Multiple sequence alignment - TraesCS2B01G409100

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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 TraesCS2B01G409100 chr2B 100.000 4072 0 0 1 4072 582315082 582311011 0.000000e+00 7520
1 TraesCS2B01G409100 chr2B 86.729 957 79 20 3085 4008 669496249 669497190 0.000000e+00 1020
2 TraesCS2B01G409100 chr2B 86.660 937 83 18 3093 4002 8622522 8623443 0.000000e+00 1000
3 TraesCS2B01G409100 chr2B 84.877 972 74 32 3091 3999 605493575 605492614 0.000000e+00 913
4 TraesCS2B01G409100 chr2B 79.433 953 125 31 3096 4003 669497177 669496251 3.480000e-170 608
5 TraesCS2B01G409100 chr2B 83.648 318 25 6 3708 3999 605493258 605493574 1.440000e-69 274
6 TraesCS2B01G409100 chr2B 90.345 145 14 0 2021 2165 785621750 785621894 1.490000e-44 191
7 TraesCS2B01G409100 chr2B 97.531 81 2 0 6 86 391452408 391452328 5.490000e-29 139
8 TraesCS2B01G409100 chr2B 97.500 80 2 0 6 85 650478248 650478327 1.970000e-28 137
9 TraesCS2B01G409100 chr2B 96.429 84 2 1 1 84 798983458 798983540 1.970000e-28 137
10 TraesCS2B01G409100 chr2B 95.294 85 3 1 1 85 606774454 606774537 2.550000e-27 134
11 TraesCS2B01G409100 chr2A 93.998 3049 100 33 100 3093 639054917 639057937 0.000000e+00 4540
12 TraesCS2B01G409100 chr2A 84.826 949 105 22 3085 4007 768980451 768981386 0.000000e+00 918
13 TraesCS2B01G409100 chr2A 93.243 74 4 1 3999 4071 639057928 639058001 1.550000e-19 108
14 TraesCS2B01G409100 chr2D 94.784 2876 87 25 255 3092 494657529 494654679 0.000000e+00 4421
15 TraesCS2B01G409100 chr2D 79.300 971 142 38 3088 4009 634646751 634645791 3.460000e-175 625
16 TraesCS2B01G409100 chr2D 89.888 178 8 5 99 266 494658037 494657860 1.910000e-53 220
17 TraesCS2B01G409100 chr2D 95.946 74 3 0 3999 4072 494654684 494654611 1.990000e-23 121
18 TraesCS2B01G409100 chr5A 96.943 916 11 5 3092 3999 697597671 697598577 0.000000e+00 1520
19 TraesCS2B01G409100 chr5A 78.006 341 57 13 1029 1360 281061687 281062018 8.930000e-47 198
20 TraesCS2B01G409100 chr5A 92.593 135 10 0 1861 1995 685018089 685017955 1.150000e-45 195
21 TraesCS2B01G409100 chrUn 85.880 949 77 25 3096 4001 272238471 272237537 0.000000e+00 957
22 TraesCS2B01G409100 chr3D 85.475 957 89 29 3088 4008 549723834 549724776 0.000000e+00 952
23 TraesCS2B01G409100 chr3D 88.482 191 20 2 3820 4009 13170783 13170972 3.170000e-56 230
24 TraesCS2B01G409100 chr1B 85.623 939 85 23 3091 3998 683781747 683782666 0.000000e+00 941
25 TraesCS2B01G409100 chr5B 85.307 946 91 24 3093 3999 597103283 597104219 0.000000e+00 933
26 TraesCS2B01G409100 chr5B 86.582 708 55 22 3092 3776 598612854 598612164 0.000000e+00 745
27 TraesCS2B01G409100 chr5B 79.623 265 46 6 1100 1360 229638595 229638855 2.500000e-42 183
28 TraesCS2B01G409100 chr5B 95.349 86 3 1 1 86 34558248 34558164 7.100000e-28 135
29 TraesCS2B01G409100 chr5B 95.294 85 3 1 1 85 578828579 578828496 2.550000e-27 134
30 TraesCS2B01G409100 chr1A 84.391 961 101 22 3091 4007 486402224 486401269 0.000000e+00 898
31 TraesCS2B01G409100 chr7A 83.844 947 109 17 3080 4002 126960702 126961628 0.000000e+00 861
32 TraesCS2B01G409100 chr7B 87.766 752 71 8 3092 3825 73716340 73717088 0.000000e+00 859
