Multiple sequence alignment - TraesCS4D01G160500

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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 TraesCS4D01G160500 chr4D 100.000 5177 0 0 808 5984 236390173 236395349 0.000000e+00 9561
1 TraesCS4D01G160500 chr4D 100.000 342 0 0 1 342 236389366 236389707 3.040000e-177 632
2 TraesCS4D01G160500 chr4D 91.803 122 10 0 69 190 278215515 278215636 2.870000e-38 171
3 TraesCS4D01G160500 chr4D 96.721 61 2 0 1 61 166043171 166043231 1.060000e-17 102
4 TraesCS4D01G160500 chrUn 96.780 5031 119 17 808 5827 57437950 57442948 0.000000e+00 8353
5 TraesCS4D01G160500 chrUn 86.957 161 5 8 198 342 57437743 57437903 3.710000e-37 167
6 TraesCS4D01G160500 chr4A 94.100 1356 47 11 4347 5685 236509693 236508354 0.000000e+00 2030
7 TraesCS4D01G160500 chr4A 94.238 1319 54 14 2260 3559 236529121 236527806 0.000000e+00 1995
8 TraesCS4D01G160500 chr4A 96.478 795 28 0 3555 4349 236519087 236518293 0.000000e+00 1314
9 TraesCS4D01G160500 chr4A 96.164 756 25 2 1515 2267 236530951 236530197 0.000000e+00 1232
10 TraesCS4D01G160500 chr4A 91.469 422 12 1 808 1229 236539121 236538724 5.240000e-155 558
11 TraesCS4D01G160500 chr4A 97.000 200 5 1 1228 1427 236531146 236530948 9.610000e-88 335
12 TraesCS4D01G160500 chr4A 90.323 217 14 5 5774 5984 236508363 236508148 1.640000e-70 278
13 TraesCS4D01G160500 chr4A 91.870 123 10 0 69 191 180756581 180756703 7.970000e-39 172
14 TraesCS4D01G160500 chr4A 87.179 117 9 2 232 342 236539293 236539177 1.750000e-25 128
15 TraesCS4D01G160500 chr3A 87.054 448 32 7 3858 4300 359347723 359347297 3.240000e-132 483
16 TraesCS4D01G160500 chr3A 90.226 133 11 2 4433 4564 359346838 359346707 7.970000e-39 172
17 TraesCS4D01G160500 chr3B 88.000 300 26 5 3863 4157 370151743 370151449 4.440000e-91 346
18 TraesCS4D01G160500 chr3B 86.310 168 16 5 4409 4571 370151019 370150854 6.160000e-40 176
19 TraesCS4D01G160500 chr5D 94.400 125 7 0 69 193 539513814 539513938 6.120000e-45 193
20 TraesCS4D01G160500 chr5D 91.870 123 10 0 69 191 432005429 432005551 7.970000e-39 172
21 TraesCS4D01G160500 chr7A 93.600 125 8 0 69 193 148016753 148016877 2.850000e-43 187
22 TraesCS4D01G160500 chr6B 93.600 125 8 0 69 193 68794567 68794443 2.850000e-43 187
23 TraesCS4D01G160500 chr2A 91.870 123 10 0 69 191 250236739 250236861 7.970000e-39 172
24 TraesCS4D01G160500 chr6A 91.200 125 11 0 69 193 212311800 212311924 2.870000e-38 171
25 TraesCS4D01G160500 chr2B 91.129 124 11 0 69 192 72548203 72548080 1.030000e-37 169


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 TraesCS4D01G160500 chr4D 236389366 236395349 5983 False 5096.500000 9561 100.000000 1 5984 2 chr4D.!!$F3 5983
1 TraesCS4D01G160500 chrUn 57437743 57442948 5205 False 4260.000000 8353 91.868500 198 5827 2 chrUn.!!$F1 5629
2 TraesCS4D01G160500 chr4A 236518293 236519087 794 True 1314.000000 1314 96.478000 3555 4349 1 chr4A.!!$R1 794
3 TraesCS4D01G160500 chr4A 236527806 236531146 3340 True 1187.333333 1995 95.800667 1228 3559 3 chr4A.!!$R3 2331
4 TraesCS4D01G160500 chr4A 236508148 236509693 1545 True 1154.000000 2030 92.211500 4347 5984 2 chr4A.!!$R2 1637
5 TraesCS4D01G160500 chr4A 236538724 236539293 569 True 343.000000 558 89.324000 232 1229 2 chr4A.!!$R4 997
6 TraesCS4D01G160500 chr3A 359346707 359347723 1016 True 327.500000 483 88.640000 3858 4564 2 chr3A.!!$R1 706
