Multiple sequence alignment - TraesCS7B01G307700

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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 TraesCS7B01G307700 chr7B 100.000 3837 0 0 1 3837 551537951 551541787 0.000000e+00 7086.0
1 TraesCS7B01G307700 chr7B 90.683 2050 107 41 873 2895 551897094 551899086 0.000000e+00 2651.0
2 TraesCS7B01G307700 chr7B 93.303 881 53 2 2945 3825 297212708 297211834 0.000000e+00 1295.0
3 TraesCS7B01G307700 chr7B 92.897 887 57 1 2939 3825 379183636 379184516 0.000000e+00 1284.0
4 TraesCS7B01G307700 chr7D 92.066 2483 130 35 172 2604 518092054 518089589 0.000000e+00 3432.0
5 TraesCS7B01G307700 chr7D 91.198 2079 121 32 873 2929 518573504 518575542 0.000000e+00 2769.0
6 TraesCS7B01G307700 chr7D 90.848 896 59 14 1973 2865 518558394 518559269 0.000000e+00 1179.0
7 TraesCS7B01G307700 chr7D 90.762 866 54 17 2007 2865 518602073 518602919 0.000000e+00 1133.0
8 TraesCS7B01G307700 chr7D 84.146 82 9 3 2787 2865 518089546 518089466 4.110000e-10 76.8
9 TraesCS7B01G307700 chr7A 93.147 2043 102 19 615 2638 593016516 593014493 0.000000e+00 2963.0
10 TraesCS7B01G307700 chr7A 91.304 2139 120 31 525 2630 593375790 593377895 0.000000e+00 2859.0
11 TraesCS7B01G307700 chr7A 92.719 879 58 1 2947 3825 552428002 552427130 0.000000e+00 1264.0
12 TraesCS7B01G307700 chr7A 86.607 224 16 6 172 382 593373645 593373867 6.410000e-58 235.0
13 TraesCS7B01G307700 chr7A 81.818 143 15 6 374 505 593375143 593375285 4.050000e-20 110.0
14 TraesCS7B01G307700 chr3A 99.444 899 5 0 2939 3837 509652 510550 0.000000e+00 1633.0
15 TraesCS7B01G307700 chr1A 98.888 899 10 0 2939 3837 335110977 335111875 0.000000e+00 1605.0
16 TraesCS7B01G307700 chr6B 95.996 899 13 7 2939 3837 247012633 247011758 0.000000e+00 1439.0
17 TraesCS7B01G307700 chr2B 93.174 879 53 2 2947 3825 127182531 127183402 0.000000e+00 1284.0
18 TraesCS7B01G307700 chr2B 94.340 106 5 1 3 108 9278584 9278688 1.100000e-35 161.0
19 TraesCS7B01G307700 chr6A 92.873 884 57 1 2942 3825 159942991 159943868 0.000000e+00 1279.0
20 TraesCS7B01G307700 chr6D 94.920 689 35 0 3137 3825 38483430 38484118 0.000000e+00 1079.0
21 TraesCS7B01G307700 chr1B 77.801 1446 264 43 1122 2536 16428287 16426868 0.000000e+00 839.0
22 TraesCS7B01G307700 chr1D 80.509 903 158 14 1643 2536 10935927 10935034 0.000000e+00 676.0
23 TraesCS7B01G307700 chr5A 92.157 459 34 2 2991 3448 219130111 219130568 0.000000e+00 647.0
24 TraesCS7B01G307700 chr3B 84.154 650 88 13 1902 2543 712559071 712559713 1.960000e-172 616.0
25 TraesCS7B01G307700 chr4D 97.500 40 1 0 243 282 460708027 460708066 6.880000e-08 69.4
26 TraesCS7B01G307700 chr4D 97.500 40 0 1 243 282 460707201 460707239 2.470000e-07 67.6


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 TraesCS7B01G307700 chr7B 551537951 551541787 3836 False 7086.0 7086 100.000000 1 3837 1 chr7B.!!$F2 3836