33 TraesCS2B01G409100 chr7B 96.471 85 2 1 1 85 80090518 80090435 5.490000e-29 139
34 TraesCS2B01G409100 chr1D 85.504 883 61 29 3171 3999 462905348 462904479 0.000000e+00 859
35 TraesCS2B01G409100 chr1D 83.627 965 81 26 3096 4000 462897733 462896786 0.000000e+00 835
36 TraesCS2B01G409100 chr4B 93.293 164 9 2 3844 4007 591275663 591275824 1.460000e-59 241
37 TraesCS2B01G409100 chr5D 77.419 341 59 13 1029 1360 214714876 214715207 1.930000e-43 187
38 TraesCS2B01G409100 chr6B 98.750 80 1 0 7 86 132430522 132430443 4.240000e-30 143
39 TraesCS2B01G409100 chr6B 95.294 85 3 1 1 85 7156936 7157019 2.550000e-27 134


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 TraesCS2B01G409100 chr2B 582311011 582315082 4071 True 7520.000000 7520 100.000000 1 4072 1 chr2B.!!$R2 4071
1 TraesCS2B01G409100 chr2B 669496249 669497190 941 False 1020.000000 1020 86.729000 3085 4008 1 chr2B.!!$F5 923
2 TraesCS2B01G409100 chr2B 8622522 8623443 921 False 1000.000000 1000 86.660000 3093 4002 1 chr2B.!!$F1 909
3 TraesCS2B01G409100 chr2B 605492614 605493575 961 True 913.000000 913 84.877000 3091 3999 1 chr2B.!!$R3 908
4 TraesCS2B01G409100 chr2B 669496251 669497177 926 True 608.000000 608 79.433000 3096 4003 1 chr2B.!!$R4 907
5 TraesCS2B01G409100 chr2A 639054917 639058001 3084 False 2324.000000 4540 93.620500 100 4071 2 chr2A.!!$F2 3971
6 TraesCS2B01G409100 chr2A 768980451 768981386 935 False 918.000000 918 84.826000 3085 4007 1 chr2A.!!$F1 922
7 TraesCS2B01G409100 chr2D 494654611 494658037 3426 True 1587.333333 4421 93.539333 99 4072 3 chr2D.!!$R2 3973
8 TraesCS2B01G409100 chr2D 634645791 634646751 960 True 625.000000 625 79.300000 3088 4009 1 chr2D.!!$R1 921
9 TraesCS2B01G409100 chr5A 697597671 697598577 906 False 1520.000000 1520 96.943000 3092 3999 1 chr5A.!!$F2 907
10 TraesCS2B01G409100 chrUn 272237537 272238471 934 True 957.000000 957 85.880000 3096 4001 1 chrUn.!!$R1 905
11 TraesCS2B01G409100 chr3D 549723834 549724776 942 False 952.000000 952 85.475000 3088 4008 1 chr3D.!!$F2 920
12 TraesCS2B01G409100 chr1B 683781747 683782666 919 False 941.000000 941 85.623000 3091 3998 1 chr1B.!!$F1 907
13 TraesCS2B01G409100 chr5B 597103283 597104219 936 False 933.000000 933 85.307000 3093 3999 1 chr5B.!!$F2 906
14 TraesCS2B01G409100 chr5B 598612164 598612854 690 True 745.000000 745 86.582000 3092 3776 1 chr5B.!!$R3 684
15 TraesCS2B01G409100 chr1A 486401269 486402224 955 True 898.000000 898 84.391000 3091 4007 1 chr1A.!!$R1 916
16 TraesCS2B01G409100 chr7A 126960702 126961628 926 False 861.000000 861 83.844000 3080 4002 1 chr7A.!!$F1 922
17 TraesCS2B01G409100 chr7B 73716340 73717088 748 False 859.000000 859 87.766000 3092 3825 1 chr7B.!!$F1 733
18 TraesCS2B01G409100 chr1D 462904479 462905348 869 True 859.000000 859 85.504000 3171 3999 1 chr1D.!!$R2 828
19 TraesCS2B01G409100 chr1D 462896786 462897733 947 True 835.000000 835 83.627000 3096 4000 1 chr1D.!!$R1 904

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
391 760 0.041238 ACCTAGCTAGCCACAGTGGA 59.959 55.0 24.96 1.8 40.96 4.02 F