7 TraesCS4D01G160500 chr3B 370150854 370151743 889 True 261.000000 346 87.155000 3863 4571 2 chr3B.!!$R1 708

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
51 52 0.034756 TACGCTCCAGCAAGCAAAGA 59.965 50.000 0.00 0.00 42.62 2.52 F
68 69 0.113776 AGACCCAGTAACGACCCAGA 59.886 55.000 0.00 0.00 0.00 3.86 F
1368 1385 0.386113 GCCTGCCTAACTAGACCTCG 59.614 60.000 0.00 0.00 0.00 4.63 F
1386 1403 1.376942 GCAGCCTCACAGTGATGCT 60.377 57.895 23.51 23.51 46.75 3.79 F
1592 1610 1.687660 TGTGTTTGCATCAAGGCACAT 59.312 42.857 11.84 0.00 44.86 3.21 F
3251 4374 1.723870 CCGGCTTGTCATTGCTAGC 59.276 57.895 8.10 8.10 36.70 3.42 F
3781 4904 2.158505 CCCGGAGATGTCCTCTTAGGTA 60.159 54.545 0.73 0.00 41.34 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1588 0.030504 TGCCTTGATGCAAACACACG 59.969 50.000 0.00 0.0 38.56 4.49 R
1592 1610 0.407528 TTAGCTGACAAATGCCCCCA 59.592 50.000 0.00 0.0 0.00 4.96 R
3209 4332 0.029834 CGGCATTGGATAGCTGCAAC 59.970 55.000 1.02 0.0 35.37 4.17 R
3251 4374 1.377072 TGCATCCCACACACCATCG 60.377 57.895 0.00 0.0 0.00 3.84 R
3630 4753 1.299648 CATTGCGGACCCCTCTTCA 59.700 57.895 0.00 0.0 0.00 3.02 R
4290 5418 1.203063 GGAAGAGCCCCCTCAAAAACT 60.203 52.381 0.00 0.0 40.68 2.66 R
5590 7071 1.858458 GCTATGCACAGCGACGAATAA 59.142 47.619 0.00 0.0 0.00 1.40 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 3.771577 ACGAGGATTCTTGACCTTTGT 57.228 42.857 0.00 0.00 36.57 2.83
22 23 3.665190 ACGAGGATTCTTGACCTTTGTC 58.335 45.455 0.00 0.00 42.12 3.18
23 24 2.668457 CGAGGATTCTTGACCTTTGTCG 59.332 50.000 0.00 0.00 44.86 4.35
24 25 3.665190 GAGGATTCTTGACCTTTGTCGT 58.335 45.455 0.00 0.00 44.86 4.34
25 26 3.403038 AGGATTCTTGACCTTTGTCGTG 58.597 45.455 0.00 0.00 44.86 4.35
26 27 2.095718 GGATTCTTGACCTTTGTCGTGC 60.096 50.000 0.00 0.00 44.86 5.34
27 28 0.934496 TTCTTGACCTTTGTCGTGCG 59.066 50.000 0.00 0.00 44.86 5.34
28 29 0.103390 TCTTGACCTTTGTCGTGCGA 59.897 50.000 0.00 0.00 44.86 5.10
29 30 1.148310 CTTGACCTTTGTCGTGCGAT 58.852 50.000 0.00 0.00 44.86 4.58
30 31 0.865111 TTGACCTTTGTCGTGCGATG 59.135 50.000 0.00 0.00 44.86 3.84
31 32 0.948623 TGACCTTTGTCGTGCGATGG 60.949 55.000 0.00 1.68 44.86 3.51
32 33 0.949105 GACCTTTGTCGTGCGATGGT 60.949 55.000 0.00 4.69 40.56 3.55
33 34 0.319083 ACCTTTGTCGTGCGATGGTA 59.681 50.000 0.00 0.00 37.28 3.25
34 35 0.719465 CCTTTGTCGTGCGATGGTAC 59.281 55.000 0.00 0.00 0.00 3.34
43 44 2.494445 CGATGGTACGCTCCAGCA 59.506 61.111 13.55 0.00 43.17 4.41
44 45 1.153647 CGATGGTACGCTCCAGCAA 60.154 57.895 13.55 0.00 43.17 3.91
45 46 1.148157 CGATGGTACGCTCCAGCAAG 61.148 60.000 13.55 0.00 43.17 4.01
46 47 1.432270 GATGGTACGCTCCAGCAAGC 61.432 60.000 9.34 0.00 42.63 4.01
47 48 2.047274 GGTACGCTCCAGCAAGCA 60.047 61.111 0.00 0.00 42.62 3.91
48 49 1.671054 GGTACGCTCCAGCAAGCAA 60.671 57.895 0.00 0.00 42.62 3.91
49 50 1.234615 GGTACGCTCCAGCAAGCAAA 61.235 55.000 0.00 0.00 42.62 3.68
50 51 0.166814 GTACGCTCCAGCAAGCAAAG 59.833 55.000 0.00 0.00 42.62 2.77
51 52 0.034756 TACGCTCCAGCAAGCAAAGA 59.965 50.000 0.00 0.00 42.62 2.52
52 53 1.208614 CGCTCCAGCAAGCAAAGAC 59.791 57.895 0.00 0.00 42.62 3.01
53 54 1.583477 GCTCCAGCAAGCAAAGACC 59.417 57.895 0.00 0.00 42.05 3.85
54 55 1.871126 GCTCCAGCAAGCAAAGACCC 61.871 60.000 0.00 0.00 42.05 4.46
55 56 0.538057 CTCCAGCAAGCAAAGACCCA 60.538 55.000 0.00 0.00 0.00 4.51
56 57 0.538057 TCCAGCAAGCAAAGACCCAG 60.538 55.000 0.00 0.00 0.00 4.45
57 58 0.825010 CCAGCAAGCAAAGACCCAGT 60.825 55.000 0.00 0.00 0.00 4.00
