Multiple sequence alignment - TraesCS2A01G230600

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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 TraesCS2A01G230600 chr2A 100.000 2402 0 0 1 2402 266908210 266905809 0.000000e+00 4436
1 TraesCS2A01G230600 chr2A 85.130 2421 289 39 1 2391 82414412 82412033 0.000000e+00 2410
2 TraesCS2A01G230600 chr2A 85.057 1218 127 29 1199 2402 679107266 679106090 0.000000e+00 1190
3 TraesCS2A01G230600 chr2A 82.917 1241 151 39 1194 2402 343445178 343443967 0.000000e+00 1061
4 TraesCS2A01G230600 chr2A 82.517 1144 147 26 1194 2319 187020240 187021348 0.000000e+00 955
5 TraesCS2A01G230600 chr2A 86.645 307 32 5 2008 2314 743379342 743379639 4.950000e-87 331
6 TraesCS2A01G230600 chr6A 90.445 2407 217 13 1 2402 462846314 462848712 0.000000e+00 3158
7 TraesCS2A01G230600 chr6A 90.233 2406 222 13 1 2402 462850860 462853256 0.000000e+00 3129
8 TraesCS2A01G230600 chr6B 87.889 2411 252 31 1 2391 272298342 272295952 0.000000e+00 2798
9 TraesCS2A01G230600 chr4B 86.888 2410 284 25 1 2391 376028084 376030480 0.000000e+00 2671
10 TraesCS2A01G230600 chr4B 86.845 2425 266 40 1 2395 230486155 230483754 0.000000e+00 2662
11 TraesCS2A01G230600 chr4D 85.260 2422 298 39 1 2402 163413561 163411179 0.000000e+00 2440
12 TraesCS2A01G230600 chr3D 85.795 2295 271 33 1 2283 402308922 402306671 0.000000e+00 2381
13 TraesCS2A01G230600 chr7D 84.407 2328 328 28 1 2316 355103484 355101180 0.000000e+00 2255
14 TraesCS2A01G230600 chr2D 88.152 1899 209 14 1 1890 323248753 323246862 0.000000e+00 2246
15 TraesCS2A01G230600 chr3B 84.254 1213 135 39 1194 2391 71910075 71911246 0.000000e+00 1131
16 TraesCS2A01G230600 chr1A 81.326 905 97 37 1493 2391 311526511 311527349 0.000000e+00 669


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 TraesCS2A01G230600 chr2A 266905809 266908210 2401 True 4436.0 4436 100.000 1 2402 1 chr2A.!!$R2 2401
1 TraesCS2A01G230600 chr2A 82412033 82414412 2379 True 2410.0 2410 85.130 1 2391 1 chr2A.!!$R1 2390
2 TraesCS2A01G230600 chr2A 679106090 679107266 1176 True 1190.0 1190 85.057 1199 2402 1 chr2A.!!$R4 1203
3 TraesCS2A01G230600 chr2A 343443967 343445178 1211 True 1061.0 1061 82.917 1194 2402 1 chr2A.!!$R3 1208
4 TraesCS2A01G230600 chr2A 187020240 187021348 1108 False 955.0 955 82.517 1194 2319 1 chr2A.!!$F1 1125
5 TraesCS2A01G230600 chr6A 462846314 462853256 6942 False 3143.5 3158 90.339 1 2402 2 chr6A.!!$F1 2401
6 TraesCS2A01G230600 chr6B 272295952 272298342 2390 True 2798.0 2798 87.889 1 2391 1 chr6B.!!$R1 2390
7 TraesCS2A01G230600 chr4B 376028084 376030480 2396 False 2671.0 2671 86.888 1 2391 1 chr4B.!!$F1 2390
8 TraesCS2A01G230600 chr4B 230483754 230486155 2401 True 2662.0 2662 86.845 1 2395 1 chr4B.!!$R1 2394
9 TraesCS2A01G230600 chr4D 163411179 163413561 2382 True 2440.0 2440 85.260 1 2402 1 chr4D.!!$R1 2401
10 TraesCS2A01G230600 chr3D 402306671 402308922 2251 True 2381.0 2381 85.795 1 2283 1 chr3D.!!$R1 2282
11 TraesCS2A01G230600 chr7D 355101180 355103484 2304 True 2255.0 2255 84.407 1 2316 1 chr7D.!!$R1 2315
12 TraesCS2A01G230600 chr2D 323246862 323248753 1891 True 2246.0 2246 88.152 1 1890 1 chr2D.!!$R1 1889
13 TraesCS2A01G230600 chr3B 71910075 71911246 1171 False 1131.0 1131 84.254 1194 2391 1 chr3B.!!$F1 1197
14 TraesCS2A01G230600 chr1A 311526511 311527349 838 False 669.0 669 81.326 1493 2391 1 chr1A.!!$F1 898