1 TraesCS7B01G307700 chr7B 551897094 551899086 1992 False 2651.0 2651 90.683000 873 2895 1 chr7B.!!$F3 2022
2 TraesCS7B01G307700 chr7B 297211834 297212708 874 True 1295.0 1295 93.303000 2945 3825 1 chr7B.!!$R1 880
3 TraesCS7B01G307700 chr7B 379183636 379184516 880 False 1284.0 1284 92.897000 2939 3825 1 chr7B.!!$F1 886
4 TraesCS7B01G307700 chr7D 518573504 518575542 2038 False 2769.0 2769 91.198000 873 2929 1 chr7D.!!$F2 2056
5 TraesCS7B01G307700 chr7D 518089466 518092054 2588 True 1754.4 3432 88.106000 172 2865 2 chr7D.!!$R1 2693
6 TraesCS7B01G307700 chr7D 518558394 518559269 875 False 1179.0 1179 90.848000 1973 2865 1 chr7D.!!$F1 892
7 TraesCS7B01G307700 chr7D 518602073 518602919 846 False 1133.0 1133 90.762000 2007 2865 1 chr7D.!!$F3 858
8 TraesCS7B01G307700 chr7A 593014493 593016516 2023 True 2963.0 2963 93.147000 615 2638 1 chr7A.!!$R2 2023
9 TraesCS7B01G307700 chr7A 552427130 552428002 872 True 1264.0 1264 92.719000 2947 3825 1 chr7A.!!$R1 878
10 TraesCS7B01G307700 chr7A 593373645 593377895 4250 False 1068.0 2859 86.576333 172 2630 3 chr7A.!!$F1 2458
11 TraesCS7B01G307700 chr3A 509652 510550 898 False 1633.0 1633 99.444000 2939 3837 1 chr3A.!!$F1 898
12 TraesCS7B01G307700 chr1A 335110977 335111875 898 False 1605.0 1605 98.888000 2939 3837 1 chr1A.!!$F1 898
13 TraesCS7B01G307700 chr6B 247011758 247012633 875 True 1439.0 1439 95.996000 2939 3837 1 chr6B.!!$R1 898
14 TraesCS7B01G307700 chr2B 127182531 127183402 871 False 1284.0 1284 93.174000 2947 3825 1 chr2B.!!$F2 878
15 TraesCS7B01G307700 chr6A 159942991 159943868 877 False 1279.0 1279 92.873000 2942 3825 1 chr6A.!!$F1 883
16 TraesCS7B01G307700 chr6D 38483430 38484118 688 False 1079.0 1079 94.920000 3137 3825 1 chr6D.!!$F1 688
17 TraesCS7B01G307700 chr1B 16426868 16428287 1419 True 839.0 839 77.801000 1122 2536 1 chr1B.!!$R1 1414
18 TraesCS7B01G307700 chr1D 10935034 10935927 893 True 676.0 676 80.509000 1643 2536 1 chr1D.!!$R1 893
19 TraesCS7B01G307700 chr3B 712559071 712559713 642 False 616.0 616 84.154000 1902 2543 1 chr3B.!!$F1 641

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
25 26 0.035458 CTCCCTTCTGGTCGCTGTTT 59.965 55.0 0.00 0.0 34.77 2.83 F
51 52 0.042131 AGGGACCCTACCGAACATCA 59.958 55.0 12.85 0.0 28.47 3.07 F
1438 3331 0.109086 CCGACGTTGATCTCAGTGCT 60.109 55.0 3.74 0.0 0.00 4.40 F
2225 4149 0.110486 TGGTGAAGAAGGCCAAGTCC 59.890 55.0 5.01 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 3073 0.609681 AGAGCGTCTTCGTCTCCCTT 60.610 55.000 0.00 0.0 39.28 3.95 R
1715 3627 3.664025 CTCGAACTGCATCCCGCCA 62.664 63.158 0.00 0.0 41.33 5.69 R
2729 4659 0.591994 TTCGACGTACCACACACACG 60.592 55.000 0.00 0.0 41.32 4.49 R
3557 5527 1.137404 GAACGTCCGCGCTTACCTA 59.863 57.895 5.56 0.0 42.83 3.08 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
18 19 2.983512 TGAGCTCTCCCTTCTGGTC 58.016 57.895 16.19 0.00 34.77 4.02
