Multiple sequence alignment - TraesCS5B01G235200

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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 TraesCS5B01G235200 chr5B 100.000 2918 0 0 1 2918 415129217 415126300 0.000000e+00 5389.0
1 TraesCS5B01G235200 chr5B 89.231 130 14 0 83 212 48418504 48418633 2.330000e-36 163.0
2 TraesCS5B01G235200 chr5D 94.610 1985 66 18 961 2918 352454952 352452982 0.000000e+00 3035.0
3 TraesCS5B01G235200 chr5D 90.185 540 31 9 433 963 352455533 352455007 0.000000e+00 684.0
4 TraesCS5B01G235200 chr5D 100.000 33 0 0 2194 2226 352451406 352451374 8.730000e-06 62.1
5 TraesCS5B01G235200 chr5A 92.800 1986 71 25 954 2899 453518951 453520904 0.000000e+00 2809.0
6 TraesCS5B01G235200 chr5A 87.069 348 25 9 621 963 453518571 453518903 2.750000e-100 375.0
7 TraesCS5B01G235200 chr5A 89.123 285 15 8 247 528 453518051 453518322 1.000000e-89 340.0
8 TraesCS5B01G235200 chr6A 99.494 1186 6 0 961 2146 116813756 116812571 0.000000e+00 2158.0
9 TraesCS5B01G235200 chr6A 99.052 211 2 0 753 963 116814021 116813811 2.120000e-101 379.0
10 TraesCS5B01G235200 chr6A 87.879 66 7 1 25 89 599172331 599172396 3.120000e-10 76.8
11 TraesCS5B01G235200 chr3A 99.462 744 4 0 1403 2146 398879899 398879156 0.000000e+00 1352.0
12 TraesCS5B01G235200 chr3A 84.076 157 22 3 1600 1755 599326213 599326367 6.520000e-32 148.0
13 TraesCS5B01G235200 chr3A 97.143 35 0 1 9 42 317275343 317275309 1.130000e-04 58.4
14 TraesCS5B01G235200 chr3A 97.143 35 0 1 9 42 317296712 317296678 1.130000e-04 58.4
15 TraesCS5B01G235200 chr3A 94.286 35 1 1 9 42 256533335 256533369 5.000000e-03 52.8
16 TraesCS5B01G235200 chr2B 99.541 436 2 0 1708 2143 712611174 712611609 0.000000e+00 795.0
17 TraesCS5B01G235200 chr2B 100.000 324 0 0 961 1284 712610854 712611177 1.500000e-167 599.0
18 TraesCS5B01G235200 chr2B 99.052 211 2 0 753 963 712610589 712610799 2.120000e-101 379.0
19 TraesCS5B01G235200 chr2B 90.076 131 12 1 85 215 147465512 147465641 5.000000e-38 169.0
20 TraesCS5B01G235200 chr2B 94.828 58 2 1 28 84 799612006 799612063 4.010000e-14 89.8
21 TraesCS5B01G235200 chr7A 90.278 288 28 0 1498 1785 258824369 258824656 7.630000e-101 377.0
22 TraesCS5B01G235200 chr7A 82.075 212 34 3 1569 1778 126122475 126122684 8.310000e-41 178.0
23 TraesCS5B01G235200 chr7D 89.931 288 29 0 1498 1785 243808054 243808341 3.550000e-99 372.0
24 TraesCS5B01G235200 chr7D 82.353 204 36 0 1569 1772 123219587 123219790 8.310000e-41 178.0
25 TraesCS5B01G235200 chr7D 94.737 57 3 0 28 84 597043667 597043611 4.010000e-14 89.8
26 TraesCS5B01G235200 chr3D 90.909 132 12 0 83 214 507038600 507038731 8.310000e-41 178.0
27 TraesCS5B01G235200 chr3D 83.439 157 23 3 1600 1755 456534488 456534642 3.030000e-30 143.0
28 TraesCS5B01G235200 chr3D 94.828 58 2 1 28 84 189039251 189039308 4.010000e-14 89.8
29 TraesCS5B01G235200 chr7B 81.604 212 35 3 1569 1778 84389122 84389331 3.870000e-39 172.0
30 TraesCS5B01G235200 chr7B 96.491 57 2 0 28 84 750584053 750583997 8.610000e-16 95.3
31 TraesCS5B01G235200 chr4A 90.152 132 13 0 83 214 300619562 300619431 3.870000e-39 172.0
32 TraesCS5B01G235200 chr4A 89.394 66 4 1 22 84 141135558 141135623 2.410000e-11 80.5
33 TraesCS5B01G235200 chr1D 90.152 132 13 0 83 214 121624601 121624470 3.870000e-39 172.0
34 TraesCS5B01G235200 chr1B 90.152 132 13 0 83 214 347665530 347665661 3.870000e-39 172.0