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
763 764 0.681733 ACCGTCACATTCAGCTGAGT 59.318 50.0 17.43 11.77 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 6755 1.929494 TGCCTCCCCAAAGGAACATAT 59.071 47.619 0.0 0.0 46.94 1.78 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
110 111 4.439426 CGATCCTTATTCTAGAGGCCATCG 60.439 50.000 5.01 1.75 35.12 3.84
193 194 2.695666 CGTGGTTACTCTCATCCTCCAT 59.304 50.000 0.00 0.00 0.00 3.41
330 331 7.047891 CACTGTTTGCCTCTAGTTATCCAATA 58.952 38.462 0.00 0.00 0.00 1.90
337 338 5.046950 GCCTCTAGTTATCCAATACAGGGAG 60.047 48.000 0.00 0.00 37.96 4.30
473 474 2.685897 GTTAACCAACAACTCCAGCACA 59.314 45.455 0.00 0.00 34.60 4.57
486 487 1.135199 CCAGCACATGTTGAGCAATCC 60.135 52.381 9.10 0.00 36.40 3.01
675 676 7.986085 AATTGAGAGGAATATTAATGTCGGG 57.014 36.000 0.00 0.00 0.00 5.14
676 677 6.494666 TTGAGAGGAATATTAATGTCGGGT 57.505 37.500 0.00 0.00 0.00 5.28
763 764 0.681733 ACCGTCACATTCAGCTGAGT 59.318 50.000 17.43 11.77 0.00 3.41
874 875 4.286808 TCCCAAGTGATCAAGATGAAGACA 59.713 41.667 0.00 0.00 0.00 3.41
875 876 5.005740 CCCAAGTGATCAAGATGAAGACAA 58.994 41.667 0.00 0.00 0.00 3.18
878 879 7.082602 CCAAGTGATCAAGATGAAGACAAAAG 58.917 38.462 0.00 0.00 0.00 2.27
890 891 9.474313 AGATGAAGACAAAAGATCTACTACTCT 57.526 33.333 0.00 0.00 0.00 3.24
1041 1042 3.355378 TGCTACTACCTTGCATTGCATT 58.645 40.909 12.95 2.77 38.76 3.56
1085 1087 9.783081 AGATTTGAAAAACTATTTGCTTGGATT 57.217 25.926 0.00 0.00 0.00 3.01
1100 1102 4.641989 GCTTGGATTTGATCATACACACCT 59.358 41.667 0.00 0.00 0.00 4.00
1112 1114 1.675552 ACACACCTTGTTAGTGGCAC 58.324 50.000 10.29 10.29 39.63 5.01
1151 1153 8.267183 TGTTCATGATACTTATGTTCCTGATGT 58.733 33.333 0.00 0.00 0.00 3.06
1223 1226 7.553044 GCTTACTGATTTGTACCATCCTAAACT 59.447 37.037 0.00 0.00 0.00 2.66
1228 1231 7.001674 TGATTTGTACCATCCTAAACTTGTGT 58.998 34.615 0.00 0.00 0.00 3.72
1300 1303 6.152323 GGGCATTACTCCTATCACTCGTATTA 59.848 42.308 0.00 0.00 0.00 0.98
1361 1364 4.345288 CATGAAACAATACATGCTGACCG 58.655 43.478 0.00 0.00 37.62 4.79
1365 1368 1.299541 CAATACATGCTGACCGGGTC 58.700 55.000 20.36 20.36 0.00 4.46
1414 1417 2.548875 GACTCTGAGCATGGTGATGAC 58.451 52.381 0.00 0.00 0.00 3.06
1476 1495 0.884704 TGCACGAGGAAGCAAAGGAC 60.885 55.000 0.00 0.00 37.90 3.85
1757 1796 6.370166 GTGAGAGCTATTAGTTTTGAGTGCTT 59.630 38.462 0.00 0.00 0.00 3.91
1759 1798 7.545965 TGAGAGCTATTAGTTTTGAGTGCTTAC 59.454 37.037 0.00 0.00 0.00 2.34
1810 1849 7.471721 TCATTTTCTGCATTTACCTTGATACG 58.528 34.615 0.00 0.00 0.00 3.06
2046 6649 0.914417 ATGTTCCCTGGATCGGTGGT 60.914 55.000 0.00 0.00 0.00 4.16
2059 6662 1.606668 TCGGTGGTTTGTGAAATCTGC 59.393 47.619 0.00 0.00 0.00 4.26
2141 6755 0.459899 CATGTTCTCGGGATCGGTGA 59.540 55.000 0.00 0.00 36.95 4.02