19 20 0.967887 TGAGCTCTCCCTTCTGGTCG 60.968 60.000 16.19 0.00 34.77 4.79
20 21 2.185608 GCTCTCCCTTCTGGTCGC 59.814 66.667 0.00 0.00 34.77 5.19
21 22 2.355193 GCTCTCCCTTCTGGTCGCT 61.355 63.158 0.00 0.00 34.77 4.93
22 23 1.515020 CTCTCCCTTCTGGTCGCTG 59.485 63.158 0.00 0.00 34.77 5.18
23 24 1.228894 TCTCCCTTCTGGTCGCTGT 60.229 57.895 0.00 0.00 34.77 4.40
24 25 0.832135 TCTCCCTTCTGGTCGCTGTT 60.832 55.000 0.00 0.00 34.77 3.16
25 26 0.035458 CTCCCTTCTGGTCGCTGTTT 59.965 55.000 0.00 0.00 34.77 2.83
26 27 0.250295 TCCCTTCTGGTCGCTGTTTG 60.250 55.000 0.00 0.00 34.77 2.93
27 28 0.535102 CCCTTCTGGTCGCTGTTTGT 60.535 55.000 0.00 0.00 0.00 2.83
28 29 0.588252 CCTTCTGGTCGCTGTTTGTG 59.412 55.000 0.00 0.00 0.00 3.33
29 30 0.588252 CTTCTGGTCGCTGTTTGTGG 59.412 55.000 0.00 0.00 0.00 4.17
30 31 1.444119 TTCTGGTCGCTGTTTGTGGC 61.444 55.000 0.00 0.00 0.00 5.01
31 32 1.893808 CTGGTCGCTGTTTGTGGCT 60.894 57.895 0.00 0.00 0.00 4.75
32 33 0.602638 CTGGTCGCTGTTTGTGGCTA 60.603 55.000 0.00 0.00 0.00 3.93
33 34 0.602638 TGGTCGCTGTTTGTGGCTAG 60.603 55.000 0.00 0.00 0.00 3.42
34 35 1.298859 GGTCGCTGTTTGTGGCTAGG 61.299 60.000 0.00 0.00 0.00 3.02
35 36 1.003839 TCGCTGTTTGTGGCTAGGG 60.004 57.895 0.00 0.00 0.00 3.53
36 37 1.003839 CGCTGTTTGTGGCTAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
37 38 1.298859 CGCTGTTTGTGGCTAGGGAC 61.299 60.000 0.00 0.00 0.00 4.46
38 39 0.960861 GCTGTTTGTGGCTAGGGACC 60.961 60.000 0.00 0.00 0.00 4.46
39 40 0.322546 CTGTTTGTGGCTAGGGACCC 60.323 60.000 0.59 0.59 0.00 4.46
40 41 0.770557 TGTTTGTGGCTAGGGACCCT 60.771 55.000 19.48 19.48 37.71 4.34
41 42 1.282382 GTTTGTGGCTAGGGACCCTA 58.718 55.000 19.65 19.65 34.61 3.53
42 43 1.065636 GTTTGTGGCTAGGGACCCTAC 60.066 57.143 16.95 10.18 34.61 3.18
43 44 0.619543 TTGTGGCTAGGGACCCTACC 60.620 60.000 16.95 20.67 34.61 3.18
44 45 2.132352 GTGGCTAGGGACCCTACCG 61.132 68.421 16.95 9.23 34.61 4.02
45 46 2.318966 TGGCTAGGGACCCTACCGA 61.319 63.158 16.95 4.74 34.61 4.69
46 47 1.075748 GGCTAGGGACCCTACCGAA 60.076 63.158 16.95 0.00 34.61 4.30
47 48 1.398174 GGCTAGGGACCCTACCGAAC 61.398 65.000 16.95 3.98 34.61 3.95
48 49 0.685458 GCTAGGGACCCTACCGAACA 60.685 60.000 16.95 0.00 34.61 3.18
49 50 2.033208 GCTAGGGACCCTACCGAACAT 61.033 57.143 16.95 0.00 34.61 2.71
50 51 1.962100 CTAGGGACCCTACCGAACATC 59.038 57.143 16.95 0.00 34.61 3.06
51 52 0.042131 AGGGACCCTACCGAACATCA 59.958 55.000 12.85 0.00 28.47 3.07
52 53 0.177373 GGGACCCTACCGAACATCAC 59.823 60.000 2.09 0.00 0.00 3.06
53 54 1.192428 GGACCCTACCGAACATCACT 58.808 55.000 0.00 0.00 0.00 3.41
54 55 1.553704 GGACCCTACCGAACATCACTT 59.446 52.381 0.00 0.00 0.00 3.16
55 56 2.618053 GACCCTACCGAACATCACTTG 58.382 52.381 0.00 0.00 0.00 3.16
56 57 1.975680 ACCCTACCGAACATCACTTGT 59.024 47.619 0.00 0.00 41.53 3.16
57 58 3.167485 ACCCTACCGAACATCACTTGTA 58.833 45.455 0.00 0.00 37.68 2.41
58 59 3.773119 ACCCTACCGAACATCACTTGTAT 59.227 43.478 0.00 0.00 37.68 2.29
