Multiple sequence alignment - TraesCS3A01G410300

Loading Multiple Alignment...

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 TraesCS3A01G410300 chr3A 100.000 3394 0 0 1 3394 654498640 654502033 0.000000e+00 6268
1 TraesCS3A01G410300 chr3A 95.612 2849 115 8 269 3108 654517753 654520600 0.000000e+00 4560
2 TraesCS3A01G410300 chr3A 85.295 2625 313 49 502 3106 654585148 654582577 0.000000e+00 2641
3 TraesCS3A01G410300 chr3A 90.229 481 41 6 2237 2714 654559975 654560452 1.030000e-174 623
4 TraesCS3A01G410300 chr3A 95.946 296 10 2 3100 3394 654520622 654520916 2.370000e-131 479
5 TraesCS3A01G410300 chr3D 95.327 2846 123 8 269 3108 519596471 519599312 0.000000e+00 4510
6 TraesCS3A01G410300 chr3D 85.315 2615 314 40 507 3106 519644709 519642150 0.000000e+00 2638
7 TraesCS3A01G410300 chr3D 88.068 880 92 12 2233 3108 519620583 519621453 0.000000e+00 1031
8 TraesCS3A01G410300 chr3D 94.915 295 14 1 3100 3393 519599334 519599628 8.580000e-126 460
9 TraesCS3A01G410300 chr3D 88.850 287 32 0 3107 3393 519642118 519641832 1.500000e-93 353
10 TraesCS3A01G410300 chr3B 92.439 2870 183 15 265 3108 684137470 684134609 0.000000e+00 4067
11 TraesCS3A01G410300 chr3B 90.816 294 16 3 3100 3392 684134587 684134304 1.910000e-102 383
12 TraesCS3A01G410300 chrUn 91.168 2638 191 22 502 3108 101062265 101064891 0.000000e+00 3542
13 TraesCS3A01G410300 chrUn 90.508 295 27 1 3100 3393 101064913 101065207 4.110000e-104 388
14 TraesCS3A01G410300 chrUn 87.983 233 26 2 270 501 314598616 314598385 1.200000e-69 274
15 TraesCS3A01G410300 chr6A 91.977 2231 160 13 886 3108 35563612 35561393 0.000000e+00 3110
16 TraesCS3A01G410300 chr6A 91.743 436 29 3 505 933 35564038 35563603 1.740000e-167 599
17 TraesCS3A01G410300 chr6A 96.970 264 8 0 1 264 466625730 466625993 8.640000e-121 444
18 TraesCS3A01G410300 chr6A 89.831 295 28 2 3100 3393 35561371 35561078 8.890000e-101 377
19 TraesCS3A01G410300 chr7A 72.583 1955 448 67 1043 2951 703549663 703551575 8.220000e-156 560
20 TraesCS3A01G410300 chr7A 96.642 268 8 1 1 267 515873180 515873447 8.640000e-121 444
21 TraesCS3A01G410300 chr7A 96.255 267 10 0 1 267 548589945 548589679 4.020000e-119 438
22 TraesCS3A01G410300 chr7B 73.706 1468 334 37 1504 2944 702196421 702194979 3.000000e-145 525
23 TraesCS3A01G410300 chr6D 96.296 270 10 0 1 270 144792578 144792847 8.640000e-121 444
24 TraesCS3A01G410300 chr2A 96.958 263 8 0 1 263 166606627 166606889 3.110000e-120 442
25 TraesCS3A01G410300 chr5A 96.591 264 9 0 1 264 413375860 413376123 4.020000e-119 438
26 TraesCS3A01G410300 chr4A 95.926 270 11 0 1 270 465322222 465322491 4.020000e-119 438
27 TraesCS3A01G410300 chr4A 88.412 233 25 2 269 500 546615894 546615663 2.580000e-71 279
28 TraesCS3A01G410300 chr4A 87.983 233 26 2 269 500 546613008 546612777 1.200000e-69 274
29 TraesCS3A01G410300 chr4A 87.983 233 26 2 270 501 652782113 652782344 1.200000e-69 274
30 TraesCS3A01G410300 chr1A 96.591 264 9 0 1 264 121989787 121989524 4.020000e-119 438
31 TraesCS3A01G410300 chr1A 94.964 278 11 3 1 278 291440868 291440594 1.870000e-117 433
32 TraesCS3A01G410300 chr1A 88.889 234 23 3 269 500 7329326 7329094 5.540000e-73 285
33 TraesCS3A01G410300 chr7D 87.931 232 28 0 269 500 39586300 39586531 1.200000e-69 274


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 TraesCS3A01G410300 chr3A 654498640 654502033 3393 False 6268.0 6268 100.000000 1 3394 1 chr3A.!!$F1 3393