741 1129 0.321122 AAAGGCGCAAGAGAGACAGG 60.321 55.0 10.83 0.0 43.02 4.00 F
1873 2288 0.667993 CAAGTGTGTCGCCATTGGTT 59.332 50.0 4.26 0.0 0.00 3.67 F
2708 3129 0.251787 TCCTGCTGCTCCTGACACTA 60.252 55.0 0.00 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2585 0.525668 CGACGGACATGAGGCAGTAC 60.526 60.0 0.00 0.00 0.00 2.73 R
2600 3021 0.618968 CCAGGTAGAAGGCCAGGAGT 60.619 60.0 5.01 0.00 34.96 3.85 R
2732 3153 0.752376 ACTTCCCGTCGATCCTCCTC 60.752 60.0 0.00 0.00 0.00 3.71 R
3589 4132 1.054231 CATATGAGGAGCTCTGGCCA 58.946 55.0 14.64 4.71 39.73 5.36 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
17 18 3.634476 TCAGGAGGGGGAGAGGTT 58.366 61.111 0.00 0.00 0.00 3.50
18 19 1.876296 TCAGGAGGGGGAGAGGTTT 59.124 57.895 0.00 0.00 0.00 3.27
19 20 0.547712 TCAGGAGGGGGAGAGGTTTG 60.548 60.000 0.00 0.00 0.00 2.93
20 21 0.842467 CAGGAGGGGGAGAGGTTTGT 60.842 60.000 0.00 0.00 0.00 2.83
21 22 0.842467 AGGAGGGGGAGAGGTTTGTG 60.842 60.000 0.00 0.00 0.00 3.33
22 23 0.840722 GGAGGGGGAGAGGTTTGTGA 60.841 60.000 0.00 0.00 0.00 3.58
23 24 1.290134 GAGGGGGAGAGGTTTGTGAT 58.710 55.000 0.00 0.00 0.00 3.06
24 25 1.636003 GAGGGGGAGAGGTTTGTGATT 59.364 52.381 0.00 0.00 0.00 2.57
25 26 1.355720 AGGGGGAGAGGTTTGTGATTG 59.644 52.381 0.00 0.00 0.00 2.67
26 27 1.616994 GGGGGAGAGGTTTGTGATTGG 60.617 57.143 0.00 0.00 0.00 3.16
27 28 1.075536 GGGGAGAGGTTTGTGATTGGT 59.924 52.381 0.00 0.00 0.00 3.67
28 29 2.490902 GGGGAGAGGTTTGTGATTGGTT 60.491 50.000 0.00 0.00 0.00 3.67
29 30 2.558359 GGGAGAGGTTTGTGATTGGTTG 59.442 50.000 0.00 0.00 0.00 3.77
30 31 3.222603 GGAGAGGTTTGTGATTGGTTGT 58.777 45.455 0.00 0.00 0.00 3.32
31 32 3.636764 GGAGAGGTTTGTGATTGGTTGTT 59.363 43.478 0.00 0.00 0.00 2.83
32 33 4.825085 GGAGAGGTTTGTGATTGGTTGTTA 59.175 41.667 0.00 0.00 0.00 2.41
33 34 5.048713 GGAGAGGTTTGTGATTGGTTGTTAG 60.049 44.000 0.00 0.00 0.00 2.34
34 35 5.690865 AGAGGTTTGTGATTGGTTGTTAGA 58.309 37.500 0.00 0.00 0.00 2.10
35 36 6.306987 AGAGGTTTGTGATTGGTTGTTAGAT 58.693 36.000 0.00 0.00 0.00 1.98
36 37 6.207417 AGAGGTTTGTGATTGGTTGTTAGATG 59.793 38.462 0.00 0.00 0.00 2.90
37 38 6.068010 AGGTTTGTGATTGGTTGTTAGATGA 58.932 36.000 0.00 0.00 0.00 2.92
38 39 6.549364 AGGTTTGTGATTGGTTGTTAGATGAA 59.451 34.615 0.00 0.00 0.00 2.57
39 40 7.069331 AGGTTTGTGATTGGTTGTTAGATGAAA 59.931 33.333 0.00 0.00 0.00 2.69
40 41 7.708752 GGTTTGTGATTGGTTGTTAGATGAAAA 59.291 33.333 0.00 0.00 0.00 2.29
41 42 8.539674 GTTTGTGATTGGTTGTTAGATGAAAAC 58.460 33.333 0.00 0.00 0.00 2.43
42 43 7.340122 TGTGATTGGTTGTTAGATGAAAACA 57.660 32.000 0.00 0.00 35.12 2.83
43 44 7.424803 TGTGATTGGTTGTTAGATGAAAACAG 58.575 34.615 0.00 0.00 38.05 3.16
44 45 7.068103 TGTGATTGGTTGTTAGATGAAAACAGT 59.932 33.333 0.00 0.00 38.05 3.55
45 46 7.920682 GTGATTGGTTGTTAGATGAAAACAGTT 59.079 33.333 0.00 0.00 38.05 3.16
46 47 8.474025 TGATTGGTTGTTAGATGAAAACAGTTT 58.526 29.630 0.00 0.00 38.05 2.66
47 48 9.959749 GATTGGTTGTTAGATGAAAACAGTTTA 57.040 29.630 0.00 0.00 38.05 2.01
48 49 9.744468 ATTGGTTGTTAGATGAAAACAGTTTAC 57.256 29.630 0.00 0.00 38.05 2.01
49 50 8.282455 TGGTTGTTAGATGAAAACAGTTTACA 57.718 30.769 0.00 0.00 38.05 2.41
50 51 8.402472 TGGTTGTTAGATGAAAACAGTTTACAG 58.598 33.333 0.00 0.00 38.05 2.74