35 TraesCS5B01G235200 chr1B 90.076 131 12 1 83 213 15725738 15725609 5.000000e-38 169.0
36 TraesCS5B01G235200 chr1A 90.226 133 12 1 83 215 575592177 575592308 3.870000e-39 172.0
37 TraesCS5B01G235200 chr1A 100.000 29 0 0 9 37 250306384 250306356 1.000000e-03 54.7
38 TraesCS5B01G235200 chrUn 89.394 132 14 0 83 214 314616604 314616473 1.800000e-37 167.0
39 TraesCS5B01G235200 chr4B 93.333 60 3 1 28 86 586994254 586994195 1.440000e-13 87.9
40 TraesCS5B01G235200 chr4B 92.982 57 2 1 28 84 454036589 454036643 6.700000e-12 82.4
41 TraesCS5B01G235200 chr4B 91.667 60 2 3 25 84 519253733 519253677 2.410000e-11 80.5
42 TraesCS5B01G235200 chr2A 100.000 28 0 0 2394 2421 344889842 344889815 5.000000e-03 52.8
43 TraesCS5B01G235200 chr2A 100.000 28 0 0 2394 2421 345161438 345161411 5.000000e-03 52.8


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 TraesCS5B01G235200 chr5B 415126300 415129217 2917 True 5389.000000 5389 100.000000 1 2918 1 chr5B.!!$R1 2917
1 TraesCS5B01G235200 chr5D 352451374 352455533 4159 True 1260.366667 3035 94.931667 433 2918 3 chr5D.!!$R1 2485
2 TraesCS5B01G235200 chr5A 453518051 453520904 2853 False 1174.666667 2809 89.664000 247 2899 3 chr5A.!!$F1 2652
3 TraesCS5B01G235200 chr6A 116812571 116814021 1450 True 1268.500000 2158 99.273000 753 2146 2 chr6A.!!$R1 1393
4 TraesCS5B01G235200 chr3A 398879156 398879899 743 True 1352.000000 1352 99.462000 1403 2146 1 chr3A.!!$R3 743
5 TraesCS5B01G235200 chr2B 712610589 712611609 1020 False 591.000000 795 99.531000 753 2143 3 chr2B.!!$F3 1390

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
407 411 0.036388 TCAACCAGATCACCTTCCGC 60.036 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2500 1.936436 ATGCATGCACGCCAACGAAT 61.936 50.0 25.37 0.0 43.93 3.34 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
20 21 3.694535 CTCGCTAGTACTCCATTCGTT 57.305 47.619 0.00 0.00 0.00 3.85
21 22 3.619729 CTCGCTAGTACTCCATTCGTTC 58.380 50.000 0.00 0.00 0.00 3.95
22 23 2.357009 TCGCTAGTACTCCATTCGTTCC 59.643 50.000 0.00 0.00 0.00 3.62
23 24 2.358267 CGCTAGTACTCCATTCGTTCCT 59.642 50.000 0.00 0.00 0.00 3.36
24 25 3.562973 CGCTAGTACTCCATTCGTTCCTA 59.437 47.826 0.00 0.00 0.00 2.94
25 26 4.036027 CGCTAGTACTCCATTCGTTCCTAA 59.964 45.833 0.00 0.00 0.00 2.69
26 27 5.449588 CGCTAGTACTCCATTCGTTCCTAAA 60.450 44.000 0.00 0.00 0.00 1.85
27 28 6.514063 GCTAGTACTCCATTCGTTCCTAAAT 58.486 40.000 0.00 0.00 0.00 1.40
28 29 7.521099 CGCTAGTACTCCATTCGTTCCTAAATA 60.521 40.741 0.00 0.00 0.00 1.40
29 30 7.594386 GCTAGTACTCCATTCGTTCCTAAATAC 59.406 40.741 0.00 0.00 0.00 1.89
30 31 7.657023 AGTACTCCATTCGTTCCTAAATACT 57.343 36.000 0.00 0.00 0.00 2.12
31 32 7.714703 AGTACTCCATTCGTTCCTAAATACTC 58.285 38.462 0.00 0.00 0.00 2.59
32 33 5.915175 ACTCCATTCGTTCCTAAATACTCC 58.085 41.667 0.00 0.00 0.00 3.85
33 34 5.163332 ACTCCATTCGTTCCTAAATACTCCC 60.163 44.000 0.00 0.00 0.00 4.30
34 35 4.966805 TCCATTCGTTCCTAAATACTCCCT 59.033 41.667 0.00 0.00 0.00 4.20
35 36 5.070047 TCCATTCGTTCCTAAATACTCCCTC 59.930 44.000 0.00 0.00 0.00 4.30
36 37 5.298347 CATTCGTTCCTAAATACTCCCTCC 58.702 45.833 0.00 0.00 0.00 4.30
37 38 2.954318 TCGTTCCTAAATACTCCCTCCG 59.046 50.000 0.00 0.00 0.00 4.63
38 39 2.692041 CGTTCCTAAATACTCCCTCCGT 59.308 50.000 0.00 0.00 0.00 4.69
39 40 3.243334 CGTTCCTAAATACTCCCTCCGTC 60.243 52.174 0.00 0.00 0.00 4.79
40 41 2.954792 TCCTAAATACTCCCTCCGTCC 58.045 52.381 0.00 0.00 0.00 4.79