58 59 1.545428 CCAGCAAGCAAAGACCCAGTA 60.545 52.381 0.00 0.00 0.00 2.74
59 60 2.229792 CAGCAAGCAAAGACCCAGTAA 58.770 47.619 0.00 0.00 0.00 2.24
60 61 2.030805 CAGCAAGCAAAGACCCAGTAAC 60.031 50.000 0.00 0.00 0.00 2.50
61 62 1.069227 GCAAGCAAAGACCCAGTAACG 60.069 52.381 0.00 0.00 0.00 3.18
62 63 2.489971 CAAGCAAAGACCCAGTAACGA 58.510 47.619 0.00 0.00 0.00 3.85
63 64 2.165319 AGCAAAGACCCAGTAACGAC 57.835 50.000 0.00 0.00 0.00 4.34
64 65 1.154197 GCAAAGACCCAGTAACGACC 58.846 55.000 0.00 0.00 0.00 4.79
65 66 1.804601 CAAAGACCCAGTAACGACCC 58.195 55.000 0.00 0.00 0.00 4.46
66 67 1.071071 CAAAGACCCAGTAACGACCCA 59.929 52.381 0.00 0.00 0.00 4.51
67 68 0.974383 AAGACCCAGTAACGACCCAG 59.026 55.000 0.00 0.00 0.00 4.45
68 69 0.113776 AGACCCAGTAACGACCCAGA 59.886 55.000 0.00 0.00 0.00 3.86
69 70 0.971386 GACCCAGTAACGACCCAGAA 59.029 55.000 0.00 0.00 0.00 3.02
70 71 1.553704 GACCCAGTAACGACCCAGAAT 59.446 52.381 0.00 0.00 0.00 2.40
71 72 2.762327 GACCCAGTAACGACCCAGAATA 59.238 50.000 0.00 0.00 0.00 1.75
72 73 2.498885 ACCCAGTAACGACCCAGAATAC 59.501 50.000 0.00 0.00 0.00 1.89
73 74 2.764572 CCCAGTAACGACCCAGAATACT 59.235 50.000 0.00 0.00 0.00 2.12
74 75 3.956199 CCCAGTAACGACCCAGAATACTA 59.044 47.826 0.00 0.00 0.00 1.82
75 76 4.202090 CCCAGTAACGACCCAGAATACTAC 60.202 50.000 0.00 0.00 0.00 2.73
76 77 4.400251 CCAGTAACGACCCAGAATACTACA 59.600 45.833 0.00 0.00 0.00 2.74
77 78 5.450137 CCAGTAACGACCCAGAATACTACAG 60.450 48.000 0.00 0.00 0.00 2.74
78 79 5.125097 CAGTAACGACCCAGAATACTACAGT 59.875 44.000 0.00 0.00 0.00 3.55
79 80 5.713861 AGTAACGACCCAGAATACTACAGTT 59.286 40.000 0.00 0.00 0.00 3.16
80 81 5.479124 AACGACCCAGAATACTACAGTTT 57.521 39.130 0.00 0.00 0.00 2.66
81 82 5.479124 ACGACCCAGAATACTACAGTTTT 57.521 39.130 0.00 0.00 0.00 2.43
82 83 6.594788 ACGACCCAGAATACTACAGTTTTA 57.405 37.500 0.00 0.00 0.00 1.52
83 84 6.996509 ACGACCCAGAATACTACAGTTTTAA 58.003 36.000 0.00 0.00 0.00 1.52
84 85 7.444299 ACGACCCAGAATACTACAGTTTTAAA 58.556 34.615 0.00 0.00 0.00 1.52
85 86 7.933033 ACGACCCAGAATACTACAGTTTTAAAA 59.067 33.333 0.00 0.00 0.00 1.52
86 87 8.225777 CGACCCAGAATACTACAGTTTTAAAAC 58.774 37.037 21.06 21.06 39.17 2.43
87 88 8.400184 ACCCAGAATACTACAGTTTTAAAACC 57.600 34.615 24.06 9.34 39.71 3.27
88 89 8.000127 ACCCAGAATACTACAGTTTTAAAACCA 59.000 33.333 24.06 11.26 39.71 3.67
89 90 8.294577 CCCAGAATACTACAGTTTTAAAACCAC 58.705 37.037 24.06 4.07 39.71 4.16
90 91 8.842280 CCAGAATACTACAGTTTTAAAACCACA 58.158 33.333 24.06 10.64 39.71 4.17
100 101 9.581099 ACAGTTTTAAAACCACAATTGTTAGAG 57.419 29.630 24.06 0.75 39.71 2.43
101 102 9.030301 CAGTTTTAAAACCACAATTGTTAGAGG 57.970 33.333 24.06 9.72 39.71 3.69
102 103 7.709182 AGTTTTAAAACCACAATTGTTAGAGGC 59.291 33.333 24.06 0.00 39.71 4.70
103 104 6.716934 TTAAAACCACAATTGTTAGAGGCA 57.283 33.333 8.77 0.00 0.00 4.75
104 105 5.606348 AAAACCACAATTGTTAGAGGCAA 57.394 34.783 8.77 0.00 0.00 4.52
105 106 4.853924 AACCACAATTGTTAGAGGCAAG 57.146 40.909 8.77 0.00 0.00 4.01
106 107 2.558359 ACCACAATTGTTAGAGGCAAGC 59.442 45.455 8.77 0.00 0.00 4.01
107 108 2.557924 CCACAATTGTTAGAGGCAAGCA 59.442 45.455 8.77 0.00 0.00 3.91
108 109 3.005684 CCACAATTGTTAGAGGCAAGCAA 59.994 43.478 8.77 0.00 0.00 3.91
109 110 4.501229 CCACAATTGTTAGAGGCAAGCAAA 60.501 41.667 8.77 0.00 0.00 3.68
110 111 4.445385 CACAATTGTTAGAGGCAAGCAAAC 59.555 41.667 8.77 0.00 0.00 2.93
111 112 4.099266 ACAATTGTTAGAGGCAAGCAAACA 59.901 37.500 4.92 0.00 0.00 2.83