51 52 7.860872 GGTTGTTAGATGAAAACAGTTTACAGG 59.139 37.037 0.00 0.00 38.05 4.00
52 53 6.966021 TGTTAGATGAAAACAGTTTACAGGC 58.034 36.000 0.00 0.00 33.13 4.85
53 54 6.770785 TGTTAGATGAAAACAGTTTACAGGCT 59.229 34.615 0.00 0.00 33.13 4.58
54 55 7.284489 TGTTAGATGAAAACAGTTTACAGGCTT 59.716 33.333 0.00 0.00 33.13 4.35
55 56 6.715347 AGATGAAAACAGTTTACAGGCTTT 57.285 33.333 0.00 0.00 0.00 3.51
56 57 7.112452 AGATGAAAACAGTTTACAGGCTTTT 57.888 32.000 0.00 0.00 0.00 2.27
57 58 8.232913 AGATGAAAACAGTTTACAGGCTTTTA 57.767 30.769 0.00 0.00 0.00 1.52
58 59 8.135529 AGATGAAAACAGTTTACAGGCTTTTAC 58.864 33.333 0.00 0.00 0.00 2.01
59 60 7.159322 TGAAAACAGTTTACAGGCTTTTACA 57.841 32.000 0.00 0.00 0.00 2.41
60 61 7.603651 TGAAAACAGTTTACAGGCTTTTACAA 58.396 30.769 0.00 0.00 0.00 2.41
61 62 8.088981 TGAAAACAGTTTACAGGCTTTTACAAA 58.911 29.630 0.00 0.00 0.00 2.83
62 63 9.093970 GAAAACAGTTTACAGGCTTTTACAAAT 57.906 29.630 0.00 0.00 0.00 2.32
63 64 8.642908 AAACAGTTTACAGGCTTTTACAAATC 57.357 30.769 0.00 0.00 0.00 2.17
64 65 7.582667 ACAGTTTACAGGCTTTTACAAATCT 57.417 32.000 0.00 0.00 0.00 2.40
65 66 8.007405 ACAGTTTACAGGCTTTTACAAATCTT 57.993 30.769 0.00 0.00 0.00 2.40
66 67 8.474831 ACAGTTTACAGGCTTTTACAAATCTTT 58.525 29.630 0.00 0.00 0.00 2.52
67 68 8.755018 CAGTTTACAGGCTTTTACAAATCTTTG 58.245 33.333 1.19 1.19 43.62 2.77
85 86 9.643693 AAATCTTTGTATGTCTAGCATTTTTGG 57.356 29.630 5.22 0.00 38.94 3.28
86 87 7.759489 TCTTTGTATGTCTAGCATTTTTGGT 57.241 32.000 5.22 0.00 38.94 3.67
87 88 8.177119 TCTTTGTATGTCTAGCATTTTTGGTT 57.823 30.769 5.22 0.00 38.94 3.67
88 89 8.637986 TCTTTGTATGTCTAGCATTTTTGGTTT 58.362 29.630 5.22 0.00 38.94 3.27
89 90 9.260002 CTTTGTATGTCTAGCATTTTTGGTTTT 57.740 29.630 5.22 0.00 38.94 2.43
90 91 8.586570 TTGTATGTCTAGCATTTTTGGTTTTG 57.413 30.769 5.22 0.00 38.94 2.44
91 92 7.946207 TGTATGTCTAGCATTTTTGGTTTTGA 58.054 30.769 5.22 0.00 38.94 2.69
92 93 8.417106 TGTATGTCTAGCATTTTTGGTTTTGAA 58.583 29.630 5.22 0.00 38.94 2.69
93 94 7.951530 ATGTCTAGCATTTTTGGTTTTGAAG 57.048 32.000 0.00 0.00 33.14 3.02
94 95 6.872920 TGTCTAGCATTTTTGGTTTTGAAGT 58.127 32.000 0.00 0.00 0.00 3.01
95 96 6.978080 TGTCTAGCATTTTTGGTTTTGAAGTC 59.022 34.615 0.00 0.00 0.00 3.01
96 97 6.420903 GTCTAGCATTTTTGGTTTTGAAGTCC 59.579 38.462 0.00 0.00 0.00 3.85
97 98 4.450976 AGCATTTTTGGTTTTGAAGTCCC 58.549 39.130 0.00 0.00 0.00 4.46
140 148 2.840974 GCGAGAAGCCTAACAAGCA 58.159 52.632 0.00 0.00 40.81 3.91
146 154 0.895559 AAGCCTAACAAGCACCTGCC 60.896 55.000 0.00 0.00 43.38 4.85
199 207 2.484287 ATCTGGTGTTGGGGCTTCCG 62.484 60.000 0.00 0.00 38.76 4.30
266 281 1.077140 TGCCAAGCCACAGTTGTCA 60.077 52.632 0.00 0.00 0.00 3.58
267 282 0.682532 TGCCAAGCCACAGTTGTCAA 60.683 50.000 0.00 0.00 0.00 3.18
288 645 2.812591 ACACAGCTGCAGAAGAATCTTG 59.187 45.455 20.43 2.06 32.03 3.02
389 758 0.898320 ACACCTAGCTAGCCACAGTG 59.102 55.000 15.74 18.02 0.00 3.66
390 759 0.176680 CACCTAGCTAGCCACAGTGG 59.823 60.000 16.16 16.16 41.55 4.00
391 760 0.041238 ACCTAGCTAGCCACAGTGGA 59.959 55.000 24.96 1.80 40.96 4.02
392 761 0.749649 CCTAGCTAGCCACAGTGGAG 59.250 60.000 24.96 13.68 40.96 3.86
393 762 1.479709 CTAGCTAGCCACAGTGGAGT 58.520 55.000 24.96 11.84 40.96 3.85
