Multiple sequence alignment - TraesCS1A01G175600

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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 TraesCS1A01G175600 chr1A 100.000 3503 0 0 1 3503 313589610 313593112 0.000000e+00 6469.0
1 TraesCS1A01G175600 chr1A 98.354 243 4 0 1 243 313495657 313495899 8.990000e-116 427.0
2 TraesCS1A01G175600 chr1D 95.249 3136 91 14 408 3503 233926146 233923029 0.000000e+00 4913.0
3 TraesCS1A01G175600 chr1D 94.304 158 9 0 250 407 233926374 233926217 3.490000e-60 243.0
4 TraesCS1A01G175600 chr1B 95.750 2353 76 13 408 2748 368681311 368678971 0.000000e+00 3770.0
5 TraesCS1A01G175600 chr1B 92.506 774 31 16 2732 3503 368677393 368676645 0.000000e+00 1083.0
6 TraesCS1A01G175600 chr5A 98.354 243 4 0 1 243 277715954 277716196 8.990000e-116 427.0
7 TraesCS1A01G175600 chr3A 97.976 247 4 1 1 247 531343104 531342859 8.990000e-116 427.0
8 TraesCS1A01G175600 chr7D 97.951 244 5 0 1 244 228363 228120 1.160000e-114 424.0
9 TraesCS1A01G175600 chr6D 97.951 244 5 0 1 244 402503380 402503137 1.160000e-114 424.0
10 TraesCS1A01G175600 chr6D 85.542 83 11 1 604 685 287891560 287891642 6.230000e-13 86.1
11 TraesCS1A01G175600 chr5D 97.951 244 5 0 1 244 426450695 426450452 1.160000e-114 424.0
12 TraesCS1A01G175600 chr5D 89.024 82 8 1 603 684 503646625 503646545 2.220000e-17 100.0
13 TraesCS1A01G175600 chr5D 82.105 95 15 2 274 367 11022406 11022499 2.900000e-11 80.5
14 TraesCS1A01G175600 chr3D 97.951 244 5 0 1 244 458816856 458817099 1.160000e-114 424.0
15 TraesCS1A01G175600 chr3D 97.561 246 6 0 1 246 226173531 226173286 4.180000e-114 422.0
16 TraesCS1A01G175600 chr3D 86.585 82 10 1 603 683 89926168 89926087 4.820000e-14 89.8
17 TraesCS1A01G175600 chr7B 96.109 257 8 2 1 256 335964503 335964758 5.410000e-113 418.0
18 TraesCS1A01G175600 chr6A 78.605 215 28 14 487 684 504475811 504476024 3.670000e-25 126.0
19 TraesCS1A01G175600 chr5B 90.789 76 7 0 608 683 149328838 149328763 6.190000e-18 102.0
20 TraesCS1A01G175600 chr2D 89.024 82 9 0 603 684 553760033 553759952 6.190000e-18 102.0
21 TraesCS1A01G175600 chr2D 75.253 198 33 10 490 671 372800818 372800621 2.900000e-11 80.5
22 TraesCS1A01G175600 chr2A 87.805 82 10 0 603 684 694150460 694150379 2.880000e-16 97.1
23 TraesCS1A01G175600 chr2B 76.064 188 26 15 490 659 442328418 442328232 2.900000e-11 80.5


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 TraesCS1A01G175600 chr1A 313589610 313593112 3502 False 6469.0 6469 100.0000 1 3503 1 chr1A.!!$F2 3502
1 TraesCS1A01G175600 chr1D 233923029 233926374 3345 True 2578.0 4913 94.7765 250 3503 2 chr1D.!!$R1 3253
2 TraesCS1A01G175600 chr1B 368676645 368681311 4666 True 2426.5 3770 94.1280 408 3503 2 chr1B.!!$R1 3095

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
858 970 0.038310 CTCCTCTTCCCCCAAACACC 59.962 60.0 0.0 0.0 0.0 4.16 F
1733 1845 0.106335 TTCAACTACCGCCCGTTCAA 59.894 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1963 1.100463 ACTTTGCACGCATGACCACA 61.100 50.000 0.0 0.0 0.0 4.17 R
2709 2822 1.678970 GCCCACCATCCTGTCCAAC 60.679 63.158 0.0 0.0 0.0 3.77 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 1.954382 TCTCCTAATGACGTGATCCCG 59.046 52.381 0.00 0.00 0.00 5.14
22 23 1.681793 CTCCTAATGACGTGATCCCGT 59.318 52.381 1.88 1.88 45.18 5.28
23 24 2.100916 CTCCTAATGACGTGATCCCGTT 59.899 50.000 4.33 0.00 41.98 4.44
24 25 2.159156 TCCTAATGACGTGATCCCGTTG 60.159 50.000 4.33 0.00 41.98 4.10
