGATACTAGCAAGAGGCCC 58.959 55.000 0.00 0.00 46.50 5.80
67 68 2.892784 AACGATACTAGCAAGAGGCC 57.107 50.000 0.00 0.00 46.50 5.19
68 69 5.184340 TCTAAACGATACTAGCAAGAGGC 57.816 43.478 0.00 0.00 45.30 4.70
69 70 7.707035 ACATTTCTAAACGATACTAGCAAGAGG 59.293 37.037 0.00 0.00 0.00 3.69
70 71 8.635877 ACATTTCTAAACGATACTAGCAAGAG 57.364 34.615 0.00 0.00 0.00 2.85
71 72 8.248253 TGACATTTCTAAACGATACTAGCAAGA 58.752 33.333 0.00 0.00 0.00 3.02
72 73 8.407457 TGACATTTCTAAACGATACTAGCAAG 57.593 34.615 0.00 0.00 0.00 4.01
73 74 8.033038 ACTGACATTTCTAAACGATACTAGCAA 58.967 33.333 0.00 0.00 0.00 3.91
74 75 7.544622 ACTGACATTTCTAAACGATACTAGCA 58.455 34.615 0.00 0.00 0.00 3.49
75 76 7.988904 ACTGACATTTCTAAACGATACTAGC 57.011 36.000 0.00 0.00 0.00 3.42
84 85 9.937175 GGCATCTTATAACTGACATTTCTAAAC 57.063 33.333 0.00 0.00 0.00 2.01
87 88 8.034313 AGGGCATCTTATAACTGACATTTCTA 57.966 34.615 0.00 0.00 0.00 2.10
148 150 0.870393 GTGTACTGAGTCACGACGGA 59.130 55.000 0.00 0.00 36.20 4.69
180 182 7.406031 AATATCAGTGACGGAGAGAAAACTA 57.594 36.000 0.00 0.00 0.00 2.24
193 195 8.451908 AGCTGGGTTAAATTAATATCAGTGAC 57.548 34.615 0.00 0.00 0.00 3.67
237 243 3.091545 ACCCAAAATACGACGGTCTAGA 58.908 45.455 6.57 0.00 0.00 2.43
245 251 6.601264 TGTCGAATTTAACCCAAAATACGAC 58.399 36.000 0.00 0.00 42.79 4.34
247 273 9.724839 ATATTGTCGAATTTAACCCAAAATACG 57.275 29.630 0.00 0.00 0.00 3.06
342 368 4.744570 TCTGTAGAAAGAGTGGTATTGCG 58.255 43.478 0.00 0.00 0.00 4.85
421 687 5.494632 ACATTTGCGTAGGGTTTATTAGC 57.505 39.130 0.00 0.00 0.00 3.09
433 699 8.500753 AAATGAAGTTCCTATACATTTGCGTA 57.499 30.769 0.00 0.00 38.92 4.42
435 701 9.950680 AATAAATGAAGTTCCTATACATTTGCG 57.049 29.630 0.00 0.00 40.03 4.85
511 850 0.391927 TCGCGGGTAGACCATTTTGG 60.392 55.000 6.13 0.00 45.02 3.28
516 855 0.322322 TTGTTTCGCGGGTAGACCAT 59.678 50.000 6.13 0.00 40.22 3.55
517 856 0.106335 TTTGTTTCGCGGGTAGACCA 59.894 50.000 6.13 0.00 40.22 4.02
520 859 2.739913 CTCATTTTGTTTCGCGGGTAGA 59.260 45.455 6.13 0.00 0.00 2.59
521 860 2.482721 ACTCATTTTGTTTCGCGGGTAG 59.517 45.455 6.13 0.00 0.00 3.18
522 861 2.224549 CACTCATTTTGTTTCGCGGGTA 59.775 45.455 6.13 0.00 0.00 3.69
523 862 1.001815 CACTCATTTTGTTTCGCGGGT 60.002 47.619 6.13 0.00 0.00 5.28