41 42 1.969208 CCTAAATACTCCCTCCGTCCC 59.031 57.143 0.00 0.00 0.00 4.46
42 43 1.612463 CTAAATACTCCCTCCGTCCCG 59.388 57.143 0.00 0.00 0.00 5.14
43 44 0.325016 AAATACTCCCTCCGTCCCGT 60.325 55.000 0.00 0.00 0.00 5.28
44 45 0.552848 AATACTCCCTCCGTCCCGTA 59.447 55.000 0.00 0.00 0.00 4.02
45 46 0.110104 ATACTCCCTCCGTCCCGTAG 59.890 60.000 0.00 0.00 0.00 3.51
46 47 1.274703 TACTCCCTCCGTCCCGTAGT 61.275 60.000 0.00 0.00 0.00 2.73
47 48 2.044650 TCCCTCCGTCCCGTAGTG 60.045 66.667 0.00 0.00 0.00 2.74
48 49 2.362120 CCCTCCGTCCCGTAGTGT 60.362 66.667 0.00 0.00 0.00 3.55
49 50 2.413142 CCCTCCGTCCCGTAGTGTC 61.413 68.421 0.00 0.00 0.00 3.67
50 51 1.676635 CCTCCGTCCCGTAGTGTCA 60.677 63.158 0.00 0.00 0.00 3.58
51 52 1.246056 CCTCCGTCCCGTAGTGTCAA 61.246 60.000 0.00 0.00 0.00 3.18
52 53 0.599558 CTCCGTCCCGTAGTGTCAAA 59.400 55.000 0.00 0.00 0.00 2.69
53 54 1.000060 CTCCGTCCCGTAGTGTCAAAA 60.000 52.381 0.00 0.00 0.00 2.44
54 55 1.411977 TCCGTCCCGTAGTGTCAAAAA 59.588 47.619 0.00 0.00 0.00 1.94
55 56 1.528161 CCGTCCCGTAGTGTCAAAAAC 59.472 52.381 0.00 0.00 0.00 2.43
56 57 1.190763 CGTCCCGTAGTGTCAAAAACG 59.809 52.381 0.00 0.00 35.20 3.60
57 58 2.204237 GTCCCGTAGTGTCAAAAACGT 58.796 47.619 0.00 0.00 33.63 3.99
58 59 2.609002 GTCCCGTAGTGTCAAAAACGTT 59.391 45.455 0.00 0.00 33.63 3.99
59 60 2.865551 TCCCGTAGTGTCAAAAACGTTC 59.134 45.455 0.00 0.00 33.63 3.95
60 61 2.867975 CCCGTAGTGTCAAAAACGTTCT 59.132 45.455 0.00 0.00 33.63 3.01
61 62 3.310501 CCCGTAGTGTCAAAAACGTTCTT 59.689 43.478 0.00 0.00 33.63 2.52
62 63 4.507388 CCCGTAGTGTCAAAAACGTTCTTA 59.493 41.667 0.00 0.00 33.63 2.10
63 64 5.178067 CCCGTAGTGTCAAAAACGTTCTTAT 59.822 40.000 0.00 0.00 33.63 1.73
64 65 6.365789 CCCGTAGTGTCAAAAACGTTCTTATA 59.634 38.462 0.00 0.00 33.63 0.98
65 66 7.063780 CCCGTAGTGTCAAAAACGTTCTTATAT 59.936 37.037 0.00 0.00 33.63 0.86
66 67 8.437742 CCGTAGTGTCAAAAACGTTCTTATATT 58.562 33.333 0.00 0.00 33.63 1.28
71 72 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
72 73 8.679100 TGTCAAAAACGTTCTTATATTATGGGG 58.321 33.333 0.00 0.00 0.00 4.96
73 74 7.646526 GTCAAAAACGTTCTTATATTATGGGGC 59.353 37.037 0.00 0.00 0.00 5.80
74 75 5.934935 AAACGTTCTTATATTATGGGGCG 57.065 39.130 0.00 0.00 0.00 6.13
75 76 3.934068 ACGTTCTTATATTATGGGGCGG 58.066 45.455 0.00 0.00 0.00 6.13
76 77 3.579586 ACGTTCTTATATTATGGGGCGGA 59.420 43.478 0.00 0.00 0.00 5.54
77 78 4.181578 CGTTCTTATATTATGGGGCGGAG 58.818 47.826 0.00 0.00 0.00 4.63
78 79 4.514401 GTTCTTATATTATGGGGCGGAGG 58.486 47.826 0.00 0.00 0.00 4.30
79 80 3.112263 TCTTATATTATGGGGCGGAGGG 58.888 50.000 0.00 0.00 0.00 4.30
80 81 2.953093 TATATTATGGGGCGGAGGGA 57.047 50.000 0.00 0.00 0.00 4.20
81 82 1.584724 ATATTATGGGGCGGAGGGAG 58.415 55.000 0.00 0.00 0.00 4.30
82 83 0.192566 TATTATGGGGCGGAGGGAGT 59.807 55.000 0.00 0.00 0.00 3.85
83 84 0.192566 ATTATGGGGCGGAGGGAGTA 59.807 55.000 0.00 0.00 0.00 2.59
84 85 0.192566 TTATGGGGCGGAGGGAGTAT 59.807 55.000 0.00 0.00 0.00 2.12
85 86 1.086565 TATGGGGCGGAGGGAGTATA 58.913 55.000 0.00 0.00 0.00 1.47
86 87 0.192566 ATGGGGCGGAGGGAGTATAA 59.807 55.000 0.00 0.00 0.00 0.98
87 88 0.471211 TGGGGCGGAGGGAGTATAAG 60.471 60.000 0.00 0.00 0.00 1.73
88 89 0.471401 GGGGCGGAGGGAGTATAAGT 60.471 60.000 0.00 0.00 0.00 2.24
89 90 0.967662 GGGCGGAGGGAGTATAAGTC 59.032 60.000 0.00 0.00 0.00 3.01
90 91 1.480869 GGGCGGAGGGAGTATAAGTCT 60.481 57.143 0.00 0.00 0.00 3.24
91 92 2.317973 GGCGGAGGGAGTATAAGTCTT 58.682 52.381 0.00 0.00 0.00 3.01