25 26 2.159156 CCTAATGACGTGATCCCGTTGA 60.159 50.000 4.33 0.00 41.98 3.18
26 27 2.691409 AATGACGTGATCCCGTTGAT 57.309 45.000 4.33 0.00 41.98 2.57
35 36 2.821546 GATCCCGTTGATCGAATGACA 58.178 47.619 0.00 0.00 40.53 3.58
36 37 2.753055 TCCCGTTGATCGAATGACAA 57.247 45.000 0.00 0.00 42.86 3.18
37 38 2.343101 TCCCGTTGATCGAATGACAAC 58.657 47.619 13.90 13.90 42.86 3.32
38 39 2.028476 TCCCGTTGATCGAATGACAACT 60.028 45.455 18.35 0.00 40.80 3.16
39 40 2.348666 CCCGTTGATCGAATGACAACTC 59.651 50.000 18.35 0.52 40.80 3.01
40 41 2.993220 CCGTTGATCGAATGACAACTCA 59.007 45.455 18.35 2.78 40.80 3.41
41 42 3.618594 CCGTTGATCGAATGACAACTCAT 59.381 43.478 18.35 0.00 40.80 2.90
42 43 4.493057 CCGTTGATCGAATGACAACTCATG 60.493 45.833 18.35 0.00 40.80 3.07
43 44 4.091945 CGTTGATCGAATGACAACTCATGT 59.908 41.667 18.35 0.00 43.47 3.21
54 55 4.679373 ACAACTCATGTCTATGGCTAGG 57.321 45.455 0.00 0.00 37.96 3.02
55 56 4.290093 ACAACTCATGTCTATGGCTAGGA 58.710 43.478 0.00 0.00 37.96 2.94
56 57 4.716784 ACAACTCATGTCTATGGCTAGGAA 59.283 41.667 0.00 0.00 37.96 3.36
57 58 5.189736 ACAACTCATGTCTATGGCTAGGAAA 59.810 40.000 0.00 0.00 37.96 3.13
58 59 5.283457 ACTCATGTCTATGGCTAGGAAAC 57.717 43.478 0.00 0.00 34.97 2.78
59 60 4.965532 ACTCATGTCTATGGCTAGGAAACT 59.034 41.667 0.00 0.00 38.55 2.66
60 61 5.069781 ACTCATGTCTATGGCTAGGAAACTC 59.930 44.000 0.00 0.00 37.07 3.01
61 62 4.962362 TCATGTCTATGGCTAGGAAACTCA 59.038 41.667 0.00 0.00 37.07 3.41
62 63 5.425217 TCATGTCTATGGCTAGGAAACTCAA 59.575 40.000 0.00 0.00 37.07 3.02
63 64 5.086104 TGTCTATGGCTAGGAAACTCAAC 57.914 43.478 0.00 0.00 43.67 3.18
64 65 4.081087 TGTCTATGGCTAGGAAACTCAACC 60.081 45.833 0.00 0.00 43.67 3.77
65 66 4.081087 GTCTATGGCTAGGAAACTCAACCA 60.081 45.833 0.00 0.00 43.67 3.67
66 67 4.721776 TCTATGGCTAGGAAACTCAACCAT 59.278 41.667 0.00 0.00 44.82 3.55
67 68 3.350219 TGGCTAGGAAACTCAACCATC 57.650 47.619 0.00 0.00 43.67 3.51
68 69 2.912956 TGGCTAGGAAACTCAACCATCT 59.087 45.455 0.00 0.00 43.67 2.90
69 70 3.330701 TGGCTAGGAAACTCAACCATCTT 59.669 43.478 0.00 0.00 43.67 2.40
70 71 3.942115 GGCTAGGAAACTCAACCATCTTC 59.058 47.826 0.00 0.00 43.67 2.87
71 72 3.619038 GCTAGGAAACTCAACCATCTTCG 59.381 47.826 0.00 0.00 43.67 3.79
72 73 4.620803 GCTAGGAAACTCAACCATCTTCGA 60.621 45.833 0.00 0.00 43.67 3.71
73 74 4.559862 AGGAAACTCAACCATCTTCGAT 57.440 40.909 0.00 0.00 32.90 3.59
74 75 4.508662 AGGAAACTCAACCATCTTCGATC 58.491 43.478 0.00 0.00 32.90 3.69
75 76 4.020218 AGGAAACTCAACCATCTTCGATCA 60.020 41.667 0.00 0.00 32.90 2.92
76 77 4.695455 GGAAACTCAACCATCTTCGATCAA 59.305 41.667 0.00 0.00 0.00 2.57
77 78 5.390991 GGAAACTCAACCATCTTCGATCAAC 60.391 44.000 0.00 0.00 0.00 3.18
78 79 3.254060 ACTCAACCATCTTCGATCAACG 58.746 45.455 0.00 0.00 44.09 4.10
89 90 3.406728 TCGATCAACGAGCTAGTCAAG 57.593 47.619 0.00 0.00 46.45 3.02
90 91 2.747989 TCGATCAACGAGCTAGTCAAGT 59.252 45.455 0.00 0.00 46.45 3.16
91 92 3.937079 TCGATCAACGAGCTAGTCAAGTA 59.063 43.478 0.00 0.00 46.45 2.24
92 93 4.034163 TCGATCAACGAGCTAGTCAAGTAG 59.966 45.833 0.00 0.00 46.45 2.57
93 94 4.034163 CGATCAACGAGCTAGTCAAGTAGA 59.966 45.833 0.00 0.00 45.77 2.59
94 95 4.948608 TCAACGAGCTAGTCAAGTAGAG 57.051 45.455 0.00 0.00 0.00 2.43
95 96 3.690139 TCAACGAGCTAGTCAAGTAGAGG 59.310 47.826 0.00 0.00 0.00 3.69
96 97 2.018515 ACGAGCTAGTCAAGTAGAGGC 58.981 52.381 0.00 0.00 0.00 4.70
97 98 2.017782 CGAGCTAGTCAAGTAGAGGCA 58.982 52.381 0.00 0.00 0.00 4.75
98 99 2.621055 CGAGCTAGTCAAGTAGAGGCAT 59.379 50.000 0.00 0.00 0.00 4.40