525 864 2.679355 TCACTCATTTTGTTTCGCGG 57.321 45.000 6.13 0.00 0.00 6.46
528 867 7.576236 AGTGTAGATTCACTCATTTTGTTTCG 58.424 34.615 0.00 0.00 44.07 3.46
575 914 9.692749 GAAGATTTCAATATAGACCACATACGA 57.307 33.333 0.00 0.00 0.00 3.43
576 915 9.476202 TGAAGATTTCAATATAGACCACATACG 57.524 33.333 0.00 0.00 36.59 3.06
600 970 9.421806 TCCGTTCGTAAATATAAGTTTCTTTGA 57.578 29.630 0.00 0.00 0.00 2.69
601 971 9.685005 CTCCGTTCGTAAATATAAGTTTCTTTG 57.315 33.333 0.00 0.00 0.00 2.77
603 973 7.493645 CCCTCCGTTCGTAAATATAAGTTTCTT 59.506 37.037 0.00 0.00 0.00 2.52
605 975 6.980397 TCCCTCCGTTCGTAAATATAAGTTTC 59.020 38.462 0.00 0.00 0.00 2.78
607 977 6.097412 ACTCCCTCCGTTCGTAAATATAAGTT 59.903 38.462 0.00 0.00 0.00 2.66
611 981 6.299141 AGTACTCCCTCCGTTCGTAAATATA 58.701 40.000 0.00 0.00 0.00 0.86
619 989 1.742761 TGTAGTACTCCCTCCGTTCG 58.257 55.000 0.00 0.00 0.00 3.95
660 1056 9.678260 AGATCTTACAAGCTGACTTCATTTATT 57.322 29.630 0.00 0.00 32.29 1.40
748 1145 4.187694 CACCAAGTTAGAAGCTGAGATCC 58.812 47.826 0.00 0.00 0.00 3.36
761 1158 3.215975 AGCTAAAAACGGCACCAAGTTA 58.784 40.909 0.00 0.00 0.00 2.24
868 1833 2.223203 ACTAGTGCACATACGACGCTAC 60.223 50.000 21.04 0.00 0.00 3.58
952 1936 4.034048 CACGCAAGGCTAACTATAGTTTGG 59.966 45.833 22.66 16.16 46.39 3.28
976 3983 1.202639 TGTGTTGTGGATCGAGCTGTT 60.203 47.619 0.00 0.00 0.00 3.16
982 3989 2.551887 CCATTGTTGTGTTGTGGATCGA 59.448 45.455 0.00 0.00 31.59 3.59
984 3991 2.297033 AGCCATTGTTGTGTTGTGGATC 59.703 45.455 0.00 0.00 31.59 3.36
985 3992 2.297033 GAGCCATTGTTGTGTTGTGGAT 59.703 45.455 0.00 0.00 31.59 3.41
1344 4398 1.817217 CGAAGTTGCACTCGTCGCAA 61.817 55.000 11.72 5.09 46.67 4.85
1401 4455 2.202623 CGGCAGAGGTCGCAGTAC 60.203 66.667 0.00 0.00 34.18 2.73
1430 4484 4.269523 TTTCCCGGCACTGCTGCT 62.270 61.111 4.10 0.00 43.66 4.24
1452 4506 1.588597 CGCAGAGCACTCCTTCTGA 59.411 57.895 5.73 0.00 32.38 3.27
1473 4531 1.476110 GGGCTCCATGGTACGCATTTA 60.476 52.381 12.58 0.00 0.00 1.40
1504 4562 7.013274 GGGCATACAACAAACACATGATACTAT 59.987 37.037 0.00 0.00 0.00 2.12
1518 4576 0.179015 ACACGGTGGGCATACAACAA 60.179 50.000 13.48 0.00 0.00 2.83
1622 4792 5.696260 TGAAATGATACGTGAGCTTTACG 57.304 39.130 18.99 18.99 46.31 3.18
1624 4794 6.345298 TGGATGAAATGATACGTGAGCTTTA 58.655 36.000 0.00 0.00 0.00 1.85