92 93 2.699321 GGCGGAGGGAGTATAAGTCTTT 59.301 50.000 0.00 0.00 0.00 2.52
93 94 3.893813 GGCGGAGGGAGTATAAGTCTTTA 59.106 47.826 0.00 0.00 0.00 1.85
94 95 4.527427 GGCGGAGGGAGTATAAGTCTTTAT 59.473 45.833 0.00 0.00 34.04 1.40
95 96 5.713861 GGCGGAGGGAGTATAAGTCTTTATA 59.286 44.000 0.00 0.00 31.97 0.98
96 97 6.127675 GGCGGAGGGAGTATAAGTCTTTATAG 60.128 46.154 0.00 0.00 33.52 1.31
97 98 6.658391 GCGGAGGGAGTATAAGTCTTTATAGA 59.342 42.308 0.00 0.00 33.52 1.98
98 99 7.148205 GCGGAGGGAGTATAAGTCTTTATAGAG 60.148 44.444 0.00 0.00 33.52 2.43
99 100 8.102047 CGGAGGGAGTATAAGTCTTTATAGAGA 58.898 40.741 0.00 0.00 33.52 3.10
100 101 9.984590 GGAGGGAGTATAAGTCTTTATAGAGAT 57.015 37.037 0.00 0.00 33.52 2.75
120 121 8.899427 AGAGATTTCACTATGAACCACATATG 57.101 34.615 0.00 0.00 40.18 1.78
121 122 8.708378 AGAGATTTCACTATGAACCACATATGA 58.292 33.333 10.38 0.00 40.18 2.15
122 123 9.330063 GAGATTTCACTATGAACCACATATGAA 57.670 33.333 10.38 0.00 40.18 2.57
123 124 9.857656 AGATTTCACTATGAACCACATATGAAT 57.142 29.630 10.38 0.00 40.18 2.57
124 125 9.888878 GATTTCACTATGAACCACATATGAATG 57.111 33.333 10.38 0.00 40.18 2.67
125 126 8.806429 TTTCACTATGAACCACATATGAATGT 57.194 30.769 10.38 0.18 40.50 2.71
126 127 9.898152 TTTCACTATGAACCACATATGAATGTA 57.102 29.630 10.38 0.00 39.05 2.29
168 169 8.594881 AGTGTAGATTCACTTGTTTTACTCTG 57.405 34.615 0.00 0.00 44.92 3.35
169 170 8.204836 AGTGTAGATTCACTTGTTTTACTCTGT 58.795 33.333 0.00 0.00 44.92 3.41
170 171 9.472361 GTGTAGATTCACTTGTTTTACTCTGTA 57.528 33.333 0.00 0.00 35.68 2.74
175 176 9.612620 GATTCACTTGTTTTACTCTGTATTTGG 57.387 33.333 0.00 0.00 0.00 3.28
176 177 8.514330 TTCACTTGTTTTACTCTGTATTTGGT 57.486 30.769 0.00 0.00 0.00 3.67
177 178 8.149973 TCACTTGTTTTACTCTGTATTTGGTC 57.850 34.615 0.00 0.00 0.00 4.02
178 179 7.990886 TCACTTGTTTTACTCTGTATTTGGTCT 59.009 33.333 0.00 0.00 0.00 3.85
179 180 9.268268 CACTTGTTTTACTCTGTATTTGGTCTA 57.732 33.333 0.00 0.00 0.00 2.59
194 195 9.699703 GTATTTGGTCTATAGTGAAATCTCTCC 57.300 37.037 0.00 0.00 0.00 3.71
195 196 7.733773 TTTGGTCTATAGTGAAATCTCTCCA 57.266 36.000 0.00 0.00 0.00 3.86
196 197 7.733773 TTGGTCTATAGTGAAATCTCTCCAA 57.266 36.000 0.00 0.00 0.00 3.53
197 198 7.733773 TGGTCTATAGTGAAATCTCTCCAAA 57.266 36.000 0.00 0.00 0.00 3.28
198 199 7.786030 TGGTCTATAGTGAAATCTCTCCAAAG 58.214 38.462 0.00 0.00 0.00 2.77
199 200 7.619698 TGGTCTATAGTGAAATCTCTCCAAAGA 59.380 37.037 0.00 0.00 0.00 2.52
200 201 7.923878 GGTCTATAGTGAAATCTCTCCAAAGAC 59.076 40.741 0.00 0.00 0.00 3.01
201 202 8.691797 GTCTATAGTGAAATCTCTCCAAAGACT 58.308 37.037 0.00 0.00 0.00 3.24
202 203 9.261035 TCTATAGTGAAATCTCTCCAAAGACTT 57.739 33.333 0.00 0.00 0.00 3.01
203 204 9.311916 CTATAGTGAAATCTCTCCAAAGACTTG 57.688 37.037 0.00 0.00 0.00 3.16
204 205 5.934781 AGTGAAATCTCTCCAAAGACTTGT 58.065 37.500 0.00 0.00 0.00 3.16
205 206 7.067496 AGTGAAATCTCTCCAAAGACTTGTA 57.933 36.000 0.00 0.00 0.00 2.41
206 207 7.684529 AGTGAAATCTCTCCAAAGACTTGTAT 58.315 34.615 0.00 0.00 0.00 2.29
207 208 8.160106 AGTGAAATCTCTCCAAAGACTTGTATT 58.840 33.333 0.00 0.00 0.00 1.89
208 209 8.787852 GTGAAATCTCTCCAAAGACTTGTATTT 58.212 33.333 0.00 0.00 0.00 1.40
211 212 9.454859 AAATCTCTCCAAAGACTTGTATTTAGG 57.545 33.333 0.00 0.00 0.00 2.69
212 213 7.792364 TCTCTCCAAAGACTTGTATTTAGGA 57.208 36.000 0.00 9.70 0.00 2.94
213 214 8.202461 TCTCTCCAAAGACTTGTATTTAGGAA 57.798 34.615 10.63 5.08 0.00 3.36