99 100 3.815962 CGAGCTAGTCAAGTAGAGGCATA 59.184 47.826 0.00 0.00 0.00 3.14
100 101 4.319911 CGAGCTAGTCAAGTAGAGGCATAC 60.320 50.000 0.00 0.00 0.00 2.39
101 102 4.798882 AGCTAGTCAAGTAGAGGCATACT 58.201 43.478 0.00 0.00 37.61 2.12
102 103 5.942961 AGCTAGTCAAGTAGAGGCATACTA 58.057 41.667 3.23 0.00 34.90 1.82
103 104 6.001460 AGCTAGTCAAGTAGAGGCATACTAG 58.999 44.000 0.00 0.00 38.50 2.57
104 105 5.766174 GCTAGTCAAGTAGAGGCATACTAGT 59.234 44.000 0.00 0.00 38.02 2.57
105 106 6.293735 GCTAGTCAAGTAGAGGCATACTAGTG 60.294 46.154 5.39 0.00 38.02 2.74
106 107 5.756918 AGTCAAGTAGAGGCATACTAGTGA 58.243 41.667 5.39 2.59 34.90 3.41
107 108 5.591067 AGTCAAGTAGAGGCATACTAGTGAC 59.409 44.000 17.97 17.97 40.57 3.67
108 109 5.357314 GTCAAGTAGAGGCATACTAGTGACA 59.643 44.000 19.41 0.00 40.28 3.58
109 110 5.357314 TCAAGTAGAGGCATACTAGTGACAC 59.643 44.000 5.39 0.00 34.90 3.67
110 111 5.118729 AGTAGAGGCATACTAGTGACACT 57.881 43.478 13.68 13.68 34.21 3.55
111 112 6.249911 AGTAGAGGCATACTAGTGACACTA 57.750 41.667 14.53 14.53 34.21 2.74
112 113 6.843752 AGTAGAGGCATACTAGTGACACTAT 58.156 40.000 15.58 8.80 33.76 2.12
113 114 6.712998 AGTAGAGGCATACTAGTGACACTATG 59.287 42.308 15.58 13.06 33.76 2.23
114 115 5.450453 AGAGGCATACTAGTGACACTATGT 58.550 41.667 15.58 16.25 29.08 2.29
115 116 5.894393 AGAGGCATACTAGTGACACTATGTT 59.106 40.000 15.58 6.32 29.08 2.71
116 117 6.381420 AGAGGCATACTAGTGACACTATGTTT 59.619 38.462 15.58 8.50 29.08 2.83
117 118 6.341316 AGGCATACTAGTGACACTATGTTTG 58.659 40.000 15.58 18.04 29.08 2.93
118 119 6.070767 AGGCATACTAGTGACACTATGTTTGT 60.071 38.462 15.58 11.73 29.08 2.83
119 120 6.255887 GGCATACTAGTGACACTATGTTTGTC 59.744 42.308 15.58 16.05 43.22 3.18
120 121 7.036220 GCATACTAGTGACACTATGTTTGTCT 58.964 38.462 15.58 0.71 43.30 3.41
121 122 8.188799 GCATACTAGTGACACTATGTTTGTCTA 58.811 37.037 15.58 1.91 43.30 2.59
124 125 8.123639 ACTAGTGACACTATGTTTGTCTATGT 57.876 34.615 15.58 3.27 43.30 2.29
125 126 9.239551 ACTAGTGACACTATGTTTGTCTATGTA 57.760 33.333 15.58 0.00 43.30 2.29
128 129 9.587772 AGTGACACTATGTTTGTCTATGTATTC 57.412 33.333 6.24 0.00 43.30 1.75
129 130 9.366216 GTGACACTATGTTTGTCTATGTATTCA 57.634 33.333 0.00 0.00 43.30 2.57
130 131 9.366216 TGACACTATGTTTGTCTATGTATTCAC 57.634 33.333 4.27 0.00 43.30 3.18
131 132 9.366216 GACACTATGTTTGTCTATGTATTCACA 57.634 33.333 0.00 0.00 40.30 3.58
132 133 9.151471 ACACTATGTTTGTCTATGTATTCACAC 57.849 33.333 0.00 0.00 37.54 3.82
133 134 9.150348 CACTATGTTTGTCTATGTATTCACACA 57.850 33.333 0.00 0.00 37.54 3.72
134 135 9.890629 ACTATGTTTGTCTATGTATTCACACAT 57.109 29.630 0.00 0.00 41.88 3.21
136 137 7.977789 TGTTTGTCTATGTATTCACACATGT 57.022 32.000 0.00 0.00 39.46 3.21
137 138 9.665719 ATGTTTGTCTATGTATTCACACATGTA 57.334 29.630 0.00 0.00 39.46 2.29
138 139 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
148 149 8.608317 TGTATTCACACATGTATTATGTTTCCG 58.392 33.333 0.00 0.00 0.00 4.30
149 150 6.429791 TTCACACATGTATTATGTTTCCGG 57.570 37.500 0.00 0.00 0.00 5.14
150 151 5.492895 TCACACATGTATTATGTTTCCGGT 58.507 37.500 0.00 0.00 0.00 5.28
151 152 5.941058 TCACACATGTATTATGTTTCCGGTT 59.059 36.000 0.00 0.00 0.00 4.44
152 153 7.104290 TCACACATGTATTATGTTTCCGGTTA 58.896 34.615 0.00 0.00 0.00 2.85
153 154 7.606839 TCACACATGTATTATGTTTCCGGTTAA 59.393 33.333 0.00 0.00 0.00 2.01
154 155 8.402472 CACACATGTATTATGTTTCCGGTTAAT 58.598 33.333 0.00 1.95 0.00 1.40
155 156 9.616156 ACACATGTATTATGTTTCCGGTTAATA 57.384 29.630 0.00 0.00 0.00 0.98