1 TraesCS3A01G410300 chr3A 654582577 654585148 2571 True 2641.0 2641 85.295000 502 3106 1 chr3A.!!$R1 2604
2 TraesCS3A01G410300 chr3A 654517753 654520916 3163 False 2519.5 4560 95.779000 269 3394 2 chr3A.!!$F3 3125
3 TraesCS3A01G410300 chr3D 519596471 519599628 3157 False 2485.0 4510 95.121000 269 3393 2 chr3D.!!$F2 3124
4 TraesCS3A01G410300 chr3D 519641832 519644709 2877 True 1495.5 2638 87.082500 507 3393 2 chr3D.!!$R1 2886
5 TraesCS3A01G410300 chr3D 519620583 519621453 870 False 1031.0 1031 88.068000 2233 3108 1 chr3D.!!$F1 875
6 TraesCS3A01G410300 chr3B 684134304 684137470 3166 True 2225.0 4067 91.627500 265 3392 2 chr3B.!!$R1 3127
7 TraesCS3A01G410300 chrUn 101062265 101065207 2942 False 1965.0 3542 90.838000 502 3393 2 chrUn.!!$F1 2891
8 TraesCS3A01G410300 chr6A 35561078 35564038 2960 True 1362.0 3110 91.183667 505 3393 3 chr6A.!!$R1 2888
9 TraesCS3A01G410300 chr7A 703549663 703551575 1912 False 560.0 560 72.583000 1043 2951 1 chr7A.!!$F2 1908
10 TraesCS3A01G410300 chr7B 702194979 702196421 1442 True 525.0 525 73.706000 1504 2944 1 chr7B.!!$R1 1440
11 TraesCS3A01G410300 chr4A 546612777 546615894 3117 True 276.5 279 88.197500 269 500 2 chr4A.!!$R1 231

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
547 550 1.067916 CCACTTTGCAAGGTGTGGC 59.932 57.895 32.0 0.0 42.55 5.01 F
1100 1199 1.656092 ATCCTCGTCAGGCTCCCCTA 61.656 60.000 0.0 0.0 40.33 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 2393 0.538516 AGACTCCTCTGTGTCGCAGT 60.539 55.000 13.0 0.0 45.23 4.40 R
3020 5129 2.627933 ACAAACCAGGACTAGCCCTTA 58.372 47.619 0.0 0.0 37.37 2.69 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
23 24 6.981762 GTCAAGTCAATCACATCATTCTCT 57.018 37.500 0.00 0.00 0.00 3.10
25 26 8.484641 GTCAAGTCAATCACATCATTCTCTAA 57.515 34.615 0.00 0.00 0.00 2.10
26 27 9.107177 GTCAAGTCAATCACATCATTCTCTAAT 57.893 33.333 0.00 0.00 0.00 1.73
27 28 9.106070 TCAAGTCAATCACATCATTCTCTAATG 57.894 33.333 0.00 0.00 43.32 1.90
38 39 5.787380 TCATTCTCTAATGATGTGATCCCG 58.213 41.667 0.00 0.00 45.17 5.14
39 40 5.305386 TCATTCTCTAATGATGTGATCCCGT 59.695 40.000 0.00 0.00 45.17 5.28
40 41 5.614324 TTCTCTAATGATGTGATCCCGTT 57.386 39.130 0.00 0.00 0.00 4.44
41 42 6.724893 TTCTCTAATGATGTGATCCCGTTA 57.275 37.500 0.00 0.00 0.00 3.18
42 43 6.724893 TCTCTAATGATGTGATCCCGTTAA 57.275 37.500 0.00 0.00 0.00 2.01
43 44 7.303182 TCTCTAATGATGTGATCCCGTTAAT 57.697 36.000 0.00 0.00 0.00 1.40
44 45 7.378966 TCTCTAATGATGTGATCCCGTTAATC 58.621 38.462 0.00 0.00 0.00 1.75
45 46 7.015195 TCTCTAATGATGTGATCCCGTTAATCA 59.985 37.037 0.00 0.00 0.00 2.57
46 47 7.505258 TCTAATGATGTGATCCCGTTAATCAA 58.495 34.615 0.00 0.00 35.04 2.57
47 48 6.624352 AATGATGTGATCCCGTTAATCAAG 57.376 37.500 0.00 0.00 35.04 3.02
48 49 5.097742 TGATGTGATCCCGTTAATCAAGT 57.902 39.130 0.00 0.00 35.04 3.16
49 50 4.875536 TGATGTGATCCCGTTAATCAAGTG 59.124 41.667 0.00 0.00 35.04 3.16
50 51 4.545208 TGTGATCCCGTTAATCAAGTGA 57.455 40.909 0.00 0.00 35.04 3.41
51 52 4.250464 TGTGATCCCGTTAATCAAGTGAC 58.750 43.478 0.00 0.00 35.04 3.67
52 53 4.250464 GTGATCCCGTTAATCAAGTGACA 58.750 43.478 0.00 0.00 35.04 3.58
53 54 4.693566 GTGATCCCGTTAATCAAGTGACAA 59.306 41.667 0.00 0.00 35.04 3.18
54 55 4.693566 TGATCCCGTTAATCAAGTGACAAC 59.306 41.667 0.00 0.00 30.37 3.32
55 56 4.345859 TCCCGTTAATCAAGTGACAACT 57.654 40.909 6.23 0.00 38.71 3.16
56 57 4.312443 TCCCGTTAATCAAGTGACAACTC 58.688 43.478 6.23 0.00 34.77 3.01
57 58 4.062293 CCCGTTAATCAAGTGACAACTCA 58.938 43.478 6.23 0.00 34.77 3.41