546 932 6.401394 TCCACATAGTTCATGAAACTCTCTG 58.599 40.000 10.35 8.74 45.28 3.35
569 955 5.172205 GCTTTATTTGTTCGGGGCATTTTA 58.828 37.500 0.00 0.00 0.00 1.52
591 977 1.512364 CGTGTTGTTGTCGTGCAAATG 59.488 47.619 0.00 0.00 39.03 2.32
593 979 3.175152 GTGTTGTTGTCGTGCAAATGAA 58.825 40.909 0.00 0.00 39.03 2.57
603 989 2.290367 CGTGCAAATGAAGAGTTCACCA 59.710 45.455 0.00 0.00 43.48 4.17
726 1114 0.433492 CGTCTGCACGTACGAAAAGG 59.567 55.000 24.41 7.87 41.55 3.11
731 1119 1.565591 CACGTACGAAAAGGCGCAA 59.434 52.632 24.41 0.00 33.86 4.85
741 1129 0.321122 AAAGGCGCAAGAGAGACAGG 60.321 55.000 10.83 0.00 43.02 4.00
742 1130 2.125350 GGCGCAAGAGAGACAGGG 60.125 66.667 10.83 0.00 43.02 4.45
746 1134 0.891373 CGCAAGAGAGACAGGGAGAA 59.109 55.000 0.00 0.00 43.02 2.87
752 1140 2.110899 AGAGAGACAGGGAGAAACCAGA 59.889 50.000 0.00 0.00 41.20 3.86
886 1278 9.623000 ACCGTCCAAATAACTAATAGCTAAAAT 57.377 29.630 0.00 0.00 0.00 1.82
1437 1845 7.334671 TGTGATCCGCAACATAATTAACAACTA 59.665 33.333 0.00 0.00 0.00 2.24
1461 1869 3.291383 CAAACGGCCGGCCAAGAA 61.291 61.111 42.78 0.00 35.37 2.52
1603 2012 2.931649 GTGGGGTTCTTCGGGGGA 60.932 66.667 0.00 0.00 0.00 4.81
1858 2273 4.889241 GTATGCATACGCGTTTTACAAGT 58.111 39.130 20.78 0.00 42.97 3.16
1873 2288 0.667993 CAAGTGTGTCGCCATTGGTT 59.332 50.000 4.26 0.00 0.00 3.67
1964 2379 1.451927 GCCTTCATCATCGTGGCCA 60.452 57.895 0.00 0.00 37.81 5.36
2170 2585 2.653448 CTCATCGTCTCCGCGCTG 60.653 66.667 5.56 0.00 0.00 5.18
2242 2657 4.135153 GAGAGCGCGCCCTTCTCA 62.135 66.667 31.94 0.00 37.78 3.27
2503 2918 6.675413 ACTCCCACTAACTTGTGTATGTAA 57.325 37.500 0.00 0.00 36.30 2.41
2504 2919 6.698380 ACTCCCACTAACTTGTGTATGTAAG 58.302 40.000 0.00 0.00 36.30 2.34
2505 2920 6.495872 ACTCCCACTAACTTGTGTATGTAAGA 59.504 38.462 0.00 0.00 36.30 2.10
2507 2922 6.495872 TCCCACTAACTTGTGTATGTAAGACT 59.504 38.462 0.00 0.00 36.30 3.24
2508 2923 7.015877 TCCCACTAACTTGTGTATGTAAGACTT 59.984 37.037 0.00 0.00 36.30 3.01
2510 2925 9.355215 CCACTAACTTGTGTATGTAAGACTTAG 57.645 37.037 0.00 0.00 36.30 2.18
2521 2938 4.663334 TGTAAGACTTAGAGGCTCTGTCA 58.337 43.478 27.17 12.19 27.04 3.58
2600 3021 4.000988 TCGAGATGATATCGATCGGAACA 58.999 43.478 16.41 9.14 43.79 3.18
2603 3024 5.303747 AGATGATATCGATCGGAACACTC 57.696 43.478 16.41 6.41 34.49 3.51
2708 3129 0.251787 TCCTGCTGCTCCTGACACTA 60.252 55.000 0.00 0.00 0.00 2.74
2732 3153 0.249238 CAATCGGCTTCTCCCTCTCG 60.249 60.000 0.00 0.00 0.00 4.04
2822 3243 0.533531 TCTTCCACTGCACAGCACAG 60.534 55.000 0.00 0.00 41.08 3.66
3011 3432 0.321564 TGCACTCCACATACACTGCC 60.322 55.000 0.00 0.00 0.00 4.85
3074 3495 6.591448 CCAATGCAGACATATTATCTTAGCGA 59.409 38.462 0.00 0.00 34.62 4.93
3076 3497 9.305925 CAATGCAGACATATTATCTTAGCGATA 57.694 33.333 0.00 0.00 34.62 2.92
3077 3498 9.526713 AATGCAGACATATTATCTTAGCGATAG 57.473 33.333 0.00 0.00 34.08 2.08
3899 4519 2.671396 CACGAGGGACAAAAACTATCCG 59.329 50.000 0.00 0.00 32.90 4.18
4058 4679 2.432444 TGGAAATGTTCGTTGCCCTAG 58.568 47.619 0.00 0.00 0.00 3.02
4064 4685 3.478857 TGTTCGTTGCCCTAGAAAAGA 57.521 42.857 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.547712 CAAACCTCTCCCCCTCCTGA 60.548 60.000 0.00 0.00 0.00 3.86