214 215 8.656806 TCTCTCCAAAGACTTGTATTTAGGAAA 58.343 33.333 10.63 2.08 0.00 3.13
215 216 9.454859 CTCTCCAAAGACTTGTATTTAGGAAAT 57.545 33.333 10.63 0.00 34.90 2.17
328 329 8.388484 ACGTATAAGTATCACGTAGGAAGAAT 57.612 34.615 0.00 0.00 46.23 2.40
341 342 4.957684 AGGAAGAATAATCTACGGTGGG 57.042 45.455 0.00 0.00 33.77 4.61
352 353 9.551734 AATAATCTACGGTGGGAACTAAAATAC 57.448 33.333 0.00 0.00 0.00 1.89
379 383 6.500041 ACTAGTATTTCTGAATCTCGTCAGC 58.500 40.000 0.00 0.00 44.01 4.26
385 389 5.843673 TTCTGAATCTCGTCAGCTTATCT 57.156 39.130 0.00 0.00 44.01 1.98
397 401 5.181748 GTCAGCTTATCTTGTCAACCAGAT 58.818 41.667 2.70 2.70 0.00 2.90
398 402 5.293079 GTCAGCTTATCTTGTCAACCAGATC 59.707 44.000 0.39 0.00 0.00 2.75
399 403 5.046376 TCAGCTTATCTTGTCAACCAGATCA 60.046 40.000 0.39 0.00 0.00 2.92
400 404 5.064452 CAGCTTATCTTGTCAACCAGATCAC 59.936 44.000 0.39 0.00 0.00 3.06
401 405 4.333926 GCTTATCTTGTCAACCAGATCACC 59.666 45.833 0.39 0.00 0.00 4.02
402 406 5.738909 CTTATCTTGTCAACCAGATCACCT 58.261 41.667 0.39 0.00 0.00 4.00
403 407 4.647564 ATCTTGTCAACCAGATCACCTT 57.352 40.909 0.00 0.00 0.00 3.50
404 408 4.008074 TCTTGTCAACCAGATCACCTTC 57.992 45.455 0.00 0.00 0.00 3.46
405 409 2.859165 TGTCAACCAGATCACCTTCC 57.141 50.000 0.00 0.00 0.00 3.46
406 410 1.001974 TGTCAACCAGATCACCTTCCG 59.998 52.381 0.00 0.00 0.00 4.30
407 411 0.036388 TCAACCAGATCACCTTCCGC 60.036 55.000 0.00 0.00 0.00 5.54
424 428 2.095110 TCCGCGTGATCGTAGAGAAAAA 60.095 45.455 4.92 0.00 43.63 1.94
460 464 1.453155 GGTTCATCGCACATGACCTT 58.547 50.000 0.00 0.00 0.00 3.50
549 689 2.166829 CTACAGAGTGCTCCACTGACT 58.833 52.381 14.46 0.00 45.44 3.41
551 691 0.669932 CAGAGTGCTCCACTGACTGC 60.670 60.000 2.12 0.00 45.44 4.40
552 692 1.735920 GAGTGCTCCACTGACTGCG 60.736 63.158 2.12 0.00 45.44 5.18
553 693 2.740055 GTGCTCCACTGACTGCGG 60.740 66.667 0.00 0.00 0.00 5.69
554 694 4.007644 TGCTCCACTGACTGCGGG 62.008 66.667 0.00 0.00 0.00 6.13
555 695 4.008933 GCTCCACTGACTGCGGGT 62.009 66.667 0.00 0.00 0.00 5.28
556 696 2.262915 CTCCACTGACTGCGGGTC 59.737 66.667 0.00 0.00 44.70 4.46
557 697 3.302347 CTCCACTGACTGCGGGTCC 62.302 68.421 0.00 0.00 43.89 4.46
558 698 3.314331 CCACTGACTGCGGGTCCT 61.314 66.667 0.00 0.00 43.89 3.85
603 755 1.252215 TAATCCACGTGTCAGGCCGA 61.252 55.000 15.65 2.65 0.00 5.54
604 756 2.507110 AATCCACGTGTCAGGCCGAG 62.507 60.000 15.65 0.00 0.00 4.63
728 892 7.100409 TGATCCGTGTTATGTGAGACATTTTA 58.900 34.615 0.00 0.00 39.88 1.52
829 993 1.303317 GGAGCGGGAAGGCAAAAGA 60.303 57.895 0.00 0.00 34.64 2.52
1525 1762 2.630098 GGGAGATGATCTTCCACATCGA 59.370 50.000 15.05 0.00 42.02 3.59
2239 2511 3.754323 TGATCCTAAAAATTCGTTGGCGT 59.246 39.130 0.00 0.00 39.49 5.68
2240 2512 3.546002 TCCTAAAAATTCGTTGGCGTG 57.454 42.857 0.00 0.00 39.49 5.34
2241 2513 1.982913 CCTAAAAATTCGTTGGCGTGC 59.017 47.619 0.00 0.00 39.49 5.34
2242 2514 2.605823 CCTAAAAATTCGTTGGCGTGCA 60.606 45.455 0.00 0.00 39.49 4.57
2292 2564 6.111768 CAATACCCATTGTCTTTTCTCTCG 57.888 41.667 0.00 0.00 37.37 4.04
2391 2663 0.742990 TGGCAATGGCAGTACTACGC 60.743 55.000 5.05 0.00 43.71 4.42
2394 2666 2.007049 GCAATGGCAGTACTACGCAGT 61.007 52.381 7.43 0.00 42.62 4.40
2408 2682 0.813184 CGCAGTACTCCCTCCGTAAA 59.187 55.000 0.00 0.00 0.00 2.01
2411 2685 2.494870 GCAGTACTCCCTCCGTAAAGAA 59.505 50.000 0.00 0.00 0.00 2.52
2422 2696 5.860716 CCCTCCGTAAAGAAATATACTACGC 59.139 44.000 0.00 0.00 35.25 4.42
2473 2747 2.486966 GCGGTGCCTTTGCTGATC 59.513 61.111 0.00 0.00 38.71 2.92