58 59 4.695455 CCCGTTAATCAAGTGACAACTCAT 59.305 41.667 6.23 0.00 34.77 2.90
59 60 5.390885 CCCGTTAATCAAGTGACAACTCATG 60.391 44.000 0.00 0.00 34.77 3.07
73 74 6.620877 ACAACTCATGTCTATGGTTAGGAA 57.379 37.500 0.00 0.00 37.96 3.36
74 75 7.016153 ACAACTCATGTCTATGGTTAGGAAA 57.984 36.000 0.00 0.00 37.96 3.13
75 76 6.879458 ACAACTCATGTCTATGGTTAGGAAAC 59.121 38.462 0.00 0.00 37.96 2.78
76 77 6.620877 ACTCATGTCTATGGTTAGGAAACA 57.379 37.500 0.00 0.00 37.34 2.83
77 78 7.200434 ACTCATGTCTATGGTTAGGAAACAT 57.800 36.000 0.00 0.00 37.34 2.71
78 79 8.319057 ACTCATGTCTATGGTTAGGAAACATA 57.681 34.615 0.00 0.00 37.34 2.29
79 80 8.768397 ACTCATGTCTATGGTTAGGAAACATAA 58.232 33.333 0.00 0.00 37.34 1.90
80 81 8.958119 TCATGTCTATGGTTAGGAAACATAAC 57.042 34.615 0.00 0.00 37.34 1.89
81 82 8.544622 TCATGTCTATGGTTAGGAAACATAACA 58.455 33.333 8.19 11.28 37.34 2.41
82 83 9.173021 CATGTCTATGGTTAGGAAACATAACAA 57.827 33.333 12.19 0.00 37.34 2.83
83 84 9.920946 ATGTCTATGGTTAGGAAACATAACAAT 57.079 29.630 12.19 5.39 37.34 2.71
84 85 9.391006 TGTCTATGGTTAGGAAACATAACAATC 57.609 33.333 8.19 0.00 37.34 2.67
85 86 9.391006 GTCTATGGTTAGGAAACATAACAATCA 57.609 33.333 8.19 0.00 37.34 2.57
89 90 8.642935 TGGTTAGGAAACATAACAATCATTGA 57.357 30.769 3.79 0.00 37.34 2.57
90 91 9.253832 TGGTTAGGAAACATAACAATCATTGAT 57.746 29.630 3.79 0.00 37.34 2.57
112 113 9.645059 TTGATTCAATGAGTTAGTCAAGTAGAG 57.355 33.333 0.00 0.00 39.19 2.43
113 114 8.253810 TGATTCAATGAGTTAGTCAAGTAGAGG 58.746 37.037 0.00 0.00 39.19 3.69
114 115 5.967088 TCAATGAGTTAGTCAAGTAGAGGC 58.033 41.667 0.00 0.00 39.19 4.70
115 116 5.480422 TCAATGAGTTAGTCAAGTAGAGGCA 59.520 40.000 0.00 0.00 39.19 4.75
116 117 6.155221 TCAATGAGTTAGTCAAGTAGAGGCAT 59.845 38.462 0.00 0.00 39.19 4.40
117 118 7.342026 TCAATGAGTTAGTCAAGTAGAGGCATA 59.658 37.037 0.00 0.00 39.19 3.14
118 119 6.452494 TGAGTTAGTCAAGTAGAGGCATAC 57.548 41.667 0.00 0.00 29.64 2.39
119 120 6.188407 TGAGTTAGTCAAGTAGAGGCATACT 58.812 40.000 0.00 0.00 37.61 2.12
120 121 7.344134 TGAGTTAGTCAAGTAGAGGCATACTA 58.656 38.462 3.23 0.00 34.90 1.82
121 122 7.499563 TGAGTTAGTCAAGTAGAGGCATACTAG 59.500 40.741 3.23 0.00 34.90 2.57
122 123 7.348033 AGTTAGTCAAGTAGAGGCATACTAGT 58.652 38.462 0.00 0.00 34.90 2.57
123 124 7.283580 AGTTAGTCAAGTAGAGGCATACTAGTG 59.716 40.741 5.39 0.00 34.90 2.74
124 125 5.756918 AGTCAAGTAGAGGCATACTAGTGA 58.243 41.667 5.39 2.59 34.90 3.41
125 126 5.591067 AGTCAAGTAGAGGCATACTAGTGAC 59.409 44.000 17.97 17.97 40.57 3.67
126 127 5.357314 GTCAAGTAGAGGCATACTAGTGACA 59.643 44.000 19.41 0.00 40.28 3.58
127 128 5.949952 TCAAGTAGAGGCATACTAGTGACAA 59.050 40.000 5.39 0.00 34.90 3.18
128 129 6.607600 TCAAGTAGAGGCATACTAGTGACAAT 59.392 38.462 5.39 0.00 34.90 2.71
129 130 6.642707 AGTAGAGGCATACTAGTGACAATC 57.357 41.667 5.39 0.00 34.21 2.67
130 131 6.369629 AGTAGAGGCATACTAGTGACAATCT 58.630 40.000 5.39 6.34 34.21 2.40
131 132 5.528043 AGAGGCATACTAGTGACAATCTG 57.472 43.478 5.39 0.00 0.00 2.90
132 133 4.959210 AGAGGCATACTAGTGACAATCTGT 59.041 41.667 5.39 0.00 0.00 3.41
133 134 5.423610 AGAGGCATACTAGTGACAATCTGTT 59.576 40.000 5.39 0.00 0.00 3.16
134 135 6.054860 AGGCATACTAGTGACAATCTGTTT 57.945 37.500 5.39 0.00 0.00 2.83
135 136 5.877012 AGGCATACTAGTGACAATCTGTTTG 59.123 40.000 5.39 0.00 41.36 2.93
149 150 8.846943 ACAATCTGTTTGTCTATGTATTCACA 57.153 30.769 0.00 0.00 45.55 3.58
150 151 8.721478 ACAATCTGTTTGTCTATGTATTCACAC 58.279 33.333 0.00 0.00 45.55 3.82
151 152 8.720562 CAATCTGTTTGTCTATGTATTCACACA 58.279 33.333 0.00 0.00 37.54 3.72