1 2 0.842467 ACAAACCTCTCCCCCTCCTG 60.842 60.000 0.00 0.00 0.00 3.86
3 4 0.840722 TCACAAACCTCTCCCCCTCC 60.841 60.000 0.00 0.00 0.00 4.30
6 7 1.616994 CCAATCACAAACCTCTCCCCC 60.617 57.143 0.00 0.00 0.00 5.40
7 8 1.075536 ACCAATCACAAACCTCTCCCC 59.924 52.381 0.00 0.00 0.00 4.81
8 9 2.558359 CAACCAATCACAAACCTCTCCC 59.442 50.000 0.00 0.00 0.00 4.30
9 10 3.222603 ACAACCAATCACAAACCTCTCC 58.777 45.455 0.00 0.00 0.00 3.71
10 11 4.918810 AACAACCAATCACAAACCTCTC 57.081 40.909 0.00 0.00 0.00 3.20
12 13 6.206634 TCATCTAACAACCAATCACAAACCTC 59.793 38.462 0.00 0.00 0.00 3.85
13 14 6.068010 TCATCTAACAACCAATCACAAACCT 58.932 36.000 0.00 0.00 0.00 3.50
14 15 6.325919 TCATCTAACAACCAATCACAAACC 57.674 37.500 0.00 0.00 0.00 3.27
15 16 8.539674 GTTTTCATCTAACAACCAATCACAAAC 58.460 33.333 0.00 0.00 0.00 2.93
16 17 8.253810 TGTTTTCATCTAACAACCAATCACAAA 58.746 29.630 0.00 0.00 32.89 2.83
17 18 7.776107 TGTTTTCATCTAACAACCAATCACAA 58.224 30.769 0.00 0.00 32.89 3.33
18 19 7.068103 ACTGTTTTCATCTAACAACCAATCACA 59.932 33.333 0.00 0.00 35.28 3.58
19 20 7.425606 ACTGTTTTCATCTAACAACCAATCAC 58.574 34.615 0.00 0.00 35.28 3.06
20 21 7.581213 ACTGTTTTCATCTAACAACCAATCA 57.419 32.000 0.00 0.00 35.28 2.57
21 22 8.871686 AAACTGTTTTCATCTAACAACCAATC 57.128 30.769 0.00 0.00 35.28 2.67
22 23 9.744468 GTAAACTGTTTTCATCTAACAACCAAT 57.256 29.630 11.48 0.00 35.28 3.16
23 24 8.740906 TGTAAACTGTTTTCATCTAACAACCAA 58.259 29.630 11.48 0.00 35.28 3.67
24 25 8.282455 TGTAAACTGTTTTCATCTAACAACCA 57.718 30.769 11.48 0.00 35.28 3.67
25 26 7.860872 CCTGTAAACTGTTTTCATCTAACAACC 59.139 37.037 11.48 0.00 35.28 3.77
26 27 7.378728 GCCTGTAAACTGTTTTCATCTAACAAC 59.621 37.037 11.48 0.25 35.28 3.32
27 28 7.284489 AGCCTGTAAACTGTTTTCATCTAACAA 59.716 33.333 11.48 0.00 35.28 2.83
28 29 6.770785 AGCCTGTAAACTGTTTTCATCTAACA 59.229 34.615 11.48 6.82 34.55 2.41
29 30 7.203255 AGCCTGTAAACTGTTTTCATCTAAC 57.797 36.000 11.48 2.37 0.00 2.34
30 31 7.817418 AAGCCTGTAAACTGTTTTCATCTAA 57.183 32.000 11.48 0.00 0.00 2.10
31 32 7.817418 AAAGCCTGTAAACTGTTTTCATCTA 57.183 32.000 11.48 0.00 0.00 1.98
32 33 6.715347 AAAGCCTGTAAACTGTTTTCATCT 57.285 33.333 11.48 9.36 0.00 2.90
33 34 7.918562 TGTAAAAGCCTGTAAACTGTTTTCATC 59.081 33.333 11.48 7.45 0.00 2.92
34 35 7.777095 TGTAAAAGCCTGTAAACTGTTTTCAT 58.223 30.769 11.48 0.00 0.00 2.57
35 36 7.159322 TGTAAAAGCCTGTAAACTGTTTTCA 57.841 32.000 11.48 11.38 0.00 2.69
36 37 8.468720 TTTGTAAAAGCCTGTAAACTGTTTTC 57.531 30.769 11.48 7.02 0.00 2.29
37 38 9.093970 GATTTGTAAAAGCCTGTAAACTGTTTT 57.906 29.630 11.48 0.00 0.00 2.43
38 39 8.474831 AGATTTGTAAAAGCCTGTAAACTGTTT 58.525 29.630 10.98 10.98 0.00 2.83
39 40 8.007405 AGATTTGTAAAAGCCTGTAAACTGTT 57.993 30.769 0.00 0.00 0.00 3.16
40 41 7.582667 AGATTTGTAAAAGCCTGTAAACTGT 57.417 32.000 0.00 0.00 0.00 3.55
41 42 8.755018 CAAAGATTTGTAAAAGCCTGTAAACTG 58.245 33.333 0.00 0.00 33.59 3.16
42 43 8.871686 CAAAGATTTGTAAAAGCCTGTAAACT 57.128 30.769 0.00 0.00 33.59 2.66
59 60 9.643693 CCAAAAATGCTAGACATACAAAGATTT 57.356 29.630 0.00 0.00 38.34 2.17
60 61 8.806146 ACCAAAAATGCTAGACATACAAAGATT 58.194 29.630 0.00 0.00 38.34 2.40