2476 2750 1.304381 GGTGCCTTTGCTGATCCCA 60.304 57.895 0.00 0.00 38.71 4.37
2485 2759 0.176449 TGCTGATCCCATGTCGTCAG 59.824 55.000 11.85 11.85 40.71 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.548415 GGAACGAATGGAGTACTAGCGAG 60.548 52.174 0.00 0.00 0.00 5.03
1 2 2.357009 GGAACGAATGGAGTACTAGCGA 59.643 50.000 0.00 0.00 0.00 4.93
2 3 2.358267 AGGAACGAATGGAGTACTAGCG 59.642 50.000 0.00 0.00 0.00 4.26
3 4 5.511234 TTAGGAACGAATGGAGTACTAGC 57.489 43.478 0.00 0.00 0.00 3.42
4 5 8.848182 AGTATTTAGGAACGAATGGAGTACTAG 58.152 37.037 0.00 0.00 0.00 2.57
5 6 8.757982 AGTATTTAGGAACGAATGGAGTACTA 57.242 34.615 0.00 0.00 0.00 1.82
6 7 7.201893 GGAGTATTTAGGAACGAATGGAGTACT 60.202 40.741 0.00 0.00 0.00 2.73
7 8 6.922407 GGAGTATTTAGGAACGAATGGAGTAC 59.078 42.308 0.00 0.00 0.00 2.73
8 9 6.041296 GGGAGTATTTAGGAACGAATGGAGTA 59.959 42.308 0.00 0.00 0.00 2.59
9 10 5.163332 GGGAGTATTTAGGAACGAATGGAGT 60.163 44.000 0.00 0.00 0.00 3.85
10 11 5.070580 AGGGAGTATTTAGGAACGAATGGAG 59.929 44.000 0.00 0.00 0.00 3.86
11 12 4.966805 AGGGAGTATTTAGGAACGAATGGA 59.033 41.667 0.00 0.00 0.00 3.41
12 13 5.291905 AGGGAGTATTTAGGAACGAATGG 57.708 43.478 0.00 0.00 0.00 3.16
13 14 5.298347 GGAGGGAGTATTTAGGAACGAATG 58.702 45.833 0.00 0.00 0.00 2.67
14 15 4.038883 CGGAGGGAGTATTTAGGAACGAAT 59.961 45.833 0.00 0.00 0.00 3.34
15 16 3.382546 CGGAGGGAGTATTTAGGAACGAA 59.617 47.826 0.00 0.00 0.00 3.85
16 17 2.954318 CGGAGGGAGTATTTAGGAACGA 59.046 50.000 0.00 0.00 0.00 3.85
17 18 2.692041 ACGGAGGGAGTATTTAGGAACG 59.308 50.000 0.00 0.00 0.00 3.95
18 19 3.069300 GGACGGAGGGAGTATTTAGGAAC 59.931 52.174 0.00 0.00 0.00 3.62
19 20 3.303049 GGACGGAGGGAGTATTTAGGAA 58.697 50.000 0.00 0.00 0.00 3.36
20 21 2.425392 GGGACGGAGGGAGTATTTAGGA 60.425 54.545 0.00 0.00 0.00 2.94
21 22 1.969208 GGGACGGAGGGAGTATTTAGG 59.031 57.143 0.00 0.00 0.00 2.69
37 38 2.204237 ACGTTTTTGACACTACGGGAC 58.796 47.619 0.00 0.00 38.26 4.46
38 39 2.600470 ACGTTTTTGACACTACGGGA 57.400 45.000 0.00 0.00 38.26 5.14
39 40 2.867975 AGAACGTTTTTGACACTACGGG 59.132 45.455 0.46 0.00 38.26 5.28
40 41 4.525411 AAGAACGTTTTTGACACTACGG 57.475 40.909 0.46 0.00 38.26 4.02
45 46 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
46 47 8.679100 CCCCATAATATAAGAACGTTTTTGACA 58.321 33.333 13.87 0.01 0.00 3.58
47 48 7.646526 GCCCCATAATATAAGAACGTTTTTGAC 59.353 37.037 13.87 0.00 0.00 3.18
48 49 7.467539 CGCCCCATAATATAAGAACGTTTTTGA 60.468 37.037 13.87 2.81 0.00 2.69
49 50 6.635239 CGCCCCATAATATAAGAACGTTTTTG 59.365 38.462 13.87 0.00 0.00 2.44
50 51 6.238814 CCGCCCCATAATATAAGAACGTTTTT 60.239 38.462 9.22 9.22 0.00 1.94
51 52 5.239963 CCGCCCCATAATATAAGAACGTTTT 59.760 40.000 0.46 0.00 0.00 2.43
52 53 4.758165 CCGCCCCATAATATAAGAACGTTT 59.242 41.667 0.46 0.00 0.00 3.60
53 54 4.040706 TCCGCCCCATAATATAAGAACGTT 59.959 41.667 0.00 0.00 0.00 3.99
54 55 3.579586 TCCGCCCCATAATATAAGAACGT 59.420 43.478 0.00 0.00 0.00 3.99
55 56 4.181578 CTCCGCCCCATAATATAAGAACG 58.818 47.826 0.00 0.00 0.00 3.95
56 57 4.514401 CCTCCGCCCCATAATATAAGAAC 58.486 47.826 0.00 0.00 0.00 3.01
57 58 3.521937 CCCTCCGCCCCATAATATAAGAA 59.478 47.826 0.00 0.00 0.00 2.52
58 59 3.112263 CCCTCCGCCCCATAATATAAGA 58.888 50.000 0.00 0.00 0.00 2.10
59 60 3.112263 TCCCTCCGCCCCATAATATAAG 58.888 50.000 0.00 0.00 0.00 1.73
60 61 3.112263 CTCCCTCCGCCCCATAATATAA 58.888 50.000 0.00 0.00 0.00 0.98