59 60 4.224370 ACCCTACCGAACATCACTTGTATT 59.776 41.667 0.00 0.00 37.68 1.89
60 61 4.809426 CCCTACCGAACATCACTTGTATTC 59.191 45.833 0.00 0.00 37.68 1.75
61 62 4.809426 CCTACCGAACATCACTTGTATTCC 59.191 45.833 0.00 0.00 37.68 3.01
62 63 4.553330 ACCGAACATCACTTGTATTCCT 57.447 40.909 0.00 0.00 37.68 3.36
63 64 4.906618 ACCGAACATCACTTGTATTCCTT 58.093 39.130 0.00 0.00 37.68 3.36
64 65 4.935808 ACCGAACATCACTTGTATTCCTTC 59.064 41.667 0.00 0.00 37.68 3.46
65 66 4.032900 CCGAACATCACTTGTATTCCTTCG 59.967 45.833 0.00 0.00 37.68 3.79
66 67 4.032900 CGAACATCACTTGTATTCCTTCGG 59.967 45.833 0.00 0.00 37.68 4.30
67 68 4.553330 ACATCACTTGTATTCCTTCGGT 57.447 40.909 0.00 0.00 36.57 4.69
68 69 4.253685 ACATCACTTGTATTCCTTCGGTG 58.746 43.478 0.00 0.00 36.57 4.94
69 70 4.253685 CATCACTTGTATTCCTTCGGTGT 58.746 43.478 0.00 0.00 0.00 4.16
70 71 4.345859 TCACTTGTATTCCTTCGGTGTT 57.654 40.909 0.00 0.00 0.00 3.32
71 72 5.471556 TCACTTGTATTCCTTCGGTGTTA 57.528 39.130 0.00 0.00 0.00 2.41
72 73 6.045072 TCACTTGTATTCCTTCGGTGTTAT 57.955 37.500 0.00 0.00 0.00 1.89
73 74 6.103997 TCACTTGTATTCCTTCGGTGTTATC 58.896 40.000 0.00 0.00 0.00 1.75
74 75 6.070995 TCACTTGTATTCCTTCGGTGTTATCT 60.071 38.462 0.00 0.00 0.00 1.98
75 76 6.594159 CACTTGTATTCCTTCGGTGTTATCTT 59.406 38.462 0.00 0.00 0.00 2.40
76 77 7.119262 CACTTGTATTCCTTCGGTGTTATCTTT 59.881 37.037 0.00 0.00 0.00 2.52
77 78 7.664318 ACTTGTATTCCTTCGGTGTTATCTTTT 59.336 33.333 0.00 0.00 0.00 2.27
78 79 7.372451 TGTATTCCTTCGGTGTTATCTTTTG 57.628 36.000 0.00 0.00 0.00 2.44
79 80 7.162761 TGTATTCCTTCGGTGTTATCTTTTGA 58.837 34.615 0.00 0.00 0.00 2.69
80 81 7.662258 TGTATTCCTTCGGTGTTATCTTTTGAA 59.338 33.333 0.00 0.00 0.00 2.69
81 82 7.703058 ATTCCTTCGGTGTTATCTTTTGAAT 57.297 32.000 0.00 0.00 0.00 2.57
82 83 8.801882 ATTCCTTCGGTGTTATCTTTTGAATA 57.198 30.769 0.00 0.00 0.00 1.75
83 84 8.624367 TTCCTTCGGTGTTATCTTTTGAATAA 57.376 30.769 0.00 0.00 0.00 1.40
84 85 8.624367 TCCTTCGGTGTTATCTTTTGAATAAA 57.376 30.769 0.00 0.00 0.00 1.40
85 86 9.069082 TCCTTCGGTGTTATCTTTTGAATAAAA 57.931 29.630 0.00 0.00 34.75 1.52
86 87 9.855021 CCTTCGGTGTTATCTTTTGAATAAAAT 57.145 29.630 0.00 0.00 35.39 1.82
89 90 9.849166 TCGGTGTTATCTTTTGAATAAAATTCC 57.151 29.630 0.00 0.00 35.39 3.01
90 91 9.855021 CGGTGTTATCTTTTGAATAAAATTCCT 57.145 29.630 0.00 0.00 35.39 3.36
101 102 9.581289 TTTGAATAAAATTCCTAGTTCACCTCA 57.419 29.630 0.00 0.00 0.00 3.86
102 103 9.581289 TTGAATAAAATTCCTAGTTCACCTCAA 57.419 29.630 0.00 0.00 0.00 3.02
103 104 9.581289 TGAATAAAATTCCTAGTTCACCTCAAA 57.419 29.630 0.00 0.00 0.00 2.69
299 305 9.750125 AAAAAGAAACTACCTAATCAAAAGCTG 57.250 29.630 0.00 0.00 0.00 4.24
424 1727 8.915871 AAACTGTTATTCAATTGATTCATCCG 57.084 30.769 9.40 0.00 0.00 4.18
425 1728 7.864108 ACTGTTATTCAATTGATTCATCCGA 57.136 32.000 9.40 0.00 0.00 4.55
426 1729 7.923888 ACTGTTATTCAATTGATTCATCCGAG 58.076 34.615 9.40 1.53 0.00 4.63