61 62 8.353423 ACCAAAAATGCTAGACATACAAAGAT 57.647 30.769 0.00 0.00 38.34 2.40
62 63 7.759489 ACCAAAAATGCTAGACATACAAAGA 57.241 32.000 0.00 0.00 38.34 2.52
63 64 8.816640 AAACCAAAAATGCTAGACATACAAAG 57.183 30.769 0.00 0.00 38.34 2.77
64 65 9.039870 CAAAACCAAAAATGCTAGACATACAAA 57.960 29.630 0.00 0.00 38.34 2.83
65 66 8.417106 TCAAAACCAAAAATGCTAGACATACAA 58.583 29.630 0.00 0.00 38.34 2.41
66 67 7.946207 TCAAAACCAAAAATGCTAGACATACA 58.054 30.769 0.00 0.00 38.34 2.29
67 68 8.810652 TTCAAAACCAAAAATGCTAGACATAC 57.189 30.769 0.00 0.00 38.34 2.39
68 69 8.637986 ACTTCAAAACCAAAAATGCTAGACATA 58.362 29.630 0.00 0.00 38.34 2.29
69 70 7.500141 ACTTCAAAACCAAAAATGCTAGACAT 58.500 30.769 0.00 0.00 42.30 3.06
70 71 6.872920 ACTTCAAAACCAAAAATGCTAGACA 58.127 32.000 0.00 0.00 0.00 3.41
71 72 6.420903 GGACTTCAAAACCAAAAATGCTAGAC 59.579 38.462 0.00 0.00 0.00 2.59
72 73 6.462347 GGGACTTCAAAACCAAAAATGCTAGA 60.462 38.462 0.00 0.00 0.00 2.43
73 74 5.696270 GGGACTTCAAAACCAAAAATGCTAG 59.304 40.000 0.00 0.00 0.00 3.42
74 75 5.454045 GGGGACTTCAAAACCAAAAATGCTA 60.454 40.000 0.00 0.00 0.00 3.49
75 76 4.450976 GGGACTTCAAAACCAAAAATGCT 58.549 39.130 0.00 0.00 0.00 3.79
76 77 3.563808 GGGGACTTCAAAACCAAAAATGC 59.436 43.478 0.00 0.00 0.00 3.56
77 78 5.034852 AGGGGACTTCAAAACCAAAAATG 57.965 39.130 0.00 0.00 37.44 2.32
78 79 6.613679 TCTTAGGGGACTTCAAAACCAAAAAT 59.386 34.615 0.00 0.00 43.67 1.82
79 80 5.958987 TCTTAGGGGACTTCAAAACCAAAAA 59.041 36.000 0.00 0.00 43.67 1.94
80 81 5.520751 TCTTAGGGGACTTCAAAACCAAAA 58.479 37.500 0.00 0.00 43.67 2.44
81 82 5.132043 TCTTAGGGGACTTCAAAACCAAA 57.868 39.130 0.00 0.00 43.67 3.28
82 83 4.799715 TCTTAGGGGACTTCAAAACCAA 57.200 40.909 0.00 0.00 43.67 3.67
83 84 4.799715 TTCTTAGGGGACTTCAAAACCA 57.200 40.909 0.00 0.00 43.67 3.67
84 85 4.280174 GGTTTCTTAGGGGACTTCAAAACC 59.720 45.833 0.00 0.00 41.89 3.27
85 86 5.009710 CAGGTTTCTTAGGGGACTTCAAAAC 59.990 44.000 0.00 0.00 43.67 2.43
86 87 5.137551 CAGGTTTCTTAGGGGACTTCAAAA 58.862 41.667 0.00 0.00 43.67 2.44
87 88 4.167307 ACAGGTTTCTTAGGGGACTTCAAA 59.833 41.667 0.00 0.00 43.67 2.69
88 89 3.720002 ACAGGTTTCTTAGGGGACTTCAA 59.280 43.478 0.00 0.00 43.67 2.69
89 90 3.323775 ACAGGTTTCTTAGGGGACTTCA 58.676 45.455 0.00 0.00 43.67 3.02
90 91 3.307550 GGACAGGTTTCTTAGGGGACTTC 60.308 52.174 0.00 0.00 43.67 3.01
91 92 2.643304 GGACAGGTTTCTTAGGGGACTT 59.357 50.000 0.00 0.00 43.67 3.01
93 94 2.267192 AGGACAGGTTTCTTAGGGGAC 58.733 52.381 0.00 0.00 0.00 4.46
94 95 2.735259 AGGACAGGTTTCTTAGGGGA 57.265 50.000 0.00 0.00 0.00 4.81
95 96 2.642807 TGAAGGACAGGTTTCTTAGGGG 59.357 50.000 0.00 0.00 0.00 4.79
96 97 3.676093 GTGAAGGACAGGTTTCTTAGGG 58.324 50.000 0.00 0.00 0.00 3.53
97 98 3.326747 CGTGAAGGACAGGTTTCTTAGG 58.673 50.000 0.00 0.00 0.00 2.69
146 154 2.049475 GATCGAGTCGTCGTCCCCTG 62.049 65.000 13.12 0.00 46.85 4.45
199 207 3.701604 CTACGTGAGCCCCGTGAGC 62.702 68.421 0.00 0.00 39.22 4.26
266 281 3.137446 AGATTCTTCTGCAGCTGTGTT 57.863 42.857 16.64 0.00 0.00 3.32
267 282 2.812591 CAAGATTCTTCTGCAGCTGTGT 59.187 45.455 16.64 0.00 30.72 3.72
389 758 5.091431 GGTGAATATATACGCACGTACTCC 58.909 45.833 4.84 0.00 33.01 3.85