152 153 9.453572 AATCTGTTTGTCTATGTATTCACACAT 57.546 29.630 0.00 0.00 41.88 3.21
153 154 8.255394 TCTGTTTGTCTATGTATTCACACATG 57.745 34.615 0.00 0.00 39.46 3.21
154 155 7.877612 TCTGTTTGTCTATGTATTCACACATGT 59.122 33.333 0.00 0.00 39.46 3.21
155 156 9.150348 CTGTTTGTCTATGTATTCACACATGTA 57.850 33.333 0.00 0.00 39.46 2.29
156 157 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
166 167 8.661257 TGTATTCACACATGTATTAAGTTTCCG 58.339 33.333 0.00 0.00 0.00 4.30
167 168 6.489127 TTCACACATGTATTAAGTTTCCGG 57.511 37.500 0.00 0.00 0.00 5.14
168 169 5.553123 TCACACATGTATTAAGTTTCCGGT 58.447 37.500 0.00 0.00 0.00 5.28
169 170 5.998981 TCACACATGTATTAAGTTTCCGGTT 59.001 36.000 0.00 0.00 0.00 4.44
170 171 7.160049 TCACACATGTATTAAGTTTCCGGTTA 58.840 34.615 0.00 0.00 0.00 2.85
171 172 7.660617 TCACACATGTATTAAGTTTCCGGTTAA 59.339 33.333 0.00 0.00 0.00 2.01
172 173 8.455682 CACACATGTATTAAGTTTCCGGTTAAT 58.544 33.333 0.00 7.17 34.13 1.40
173 174 9.669887 ACACATGTATTAAGTTTCCGGTTAATA 57.330 29.630 0.00 6.13 32.39 0.98
174 175 9.925268 CACATGTATTAAGTTTCCGGTTAATAC 57.075 33.333 24.77 24.77 44.86 1.89
183 184 7.549615 AGTTTCCGGTTAATACAATTCTAGC 57.450 36.000 0.00 0.00 0.00 3.42
184 185 7.107542 AGTTTCCGGTTAATACAATTCTAGCA 58.892 34.615 0.00 0.00 0.00 3.49
185 186 7.773690 AGTTTCCGGTTAATACAATTCTAGCAT 59.226 33.333 0.00 0.00 0.00 3.79
186 187 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
187 188 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
188 189 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
189 190 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
190 191 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
250 251 8.521170 AACAACTTTATTATTTCCTCTAGGGC 57.479 34.615 0.00 0.00 35.41 5.19
251 252 7.639378 ACAACTTTATTATTTCCTCTAGGGCA 58.361 34.615 0.00 0.00 35.41 5.36
252 253 8.282256 ACAACTTTATTATTTCCTCTAGGGCAT 58.718 33.333 0.00 0.00 35.41 4.40
253 254 9.793259 CAACTTTATTATTTCCTCTAGGGCATA 57.207 33.333 0.00 0.00 35.41 3.14
260 261 8.933522 TTATTTCCTCTAGGGCATATATCCTT 57.066 34.615 0.00 0.00 34.75 3.36
261 262 6.875972 TTTCCTCTAGGGCATATATCCTTC 57.124 41.667 0.00 0.00 34.75 3.46
262 263 5.552430 TCCTCTAGGGCATATATCCTTCA 57.448 43.478 0.00 0.00 34.75 3.02
263 264 5.523588 TCCTCTAGGGCATATATCCTTCAG 58.476 45.833 0.00 0.00 34.75 3.02
267 268 4.500499 AGGGCATATATCCTTCAGCATC 57.500 45.455 0.00 0.00 0.00 3.91
306 307 1.884075 AATAGCACAGACACGCGGGA 61.884 55.000 19.19 0.00 0.00 5.14
313 314 3.429141 GACACGCGGGAGAGTCGA 61.429 66.667 19.19 0.00 42.38 4.20
323 324 1.568514 GAGAGTCGACGACGTGTGT 59.431 57.895 21.44 4.30 37.67 3.72
398 400 3.776016 ATAGTCAGGCCCCGGGGAG 62.776 68.421 44.86 30.04 37.50 4.30
432 435 5.047802 TCGGGTAAACTCGTTAACAGATCTT 60.048 40.000 6.39 3.75 29.79 2.40
494 497 2.766313 CGATGGCCTCGGATTTATTCA 58.234 47.619 14.53 0.00 43.82 2.57
547 550 1.067916 CCACTTTGCAAGGTGTGGC 59.932 57.895 32.00 0.00 42.55 5.01
898 970 3.368501 CCTCCCTCCCCTCTCCCA 61.369 72.222 0.00 0.00 0.00 4.37
1019 1118 2.033424 CGATGGAGTTCAGATCTGCGTA 59.967 50.000 18.36 2.97 0.00 4.42
1022 1121 3.291584 TGGAGTTCAGATCTGCGTATCT 58.708 45.455 18.36 10.50 36.64 1.98
1100 1199 1.656092 ATCCTCGTCAGGCTCCCCTA 61.656 60.000 0.00 0.00 40.33 3.53
1342 1444 4.142038 GGAACTTAAGCCAAAGGAGTTCA 58.858 43.478 14.25 0.00 44.86 3.18
1393 1495 5.848286 ATTAGGCAGGTCCATCATCATTA 57.152 39.130 0.00 0.00 37.29 1.90
1398 1500 5.901276 AGGCAGGTCCATCATCATTAATTTT 59.099 36.000 0.00 0.00 37.29 1.82