427 1730 7.554118 ACTGTTATTCAATTGATTCATCCGAGT 59.446 33.333 9.40 2.11 0.00 4.18
428 1731 7.919690 TGTTATTCAATTGATTCATCCGAGTC 58.080 34.615 9.40 0.00 0.00 3.36
429 1732 5.663795 ATTCAATTGATTCATCCGAGTCG 57.336 39.130 9.40 5.29 30.69 4.18
440 1772 3.628005 CCGAGTCGGCGTTTATACA 57.372 52.632 20.50 0.00 41.17 2.29
452 1784 9.345517 GTCGGCGTTTATACATACTATGATTTA 57.654 33.333 6.85 0.00 0.00 1.40
516 2337 0.883833 CAAAGGCACGGAGATGCTTT 59.116 50.000 0.00 0.00 45.87 3.51
518 2339 0.326264 AAGGCACGGAGATGCTTTCT 59.674 50.000 0.00 0.00 40.56 2.52
539 2360 0.960861 CTCTCCCCCGGTCAAAAAGC 60.961 60.000 0.00 0.00 0.00 3.51
540 2361 1.074951 CTCCCCCGGTCAAAAAGCT 59.925 57.895 0.00 0.00 0.00 3.74
541 2362 0.960861 CTCCCCCGGTCAAAAAGCTC 60.961 60.000 0.00 0.00 0.00 4.09
543 2364 2.332654 CCCCGGTCAAAAAGCTCCG 61.333 63.158 0.00 2.41 42.22 4.63
544 2365 1.302192 CCCGGTCAAAAAGCTCCGA 60.302 57.895 10.61 0.00 44.86 4.55
545 2366 1.298859 CCCGGTCAAAAAGCTCCGAG 61.299 60.000 10.61 0.00 44.86 4.63
703 2533 2.993937 TCTCGCCGGGAATTTGTTTAT 58.006 42.857 2.18 0.00 0.00 1.40
749 2579 3.207778 GCACGAGATCTACTGGAGTAGT 58.792 50.000 12.51 2.19 46.08 2.73
751 2581 4.211794 GCACGAGATCTACTGGAGTAGTAC 59.788 50.000 12.51 8.56 46.08 2.73
807 2643 2.707039 GTTCTTGTGTGCGCGTGT 59.293 55.556 8.43 0.00 0.00 4.49
871 2711 1.055551 ACTAACCCCCACCACACGAA 61.056 55.000 0.00 0.00 0.00 3.85
1044 2910 1.032114 GTACTGCATTCCCCACAGCC 61.032 60.000 0.00 0.00 34.72 4.85
1198 3091 0.456995 CAAGGGAGACGAAGACGCTC 60.457 60.000 0.00 0.00 43.96 5.03
1300 3193 3.845259 GACCCTGCCGCCGTCATA 61.845 66.667 0.00 0.00 0.00 2.15
1434 3327 0.526524 GAGGCCGACGTTGATCTCAG 60.527 60.000 3.74 0.00 0.00 3.35
1438 3331 0.109086 CCGACGTTGATCTCAGTGCT 60.109 55.000 3.74 0.00 0.00 4.40
1559 3461 2.975489 CCCTTGCTCTACATCCAGGTAT 59.025 50.000 0.00 0.00 0.00 2.73
2066 3990 3.733960 CACGACGAGGAGGTGCGA 61.734 66.667 0.00 0.00 0.00 5.10
2225 4149 0.110486 TGGTGAAGAAGGCCAAGTCC 59.890 55.000 5.01 0.00 0.00 3.85
2672 4600 2.283145 ATAAGTGCATCTCCATGGGC 57.717 50.000 13.02 7.91 0.00 5.36
2676 4604 2.190313 GCATCTCCATGGGCGACA 59.810 61.111 13.02 0.00 0.00 4.35
2716 4644 4.044426 CCAAGTTTTGCTCTTGTGCTTAC 58.956 43.478 0.00 0.00 40.15 2.34
2729 4659 8.713271 GCTCTTGTGCTTACTATTTACATATCC 58.287 37.037 0.00 0.00 0.00 2.59
2742 4672 3.241067 ACATATCCGTGTGTGTGGTAC 57.759 47.619 0.00 0.00 0.00 3.34
2745 4675 0.038892 ATCCGTGTGTGTGGTACGTC 60.039 55.000 0.00 0.00 36.17 4.34
2807 4737 5.815222 GTGCAATTTGTATGTAATTTCCCCC 59.185 40.000 0.00 0.00 0.00 5.40
2865 4811 9.268282 ACTGGATCTACTAGTAAGGAATGAAAA 57.732 33.333 3.76 0.00 38.52 2.29
2867 4813 8.705594 TGGATCTACTAGTAAGGAATGAAAAGG 58.294 37.037 3.76 0.00 0.00 3.11
2924 4874 5.310451 GGGAGTGGATTAACAACTACACAA 58.690 41.667 0.00 0.00 0.00 3.33
2932 4882 8.281212 GGATTAACAACTACACAATCCAATCT 57.719 34.615 6.75 0.00 42.72 2.40
2933 4883 8.739972 GGATTAACAACTACACAATCCAATCTT 58.260 33.333 6.75 0.00 42.72 2.40