156 157 9.872757 CACATGTATTATGTTTCCGGTTAATAC 57.127 33.333 0.00 12.47 37.73 1.89
157 158 9.616156 ACATGTATTATGTTTCCGGTTAATACA 57.384 29.630 22.83 22.83 44.85 2.29
165 166 7.311364 TGTTTCCGGTTAATACAATTCTAGC 57.689 36.000 0.00 0.00 0.00 3.42
166 167 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.00 0.00 3.49
167 168 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
168 169 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
169 170 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
170 171 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
171 172 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
172 173 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
230 231 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
242 243 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
243 244 5.310409 CCTCTAGGGCATATTTCCTTCAA 57.690 43.478 0.00 0.00 34.75 2.69
244 245 5.312079 CCTCTAGGGCATATTTCCTTCAAG 58.688 45.833 0.00 0.00 34.75 3.02
245 246 5.310409 TCTAGGGCATATTTCCTTCAAGG 57.690 43.478 0.00 0.00 36.46 3.61
246 247 4.726825 TCTAGGGCATATTTCCTTCAAGGT 59.273 41.667 2.50 0.00 36.53 3.50
247 248 3.635591 AGGGCATATTTCCTTCAAGGTG 58.364 45.455 2.50 0.00 36.53 4.00
248 249 2.695147 GGGCATATTTCCTTCAAGGTGG 59.305 50.000 2.50 0.00 36.53 4.61
262 263 0.332972 AGGTGGAGCTGGATTTTCCC 59.667 55.000 0.00 0.00 35.03 3.97
286 287 2.646175 GGCGCCCCTATATCTCGCA 61.646 63.158 18.11 0.00 46.60 5.10
291 292 2.736719 CGCCCCTATATCTCGCATTCAG 60.737 54.545 0.00 0.00 0.00 3.02
292 293 2.234908 GCCCCTATATCTCGCATTCAGT 59.765 50.000 0.00 0.00 0.00 3.41
310 311 1.689273 AGTGAGTCAAGCTTCCGACTT 59.311 47.619 17.73 3.14 42.48 3.01
327 328 0.471617 CTTGATGAAGGGGGAGCGAT 59.528 55.000 0.00 0.00 0.00 4.58
372 373 0.171231 GCCACGGCCTCTTTGATTTC 59.829 55.000 0.00 0.00 34.56 2.17
380 381 4.074970 GGCCTCTTTGATTTCAGAGTGAA 58.925 43.478 0.00 0.00 35.64 3.18
421 492 6.743575 AGTTTTAGGAGGATTGAAATGTCG 57.256 37.500 0.00 0.00 0.00 4.35
462 533 3.821841 AGATTTTGGTTCGTTCGATTGC 58.178 40.909 0.00 0.00 0.00 3.56
464 535 3.422417 TTTTGGTTCGTTCGATTGCAA 57.578 38.095 0.00 0.00 0.00 4.08
559 641 6.413783 TTTAAAAAGGTTTGAGTGGATCCC 57.586 37.500 9.90 0.11 0.00 3.85
635 721 5.975693 TCCTATGAATCAAACAACCAACC 57.024 39.130 0.00 0.00 0.00 3.77
639 726 5.982890 ATGAATCAAACAACCAACCTAGG 57.017 39.130 7.41 7.41 0.00 3.02
719 831 5.606348 AGGATGGTTTAGAGTTGCTCTAG 57.394 43.478 6.07 0.00 42.92 2.43
781 893 2.101575 GGCACGAGCGTGTATCGA 59.898 61.111 22.06 0.00 46.90 3.59
782 894 2.222217 GGCACGAGCGTGTATCGAC 61.222 63.158 22.06 6.26 46.90 4.20
783 895 2.556677 GCACGAGCGTGTATCGACG 61.557 63.158 22.06 0.00 46.90 5.12
784 896 1.933041 CACGAGCGTGTATCGACGG 60.933 63.158 14.36 0.00 42.76 4.79
785 897 2.352001 CGAGCGTGTATCGACGGG 60.352 66.667 0.00 0.00 42.76 5.28
786 898 2.816360 CGAGCGTGTATCGACGGGA 61.816 63.158 0.00 0.00 42.76 5.14
801 913 2.264794 GGACGGCAACACCTCGAT 59.735 61.111 0.00 0.00 35.61 3.59
858 970 0.038310 CTCCTCTTCCCCCAAACACC 59.962 60.000 0.00 0.00 0.00 4.16
1097 1209 2.027625 CAAGAACCGGTGTCGAGGC 61.028 63.158 8.52 0.00 39.00 4.70
1165 1277 4.541648 AGGCGGGCCTAGATCCGT 62.542 66.667 11.22 4.10 46.14 4.69
1326 1438 4.556697 TGGCAGATAGGATTCTCAAGGTA 58.443 43.478 0.00 0.00 0.00 3.08
1733 1845 0.106335 TTCAACTACCGCCCGTTCAA 59.894 50.000 0.00 0.00 0.00 2.69
1770 1882 0.735978 TATTGCACACGCTCCTGACG 60.736 55.000 0.00 0.00 39.64 4.35
1773 1885 2.161486 GCACACGCTCCTGACGATC 61.161 63.158 0.00 0.00 34.30 3.69