112 113 4.935352 ATTGTTAGAGGCAAGCAAACAA 57.065 36.364 12.94 12.94 42.35 2.83
113 114 3.708563 TGTTAGAGGCAAGCAAACAAC 57.291 42.857 0.00 0.00 0.00 3.32
114 115 3.287222 TGTTAGAGGCAAGCAAACAACT 58.713 40.909 0.00 0.00 0.00 3.16
115 116 3.315191 TGTTAGAGGCAAGCAAACAACTC 59.685 43.478 0.00 0.00 0.00 3.01
116 117 2.057137 AGAGGCAAGCAAACAACTCA 57.943 45.000 0.00 0.00 0.00 3.41
117 118 2.590821 AGAGGCAAGCAAACAACTCAT 58.409 42.857 0.00 0.00 0.00 2.90
118 119 2.961062 AGAGGCAAGCAAACAACTCATT 59.039 40.909 0.00 0.00 0.00 2.57
119 120 3.385755 AGAGGCAAGCAAACAACTCATTT 59.614 39.130 0.00 0.00 0.00 2.32
120 121 4.122046 GAGGCAAGCAAACAACTCATTTT 58.878 39.130 0.00 0.00 0.00 1.82
121 122 5.068987 AGAGGCAAGCAAACAACTCATTTTA 59.931 36.000 0.00 0.00 0.00 1.52
122 123 5.669477 AGGCAAGCAAACAACTCATTTTAA 58.331 33.333 0.00 0.00 0.00 1.52
123 124 6.112058 AGGCAAGCAAACAACTCATTTTAAA 58.888 32.000 0.00 0.00 0.00 1.52
124 125 6.767423 AGGCAAGCAAACAACTCATTTTAAAT 59.233 30.769 0.00 0.00 0.00 1.40
125 126 7.930865 AGGCAAGCAAACAACTCATTTTAAATA 59.069 29.630 0.00 0.00 0.00 1.40
126 127 8.555361 GGCAAGCAAACAACTCATTTTAAATAA 58.445 29.630 0.00 0.00 0.00 1.40
127 128 9.928236 GCAAGCAAACAACTCATTTTAAATAAA 57.072 25.926 0.00 0.00 0.00 1.40
206 207 3.066380 TCAAACAGACATGATGTGGTCG 58.934 45.455 1.23 0.00 39.01 4.79
215 216 7.121168 ACAGACATGATGTGGTCGAAATAAAAT 59.879 33.333 1.23 0.00 39.01 1.82
305 316 2.293184 ACTAATTCCTGCCTCCTCCAGA 60.293 50.000 0.00 0.00 32.03 3.86
306 317 1.904440 AATTCCTGCCTCCTCCAGAT 58.096 50.000 0.00 0.00 32.03 2.90
307 318 1.433121 ATTCCTGCCTCCTCCAGATC 58.567 55.000 0.00 0.00 32.03 2.75
308 319 1.045350 TTCCTGCCTCCTCCAGATCG 61.045 60.000 0.00 0.00 32.03 3.69
309 320 1.456518 CCTGCCTCCTCCAGATCGA 60.457 63.158 0.00 0.00 32.03 3.59
311 322 1.743321 CTGCCTCCTCCAGATCGACC 61.743 65.000 0.00 0.00 32.03 4.79
312 323 2.503382 GCCTCCTCCAGATCGACCC 61.503 68.421 0.00 0.00 0.00 4.46
844 861 3.151710 CGGCCACATCTCCGGGTA 61.152 66.667 2.24 0.00 41.82 3.69
871 888 1.536331 CTAGAGGTAATCTCCGCCGTC 59.464 57.143 0.00 0.00 43.44 4.79
982 999 5.804944 TTCTTGGAATTGAAGGATTTGCA 57.195 34.783 0.00 0.00 0.00 4.08
1368 1385 0.386113 GCCTGCCTAACTAGACCTCG 59.614 60.000 0.00 0.00 0.00 4.63
1386 1403 1.376942 GCAGCCTCACAGTGATGCT 60.377 57.895 23.51 23.51 46.75 3.79
1408 1425 5.106712 GCTTTTGAAGTCGATGAACCATGTA 60.107 40.000 0.00 0.00 0.00 2.29
1570 1588 8.400409 GACCATGTCATAGGCCTTATTTTGCC 62.400 46.154 12.58 0.00 39.01 4.52
1592 1610 1.687660 TGTGTTTGCATCAAGGCACAT 59.312 42.857 11.84 0.00 44.86 3.21
1740 1761 2.560105 GGCTTCCAGCAGTTCTCAAAAT 59.440 45.455 0.00 0.00 44.75 1.82
1876 1897 8.972127 ACACTGAGTTTATCACTATACTGTCAT 58.028 33.333 0.00 0.00 35.01 3.06
2224 2245 5.435373 AGGTTTATAGCATTACCCCCTCTTT 59.565 40.000 0.00 0.00 0.00 2.52
2549 3653 4.256110 CTGTAGCATCAGTTGGTGATTCA 58.744 43.478 0.00 0.00 44.05 2.57
2637 3741 5.757320 GTCAATGAGGAGGAGTATGTTCATG 59.243 44.000 0.00 0.00 0.00 3.07
2658 3762 2.423538 GCATCCAGGCTTCGTTGTATTT 59.576 45.455 0.00 0.00 0.00 1.40
2807 3911 7.500892 TCATTTGTGTATGTTTGTCAGTTACCT 59.499 33.333 0.00 0.00 0.00 3.08
3103 4226 9.994432 GTGGAAAAGATTCTGTCATGTTATAAG 57.006 33.333 0.00 0.00 35.79 1.73
3209 4332 5.716094 TGAGATTTGATGCATCCAAACTTG 58.284 37.500 23.67 0.00 36.48 3.16
3251 4374 1.723870 CCGGCTTGTCATTGCTAGC 59.276 57.895 8.10 8.10 36.70 3.42
