Multiple sequence alignment - TraesCS4D01G127700

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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 TraesCS4D01G127700 chr4D 100.000 3530 0 0 1 3530 111981240 111977711 0.000000e+00 6519
1 TraesCS4D01G127700 chr4D 87.500 192 20 4 3339 3528 214938736 214938925 5.930000e-53 219
2 TraesCS4D01G127700 chr4A 92.840 3380 172 39 1 3332 465274427 465277784 0.000000e+00 4837
3 TraesCS4D01G127700 chr4A 89.055 201 19 1 3329 3529 465278098 465278295 2.720000e-61 246
4 TraesCS4D01G127700 chr4A 88.889 189 19 2 3343 3530 623350150 623349963 7.620000e-57 231
5 TraesCS4D01G127700 chr4B 94.954 2814 123 15 547 3345 172722772 172719963 0.000000e+00 4392
6 TraesCS4D01G127700 chr4B 91.525 531 38 6 1 525 172723620 172723091 0.000000e+00 725
7 TraesCS4D01G127700 chr7D 88.830 188 21 0 3343 3530 427145807 427145620 7.620000e-57 231
8 TraesCS4D01G127700 chr5A 86.559 186 21 4 3343 3526 25021966 25022149 5.980000e-48 202
9 TraesCS4D01G127700 chr1D 86.813 182 23 1 3348 3528 131981930 131981749 5.980000e-48 202
10 TraesCS4D01G127700 chr7B 85.714 189 26 1 3343 3530 750032969 750032781 7.730000e-47 198
11 TraesCS4D01G127700 chr1B 85.714 189 26 1 3343 3530 294490427 294490615 7.730000e-47 198
12 TraesCS4D01G127700 chr2B 85.561 187 26 1 3342 3527 134542061 134542247 1.000000e-45 195


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 TraesCS4D01G127700 chr4D 111977711 111981240 3529 True 6519.0 6519 100.0000 1 3530 1 chr4D.!!$R1 3529
1 TraesCS4D01G127700 chr4A 465274427 465278295 3868 False 2541.5 4837 90.9475 1 3529 2 chr4A.!!$F1 3528
2 TraesCS4D01G127700 chr4B 172719963 172723620 3657 True 2558.5 4392 93.2395 1 3345 2 chr4B.!!$R1 3344