1851 1963 7.496920 CACACTCCTGATGTATTGACATACAAT 59.503 37.037 0.00 0.00 46.76 2.71
1935 2047 2.122783 TGGGAAAGAATGGGCTTACG 57.877 50.000 0.00 0.00 0.00 3.18
2043 2155 0.743688 GTGATGTTGGTTGTGTGCCA 59.256 50.000 0.00 0.00 0.00 4.92
2121 2233 5.713861 AGAAGCTTGCAGGTATTTCTTTGAT 59.286 36.000 2.10 0.00 0.00 2.57
2346 2458 2.615912 GCTGAAGGATATGGACTTGCAC 59.384 50.000 0.00 0.00 0.00 4.57
2373 2485 3.815401 GCACACCAAACTTCTCAGTGTAT 59.185 43.478 0.00 0.00 39.56 2.29
2475 2587 5.716228 AGGCCAATATCTTCATTTGTTGTCA 59.284 36.000 5.01 0.00 0.00 3.58
2791 4498 8.598916 TCAATAGTCCTAATTCCTACACACAAA 58.401 33.333 0.00 0.00 0.00 2.83
2792 4499 9.226606 CAATAGTCCTAATTCCTACACACAAAA 57.773 33.333 0.00 0.00 0.00 2.44
2817 4524 3.769536 ACGTTTTCCTTTTGTTGAGCTG 58.230 40.909 0.00 0.00 0.00 4.24
2983 4690 7.582667 ATGTTAAATGGTAAGTAAGATGCCC 57.417 36.000 0.00 0.00 0.00 5.36
3083 4790 7.450903 AGTAATAGGGTTAGTGGATTACATGC 58.549 38.462 0.00 0.00 36.08 4.06
3219 4927 7.598759 TTTTAAGGGTTAACAATAGGTGCAA 57.401 32.000 8.10 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.361119 CGGGATCACGTCATTAGGAGAA 59.639 50.000 9.83 0.00 0.00 2.87
1 2 1.954382 CGGGATCACGTCATTAGGAGA 59.046 52.381 9.83 0.00 0.00 3.71
2 3 1.681793 ACGGGATCACGTCATTAGGAG 59.318 52.381 19.33 0.00 45.08 3.69
3 4 1.771565 ACGGGATCACGTCATTAGGA 58.228 50.000 19.33 0.00 45.08 2.94
16 17 2.936498 GTTGTCATTCGATCAACGGGAT 59.064 45.455 0.00 0.00 42.82 3.85
17 18 2.028476 AGTTGTCATTCGATCAACGGGA 60.028 45.455 13.41 0.00 43.87 5.14
18 19 2.346803 AGTTGTCATTCGATCAACGGG 58.653 47.619 13.41 0.00 43.87 5.28
19 20 2.993220 TGAGTTGTCATTCGATCAACGG 59.007 45.455 13.41 0.00 43.87 4.44
20 21 4.091945 ACATGAGTTGTCATTCGATCAACG 59.908 41.667 0.00 0.00 40.84 4.10
21 22 5.536554 ACATGAGTTGTCATTCGATCAAC 57.463 39.130 0.00 12.20 40.84 3.18
33 34 4.290093 TCCTAGCCATAGACATGAGTTGT 58.710 43.478 0.00 0.00 42.79 3.32
34 35 4.944619 TCCTAGCCATAGACATGAGTTG 57.055 45.455 0.00 0.00 33.67 3.16
35 36 5.426833 AGTTTCCTAGCCATAGACATGAGTT 59.573 40.000 0.00 0.00 33.67 3.01
36 37 4.965532 AGTTTCCTAGCCATAGACATGAGT 59.034 41.667 0.00 0.00 33.67 3.41
37 38 5.069648 TGAGTTTCCTAGCCATAGACATGAG 59.930 44.000 0.00 0.00 33.67 2.90
38 39 4.962362 TGAGTTTCCTAGCCATAGACATGA 59.038 41.667 0.00 0.00 33.67 3.07
39 40 5.282055 TGAGTTTCCTAGCCATAGACATG 57.718 43.478 0.00 0.00 0.00 3.21
40 41 5.396884 GGTTGAGTTTCCTAGCCATAGACAT 60.397 44.000 0.00 0.00 0.00 3.06
41 42 4.081087 GGTTGAGTTTCCTAGCCATAGACA 60.081 45.833 0.00 0.00 0.00 3.41
42 43 4.081087 TGGTTGAGTTTCCTAGCCATAGAC 60.081 45.833 0.00 0.00 0.00 2.59
43 44 4.101114 TGGTTGAGTTTCCTAGCCATAGA 58.899 43.478 0.00 0.00 0.00 1.98
44 45 4.487714 TGGTTGAGTTTCCTAGCCATAG 57.512 45.455 0.00 0.00 0.00 2.23
45 46 4.721776 AGATGGTTGAGTTTCCTAGCCATA 59.278 41.667 0.00 0.00 35.64 2.74
46 47 3.525199 AGATGGTTGAGTTTCCTAGCCAT 59.475 43.478 0.00 0.00 37.88 4.40
47 48 2.912956 AGATGGTTGAGTTTCCTAGCCA 59.087 45.455 0.00 0.00 0.00 4.75
48 49 3.636153 AGATGGTTGAGTTTCCTAGCC 57.364 47.619 0.00 0.00 0.00 3.93
49 50 3.619038 CGAAGATGGTTGAGTTTCCTAGC 59.381 47.826 0.00 0.00 0.00 3.42
50 51 5.073311 TCGAAGATGGTTGAGTTTCCTAG 57.927 43.478 0.00 0.00 0.00 3.02
51 52 5.186992 TGATCGAAGATGGTTGAGTTTCCTA 59.813 40.000 0.00 0.00 45.12 2.94
52 53 4.020218 TGATCGAAGATGGTTGAGTTTCCT 60.020 41.667 0.00 0.00 45.12 3.36
53 54 4.253685 TGATCGAAGATGGTTGAGTTTCC 58.746 43.478 0.00 0.00 45.12 3.13
54 55 5.622378 GTTGATCGAAGATGGTTGAGTTTC 58.378 41.667 0.00 0.00 45.12 2.78