3630 4753 8.554490 AACCTGATGTTGTAGAGGAACTATAT 57.446 34.615 0.00 0.00 34.95 0.86
3781 4904 2.158505 CCCGGAGATGTCCTCTTAGGTA 60.159 54.545 0.73 0.00 41.34 3.08
3986 5110 7.322664 CAAATTTTTCATTTAGCTGGCCTCTA 58.677 34.615 3.32 2.40 0.00 2.43
4091 5218 6.821665 GGAAACCATATAACACTTGCTCACTA 59.178 38.462 0.00 0.00 0.00 2.74
4290 5418 5.645056 TTTGGAAGCATAGGTATGGATGA 57.355 39.130 0.00 0.00 34.32 2.92
4368 5496 1.851304 CCCATTTGTGGTGTATGGCT 58.149 50.000 0.00 0.00 37.97 4.75
4372 5500 0.774276 TTTGTGGTGTATGGCTGGGA 59.226 50.000 0.00 0.00 0.00 4.37
4379 5507 1.072266 TGTATGGCTGGGACCAAAGT 58.928 50.000 0.00 0.00 44.65 2.66
4423 5728 0.035343 TGTGTGGTTTTGGGTCGTGA 60.035 50.000 0.00 0.00 0.00 4.35
4426 5731 1.134068 TGTGGTTTTGGGTCGTGATCA 60.134 47.619 0.00 0.00 0.00 2.92
4535 5992 9.334693 CTTTCTTTCTTAATATAATGATGCGCC 57.665 33.333 4.18 0.00 0.00 6.53
4818 6286 3.129287 CAGCCGGAAATATGTTCAAGCTT 59.871 43.478 5.05 0.00 0.00 3.74
4929 6397 1.074951 CTGGGGCGGTCCTTTTCTT 59.925 57.895 0.00 0.00 35.33 2.52
5127 6597 7.309805 GCCTTCCTCAATGGTTTTGTATACTTT 60.310 37.037 4.17 0.00 37.07 2.66
5480 6959 6.116680 CAGTCATGGAGTCATTTTTAGCTC 57.883 41.667 0.00 0.00 0.00 4.09
5589 7070 1.872773 TTTCCTTGCACCCCAGTTTT 58.127 45.000 0.00 0.00 0.00 2.43
5590 7071 1.872773 TTCCTTGCACCCCAGTTTTT 58.127 45.000 0.00 0.00 0.00 1.94
5724 7205 6.636562 ACATATAGTGGAAGTTCTACCTCG 57.363 41.667 15.09 3.65 0.00 4.63
5737 7218 6.989659 AGTTCTACCTCGATTTTGTACTTGA 58.010 36.000 0.00 0.00 0.00 3.02
5967 7453 9.841880 GAACTATTTGAACAATAAGGGAGTTTC 57.158 33.333 0.00 0.00 0.00 2.78
5973 7459 3.863041 ACAATAAGGGAGTTTCGCTCTC 58.137 45.455 0.00 0.00 45.09 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.065789 GACAAAGGTCAAGAATCCTCGTT 58.934 43.478 0.00 0.00 43.73 3.85
1 2 3.665190 GACAAAGGTCAAGAATCCTCGT 58.335 45.455 0.00 0.00 43.73 4.18
2 3 2.668457 CGACAAAGGTCAAGAATCCTCG 59.332 50.000 0.00 0.00 44.54 4.63
3 4 3.433615 CACGACAAAGGTCAAGAATCCTC 59.566 47.826 0.00 0.00 44.54 3.71
4 5 3.403038 CACGACAAAGGTCAAGAATCCT 58.597 45.455 0.00 0.00 44.54 3.24
5 6 2.095718 GCACGACAAAGGTCAAGAATCC 60.096 50.000 0.00 0.00 44.54 3.01
6 7 2.411547 CGCACGACAAAGGTCAAGAATC 60.412 50.000 0.00 0.00 44.54 2.52
7 8 1.531149 CGCACGACAAAGGTCAAGAAT 59.469 47.619 0.00 0.00 44.54 2.40
8 9 0.934496 CGCACGACAAAGGTCAAGAA 59.066 50.000 0.00 0.00 44.54 2.52
9 10 0.103390 TCGCACGACAAAGGTCAAGA 59.897 50.000 0.00 0.00 44.54 3.02
10 11 1.136252 CATCGCACGACAAAGGTCAAG 60.136 52.381 0.00 0.00 44.54 3.02
11 12 0.865111 CATCGCACGACAAAGGTCAA 59.135 50.000 0.00 0.00 44.54 3.18
12 13 0.948623 CCATCGCACGACAAAGGTCA 60.949 55.000 0.00 0.00 44.54 4.02
13 14 0.949105 ACCATCGCACGACAAAGGTC 60.949 55.000 0.00 0.00 40.77 3.85
14 15 0.319083 TACCATCGCACGACAAAGGT 59.681 50.000 11.35 11.35 0.00 3.50
15 16 0.719465 GTACCATCGCACGACAAAGG 59.281 55.000 0.00 0.00 0.00 3.11
16 17 0.365523 CGTACCATCGCACGACAAAG 59.634 55.000 0.00 0.00 40.56 2.77
17 18 2.436795 CGTACCATCGCACGACAAA 58.563 52.632 0.00 0.00 40.56 2.83
18 19 4.156214 CGTACCATCGCACGACAA 57.844 55.556 0.00 0.00 40.56 3.18
26 27 1.148157 CTTGCTGGAGCGTACCATCG 61.148 60.000 3.46 0.00 45.83 3.84
27 28 1.432270 GCTTGCTGGAGCGTACCATC 61.432 60.000 3.46 0.95 45.83 3.51
28 29 1.450312 GCTTGCTGGAGCGTACCAT 60.450 57.895 3.46 0.00 45.83 3.55
29 30 2.047274 GCTTGCTGGAGCGTACCA 60.047 61.111 3.07 3.07 45.83 3.25
30 31 1.234615 TTTGCTTGCTGGAGCGTACC 61.235 55.000 0.00 0.00 45.64 3.34