2159 6773 3.555966 GTGATATGTTCCTTTGGGGAGG 58.444 50.000 0.00 0.00 46.01 4.30
2232 6853 1.548081 TCGGTGGTATGTTCCTTCGA 58.452 50.000 0.00 0.00 33.39 3.71
2235 6856 2.418197 CGGTGGTATGTTCCTTCGATGT 60.418 50.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.433615 CCTCAAAAACTACTTCTCGCTGG 59.566 47.826 0.00 0.0 0.00 4.85
110 111 2.289565 GGCAGGTAGGAGCAACATAAC 58.710 52.381 0.00 0.0 0.00 1.89
160 161 4.021368 AGAGTAACCACGCTAACATTCAGT 60.021 41.667 0.00 0.0 32.47 3.41
169 170 2.950309 GAGGATGAGAGTAACCACGCTA 59.050 50.000 0.00 0.0 34.64 4.26
193 194 4.095410 CGAAGCTCATGCCAAAACAATA 57.905 40.909 0.00 0.0 40.80 1.90
270 271 7.448469 GGGTTGTTGCTCCTATATGACATATTT 59.552 37.037 13.09 0.0 0.00 1.40
330 331 4.016479 TCCTCTTCATACCTAACTCCCTGT 60.016 45.833 0.00 0.0 0.00 4.00
337 338 5.105310 TGTTGCTCTCCTCTTCATACCTAAC 60.105 44.000 0.00 0.0 0.00 2.34
454 455 2.719531 TGTGCTGGAGTTGTTGGTTA 57.280 45.000 0.00 0.0 0.00 2.85
473 474 1.479323 GTGCATGGGATTGCTCAACAT 59.521 47.619 0.00 0.0 43.18 2.71
486 487 2.201708 TGTGGGCACTTGTGCATGG 61.202 57.895 24.34 0.0 36.33 3.66
671 672 1.040646 GGATGAGATAGTGCACCCGA 58.959 55.000 14.63 0.0 0.00 5.14
672 673 0.034059 GGGATGAGATAGTGCACCCG 59.966 60.000 14.63 0.0 0.00 5.28
675 676 2.324541 AGGAGGGATGAGATAGTGCAC 58.675 52.381 9.40 9.4 0.00 4.57
676 677 2.702478 CAAGGAGGGATGAGATAGTGCA 59.298 50.000 0.00 0.0 0.00 4.57
763 764 5.500546 TCCTATGGACTCTCGCTATCTTA 57.499 43.478 0.00 0.0 0.00 2.10
1041 1042 7.801104 TCAAATCTACCTTAAGTGATGGCATA 58.199 34.615 0.00 0.0 0.00 3.14
1085 1087 5.937540 CCACTAACAAGGTGTGTATGATCAA 59.062 40.000 0.00 0.0 40.60 2.57
1100 1102 2.566833 ATGAGCAGTGCCACTAACAA 57.433 45.000 12.58 0.0 0.00 2.83
1112 1114 7.604549 AGTATCATGAACAGAGATATGAGCAG 58.395 38.462 0.00 0.0 33.53 4.24
1151 1153 6.600032 ACACGTTTCATTAAGCATGGGTATAA 59.400 34.615 0.00 0.0 33.07 0.98
1300 1303 3.515602 AAGGCACTCAACCAAAGAGAT 57.484 42.857 0.00 0.0 38.49 2.75
1345 1348 0.618458 ACCCGGTCAGCATGTATTGT 59.382 50.000 0.00 0.0 37.40 2.71
1361 1364 1.221021 GGAATGTCACCTCGGACCC 59.779 63.158 0.00 0.0 36.97 4.46
1365 1368 0.392998 CCCAAGGAATGTCACCTCGG 60.393 60.000 0.00 0.0 36.67 4.63
1414 1417 4.020617 TGTGCCCCCTGCTTCTCG 62.021 66.667 0.00 0.0 42.00 4.04
1476 1495 3.679025 CACTCTCTAAGCTGCAACTCTTG 59.321 47.826 1.02 0.0 0.00 3.02
1810 1849 6.338214 TCATCTGAACATAGTGATCTAGGC 57.662 41.667 0.00 0.0 32.01 3.93
2005 6608 5.339008 TGACATGCTACTGTTAGGTAAGG 57.661 43.478 0.00 0.0 0.00 2.69
2046 6649 3.191162 CCGATCCAAGCAGATTTCACAAA 59.809 43.478 0.00 0.0 0.00 2.83
2141 6755 1.929494 TGCCTCCCCAAAGGAACATAT 59.071 47.619 0.00 0.0 46.94 1.78


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

AutoCloner maintained by Alex Coulton.