55 56 4.152402 CGTTGATCGAAGATGGTTGAGTTT 59.848 41.667 0.00 0.00 45.12 2.66
56 57 3.679980 CGTTGATCGAAGATGGTTGAGTT 59.320 43.478 0.00 0.00 45.12 3.01
57 58 3.056821 TCGTTGATCGAAGATGGTTGAGT 60.057 43.478 0.00 0.00 45.98 3.41
58 59 3.511699 TCGTTGATCGAAGATGGTTGAG 58.488 45.455 0.00 0.00 45.98 3.02
59 60 3.586100 TCGTTGATCGAAGATGGTTGA 57.414 42.857 0.00 0.00 45.98 3.18
69 70 2.747989 ACTTGACTAGCTCGTTGATCGA 59.252 45.455 0.00 0.00 46.83 3.59
70 71 3.138205 ACTTGACTAGCTCGTTGATCG 57.862 47.619 0.00 0.00 41.41 3.69
71 72 5.487153 TCTACTTGACTAGCTCGTTGATC 57.513 43.478 0.00 0.00 0.00 2.92
72 73 4.336993 CCTCTACTTGACTAGCTCGTTGAT 59.663 45.833 0.00 0.00 0.00 2.57
73 74 3.690139 CCTCTACTTGACTAGCTCGTTGA 59.310 47.826 0.00 0.00 0.00 3.18
74 75 3.732471 GCCTCTACTTGACTAGCTCGTTG 60.732 52.174 0.00 0.00 0.00 4.10
75 76 2.424246 GCCTCTACTTGACTAGCTCGTT 59.576 50.000 0.00 0.00 0.00 3.85
76 77 2.018515 GCCTCTACTTGACTAGCTCGT 58.981 52.381 0.00 0.00 0.00 4.18
77 78 2.017782 TGCCTCTACTTGACTAGCTCG 58.982 52.381 0.00 0.00 0.00 5.03
78 79 4.825085 AGTATGCCTCTACTTGACTAGCTC 59.175 45.833 0.00 0.00 0.00 4.09
79 80 4.798882 AGTATGCCTCTACTTGACTAGCT 58.201 43.478 0.00 0.00 0.00 3.32
80 81 5.766174 ACTAGTATGCCTCTACTTGACTAGC 59.234 44.000 0.00 0.00 38.86 3.42
81 82 6.993308 TCACTAGTATGCCTCTACTTGACTAG 59.007 42.308 0.00 0.00 40.35 2.57
82 83 6.766944 GTCACTAGTATGCCTCTACTTGACTA 59.233 42.308 0.00 0.00 36.95 2.59
83 84 5.591067 GTCACTAGTATGCCTCTACTTGACT 59.409 44.000 0.00 0.00 36.95 3.41
84 85 5.357314 TGTCACTAGTATGCCTCTACTTGAC 59.643 44.000 0.00 11.98 38.64 3.18
85 86 5.357314 GTGTCACTAGTATGCCTCTACTTGA 59.643 44.000 0.00 0.18 33.96 3.02
86 87 5.358442 AGTGTCACTAGTATGCCTCTACTTG 59.642 44.000 2.87 0.00 33.96 3.16
87 88 5.511363 AGTGTCACTAGTATGCCTCTACTT 58.489 41.667 2.87 0.00 33.96 2.24
88 89 5.118729 AGTGTCACTAGTATGCCTCTACT 57.881 43.478 2.87 0.00 36.04 2.57
89 90 6.487331 ACATAGTGTCACTAGTATGCCTCTAC 59.513 42.308 17.43 0.00 37.44 2.59
90 91 6.602278 ACATAGTGTCACTAGTATGCCTCTA 58.398 40.000 17.43 0.00 37.44 2.43
91 92 5.450453 ACATAGTGTCACTAGTATGCCTCT 58.550 41.667 17.43 0.00 37.44 3.69
92 93 5.776173 ACATAGTGTCACTAGTATGCCTC 57.224 43.478 17.43 0.00 37.44 4.70
93 94 6.070767 ACAAACATAGTGTCACTAGTATGCCT 60.071 38.462 17.43 2.21 37.44 4.75
94 95 6.106673 ACAAACATAGTGTCACTAGTATGCC 58.893 40.000 17.43 0.00 37.44 4.40
95 96 7.036220 AGACAAACATAGTGTCACTAGTATGC 58.964 38.462 17.43 9.88 46.44 3.14
98 99 9.239551 ACATAGACAAACATAGTGTCACTAGTA 57.760 33.333 17.43 0.00 46.44 1.82
99 100 8.123639 ACATAGACAAACATAGTGTCACTAGT 57.876 34.615 17.43 12.40 46.44 2.57
102 103 9.587772 GAATACATAGACAAACATAGTGTCACT 57.412 33.333 10.99 10.99 46.44 3.41
103 104 9.366216 TGAATACATAGACAAACATAGTGTCAC 57.634 33.333 7.26 0.00 46.44 3.67
104 105 9.366216 GTGAATACATAGACAAACATAGTGTCA 57.634 33.333 7.26 0.00 46.44 3.58
105 106 9.366216 TGTGAATACATAGACAAACATAGTGTC 57.634 33.333 0.00 0.00 44.75 3.67
106 107 9.151471 GTGTGAATACATAGACAAACATAGTGT 57.849 33.333 0.00 0.00 39.39 3.55
107 108 9.150348 TGTGTGAATACATAGACAAACATAGTG 57.850 33.333 0.00 0.00 39.39 2.74
108 109 9.890629 ATGTGTGAATACATAGACAAACATAGT 57.109 29.630 0.00 0.00 38.77 2.12
110 111 9.665719 ACATGTGTGAATACATAGACAAACATA 57.334 29.630 0.00 0.00 38.58 2.29
111 112 8.565896 ACATGTGTGAATACATAGACAAACAT 57.434 30.769 0.00 0.00 40.42 2.71
112 113 7.977789 ACATGTGTGAATACATAGACAAACA 57.022 32.000 0.00 0.00 39.17 2.83