31 32 0.166814 CTTTGCTTGCTGGAGCGTAC 59.833 55.000 0.00 0.00 45.64 3.67
32 33 0.034756 TCTTTGCTTGCTGGAGCGTA 59.965 50.000 0.00 0.00 45.64 4.42
33 34 1.227943 TCTTTGCTTGCTGGAGCGT 60.228 52.632 0.00 0.00 45.64 5.07
34 35 1.208614 GTCTTTGCTTGCTGGAGCG 59.791 57.895 0.00 0.00 45.64 5.03
35 36 1.583477 GGTCTTTGCTTGCTGGAGC 59.417 57.895 0.00 0.00 43.00 4.70
36 37 0.538057 TGGGTCTTTGCTTGCTGGAG 60.538 55.000 0.00 0.00 0.00 3.86
37 38 0.538057 CTGGGTCTTTGCTTGCTGGA 60.538 55.000 0.00 0.00 0.00 3.86
38 39 0.825010 ACTGGGTCTTTGCTTGCTGG 60.825 55.000 0.00 0.00 0.00 4.85
39 40 1.896220 TACTGGGTCTTTGCTTGCTG 58.104 50.000 0.00 0.00 0.00 4.41
40 41 2.230660 GTTACTGGGTCTTTGCTTGCT 58.769 47.619 0.00 0.00 0.00 3.91
41 42 1.069227 CGTTACTGGGTCTTTGCTTGC 60.069 52.381 0.00 0.00 0.00 4.01
42 43 2.223377 GTCGTTACTGGGTCTTTGCTTG 59.777 50.000 0.00 0.00 0.00 4.01
43 44 2.490991 GTCGTTACTGGGTCTTTGCTT 58.509 47.619 0.00 0.00 0.00 3.91
44 45 1.270678 GGTCGTTACTGGGTCTTTGCT 60.271 52.381 0.00 0.00 0.00 3.91
45 46 1.154197 GGTCGTTACTGGGTCTTTGC 58.846 55.000 0.00 0.00 0.00 3.68
46 47 1.071071 TGGGTCGTTACTGGGTCTTTG 59.929 52.381 0.00 0.00 0.00 2.77
47 48 1.346722 CTGGGTCGTTACTGGGTCTTT 59.653 52.381 0.00 0.00 0.00 2.52
48 49 0.974383 CTGGGTCGTTACTGGGTCTT 59.026 55.000 0.00 0.00 0.00 3.01
49 50 0.113776 TCTGGGTCGTTACTGGGTCT 59.886 55.000 0.00 0.00 0.00 3.85
50 51 0.971386 TTCTGGGTCGTTACTGGGTC 59.029 55.000 0.00 0.00 0.00 4.46
51 52 1.652947 ATTCTGGGTCGTTACTGGGT 58.347 50.000 0.00 0.00 0.00 4.51
52 53 2.764572 AGTATTCTGGGTCGTTACTGGG 59.235 50.000 0.00 0.00 0.00 4.45
53 54 4.400251 TGTAGTATTCTGGGTCGTTACTGG 59.600 45.833 0.00 0.00 0.00 4.00
54 55 5.125097 ACTGTAGTATTCTGGGTCGTTACTG 59.875 44.000 0.00 0.00 0.00 2.74
55 56 5.259632 ACTGTAGTATTCTGGGTCGTTACT 58.740 41.667 0.00 0.00 0.00 2.24
56 57 5.573337 ACTGTAGTATTCTGGGTCGTTAC 57.427 43.478 0.00 0.00 0.00 2.50
57 58 6.594788 AAACTGTAGTATTCTGGGTCGTTA 57.405 37.500 0.00 0.00 0.00 3.18
58 59 5.479124 AAACTGTAGTATTCTGGGTCGTT 57.521 39.130 0.00 0.00 0.00 3.85
59 60 5.479124 AAAACTGTAGTATTCTGGGTCGT 57.521 39.130 0.00 0.00 0.00 4.34
60 61 7.894376 TTTAAAACTGTAGTATTCTGGGTCG 57.106 36.000 0.00 0.00 0.00 4.79
61 62 8.509690 GGTTTTAAAACTGTAGTATTCTGGGTC 58.490 37.037 25.89 4.20 38.89 4.46
62 63 8.000127 TGGTTTTAAAACTGTAGTATTCTGGGT 59.000 33.333 25.89 0.00 38.89 4.51
63 64 8.294577 GTGGTTTTAAAACTGTAGTATTCTGGG 58.705 37.037 25.89 0.00 38.89 4.45
64 65 8.842280 TGTGGTTTTAAAACTGTAGTATTCTGG 58.158 33.333 25.89 0.00 38.89 3.86
74 75 9.581099 CTCTAACAATTGTGGTTTTAAAACTGT 57.419 29.630 25.89 19.01 38.89 3.55
75 76 9.030301 CCTCTAACAATTGTGGTTTTAAAACTG 57.970 33.333 25.89 18.47 38.89 3.16
76 77 7.709182 GCCTCTAACAATTGTGGTTTTAAAACT 59.291 33.333 25.89 7.38 38.89 2.66
77 78 7.492994 TGCCTCTAACAATTGTGGTTTTAAAAC 59.507 33.333 20.58 20.58 38.17 2.43
78 79 7.556844 TGCCTCTAACAATTGTGGTTTTAAAA 58.443 30.769 12.82 0.00 0.00 1.52
79 80 7.113658 TGCCTCTAACAATTGTGGTTTTAAA 57.886 32.000 12.82 0.00 0.00 1.52
80 81 6.716934 TGCCTCTAACAATTGTGGTTTTAA 57.283 33.333 12.82 0.00 0.00 1.52
81 82 6.716934 TTGCCTCTAACAATTGTGGTTTTA 57.283 33.333 12.82 0.00 0.00 1.52
82 83 5.600696 CTTGCCTCTAACAATTGTGGTTTT 58.399 37.500 12.82 0.00 0.00 2.43
83 84 4.501400 GCTTGCCTCTAACAATTGTGGTTT 60.501 41.667 12.82 0.00 0.00 3.27
84 85 3.005791 GCTTGCCTCTAACAATTGTGGTT 59.994 43.478 12.82 0.00 0.00 3.67