1399 1501 7.068702 AGGCAGGTCCATCATCATTAATTTTA 58.931 34.615 0.00 0.00 37.29 1.52
1418 1520 1.973281 CTTGCTTCCACCGCACCAT 60.973 57.895 0.00 0.00 37.07 3.55
1760 2393 2.313643 TGGAGGATGTCTGGTGGTACTA 59.686 50.000 0.00 0.00 0.00 1.82
1765 2398 0.885879 TGTCTGGTGGTACTACTGCG 59.114 55.000 9.41 0.00 0.00 5.18
1783 2416 3.617284 TGCGACACAGAGGAGTCTATTA 58.383 45.455 0.00 0.00 33.12 0.98
1800 2434 6.602009 AGTCTATTATGTTTGGCCTTTGGTAC 59.398 38.462 3.32 0.00 0.00 3.34
1840 2474 2.028130 AGGCGACAGATAGACAAGGAG 58.972 52.381 0.00 0.00 0.00 3.69
1965 2601 8.366401 TCTTGCATAATTGTTTTTCAGGATTCA 58.634 29.630 0.00 0.00 0.00 2.57
1983 2619 6.103797 AGGATTCATCACTTTTCCCCTATGAT 59.896 38.462 0.00 0.00 0.00 2.45
1994 2630 3.469859 TCCCCTATGATCCCAACTTTGA 58.530 45.455 0.00 0.00 0.00 2.69
2301 4385 3.961408 GTCCCAAGCTATCTCCTTGACTA 59.039 47.826 2.93 0.00 41.64 2.59
2447 4531 2.924903 TCAAGTAACACTAGACGCACG 58.075 47.619 0.00 0.00 0.00 5.34
2721 4816 7.609532 GCTAATTCTGAATGCTATAATCCCACT 59.390 37.037 3.22 0.00 0.00 4.00
2864 4970 2.092323 GTTCTGTAATGGTCAAGCCCC 58.908 52.381 0.00 0.00 36.04 5.80
2893 4999 8.394877 TGTTTTGCATATGTATTCTACTTTCCG 58.605 33.333 4.29 0.00 0.00 4.30
3042 5151 1.907255 AGGGCTAGTCCTGGTTTGTAC 59.093 52.381 17.14 0.00 35.47 2.90
3112 5252 0.609151 TTGGGATTTGGCACATGCAG 59.391 50.000 7.45 0.00 44.36 4.41
3374 5514 6.577103 TCCATTCAACATGTTGTTTTGCTAA 58.423 32.000 31.99 20.05 38.77 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.981762 AGAGAATGATGTGATTGACTTGAC 57.018 37.500 0.00 0.00 0.00 3.18
1 2 9.106070 CATTAGAGAATGATGTGATTGACTTGA 57.894 33.333 0.00 0.00 44.59 3.02
2 3 9.106070 TCATTAGAGAATGATGTGATTGACTTG 57.894 33.333 0.00 0.00 45.26 3.16
16 17 5.545588 ACGGGATCACATCATTAGAGAATG 58.454 41.667 0.00 0.00 43.39 2.67
17 18 5.815233 ACGGGATCACATCATTAGAGAAT 57.185 39.130 0.00 0.00 0.00 2.40
18 19 5.614324 AACGGGATCACATCATTAGAGAA 57.386 39.130 0.00 0.00 0.00 2.87
19 20 6.724893 TTAACGGGATCACATCATTAGAGA 57.275 37.500 0.00 0.00 0.00 3.10
20 21 7.154656 TGATTAACGGGATCACATCATTAGAG 58.845 38.462 0.00 0.00 0.00 2.43
21 22 7.061566 TGATTAACGGGATCACATCATTAGA 57.938 36.000 0.00 0.00 0.00 2.10
22 23 7.442364 ACTTGATTAACGGGATCACATCATTAG 59.558 37.037 0.00 0.00 33.51 1.73
23 24 7.226523 CACTTGATTAACGGGATCACATCATTA 59.773 37.037 0.00 0.00 33.51 1.90
24 25 6.038603 CACTTGATTAACGGGATCACATCATT 59.961 38.462 0.00 0.00 33.51 2.57
25 26 5.528690 CACTTGATTAACGGGATCACATCAT 59.471 40.000 0.00 0.00 33.51 2.45
26 27 4.875536 CACTTGATTAACGGGATCACATCA 59.124 41.667 0.00 0.00 33.51 3.07
27 28 5.006746 GTCACTTGATTAACGGGATCACATC 59.993 44.000 0.00 0.00 33.51 3.06
28 29 4.876107 GTCACTTGATTAACGGGATCACAT 59.124 41.667 0.00 0.00 33.51 3.21
29 30 4.250464 GTCACTTGATTAACGGGATCACA 58.750 43.478 0.00 0.00 33.51 3.58
30 31 4.250464 TGTCACTTGATTAACGGGATCAC 58.750 43.478 0.00 0.00 33.51 3.06
31 32 4.545208 TGTCACTTGATTAACGGGATCA 57.455 40.909 0.00 0.00 0.00 2.92
32 33 4.935808 AGTTGTCACTTGATTAACGGGATC 59.064 41.667 0.00 0.00 32.73 3.36
33 34 4.906618 AGTTGTCACTTGATTAACGGGAT 58.093 39.130 0.00 0.00 32.73 3.85
34 35 4.202274 TGAGTTGTCACTTGATTAACGGGA 60.202 41.667 0.00 0.00 31.22 5.14
35 36 4.062293 TGAGTTGTCACTTGATTAACGGG 58.938 43.478 0.00 0.00 31.22 5.28
36 37 5.179368 ACATGAGTTGTCACTTGATTAACGG 59.821 40.000 0.00 0.00 34.75 4.44
37 38 6.228273 ACATGAGTTGTCACTTGATTAACG 57.772 37.500 0.00 0.00 34.75 3.18
50 51 6.620877 TTCCTAACCATAGACATGAGTTGT 57.379 37.500 0.00 0.00 42.79 3.32