61 62 2.045326 ACTCCCTCCGCCCCATAATATA 59.955 50.000 0.00 0.00 0.00 0.86
62 63 1.203440 ACTCCCTCCGCCCCATAATAT 60.203 52.381 0.00 0.00 0.00 1.28
63 64 0.192566 ACTCCCTCCGCCCCATAATA 59.807 55.000 0.00 0.00 0.00 0.98
64 65 0.192566 TACTCCCTCCGCCCCATAAT 59.807 55.000 0.00 0.00 0.00 1.28
65 66 0.192566 ATACTCCCTCCGCCCCATAA 59.807 55.000 0.00 0.00 0.00 1.90
66 67 1.086565 TATACTCCCTCCGCCCCATA 58.913 55.000 0.00 0.00 0.00 2.74
67 68 0.192566 TTATACTCCCTCCGCCCCAT 59.807 55.000 0.00 0.00 0.00 4.00
68 69 0.471211 CTTATACTCCCTCCGCCCCA 60.471 60.000 0.00 0.00 0.00 4.96
69 70 0.471401 ACTTATACTCCCTCCGCCCC 60.471 60.000 0.00 0.00 0.00 5.80
70 71 0.967662 GACTTATACTCCCTCCGCCC 59.032 60.000 0.00 0.00 0.00 6.13
71 72 1.998222 AGACTTATACTCCCTCCGCC 58.002 55.000 0.00 0.00 0.00 6.13
72 73 5.725325 ATAAAGACTTATACTCCCTCCGC 57.275 43.478 0.00 0.00 0.00 5.54
73 74 8.102047 TCTCTATAAAGACTTATACTCCCTCCG 58.898 40.741 0.00 0.00 0.00 4.63
74 75 9.984590 ATCTCTATAAAGACTTATACTCCCTCC 57.015 37.037 0.00 0.00 0.00 4.30
94 95 9.987272 CATATGTGGTTCATAGTGAAATCTCTA 57.013 33.333 0.00 0.00 41.55 2.43
95 96 8.708378 TCATATGTGGTTCATAGTGAAATCTCT 58.292 33.333 1.90 0.00 41.55 3.10
96 97 8.893219 TCATATGTGGTTCATAGTGAAATCTC 57.107 34.615 1.90 0.00 41.55 2.75
97 98 9.857656 ATTCATATGTGGTTCATAGTGAAATCT 57.142 29.630 1.90 0.00 41.55 2.40
98 99 9.888878 CATTCATATGTGGTTCATAGTGAAATC 57.111 33.333 1.90 0.00 41.55 2.17
99 100 9.412460 ACATTCATATGTGGTTCATAGTGAAAT 57.588 29.630 1.90 0.00 43.29 2.17
100 101 8.806429 ACATTCATATGTGGTTCATAGTGAAA 57.194 30.769 1.90 0.00 43.29 2.69
144 145 8.366671 ACAGAGTAAAACAAGTGAATCTACAC 57.633 34.615 0.00 0.00 40.60 2.90
149 150 9.612620 CCAAATACAGAGTAAAACAAGTGAATC 57.387 33.333 0.00 0.00 0.00 2.52
150 151 9.131791 ACCAAATACAGAGTAAAACAAGTGAAT 57.868 29.630 0.00 0.00 0.00 2.57
151 152 8.514330 ACCAAATACAGAGTAAAACAAGTGAA 57.486 30.769 0.00 0.00 0.00 3.18
152 153 7.990886 AGACCAAATACAGAGTAAAACAAGTGA 59.009 33.333 0.00 0.00 0.00 3.41
153 154 8.154649 AGACCAAATACAGAGTAAAACAAGTG 57.845 34.615 0.00 0.00 0.00 3.16
168 169 9.699703 GGAGAGATTTCACTATAGACCAAATAC 57.300 37.037 6.78 5.85 0.00 1.89
169 170 9.434275 TGGAGAGATTTCACTATAGACCAAATA 57.566 33.333 6.78 0.00 0.00 1.40
170 171 8.324191 TGGAGAGATTTCACTATAGACCAAAT 57.676 34.615 6.78 7.28 0.00 2.32
171 172 7.733773 TGGAGAGATTTCACTATAGACCAAA 57.266 36.000 6.78 2.69 0.00 3.28
172 173 7.733773 TTGGAGAGATTTCACTATAGACCAA 57.266 36.000 6.78 0.00 0.00 3.67
173 174 7.619698 TCTTTGGAGAGATTTCACTATAGACCA 59.380 37.037 6.78 0.00 0.00 4.02
174 175 7.923878 GTCTTTGGAGAGATTTCACTATAGACC 59.076 40.741 6.78 0.00 32.29 3.85
175 176 8.691797 AGTCTTTGGAGAGATTTCACTATAGAC 58.308 37.037 6.78 8.58 35.52 2.59
176 177 8.830915 AGTCTTTGGAGAGATTTCACTATAGA 57.169 34.615 6.78 0.00 31.07 1.98
177 178 9.311916 CAAGTCTTTGGAGAGATTTCACTATAG 57.688 37.037 0.00 0.00 31.07 1.31
178 179 8.816894 ACAAGTCTTTGGAGAGATTTCACTATA 58.183 33.333 0.00 0.00 38.66 1.31
179 180 7.684529 ACAAGTCTTTGGAGAGATTTCACTAT 58.315 34.615 0.00 0.00 38.66 2.12
180 181 7.067496 ACAAGTCTTTGGAGAGATTTCACTA 57.933 36.000 0.00 0.00 38.66 2.74
181 182 5.934781 ACAAGTCTTTGGAGAGATTTCACT 58.065 37.500 0.00 0.00 38.66 3.41
182 183 7.913674 ATACAAGTCTTTGGAGAGATTTCAC 57.086 36.000 0.00 0.00 38.66 3.18
183 184 8.924511 AAATACAAGTCTTTGGAGAGATTTCA 57.075 30.769 0.00 0.00 38.66 2.69
185 186 9.454859 CCTAAATACAAGTCTTTGGAGAGATTT 57.545 33.333 0.00 0.00 38.66 2.17