85 86 2.558359 GCTTGCCTCTAACAATTGTGGT 59.442 45.455 12.82 0.00 0.00 4.16
86 87 2.557924 TGCTTGCCTCTAACAATTGTGG 59.442 45.455 12.82 10.04 0.00 4.17
87 88 3.921119 TGCTTGCCTCTAACAATTGTG 57.079 42.857 12.82 0.12 0.00 3.33
88 89 4.099266 TGTTTGCTTGCCTCTAACAATTGT 59.901 37.500 4.92 4.92 0.00 2.71
89 90 4.619973 TGTTTGCTTGCCTCTAACAATTG 58.380 39.130 3.24 3.24 0.00 2.32
90 91 4.935352 TGTTTGCTTGCCTCTAACAATT 57.065 36.364 0.00 0.00 0.00 2.32
91 92 4.342092 AGTTGTTTGCTTGCCTCTAACAAT 59.658 37.500 0.00 0.00 39.73 2.71
92 93 3.699038 AGTTGTTTGCTTGCCTCTAACAA 59.301 39.130 0.00 0.00 37.03 2.83
93 94 3.287222 AGTTGTTTGCTTGCCTCTAACA 58.713 40.909 0.00 0.00 0.00 2.41
94 95 3.315191 TGAGTTGTTTGCTTGCCTCTAAC 59.685 43.478 0.00 0.00 0.00 2.34
95 96 3.550820 TGAGTTGTTTGCTTGCCTCTAA 58.449 40.909 0.00 0.00 0.00 2.10
96 97 3.207265 TGAGTTGTTTGCTTGCCTCTA 57.793 42.857 0.00 0.00 0.00 2.43
97 98 2.057137 TGAGTTGTTTGCTTGCCTCT 57.943 45.000 0.00 0.00 0.00 3.69
98 99 3.375782 AATGAGTTGTTTGCTTGCCTC 57.624 42.857 0.00 0.00 0.00 4.70
99 100 3.825143 AAATGAGTTGTTTGCTTGCCT 57.175 38.095 0.00 0.00 0.00 4.75
100 101 5.982465 TTAAAATGAGTTGTTTGCTTGCC 57.018 34.783 0.00 0.00 0.00 4.52
101 102 9.928236 TTTATTTAAAATGAGTTGTTTGCTTGC 57.072 25.926 0.00 0.00 0.00 4.01
175 176 9.283768 ACATCATGTCTGTTTGATAACAAAGTA 57.716 29.630 0.00 0.00 44.97 2.24
176 177 8.077991 CACATCATGTCTGTTTGATAACAAAGT 58.922 33.333 0.00 0.00 44.97 2.66
177 178 7.539710 CCACATCATGTCTGTTTGATAACAAAG 59.460 37.037 0.00 0.00 44.97 2.77
178 179 7.014134 ACCACATCATGTCTGTTTGATAACAAA 59.986 33.333 0.00 0.00 43.33 2.83
179 180 6.489700 ACCACATCATGTCTGTTTGATAACAA 59.510 34.615 0.00 0.00 43.33 2.83
180 181 6.003326 ACCACATCATGTCTGTTTGATAACA 58.997 36.000 0.00 0.00 41.82 2.41
181 182 6.500684 ACCACATCATGTCTGTTTGATAAC 57.499 37.500 0.00 0.00 31.50 1.89
182 183 5.351189 CGACCACATCATGTCTGTTTGATAA 59.649 40.000 0.00 0.00 31.50 1.75
183 184 4.869861 CGACCACATCATGTCTGTTTGATA 59.130 41.667 0.00 0.00 31.50 2.15
184 185 3.686241 CGACCACATCATGTCTGTTTGAT 59.314 43.478 0.00 0.00 32.87 2.57
185 186 3.066380 CGACCACATCATGTCTGTTTGA 58.934 45.455 0.00 0.00 0.00 2.69
186 187 3.066380 TCGACCACATCATGTCTGTTTG 58.934 45.455 0.00 0.00 0.00 2.93
187 188 3.401033 TCGACCACATCATGTCTGTTT 57.599 42.857 0.00 0.00 0.00 2.83
188 189 3.401033 TTCGACCACATCATGTCTGTT 57.599 42.857 0.00 0.00 0.00 3.16
189 190 3.401033 TTTCGACCACATCATGTCTGT 57.599 42.857 0.00 0.00 0.00 3.41
190 191 6.421377 TTTATTTCGACCACATCATGTCTG 57.579 37.500 0.00 0.00 0.00 3.51
191 192 7.630242 ATTTTATTTCGACCACATCATGTCT 57.370 32.000 0.00 0.00 0.00 3.41
192 193 9.385902 CATATTTTATTTCGACCACATCATGTC 57.614 33.333 0.00 0.00 0.00 3.06
193 194 9.119418 TCATATTTTATTTCGACCACATCATGT 57.881 29.630 0.00 0.00 0.00 3.21
194 195 9.603298 CTCATATTTTATTTCGACCACATCATG 57.397 33.333 0.00 0.00 0.00 3.07
195 196 9.342308 ACTCATATTTTATTTCGACCACATCAT 57.658 29.630 0.00 0.00 0.00 2.45
196 197 8.731275 ACTCATATTTTATTTCGACCACATCA 57.269 30.769 0.00 0.00 0.00 3.07
305 316 2.038557 CGGAATGGATTAAGGGGTCGAT 59.961 50.000 0.00 0.00 0.00 3.59
306 317 1.414919 CGGAATGGATTAAGGGGTCGA 59.585 52.381 0.00 0.00 0.00 4.20
307 318 1.140252 ACGGAATGGATTAAGGGGTCG 59.860 52.381 0.00 0.00 0.00 4.79
308 319 4.635699 ATACGGAATGGATTAAGGGGTC 57.364 45.455 0.00 0.00 0.00 4.46
309 320 5.382616 GAAATACGGAATGGATTAAGGGGT 58.617 41.667 0.00 0.00 0.00 4.95