51 52 6.878923 TGTTTCCTAACCATAGACATGAGTTG 59.121 38.462 0.00 0.00 33.15 3.16
52 53 7.016153 TGTTTCCTAACCATAGACATGAGTT 57.984 36.000 0.00 0.00 33.15 3.01
53 54 6.620877 TGTTTCCTAACCATAGACATGAGT 57.379 37.500 0.00 0.00 33.15 3.41
54 55 9.046296 GTTATGTTTCCTAACCATAGACATGAG 57.954 37.037 0.00 0.00 30.80 2.90
55 56 8.544622 TGTTATGTTTCCTAACCATAGACATGA 58.455 33.333 0.00 0.00 30.80 3.07
56 57 8.731275 TGTTATGTTTCCTAACCATAGACATG 57.269 34.615 0.00 0.00 30.80 3.21
57 58 9.920946 ATTGTTATGTTTCCTAACCATAGACAT 57.079 29.630 0.00 0.00 32.18 3.06
58 59 9.391006 GATTGTTATGTTTCCTAACCATAGACA 57.609 33.333 0.00 0.00 33.15 3.41
59 60 9.391006 TGATTGTTATGTTTCCTAACCATAGAC 57.609 33.333 0.00 0.00 33.15 2.59
63 64 9.253832 TCAATGATTGTTATGTTTCCTAACCAT 57.746 29.630 4.93 0.00 33.15 3.55
64 65 8.642935 TCAATGATTGTTATGTTTCCTAACCA 57.357 30.769 4.93 0.00 33.15 3.67
86 87 9.645059 CTCTACTTGACTAACTCATTGAATCAA 57.355 33.333 0.00 0.00 0.00 2.57
87 88 8.253810 CCTCTACTTGACTAACTCATTGAATCA 58.746 37.037 0.00 0.00 0.00 2.57
88 89 7.223777 GCCTCTACTTGACTAACTCATTGAATC 59.776 40.741 0.00 0.00 0.00 2.52
89 90 7.044798 GCCTCTACTTGACTAACTCATTGAAT 58.955 38.462 0.00 0.00 0.00 2.57
90 91 6.014584 TGCCTCTACTTGACTAACTCATTGAA 60.015 38.462 0.00 0.00 0.00 2.69
91 92 5.480422 TGCCTCTACTTGACTAACTCATTGA 59.520 40.000 0.00 0.00 0.00 2.57
92 93 5.724328 TGCCTCTACTTGACTAACTCATTG 58.276 41.667 0.00 0.00 0.00 2.82
93 94 6.552445 ATGCCTCTACTTGACTAACTCATT 57.448 37.500 0.00 0.00 0.00 2.57
94 95 6.836527 AGTATGCCTCTACTTGACTAACTCAT 59.163 38.462 0.00 0.00 0.00 2.90
95 96 6.188407 AGTATGCCTCTACTTGACTAACTCA 58.812 40.000 0.00 0.00 0.00 3.41
96 97 6.702716 AGTATGCCTCTACTTGACTAACTC 57.297 41.667 0.00 0.00 0.00 3.01
97 98 7.283580 CACTAGTATGCCTCTACTTGACTAACT 59.716 40.741 0.00 0.00 33.96 2.24
98 99 7.282675 TCACTAGTATGCCTCTACTTGACTAAC 59.717 40.741 0.00 0.00 33.96 2.34
99 100 7.282675 GTCACTAGTATGCCTCTACTTGACTAA 59.717 40.741 0.00 0.00 36.95 2.24
100 101 6.766944 GTCACTAGTATGCCTCTACTTGACTA 59.233 42.308 0.00 0.00 36.95 2.59
101 102 5.591067 GTCACTAGTATGCCTCTACTTGACT 59.409 44.000 0.00 0.00 36.95 3.41
102 103 5.357314 TGTCACTAGTATGCCTCTACTTGAC 59.643 44.000 0.00 11.98 38.64 3.18
103 104 5.506708 TGTCACTAGTATGCCTCTACTTGA 58.493 41.667 0.00 0.18 33.96 3.02
104 105 5.836821 TGTCACTAGTATGCCTCTACTTG 57.163 43.478 0.00 0.00 33.96 3.16
105 106 6.836527 AGATTGTCACTAGTATGCCTCTACTT 59.163 38.462 0.00 0.00 33.96 2.24
106 107 6.264292 CAGATTGTCACTAGTATGCCTCTACT 59.736 42.308 0.00 0.00 36.04 2.57
107 108 6.039941 ACAGATTGTCACTAGTATGCCTCTAC 59.960 42.308 0.00 0.00 0.00 2.59
108 109 6.129874 ACAGATTGTCACTAGTATGCCTCTA 58.870 40.000 0.00 0.00 0.00 2.43
109 110 4.959210 ACAGATTGTCACTAGTATGCCTCT 59.041 41.667 0.00 0.00 0.00 3.69
110 111 5.269505 ACAGATTGTCACTAGTATGCCTC 57.730 43.478 0.00 0.00 0.00 4.70
111 112 5.683876 AACAGATTGTCACTAGTATGCCT 57.316 39.130 0.00 0.00 0.00 4.75
112 113 6.111768 CAAACAGATTGTCACTAGTATGCC 57.888 41.667 0.00 0.00 34.16 4.40
124 125 8.721478 GTGTGAATACATAGACAAACAGATTGT 58.279 33.333 0.00 0.00 46.15 2.71
125 126 8.720562 TGTGTGAATACATAGACAAACAGATTG 58.279 33.333 0.00 0.00 40.98 2.67
126 127 8.846943 TGTGTGAATACATAGACAAACAGATT 57.153 30.769 0.00 0.00 39.39 2.40
127 128 8.886719 CATGTGTGAATACATAGACAAACAGAT 58.113 33.333 0.00 0.00 39.17 2.90
128 129 7.877612 ACATGTGTGAATACATAGACAAACAGA 59.122 33.333 0.00 0.00 39.17 3.41
129 130 8.032952 ACATGTGTGAATACATAGACAAACAG 57.967 34.615 0.00 0.00 39.17 3.16