1629 4799 5.178252 GGTGATGGATGAAATGATACGTGAG 59.822 44.000 0.00 0.00 0.00 3.51
1631 4801 4.815846 TGGTGATGGATGAAATGATACGTG 59.184 41.667 0.00 0.00 0.00 4.49
1667 4839 2.225343 TGATTGTTTGGATCTGCCCCTT 60.225 45.455 0.00 0.00 34.97 3.95
1696 4868 9.964354 TTAAGGACCATTAGATTATGATGATGG 57.036 33.333 0.00 0.00 39.84 3.51
1739 4911 3.749609 GTCTTTATTGCGTGGTTGGTAGT 59.250 43.478 0.00 0.00 0.00 2.73
1772 4944 1.292223 GCGGGGCAGATTAGCGATA 59.708 57.895 0.00 0.00 34.64 2.92
1799 4971 2.171489 GAGGTCGTGCGGCAGTTTTC 62.171 60.000 1.18 0.00 0.00 2.29
1804 4976 4.803426 GAGGAGGTCGTGCGGCAG 62.803 72.222 1.18 0.00 0.00 4.85
1806 4978 3.665675 AATGAGGAGGTCGTGCGGC 62.666 63.158 0.00 0.00 0.00 6.53
1910 5104 4.069232 CGACCCGCAGAGGCTTCA 62.069 66.667 0.00 0.00 39.21 3.02
2090 5974 5.556915 TGACCTTTTCCTGAATTCGTATGT 58.443 37.500 0.04 0.00 0.00 2.29
2095 5979 6.072112 TCTTTTGACCTTTTCCTGAATTCG 57.928 37.500 0.04 0.00 0.00 3.34
2097 5981 9.112725 CAATTTCTTTTGACCTTTTCCTGAATT 57.887 29.630 0.00 0.00 0.00 2.17
2106 5990 6.183360 CCTGGTACCAATTTCTTTTGACCTTT 60.183 38.462 17.11 0.00 29.32 3.11
2119 6003 1.618343 GCACAAAGCCTGGTACCAATT 59.382 47.619 17.11 8.38 37.23 2.32
2188 6072 5.240623 CCCTGCTTTGTTGACTGTTGTAATA 59.759 40.000 0.00 0.00 0.00 0.98
2267 6151 9.855021 GATACCTTAGCACACAAACAATTTATT 57.145 29.630 0.00 0.00 0.00 1.40
2268 6152 9.019656 TGATACCTTAGCACACAAACAATTTAT 57.980 29.630 0.00 0.00 0.00 1.40
2331 6215 5.066764 GTCTAGAAGTGTGGTAGATGGAGAC 59.933 48.000 0.00 0.00 0.00 3.36
2332 6216 5.194432 GTCTAGAAGTGTGGTAGATGGAGA 58.806 45.833 0.00 0.00 0.00 3.71
2333 6217 4.950475 TGTCTAGAAGTGTGGTAGATGGAG 59.050 45.833 0.00 0.00 0.00 3.86
2334 6218 4.930696 TGTCTAGAAGTGTGGTAGATGGA 58.069 43.478 0.00 0.00 0.00 3.41
2335 6219 5.661056 TTGTCTAGAAGTGTGGTAGATGG 57.339 43.478 0.00 0.00 0.00 3.51
2336 6220 8.633561 TGATATTGTCTAGAAGTGTGGTAGATG 58.366 37.037 0.00 0.00 0.00 2.90
2337 6221 8.634444 GTGATATTGTCTAGAAGTGTGGTAGAT 58.366 37.037 0.00 0.00 0.00 1.98
2338 6222 7.068348 GGTGATATTGTCTAGAAGTGTGGTAGA 59.932 40.741 0.00 0.00 0.00 2.59
2468 6352 3.562973 GGCACAATATGAGTGAGATGTGG 59.437 47.826 11.58 0.00 39.30 4.17


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

AutoCloner maintained by Alex Coulton.