311 322 5.381757 TGGAAATACGGAATGGATTAAGGG 58.618 41.667 0.00 0.00 0.00 3.95
312 323 6.238925 GGTTGGAAATACGGAATGGATTAAGG 60.239 42.308 0.00 0.00 0.00 2.69
817 834 2.159382 AGATGTGGCCGAATTCGTTTT 58.841 42.857 25.10 5.07 37.74 2.43
844 861 4.658063 CGGAGATTACCTCTAGTGGATCT 58.342 47.826 17.66 14.70 41.66 2.75
871 888 7.639072 CGATTGAACAAATTCTTCTAGAGCATG 59.361 37.037 0.00 0.00 35.69 4.06
1189 1206 3.643978 GTCATCGCCGCCTGCATC 61.644 66.667 0.00 0.00 41.33 3.91
1386 1403 5.106712 GCTACATGGTTCATCGACTTCAAAA 60.107 40.000 0.00 0.00 0.00 2.44
1408 1425 8.677148 TCTAAGTTACAAAAGATGAAACAGCT 57.323 30.769 0.00 0.00 0.00 4.24
1570 1588 0.030504 TGCCTTGATGCAAACACACG 59.969 50.000 0.00 0.00 38.56 4.49
1592 1610 0.407528 TTAGCTGACAAATGCCCCCA 59.592 50.000 0.00 0.00 0.00 4.96
1809 1830 7.451255 ACAGGAATAAATTCATTGTGACTTGGA 59.549 33.333 5.15 0.00 38.53 3.53
1876 1897 7.012138 TGGTGTACGCACAACTTTAAAAATAGA 59.988 33.333 5.24 0.00 46.95 1.98
1887 1908 1.134640 TCAGTTGGTGTACGCACAACT 60.135 47.619 25.08 25.08 46.95 3.16
2549 3653 6.208988 TCAGCAGATTCTAGAATACAACGT 57.791 37.500 17.94 0.00 0.00 3.99
2637 3741 1.668419 ATACAACGAAGCCTGGATGC 58.332 50.000 0.00 0.00 0.00 3.91
2807 3911 3.700038 GCCTAGGAGACAGCTGTTAACTA 59.300 47.826 22.65 19.86 0.00 2.24
3146 4269 6.473455 GCAAGAATGCGCTGTTTTAATCTAAT 59.527 34.615 9.73 0.00 43.83 1.73
3209 4332 0.029834 CGGCATTGGATAGCTGCAAC 59.970 55.000 1.02 0.00 35.37 4.17
3233 4356 1.723870 GCTAGCAATGACAAGCCGG 59.276 57.895 10.63 0.00 0.00 6.13
3251 4374 1.377072 TGCATCCCACACACCATCG 60.377 57.895 0.00 0.00 0.00 3.84
3630 4753 1.299648 CATTGCGGACCCCTCTTCA 59.700 57.895 0.00 0.00 0.00 3.02
3781 4904 4.071961 TGCACTAACAAGTGTCAGTGAT 57.928 40.909 17.26 0.00 40.67 3.06
3986 5110 4.769688 TCAGCAGTCCAACATCGATTTAT 58.230 39.130 0.00 0.00 0.00 1.40
4091 5218 3.508012 ACTTCTCTAGAGAACACGCATGT 59.492 43.478 27.71 19.61 42.06 3.21
4232 5360 5.176958 ACCAACACGACTAAAGAATCGAAAG 59.823 40.000 0.00 0.00 40.86 2.62
4290 5418 1.203063 GGAAGAGCCCCCTCAAAAACT 60.203 52.381 0.00 0.00 40.68 2.66
4368 5496 2.594303 CGCAGCACTTTGGTCCCA 60.594 61.111 0.00 0.00 0.00 4.37
4372 5500 4.974721 CCCCCGCAGCACTTTGGT 62.975 66.667 0.00 0.00 0.00 3.67
4426 5731 8.613482 CCGAGAAAGAAAGAAAGAAACTACTTT 58.387 33.333 0.00 0.00 41.86 2.66
4748 6216 7.750947 ACCAGTTAAAAGGGATAGACTGTAT 57.249 36.000 0.00 0.00 34.26 2.29
4929 6397 2.655090 TCACTTGGCAGGATGAACAA 57.345 45.000 2.65 0.00 39.69 2.83
5127 6597 9.803315 CTGTTAGTAATATTAGCTTGTCTGACA 57.197 33.333 6.36 6.36 0.00 3.58
5468 6947 3.741388 GCCTAGGCTCGAGCTAAAAATGA 60.741 47.826 34.46 11.59 41.70 2.57
5589 7070 2.284150 GCTATGCACAGCGACGAATAAA 59.716 45.455 0.00 0.00 0.00 1.40
5590 7071 1.858458 GCTATGCACAGCGACGAATAA 59.142 47.619 0.00 0.00 0.00 1.40
5895 7376 3.726557 TCTGACCAGCATCCAAGATTT 57.273 42.857 0.00 0.00 0.00 2.17
5896 7377 3.726557 TTCTGACCAGCATCCAAGATT 57.273 42.857 0.00 0.00 0.00 2.40
5897 7378 3.947612 ATTCTGACCAGCATCCAAGAT 57.052 42.857 0.00 0.00 0.00 2.40
5899 7380 5.902613 TTTAATTCTGACCAGCATCCAAG 57.097 39.130 0.00 0.00 0.00 3.61
5902 7383 6.455360 TCAATTTAATTCTGACCAGCATCC 57.545 37.500 0.00 0.00 0.00 3.51
5903 7384 7.315142 TGTTCAATTTAATTCTGACCAGCATC 58.685 34.615 0.00 0.00 0.00 3.91
5906 7387 9.294030 CTATTGTTCAATTTAATTCTGACCAGC 57.706 33.333 3.36 0.00 0.00 4.85
5940 7426 9.588096 AAACTCCCTTATTGTTCAAATAGTTCT 57.412 29.630 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.