130 131 7.977789 ACATGTGTGAATACATAGACAAACA 57.022 32.000 0.00 0.00 39.17 2.83
140 141 8.661257 CGGAAACTTAATACATGTGTGAATACA 58.339 33.333 9.11 0.00 34.63 2.29
141 142 8.120465 CCGGAAACTTAATACATGTGTGAATAC 58.880 37.037 9.11 0.00 0.00 1.89
142 143 7.825270 ACCGGAAACTTAATACATGTGTGAATA 59.175 33.333 9.46 0.00 0.00 1.75
143 144 6.657541 ACCGGAAACTTAATACATGTGTGAAT 59.342 34.615 9.46 0.00 0.00 2.57
144 145 5.998981 ACCGGAAACTTAATACATGTGTGAA 59.001 36.000 9.46 0.00 0.00 3.18
145 146 5.553123 ACCGGAAACTTAATACATGTGTGA 58.447 37.500 9.46 0.00 0.00 3.58
146 147 5.873179 ACCGGAAACTTAATACATGTGTG 57.127 39.130 9.46 0.00 0.00 3.82
147 148 7.982761 TTAACCGGAAACTTAATACATGTGT 57.017 32.000 9.46 0.00 0.00 3.72
148 149 9.925268 GTATTAACCGGAAACTTAATACATGTG 57.075 33.333 25.71 0.00 40.33 3.21
149 150 9.669887 TGTATTAACCGGAAACTTAATACATGT 57.330 29.630 27.66 2.69 42.66 3.21
157 158 9.101655 GCTAGAATTGTATTAACCGGAAACTTA 57.898 33.333 9.46 0.00 0.00 2.24
158 159 7.608761 TGCTAGAATTGTATTAACCGGAAACTT 59.391 33.333 9.46 0.00 0.00 2.66
159 160 7.107542 TGCTAGAATTGTATTAACCGGAAACT 58.892 34.615 9.46 0.00 0.00 2.66
160 161 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
161 162 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
162 163 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
163 164 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
164 165 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
224 225 9.623000 GCCCTAGAGGAAATAATAAAGTTGTTA 57.377 33.333 0.00 0.00 38.24 2.41
225 226 8.113462 TGCCCTAGAGGAAATAATAAAGTTGTT 58.887 33.333 0.00 0.00 38.24 2.83
226 227 7.639378 TGCCCTAGAGGAAATAATAAAGTTGT 58.361 34.615 0.00 0.00 38.24 3.32
227 228 8.697507 ATGCCCTAGAGGAAATAATAAAGTTG 57.302 34.615 0.00 0.00 38.24 3.16
234 235 9.526261 AAGGATATATGCCCTAGAGGAAATAAT 57.474 33.333 0.00 0.00 38.24 1.28
235 236 8.933522 AAGGATATATGCCCTAGAGGAAATAA 57.066 34.615 0.00 0.00 38.24 1.40
236 237 8.129001 TGAAGGATATATGCCCTAGAGGAAATA 58.871 37.037 0.00 0.00 38.24 1.40
237 238 6.968248 TGAAGGATATATGCCCTAGAGGAAAT 59.032 38.462 0.00 0.00 38.24 2.17
238 239 6.331032 TGAAGGATATATGCCCTAGAGGAAA 58.669 40.000 0.00 0.00 38.24 3.13
239 240 5.915628 TGAAGGATATATGCCCTAGAGGAA 58.084 41.667 0.00 0.00 38.24 3.36
240 241 5.523588 CTGAAGGATATATGCCCTAGAGGA 58.476 45.833 0.00 0.00 38.24 3.71
241 242 4.100808 GCTGAAGGATATATGCCCTAGAGG 59.899 50.000 0.00 0.00 39.47 3.69
242 243 4.713814 TGCTGAAGGATATATGCCCTAGAG 59.286 45.833 0.00 0.00 31.36 2.43
243 244 4.687976 TGCTGAAGGATATATGCCCTAGA 58.312 43.478 0.00 0.00 31.36 2.43
244 245 5.129980 TGATGCTGAAGGATATATGCCCTAG 59.870 44.000 0.00 0.00 31.36 3.02
245 246 5.032170 TGATGCTGAAGGATATATGCCCTA 58.968 41.667 0.00 0.00 31.36 3.53
246 247 3.848377 TGATGCTGAAGGATATATGCCCT 59.152 43.478 0.00 0.00 0.00 5.19
247 248 4.226427 TGATGCTGAAGGATATATGCCC 57.774 45.455 0.00 0.00 0.00 5.36
248 249 5.191426 ACATGATGCTGAAGGATATATGCC 58.809 41.667 0.00 0.00 29.74 4.40
249 250 7.201679 GGTTACATGATGCTGAAGGATATATGC 60.202 40.741 0.00 0.00 29.74 3.14
250 251 8.045507 AGGTTACATGATGCTGAAGGATATATG 58.954 37.037 0.00 6.86 31.56 1.78
251 252 8.155620 AGGTTACATGATGCTGAAGGATATAT 57.844 34.615 0.00 0.00 0.00 0.86
252 253 7.559335 AGGTTACATGATGCTGAAGGATATA 57.441 36.000 0.00 0.00 0.00 0.86
253 254 6.445451 AGGTTACATGATGCTGAAGGATAT 57.555 37.500 0.00 0.00 0.00 1.63
254 255 5.894298 AGGTTACATGATGCTGAAGGATA 57.106 39.130 0.00 0.00 0.00 2.59
255 256 4.785346 AGGTTACATGATGCTGAAGGAT 57.215 40.909 0.00 0.00 0.00 3.24