122 123 8.608317 CGGAAACATAATACATGTGTGAATACA 58.392 33.333 9.11 0.00 34.63 2.29
123 124 8.067784 CCGGAAACATAATACATGTGTGAATAC 58.932 37.037 9.11 0.00 31.80 1.89
124 125 7.771361 ACCGGAAACATAATACATGTGTGAATA 59.229 33.333 9.46 0.00 31.80 1.75
125 126 6.601613 ACCGGAAACATAATACATGTGTGAAT 59.398 34.615 9.46 0.00 31.80 2.57
126 127 5.941058 ACCGGAAACATAATACATGTGTGAA 59.059 36.000 9.46 0.00 31.80 3.18
127 128 5.492895 ACCGGAAACATAATACATGTGTGA 58.507 37.500 9.46 0.00 31.80 3.58
128 129 5.811399 ACCGGAAACATAATACATGTGTG 57.189 39.130 9.46 4.81 31.80 3.82
129 130 7.925043 TTAACCGGAAACATAATACATGTGT 57.075 32.000 9.46 0.00 31.80 3.72
130 131 9.872757 GTATTAACCGGAAACATAATACATGTG 57.127 33.333 9.46 0.00 39.40 3.21
131 132 9.616156 TGTATTAACCGGAAACATAATACATGT 57.384 29.630 22.31 2.69 42.13 3.21
139 140 9.048446 GCTAGAATTGTATTAACCGGAAACATA 57.952 33.333 9.46 0.00 0.00 2.29
140 141 7.554835 TGCTAGAATTGTATTAACCGGAAACAT 59.445 33.333 9.46 0.00 0.00 2.71
141 142 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
142 143 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
143 144 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
144 145 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
145 146 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
146 147 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
221 222 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
222 223 5.163152 ACCTTGAAGGAAATATGCCCTAGAG 60.163 44.000 19.83 0.00 37.67 2.43
223 224 4.726825 ACCTTGAAGGAAATATGCCCTAGA 59.273 41.667 19.83 0.00 37.67 2.43
224 225 4.823989 CACCTTGAAGGAAATATGCCCTAG 59.176 45.833 19.83 0.00 37.67 3.02
225 226 4.386312 CCACCTTGAAGGAAATATGCCCTA 60.386 45.833 19.83 0.00 37.67 3.53
226 227 3.628257 CCACCTTGAAGGAAATATGCCCT 60.628 47.826 19.83 0.00 37.67 5.19
227 228 2.695147 CCACCTTGAAGGAAATATGCCC 59.305 50.000 19.83 0.00 37.67 5.36
228 229 3.631250 TCCACCTTGAAGGAAATATGCC 58.369 45.455 19.83 0.00 37.67 4.40
229 230 3.067320 GCTCCACCTTGAAGGAAATATGC 59.933 47.826 19.83 10.10 37.67 3.14
230 231 4.337555 CAGCTCCACCTTGAAGGAAATATG 59.662 45.833 19.83 4.95 37.67 1.78
231 232 4.530875 CAGCTCCACCTTGAAGGAAATAT 58.469 43.478 19.83 0.00 37.67 1.28
232 233 3.308402 CCAGCTCCACCTTGAAGGAAATA 60.308 47.826 19.83 0.00 37.67 1.40
233 234 2.556114 CCAGCTCCACCTTGAAGGAAAT 60.556 50.000 19.83 0.00 37.67 2.17
234 235 1.202927 CCAGCTCCACCTTGAAGGAAA 60.203 52.381 19.83 1.52 37.67 3.13
235 236 0.401738 CCAGCTCCACCTTGAAGGAA 59.598 55.000 19.83 1.90 37.67 3.36
236 237 0.473694 TCCAGCTCCACCTTGAAGGA 60.474 55.000 19.83 0.00 37.67 3.36
237 238 0.622665 ATCCAGCTCCACCTTGAAGG 59.377 55.000 10.24 10.24 42.49 3.46
238 239 2.503895 AATCCAGCTCCACCTTGAAG 57.496 50.000 0.00 0.00 0.00 3.02
239 240 2.978156 AAATCCAGCTCCACCTTGAA 57.022 45.000 0.00 0.00 0.00 2.69
240 241 2.555227 GGAAAATCCAGCTCCACCTTGA 60.555 50.000 0.00 0.00 36.28 3.02
241 242 1.821136 GGAAAATCCAGCTCCACCTTG 59.179 52.381 0.00 0.00 36.28 3.61
242 243 1.272704 GGGAAAATCCAGCTCCACCTT 60.273 52.381 0.00 0.00 38.64 3.50
243 244 0.332972 GGGAAAATCCAGCTCCACCT 59.667 55.000 0.00 0.00 38.64 4.00
244 245 1.032114 CGGGAAAATCCAGCTCCACC 61.032 60.000 0.00 0.00 38.64 4.61
245 246 2.482326 CGGGAAAATCCAGCTCCAC 58.518 57.895 0.00 0.00 38.64 4.02
286 287 2.300152 TCGGAAGCTTGACTCACTGAAT 59.700 45.455 2.10 0.00 0.00 2.57
291 292 1.795286 CAAGTCGGAAGCTTGACTCAC 59.205 52.381 17.16 4.81 44.36 3.51
292 293 1.686587 TCAAGTCGGAAGCTTGACTCA 59.313 47.619 17.16 7.04 44.36 3.41