390 759 5.692814 TGGTGAATATATACGCACGTACTC 58.307 41.667 4.84 0.00 33.01 2.59
391 760 5.471116 TCTGGTGAATATATACGCACGTACT 59.529 40.000 4.84 0.00 33.01 2.73
392 761 5.566774 GTCTGGTGAATATATACGCACGTAC 59.433 44.000 4.84 0.00 33.01 3.67
393 762 5.239087 TGTCTGGTGAATATATACGCACGTA 59.761 40.000 5.24 5.24 34.87 3.57
546 932 2.959507 ATGCCCCGAACAAATAAAGC 57.040 45.000 0.00 0.00 0.00 3.51
569 955 1.010580 TTGCACGACAACAACACGAT 58.989 45.000 0.00 0.00 31.73 3.73
591 977 4.557205 ACTTCGTATGTGGTGAACTCTTC 58.443 43.478 0.00 0.00 0.00 2.87
593 979 4.557205 GAACTTCGTATGTGGTGAACTCT 58.443 43.478 0.00 0.00 0.00 3.24
603 989 2.423577 GCCACTTGGAACTTCGTATGT 58.576 47.619 0.00 0.00 37.39 2.29
726 1114 1.153667 CTCCCTGTCTCTCTTGCGC 60.154 63.158 0.00 0.00 0.00 6.09
731 1119 2.110899 TCTGGTTTCTCCCTGTCTCTCT 59.889 50.000 0.00 0.00 34.77 3.10
741 1129 3.493767 AGTTCAAGGTCTGGTTTCTCC 57.506 47.619 0.00 0.00 0.00 3.71
742 1130 5.470047 TCTAGTTCAAGGTCTGGTTTCTC 57.530 43.478 0.00 0.00 0.00 2.87
746 1134 3.648545 AGCTTCTAGTTCAAGGTCTGGTT 59.351 43.478 0.00 0.00 0.00 3.67
752 1140 3.142174 GTTGCAGCTTCTAGTTCAAGGT 58.858 45.455 0.00 0.00 31.67 3.50
886 1278 3.733443 TCATCAATTCAGCTAGCGCTA 57.267 42.857 17.75 17.75 46.99 4.26
888 1280 2.598439 CGTTCATCAATTCAGCTAGCGC 60.598 50.000 9.55 0.00 0.00 5.92
1461 1869 9.807649 GACAATGGCATTAGAAATTTAGAATGT 57.192 29.630 13.23 1.72 32.89 2.71
1544 1952 7.590279 AGTAGTATACAAACATTTGCAACCAC 58.410 34.615 0.00 0.93 46.26 4.16
1711 2120 4.899239 GCGATGGCCTCCACCTCG 62.899 72.222 3.32 4.26 35.80 4.63
1964 2379 2.359230 GCTGCCGTTCCAGAAGCT 60.359 61.111 0.00 0.00 34.77 3.74
1987 2402 3.124921 CCGGGCGTCACCATGTTC 61.125 66.667 0.00 0.00 42.05 3.18
2146 2561 1.736586 GGAGACGATGAGCACCGAT 59.263 57.895 0.00 0.00 0.00 4.18
2170 2585 0.525668 CGACGGACATGAGGCAGTAC 60.526 60.000 0.00 0.00 0.00 2.73
2242 2657 1.079127 CTTGTCCCTGAACGCCGAT 60.079 57.895 0.00 0.00 0.00 4.18
2503 2918 5.538433 GGATATTGACAGAGCCTCTAAGTCT 59.462 44.000 12.00 0.00 0.00 3.24
2504 2919 5.303078 TGGATATTGACAGAGCCTCTAAGTC 59.697 44.000 5.48 5.48 0.00 3.01
2505 2920 5.211973 TGGATATTGACAGAGCCTCTAAGT 58.788 41.667 0.00 0.00 0.00 2.24
2507 2922 4.590647 CCTGGATATTGACAGAGCCTCTAA 59.409 45.833 0.00 0.00 36.86 2.10
2508 2923 4.140924 TCCTGGATATTGACAGAGCCTCTA 60.141 45.833 0.00 0.00 36.86 2.43
2510 2925 2.968574 TCCTGGATATTGACAGAGCCTC 59.031 50.000 0.00 0.00 36.86 4.70
2521 2938 1.414181 CCGTGCAGAGTCCTGGATATT 59.586 52.381 0.00 0.00 42.72 1.28
2600 3021 0.618968 CCAGGTAGAAGGCCAGGAGT 60.619 60.000 5.01 0.00 34.96 3.85
2603 3024 1.604378 CACCAGGTAGAAGGCCAGG 59.396 63.158 5.01 0.00 38.47 4.45
2732 3153 0.752376 ACTTCCCGTCGATCCTCCTC 60.752 60.000 0.00 0.00 0.00 3.71
3011 3432 4.551603 GCATTGACGATCTCATTTTCCTCG 60.552 45.833 0.00 0.00 35.56 4.63
3588 4131 1.419012 CATATGAGGAGCTCTGGCCAA 59.581 52.381 14.64 0.00 39.73 4.52
3589 4132 1.054231 CATATGAGGAGCTCTGGCCA 58.946 55.000 14.64 4.71 39.73 5.36
3852 4456 1.681076 GGGCGGTTTTAGTCTGGGA 59.319 57.895 0.00 0.00 0.00 4.37
3899 4519 4.320870 TCGTCCCTCAACTATCAAAAACC 58.679 43.478 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.