186 187 8.826765 TCCTAAATACAAGTCTTTGGAGAGATT 58.173 33.333 0.00 0.00 38.66 2.40
187 188 8.380742 TCCTAAATACAAGTCTTTGGAGAGAT 57.619 34.615 0.00 0.00 38.66 2.75
188 189 7.792364 TCCTAAATACAAGTCTTTGGAGAGA 57.208 36.000 0.00 0.00 38.66 3.10
189 190 8.848474 TTTCCTAAATACAAGTCTTTGGAGAG 57.152 34.615 0.00 0.00 38.66 3.20
328 329 7.500141 GGTATTTTAGTTCCCACCGTAGATTA 58.500 38.462 0.00 0.00 0.00 1.75
352 353 6.062434 ACGAGATTCAGAAATACTAGTCGG 57.938 41.667 0.00 0.00 0.00 4.79
379 383 5.738909 AGGTGATCTGGTTGACAAGATAAG 58.261 41.667 1.05 0.00 0.00 1.73
385 389 2.549992 CGGAAGGTGATCTGGTTGACAA 60.550 50.000 0.00 0.00 0.00 3.18
398 402 0.866061 CTACGATCACGCGGAAGGTG 60.866 60.000 12.47 0.00 43.96 4.00
399 403 1.028330 TCTACGATCACGCGGAAGGT 61.028 55.000 12.47 9.62 43.96 3.50
400 404 0.317103 CTCTACGATCACGCGGAAGG 60.317 60.000 12.47 4.07 43.96 3.46
401 405 0.656259 TCTCTACGATCACGCGGAAG 59.344 55.000 12.47 6.49 43.96 3.46
402 406 1.089112 TTCTCTACGATCACGCGGAA 58.911 50.000 12.47 0.00 43.96 4.30
403 407 1.089112 TTTCTCTACGATCACGCGGA 58.911 50.000 12.47 5.24 43.96 5.54
404 408 1.904144 TTTTCTCTACGATCACGCGG 58.096 50.000 12.47 0.00 43.96 6.46
424 428 3.118454 CGCGCGTGGGTGATCTTT 61.118 61.111 24.19 0.00 0.00 2.52
442 446 2.076100 TGAAGGTCATGTGCGATGAAC 58.924 47.619 5.60 5.60 36.05 3.18
455 459 0.526662 ACGTCGGACTGATGAAGGTC 59.473 55.000 10.57 0.00 37.05 3.85
460 464 1.934220 GCTCCACGTCGGACTGATGA 61.934 60.000 10.57 0.00 39.64 2.92
494 498 3.243367 CGAAAAGGAAAACATGCAGTGGA 60.243 43.478 0.00 0.00 0.00 4.02
549 689 4.329545 GCTGTCCAAGGACCCGCA 62.330 66.667 16.18 0.00 43.97 5.69
551 691 0.821711 TTTTGCTGTCCAAGGACCCG 60.822 55.000 16.18 8.69 43.97 5.28
552 692 0.961753 CTTTTGCTGTCCAAGGACCC 59.038 55.000 16.18 8.17 43.97 4.46
553 693 0.315251 GCTTTTGCTGTCCAAGGACC 59.685 55.000 16.18 2.94 43.35 4.46
554 694 0.040067 CGCTTTTGCTGTCCAAGGAC 60.040 55.000 12.30 12.30 44.80 3.85
555 695 0.179032 TCGCTTTTGCTGTCCAAGGA 60.179 50.000 0.00 0.00 44.80 3.36
556 696 0.040067 GTCGCTTTTGCTGTCCAAGG 60.040 55.000 0.00 0.00 44.80 3.61
557 697 0.040067 GGTCGCTTTTGCTGTCCAAG 60.040 55.000 0.00 0.00 44.80 3.61
558 698 1.781025 CGGTCGCTTTTGCTGTCCAA 61.781 55.000 0.00 0.00 44.80 3.53
603 755 2.571216 CGGGTCGGTCAGTTCACCT 61.571 63.158 0.00 0.00 33.77 4.00
604 756 2.048503 CGGGTCGGTCAGTTCACC 60.049 66.667 0.00 0.00 0.00 4.02
714 878 7.203910 GGACGTCTCTATAAAATGTCTCACAT 58.796 38.462 16.46 0.00 41.31 3.21
728 892 2.243602 GTCGAGAGGGACGTCTCTAT 57.756 55.000 20.17 16.83 43.51 1.98
2228 2500 1.936436 ATGCATGCACGCCAACGAAT 61.936 50.000 25.37 0.00 43.93 3.34
2283 2555 6.154445 ACTAAATGTAGCGAACGAGAGAAAA 58.846 36.000 0.00 0.00 0.00 2.29
2391 2663 4.796038 TTTCTTTACGGAGGGAGTACTG 57.204 45.455 0.00 0.00 0.00 2.74
2394 2666 9.289782 GTAGTATATTTCTTTACGGAGGGAGTA 57.710 37.037 0.00 0.00 0.00 2.59
2408 2682 5.759963 CGAACCTCTGCGTAGTATATTTCT 58.240 41.667 0.00 0.00 0.00 2.52
2411 2685 3.305199 GGCGAACCTCTGCGTAGTATATT 60.305 47.826 0.00 0.00 0.00 1.28
2473 2747 4.082523 ACGGCCTGACGACATGGG 62.083 66.667 0.00 0.00 37.61 4.00
2476 2750 4.129737 CCGACGGCCTGACGACAT 62.130 66.667 17.28 0.00 37.99 3.06
2552 2831 6.310149 AGTAGCTACTTATTACGTACCCCAT 58.690 40.000 20.95 0.00 31.13 4.00
2553 2832 5.694995 AGTAGCTACTTATTACGTACCCCA 58.305 41.667 20.95 0.00 31.13 4.96


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

AutoCloner maintained by Alex Coulton.