298 299 2.616510 CCCTTCATCAAGTCGGAAGCTT 60.617 50.000 0.00 0.00 37.34 3.74
310 311 1.625315 CATATCGCTCCCCCTTCATCA 59.375 52.381 0.00 0.00 0.00 3.07
372 373 2.417933 CAGCTCCCGAAAATTCACTCTG 59.582 50.000 0.00 0.00 0.00 3.35
380 381 4.937201 AACTTTTTCAGCTCCCGAAAAT 57.063 36.364 10.28 0.00 40.87 1.82
538 620 5.068215 TGGGATCCACTCAAACCTTTTTA 57.932 39.130 15.23 0.00 0.00 1.52
557 639 0.179000 CCTCTCACGGGATTTCTGGG 59.821 60.000 0.00 0.00 0.00 4.45
559 641 2.761208 ACTACCTCTCACGGGATTTCTG 59.239 50.000 0.00 0.00 0.00 3.02
610 696 7.893302 AGGTTGGTTGTTTGATTCATAGGATTA 59.107 33.333 0.00 0.00 0.00 1.75
673 760 7.285401 CCTAAGGGCTGCTTTAATTTTCATAGA 59.715 37.037 0.00 0.00 0.00 1.98
684 772 2.205342 ACCATCCTAAGGGCTGCTTTA 58.795 47.619 0.00 0.00 0.00 1.85
689 777 3.456277 ACTCTAAACCATCCTAAGGGCTG 59.544 47.826 0.00 0.00 0.00 4.85
703 791 4.749976 CCCACTCTAGAGCAACTCTAAAC 58.250 47.826 19.97 0.00 41.74 2.01
719 831 0.537653 GTCCTAGTCCAAGCCCACTC 59.462 60.000 0.00 0.00 0.00 3.51
781 893 4.309950 GAGGTGTTGCCGTCCCGT 62.310 66.667 0.00 0.00 43.70 5.28
783 895 3.310860 ATCGAGGTGTTGCCGTCCC 62.311 63.158 0.00 0.00 43.70 4.46
784 896 2.100631 CATCGAGGTGTTGCCGTCC 61.101 63.158 0.00 0.00 43.70 4.79
785 897 2.100631 CCATCGAGGTGTTGCCGTC 61.101 63.158 0.00 0.00 43.70 4.79
786 898 2.047274 CCATCGAGGTGTTGCCGT 60.047 61.111 0.00 0.00 43.70 5.68
801 913 0.538977 AGAGGAGGAAACGTCGACCA 60.539 55.000 10.58 0.00 0.00 4.02
858 970 1.391485 CTCGAGATGGTTTGAGTTGCG 59.609 52.381 6.58 0.00 0.00 4.85
969 1081 2.433145 TCAGGAGCTCGCGCAAAG 60.433 61.111 8.75 5.15 39.10 2.77
1165 1277 3.326889 CTTCGGGCGTAACGGTCGA 62.327 63.158 0.00 0.00 0.00 4.20
1302 1414 3.390639 CCTTGAGAATCCTATCTGCCAGT 59.609 47.826 0.00 0.00 0.00 4.00
1326 1438 4.437587 GGGCCATCCTGCAGCAGT 62.438 66.667 21.26 0.04 0.00 4.40
1473 1585 1.529865 GCCCACACGAAGAACTTGTAC 59.470 52.381 0.00 0.00 29.89 2.90
1733 1845 4.260375 GCAATATCGCATTGAACGAACTCT 60.260 41.667 12.18 0.00 43.71 3.24
1773 1885 6.402550 CCCATTCGATCAAAGAGTACTGTTTG 60.403 42.308 30.14 30.14 42.89 2.93
1851 1963 1.100463 ACTTTGCACGCATGACCACA 61.100 50.000 0.00 0.00 0.00 4.17
1935 2047 5.675538 AGATTGTAAGTATGAAGGTCAGGC 58.324 41.667 0.00 0.00 0.00 4.85
2043 2155 3.701040 AGTTTGTGAAATGGAGCACACTT 59.299 39.130 0.00 0.00 43.97 3.16
2121 2233 2.711009 ACACCCTTTCTTCACCATCTCA 59.289 45.455 0.00 0.00 0.00 3.27
2346 2458 1.197721 GAGAAGTTTGGTGTGCATCCG 59.802 52.381 0.00 0.00 0.00 4.18
2373 2485 7.381766 TCGCAATCTACACACTAAAGTACTA 57.618 36.000 0.00 0.00 0.00 1.82
2451 2563 5.716228 TGACAACAAATGAAGATATTGGCCT 59.284 36.000 3.32 0.00 0.00 5.19
2475 2587 5.458215 GCATCTTCTATATCCCCCAAACCTT 60.458 44.000 0.00 0.00 0.00 3.50
2652 2765 3.980646 ACATTTGTGCACTTCGCTAAA 57.019 38.095 19.41 9.27 43.06 1.85
2709 2822 1.678970 GCCCACCATCCTGTCCAAC 60.679 63.158 0.00 0.00 0.00 3.77
2757 4464 5.008118 GGAATTAGGACTATTGAAGCAGTGC 59.992 44.000 7.13 7.13 33.69 4.40
2792 4499 5.699001 AGCTCAACAAAAGGAAAACGTTTTT 59.301 32.000 25.86 9.80 0.00 1.94
2797 4504 3.769536 ACAGCTCAACAAAAGGAAAACG 58.230 40.909 0.00 0.00 0.00 3.60
2817 4524 7.900782 TTAGGAGCAAAACTACTGTGAATAC 57.099 36.000 0.00 0.00 40.99 1.89
3246 4954 6.183361 ACAGAAGGTTGACATTGACTAGAACT 60.183 38.462 0.00 0.00 0.00 3.01
3324 5032 1.825090 TTGAAGGCATGCACCTACTG 58.175 50.000 21.36 0.00 39.93 2.74
3409 5117 2.880268 TCATCCATGCCTAAAATGCTCG 59.120 45.455 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.