256 257 5.614308 CATAGGTTACATGATGCTGAAGGA 58.386 41.667 0.00 0.00 0.00 3.36
257 258 4.214971 GCATAGGTTACATGATGCTGAAGG 59.785 45.833 0.00 0.00 41.19 3.46
258 259 4.214971 GGCATAGGTTACATGATGCTGAAG 59.785 45.833 12.80 0.00 43.39 3.02
259 260 4.136796 GGCATAGGTTACATGATGCTGAA 58.863 43.478 12.80 0.00 43.39 3.02
260 261 3.136260 TGGCATAGGTTACATGATGCTGA 59.864 43.478 12.80 0.73 43.39 4.26
261 262 3.479489 TGGCATAGGTTACATGATGCTG 58.521 45.455 12.80 0.00 43.39 4.41
262 263 3.862877 TGGCATAGGTTACATGATGCT 57.137 42.857 12.80 0.00 43.39 3.79
263 264 3.631686 TGTTGGCATAGGTTACATGATGC 59.368 43.478 0.00 2.65 43.19 3.91
267 268 7.174772 TGCTATTATGTTGGCATAGGTTACATG 59.825 37.037 9.82 0.00 38.64 3.21
306 307 1.568514 GACACACGTCGTCGACTCT 59.431 57.895 22.18 5.29 40.62 3.24
398 400 4.219288 ACGAGTTTACCCGATATGGATACC 59.781 45.833 0.00 0.00 42.00 2.73
432 435 3.366577 GCAATCACACAAGCATGACATCA 60.367 43.478 0.00 0.00 0.00 3.07
547 550 9.465985 CAGAATATTCTCATATGGATCATCTCG 57.534 37.037 15.24 0.00 34.74 4.04
719 769 9.981114 TTTGACCCTAGAGATTTCAAATTTTTC 57.019 29.630 0.00 0.00 32.57 2.29
969 1068 3.802852 AAAACACCACCGCCCCCTC 62.803 63.158 0.00 0.00 0.00 4.30
970 1069 3.828023 AAAACACCACCGCCCCCT 61.828 61.111 0.00 0.00 0.00 4.79
1019 1118 4.635473 TGAATCTAGGAAACCCAGGAGAT 58.365 43.478 0.00 0.00 0.00 2.75
1022 1121 4.074799 TCTGAATCTAGGAAACCCAGGA 57.925 45.455 0.00 0.00 0.00 3.86
1100 1199 2.255252 GCGCCGCAACTTTGATGT 59.745 55.556 3.15 0.00 0.00 3.06
1327 1429 1.168714 GCGATGAACTCCTTTGGCTT 58.831 50.000 0.00 0.00 0.00 4.35
1342 1444 1.306997 TTGAGGGGAAGGAGGCGAT 60.307 57.895 0.00 0.00 0.00 4.58
1393 1495 2.625790 TGCGGTGGAAGCAAGTAAAATT 59.374 40.909 0.00 0.00 42.18 1.82
1398 1500 1.302192 GGTGCGGTGGAAGCAAGTA 60.302 57.895 0.00 0.00 46.97 2.24
1399 1501 2.594592 GGTGCGGTGGAAGCAAGT 60.595 61.111 0.00 0.00 46.97 3.16
1760 2393 0.538516 AGACTCCTCTGTGTCGCAGT 60.539 55.000 13.00 0.00 45.23 4.40
1765 2398 6.758886 CCAAACATAATAGACTCCTCTGTGTC 59.241 42.308 0.00 0.00 35.67 3.67
1783 2416 2.632512 CAAGGTACCAAAGGCCAAACAT 59.367 45.455 15.94 0.00 0.00 2.71
1800 2434 3.256631 CCTGAAATCCCAACAACTCAAGG 59.743 47.826 0.00 0.00 0.00 3.61
1840 2474 4.156008 ACGAATATGCAACAAAGGGAGTTC 59.844 41.667 0.00 0.00 0.00 3.01
1965 2601 4.054369 TGGGATCATAGGGGAAAAGTGAT 58.946 43.478 0.00 0.00 32.59 3.06
1983 2619 4.844085 TCTATCTCCTGTTCAAAGTTGGGA 59.156 41.667 0.00 0.00 0.00 4.37
1994 2630 5.843421 ACCATATGCTTCTCTATCTCCTGTT 59.157 40.000 0.00 0.00 0.00 3.16
2119 4202 5.108187 AGGATGATCTTAAGCTTCTGCAA 57.892 39.130 0.00 0.00 42.74 4.08
2301 4385 6.208204 CCATTGATTTCCACTTCTTCAAGAGT 59.792 38.462 0.00 0.00 33.34 3.24
2447 4531 6.371825 AGGTCTCCAAGACGTTGAATATTTTC 59.628 38.462 0.00 0.00 45.96 2.29
2503 4587 5.652014 TGCCAAATAAAATACTCACCAGAGG 59.348 40.000 0.00 0.00 46.44 3.69
2704 4799 5.972107 AATGCAGTGGGATTATAGCATTC 57.028 39.130 0.00 0.00 46.21 2.67
2817 4920 6.921914 TGTAAACGAAAAAGGGAAACAAAGA 58.078 32.000 0.00 0.00 0.00 2.52
2946 5055 7.816031 CCTTTAACATGAGTCAAAAAGATGCAT 59.184 33.333 0.00 0.00 29.96 3.96
2955 5064 3.751175 CCGAGCCTTTAACATGAGTCAAA 59.249 43.478 0.00 0.00 0.00 2.69
3013 5122 3.202151 CCAGGACTAGCCCTTAATGGAAA 59.798 47.826 0.00 0.00 38.35 3.13
3020 5129 2.627933 ACAAACCAGGACTAGCCCTTA 58.372 47.619 0.00 0.00 37.37 2.69
3085 5194 3.245586 TGTGCCAAATCCCAAGGATAGTT 60.246 43.478 0.00 0.00 42.27 2.24


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

AutoCloner maintained by Alex Coulton.