2936 4886 6.575162 ACAACTACACAATCCAATCTTTCC 57.425 37.500 0.00 0.00 0.00 3.13
2937 4887 5.476945 ACAACTACACAATCCAATCTTTCCC 59.523 40.000 0.00 0.00 0.00 3.97
3557 5527 1.215647 GTCACCGTCCATCTTCGCT 59.784 57.895 0.00 0.00 0.00 4.93
3723 5693 4.030452 GCAACAGCCACTGGACGC 62.030 66.667 0.00 0.00 35.51 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.813192 CGACCAGAAGGGAGAGCTC 59.187 63.158 5.27 5.27 41.15 4.09
2 3 2.355193 GCGACCAGAAGGGAGAGCT 61.355 63.158 0.00 0.00 41.15 4.09
3 4 2.185608 GCGACCAGAAGGGAGAGC 59.814 66.667 0.00 0.00 41.15 4.09
4 5 1.254284 ACAGCGACCAGAAGGGAGAG 61.254 60.000 0.00 0.00 41.15 3.20
5 6 0.832135 AACAGCGACCAGAAGGGAGA 60.832 55.000 0.00 0.00 41.15 3.71
6 7 0.035458 AAACAGCGACCAGAAGGGAG 59.965 55.000 0.00 0.00 41.15 4.30
7 8 0.250295 CAAACAGCGACCAGAAGGGA 60.250 55.000 0.00 0.00 41.15 4.20
8 9 0.535102 ACAAACAGCGACCAGAAGGG 60.535 55.000 0.00 0.00 44.81 3.95
9 10 0.588252 CACAAACAGCGACCAGAAGG 59.412 55.000 0.00 0.00 42.21 3.46
10 11 0.588252 CCACAAACAGCGACCAGAAG 59.412 55.000 0.00 0.00 0.00 2.85
11 12 1.444119 GCCACAAACAGCGACCAGAA 61.444 55.000 0.00 0.00 0.00 3.02
12 13 1.891919 GCCACAAACAGCGACCAGA 60.892 57.895 0.00 0.00 0.00 3.86
13 14 0.602638 TAGCCACAAACAGCGACCAG 60.603 55.000 0.00 0.00 0.00 4.00
14 15 0.602638 CTAGCCACAAACAGCGACCA 60.603 55.000 0.00 0.00 0.00 4.02
15 16 1.298859 CCTAGCCACAAACAGCGACC 61.299 60.000 0.00 0.00 0.00 4.79
16 17 1.298859 CCCTAGCCACAAACAGCGAC 61.299 60.000 0.00 0.00 0.00 5.19
17 18 1.003839 CCCTAGCCACAAACAGCGA 60.004 57.895 0.00 0.00 0.00 4.93
18 19 1.003839 TCCCTAGCCACAAACAGCG 60.004 57.895 0.00 0.00 0.00 5.18
19 20 0.960861 GGTCCCTAGCCACAAACAGC 60.961 60.000 0.00 0.00 0.00 4.40
20 21 0.322546 GGGTCCCTAGCCACAAACAG 60.323 60.000 0.00 0.00 43.18 3.16
21 22 0.770557 AGGGTCCCTAGCCACAAACA 60.771 55.000 9.39 0.00 46.32 2.83
22 23 1.065636 GTAGGGTCCCTAGCCACAAAC 60.066 57.143 18.75 2.46 46.32 2.93
23 24 1.282382 GTAGGGTCCCTAGCCACAAA 58.718 55.000 18.75 0.00 46.32 2.83
24 25 0.619543 GGTAGGGTCCCTAGCCACAA 60.620 60.000 29.98 2.98 45.66 3.33
25 26 1.002533 GGTAGGGTCCCTAGCCACA 59.997 63.158 29.98 3.74 45.66 4.17
26 27 3.967215 GGTAGGGTCCCTAGCCAC 58.033 66.667 29.98 16.47 45.66 5.01
30 31 1.962100 GATGTTCGGTAGGGTCCCTAG 59.038 57.143 18.75 7.86 36.71 3.02
31 32 1.288633 TGATGTTCGGTAGGGTCCCTA 59.711 52.381 14.22 14.22 34.61 3.53
32 33 0.042131 TGATGTTCGGTAGGGTCCCT 59.958 55.000 16.73 16.73 37.71 4.20
33 34 0.177373 GTGATGTTCGGTAGGGTCCC 59.823 60.000 0.00 0.00 0.00 4.46
34 35 1.192428 AGTGATGTTCGGTAGGGTCC 58.808 55.000 0.00 0.00 0.00 4.46
35 36 2.028385 ACAAGTGATGTTCGGTAGGGTC 60.028 50.000 0.00 0.00 40.06 4.46
36 37 1.975680 ACAAGTGATGTTCGGTAGGGT 59.024 47.619 0.00 0.00 40.06 4.34
37 38 2.762535 ACAAGTGATGTTCGGTAGGG 57.237 50.000 0.00 0.00 40.06 3.53
38 39 4.809426 GGAATACAAGTGATGTTCGGTAGG 59.191 45.833 0.00 0.00 43.63 3.18
39 40 5.661458 AGGAATACAAGTGATGTTCGGTAG 58.339 41.667 0.00 0.00 43.63 3.18
40 41 5.670792 AGGAATACAAGTGATGTTCGGTA 57.329 39.130 0.00 0.00 43.63 4.02
41 42 4.553330 AGGAATACAAGTGATGTTCGGT 57.447 40.909 0.00 0.00 43.63 4.69
42 43 4.032900 CGAAGGAATACAAGTGATGTTCGG 59.967 45.833 0.00 0.00 43.63 4.30
43 44 5.131168 CGAAGGAATACAAGTGATGTTCG 57.869 43.478 0.00 0.00 43.63 3.95
60 61 9.855021 ATTTTATTCAAAAGATAACACCGAAGG 57.145 29.630 0.00 0.00 45.42 3.46
63 64 9.849166 GGAATTTTATTCAAAAGATAACACCGA 57.151 29.630 2.24 0.00 37.08 4.69
64 65 9.855021 AGGAATTTTATTCAAAAGATAACACCG 57.145 29.630 2.24 0.00 37.08 4.94
75 76 9.581289 TGAGGTGAACTAGGAATTTTATTCAAA 57.419 29.630 0.00 0.00 0.00 2.69
76 77 9.581289 TTGAGGTGAACTAGGAATTTTATTCAA 57.419 29.630 0.00 0.00 0.00 2.69
77 78 9.581289 TTTGAGGTGAACTAGGAATTTTATTCA 57.419 29.630 0.00 0.00 0.00 2.57
162 163 3.716601 CAACGCACAGGAATTCCTTTTT 58.283 40.909 24.93 9.16 46.09 1.94
163 164 2.545742 GCAACGCACAGGAATTCCTTTT 60.546 45.455 24.93 11.80 46.09 2.27
164 165 1.000274 GCAACGCACAGGAATTCCTTT 60.000 47.619 24.93 16.21 46.09 3.11
165 166 0.598065 GCAACGCACAGGAATTCCTT 59.402 50.000 24.93 13.10 46.09 3.36
167 168 0.109597 CAGCAACGCACAGGAATTCC 60.110 55.000 17.31 17.31 0.00 3.01
168 169 0.730494 GCAGCAACGCACAGGAATTC 60.730 55.000 0.00 0.00 0.00 2.17
169 170 1.286880 GCAGCAACGCACAGGAATT 59.713 52.632 0.00 0.00 0.00 2.17
170 171 1.859427 CTGCAGCAACGCACAGGAAT 61.859 55.000 0.00 0.00 36.86 3.01
175 176 1.375853 AACTTCTGCAGCAACGCACA 61.376 50.000 9.47 0.00 36.86 4.57
179 180 7.566858 AATATTTTTAACTTCTGCAGCAACG 57.433 32.000 9.47 0.00 0.00 4.10
319 327 8.561212 GGGTCGCATTTACATAATTGTACAATA 58.439 33.333 21.07 10.20 38.05 1.90
423 1726 3.881795 AGTATGTATAAACGCCGACTCG 58.118 45.455 0.00 0.00 0.00 4.18
424 1727 6.605849 TCATAGTATGTATAAACGCCGACTC 58.394 40.000 9.94 0.00 0.00 3.36
425 1728 6.564709 TCATAGTATGTATAAACGCCGACT 57.435 37.500 9.94 0.00 0.00 4.18
426 1729 7.807687 AATCATAGTATGTATAAACGCCGAC 57.192 36.000 9.94 0.00 0.00 4.79
427 1730 9.911138 TTAAATCATAGTATGTATAAACGCCGA 57.089 29.630 9.94 0.00 0.00 5.54
440 1772 6.148811 CCGGCCGTCAAATTAAATCATAGTAT 59.851 38.462 26.12 0.00 0.00 2.12
452 1784 2.675075 CCACCCGGCCGTCAAATT 60.675 61.111 26.12 0.00 0.00 1.82
516 2337 2.101801 TTTGACCGGGGGAGAGGAGA 62.102 60.000 6.32 0.00 0.00 3.71
518 2339 0.768997 TTTTTGACCGGGGGAGAGGA 60.769 55.000 6.32 0.00 0.00 3.71
521 2342 1.074248 GCTTTTTGACCGGGGGAGA 59.926 57.895 6.32 0.00 0.00 3.71
539 2360 1.268285 CGTGCAGATCAGTACTCGGAG 60.268 57.143 2.83 2.83 0.00 4.63
540 2361 0.733150 CGTGCAGATCAGTACTCGGA 59.267 55.000 4.92 0.00 0.00 4.55
541 2362 0.452184 ACGTGCAGATCAGTACTCGG 59.548 55.000 4.92 0.00 0.00 4.63
543 2364 2.420372 TCAGACGTGCAGATCAGTACTC 59.580 50.000 0.00 2.33 0.00 2.59
544 2365 2.437413 TCAGACGTGCAGATCAGTACT 58.563 47.619 0.00 0.00 0.00 2.73
545 2366 2.917971 GTTCAGACGTGCAGATCAGTAC 59.082 50.000 0.00 0.00 0.00 2.73
703 2533 2.181521 AAAGTCGCGCGGAAAACCA 61.182 52.632 31.69 5.26 0.00 3.67
749 2579 7.347448 CAATGATAGTAAGCACGTACGTAGTA 58.653 38.462 22.34 12.87 45.11 1.82
751 2581 5.115171 GCAATGATAGTAAGCACGTACGTAG 59.885 44.000 22.34 16.04 0.00 3.51
807 2643 1.876416 GCTAAGCAAAGACCCGACACA 60.876 52.381 0.00 0.00 0.00 3.72
871 2711 2.428890 GGACTGAGAATGAGATCGGTGT 59.571 50.000 0.00 0.00 35.18 4.16
1058 2924 3.176924 AGAGACTCTGTGGGTATGTGT 57.823 47.619 3.56 0.00 0.00 3.72
1062 2928 3.963476 AGCTAGAGACTCTGTGGGTAT 57.037 47.619 15.55 0.00 0.00 2.73
1180 3073 0.609681 AGAGCGTCTTCGTCTCCCTT 60.610 55.000 0.00 0.00 39.28 3.95
1434 3327 3.782244 CGCCGAAGTCAGCAGCAC 61.782 66.667 0.00 0.00 0.00 4.40
1438 3331 3.973516 ACGTCGCCGAAGTCAGCA 61.974 61.111 0.00 0.00 37.88 4.41
1715 3627 3.664025 CTCGAACTGCATCCCGCCA 62.664 63.158 0.00 0.00 41.33 5.69
2049 3973 3.733960 TCGCACCTCCTCGTCGTG 61.734 66.667 0.00 0.00 0.00 4.35
2050 3974 3.735029 GTCGCACCTCCTCGTCGT 61.735 66.667 0.00 0.00 0.00 4.34
2066 3990 1.935300 GCGTTCACGATGAAGGACAGT 60.935 52.381 18.20 0.00 42.87 3.55
2606 4530 2.438583 GTGACGACGTATGCTCTGTAC 58.561 52.381 0.00 0.00 0.00 2.90
2672 4600 4.355437 GTCAGTCAGAATATCACCTGTCG 58.645 47.826 0.00 0.00 0.00 4.35
2676 4604 4.780021 ACTTGGTCAGTCAGAATATCACCT 59.220 41.667 0.00 0.00 0.00 4.00
2716 4644 6.046593 ACCACACACACGGATATGTAAATAG 58.953 40.000 0.00 0.00 0.00 1.73
2729 4659 0.591994 TTCGACGTACCACACACACG 60.592 55.000 0.00 0.00 41.32 4.49
2742 4672 1.002900 ACACTGTTGGCAATTTCGACG 60.003 47.619 1.92 0.00 0.00 5.12
2745 4675 3.617540 TGTACACTGTTGGCAATTTCG 57.382 42.857 1.92 0.00 0.00 3.46
2890 4840 4.308458 CACTCCCCGTGTTCCGCA 62.308 66.667 0.00 0.00 38.84 5.69
2911 4861 7.175990 GGGAAAGATTGGATTGTGTAGTTGTTA 59.824 37.037 0.00 0.00 0.00 2.41
2924 4874 3.861082 AGGGAAAGAGGGAAAGATTGGAT 59.139 43.478 0.00 0.00 0.00 3.41
2929 4879 8.871570 TTATTAGTAGGGAAAGAGGGAAAGAT 57.128 34.615 0.00 0.00 0.00 2.40
2930 4880 8.689707 TTTATTAGTAGGGAAAGAGGGAAAGA 57.310 34.615 0.00 0.00 0.00 2.52
2931 4881 7.499563 GCTTTATTAGTAGGGAAAGAGGGAAAG 59.500 40.741 0.00 0.00 31.83 2.62
2932 4882 7.037153 TGCTTTATTAGTAGGGAAAGAGGGAAA 60.037 37.037 0.00 0.00 31.83 3.13
2933 4883 6.445786 TGCTTTATTAGTAGGGAAAGAGGGAA 59.554 38.462 0.00 0.00 31.83 3.97
2934 4884 5.968167 TGCTTTATTAGTAGGGAAAGAGGGA 59.032 40.000 0.00 0.00 31.83 4.20
2935 4885 6.248569 TGCTTTATTAGTAGGGAAAGAGGG 57.751 41.667 0.00 0.00 31.83 4.30
2936 4886 8.753497 AATTGCTTTATTAGTAGGGAAAGAGG 57.247 34.615 0.00 0.00 31.83 3.69
3320 5290 1.915769 GCCACACCAGGAGAGGAGT 60.916 63.158 4.47 0.00 32.39 3.85
3557 5527 1.137404 GAACGTCCGCGCTTACCTA 59.863 57.895 5.56 0.00 42.83 3.08
3723 5693 3.884693 TCATACAATGCATGCTTACCTGG 59.115 43.478 20.33 4.23 0.00 4.45


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

AutoCloner maintained by Alex Coulton.