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
334 338 1.186267 GGGCGACGAAGGAGGGATAT 61.186 60.000 0.0 0.0 0.00 1.63 F
518 528 1.282817 CGGCGTTTCAATCATACGGA 58.717 50.000 0.0 0.0 35.91 4.69 F
1307 1634 1.666189 GTTTCTTAGCATGACCGGCTC 59.334 52.381 0.0 0.0 42.62 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1162 1489 2.192443 CTCCATCAGGCCCAGCTG 59.808 66.667 6.78 6.78 33.74 4.24 R
2309 2636 2.261430 AATCGCAGCATCCCTCAGCA 62.261 55.000 0.00 0.00 0.00 4.41 R
3294 3635 0.318614 GTCCAACACATTTGGGTGCG 60.319 55.000 3.25 0.00 42.55 5.34 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
265 268 1.745489 GGACGCCCATGAACCTGAC 60.745 63.158 0.00 0.00 0.00 3.51
303 307 2.045829 TCCAGCGACGCTCTCTCT 60.046 61.111 21.67 0.00 36.40 3.10
305 309 2.579249 CAGCGACGCTCTCTCTGC 60.579 66.667 21.67 0.00 36.40 4.26
334 338 1.186267 GGGCGACGAAGGAGGGATAT 61.186 60.000 0.00 0.00 0.00 1.63
339 343 3.676324 GCGACGAAGGAGGGATATAATGG 60.676 52.174 0.00 0.00 0.00 3.16
342 346 3.181399 ACGAAGGAGGGATATAATGGGGA 60.181 47.826 0.00 0.00 0.00 4.81
343 347 3.452627 CGAAGGAGGGATATAATGGGGAG 59.547 52.174 0.00 0.00 0.00 4.30
345 349 3.018788 AGGAGGGATATAATGGGGAGGA 58.981 50.000 0.00 0.00 0.00 3.71
346 350 3.014574 AGGAGGGATATAATGGGGAGGAG 59.985 52.174 0.00 0.00 0.00 3.69
347 351 2.774809 GAGGGATATAATGGGGAGGAGC 59.225 54.545 0.00 0.00 0.00 4.70
405 414 1.534729 GCGTGGGGAAAAGTGAAGAT 58.465 50.000 0.00 0.00 0.00 2.40
428 437 1.776710 TAGTGGGGTGGCTGGGTTT 60.777 57.895 0.00 0.00 0.00 3.27
436 445 2.203437 GGCTGGGTTTGTTCGGGT 60.203 61.111 0.00 0.00 0.00 5.28
499 508 4.492160 TCGGGAGCGTCGTGATGC 62.492 66.667 5.93 5.93 43.42 3.91
518 528 1.282817 CGGCGTTTCAATCATACGGA 58.717 50.000 0.00 0.00 35.91 4.69
532 830 6.672266 ATCATACGGAGTTAAGGACATCAT 57.328 37.500 0.00 0.00 37.78 2.45
536 834 3.118738 ACGGAGTTAAGGACATCATGACC 60.119 47.826 0.00 0.00 37.78 4.02
601 928 8.574196 ACTTTGATCAAATTTGTAAAACCTCG 57.426 30.769 20.76 6.99 0.00 4.63
643 970 5.108517 GTGAAAAAGAACTCATTGCCACAA 58.891 37.500 0.00 0.00 0.00 3.33
1074 1401 4.077184 TGCGGCGTTGACCTAGGG 62.077 66.667 14.81 0.00 0.00 3.53
1125 1452 4.778143 GCCGGGGTGTTCGCAGAT 62.778 66.667 2.18 0.00 35.04 2.90
1162 1489 2.412847 GGTTTCATCAAGCTGTACGCAC 60.413 50.000 11.30 0.00 42.61 5.34
1250 1577 1.830587 AATGTGCTCCTGGACTGCGA 61.831 55.000 0.00 0.00 35.45 5.10
1269 1596 4.452733 GTGAGGTCCGGGGAAGCG 62.453 72.222 0.00 0.00 0.00 4.68
1307 1634 1.666189 GTTTCTTAGCATGACCGGCTC 59.334 52.381 0.00 0.00 42.62 4.70
1437 1764 8.267894 TCTGGGTATCTTAAGGATCTTTTTCTG 58.732 37.037 1.85 0.00 35.98 3.02
1524 1851 3.801698 TGCTATGCTTGAGAAGGATGTC 58.198 45.455 0.98 0.00 40.04 3.06
1925 2252 5.571784 ATGATGCGACTTCATTGTGAATT 57.428 34.783 0.00 0.00 35.59 2.17
2114 2441 5.078411 TGGTTAGATGAAGCAGAAGAGAC 57.922 43.478 0.00 0.00 40.60 3.36
2309 2636 2.119495 AGAATGGAGTAATGCCTCGGT 58.881 47.619 0.00 0.00 31.98 4.69
2439 2766 7.177498 TGCACAATTCGAACAGATATATGAC 57.823 36.000 3.93 0.00 0.00 3.06
2494 2821 0.179048 TGACAAGCTGGTCACACAGG 60.179 55.000 20.42 0.00 42.56 4.00
2505 2832 2.213499 GTCACACAGGTCAACTCCTTG 58.787 52.381 0.00 0.00 35.37 3.61
2626 2954 9.490379 AATGACCGATTTGGATAGTATTTCTAC 57.510 33.333 0.00 0.00 42.00 2.59
2655 2983 5.734855 AGGTTAGTTACTTATGCAATGCG 57.265 39.130 0.00 0.00 0.00 4.73
2794 3122 7.397476 TGGTTTTATGCCAATAAATGTCCACTA 59.603 33.333 0.00 0.00 37.92 2.74
2809 3137 9.533831 AAATGTCCACTATTCTTTTAGATGGTT 57.466 29.630 0.00 0.00 0.00 3.67
2863 3191 2.381911 GGTTCAGATGTGCCCATTCAT 58.618 47.619 0.00 0.00 0.00 2.57
2873 3201 3.450457 TGTGCCCATTCATTGGTATTTCC 59.550 43.478 0.00 0.00 44.83 3.13
2883 3211 4.833380 TCATTGGTATTTCCGGTTTTCCAA 59.167 37.500 17.41 17.41 40.70 3.53
2950 3278 1.009829 GCGGCGACTTCATCAATCTT 58.990 50.000 12.98 0.00 0.00 2.40
2970 3298 7.825331 ATCTTAAGATCTATCGGTTCAGTCA 57.175 36.000 12.37 0.00 0.00 3.41
2971 3299 7.825331 TCTTAAGATCTATCGGTTCAGTCAT 57.175 36.000 0.00 0.00 0.00 3.06
3015 3345 5.132312 TCGTAGGAAGAAAGATAGAGGAGGA 59.868 44.000 0.00 0.00 0.00 3.71
3048 3379 7.824779 GGTGGTAGGGCTAGAATGAATTAATAG 59.175 40.741 0.00 0.00 0.00 1.73
3112 3447 2.723719 GGCGCGACGAGGTTACAAC 61.724 63.158 12.10 0.00 0.00 3.32
3143 3478 2.293399 GGACCATTTCGCAGAAGTGTTT 59.707 45.455 10.90 1.37 45.90 2.83
3162 3498 4.436998 GGACGCACGAGGAGGGTG 62.437 72.222 0.00 0.00 40.26 4.61
3211 3548 7.332678 AGCTTTATTCAAAAGAATGCATTCACC 59.667 33.333 34.59 14.41 39.23 4.02
3237 3578 5.128827 AGTTGTTAACCAGAAGACTGTCAGA 59.871 40.000 10.88 0.00 42.05 3.27
3243 3584 3.244044 ACCAGAAGACTGTCAGAAAGCTC 60.244 47.826 10.88 0.00 42.05 4.09
3274 3615 0.250901 AAGCCAGCTTTCGGTGACAT 60.251 50.000 0.00 0.00 41.05 3.06
3278 3619 0.806868 CAGCTTTCGGTGACATGCAT 59.193 50.000 0.00 0.00 41.05 3.96
3299 3640 4.683334 GCAACCACGCTTCGCACC 62.683 66.667 0.00 0.00 0.00 5.01
3326 3668 2.557924 GTGTTGGACCATTTGCTGATCA 59.442 45.455 0.00 0.00 0.00 2.92
3337 3996 5.803461 CCATTTGCTGATCAACTTACATGTG 59.197 40.000 9.11 0.00 33.73 3.21
3347 4006 8.946085 TGATCAACTTACATGTGGAATTACTTC 58.054 33.333 9.11 0.00 0.00 3.01
3374 4033 5.868801 CCATTTTTGTATACAAGGCCACAAG 59.131 40.000 17.36 5.13 37.15 3.16
3375 4034 6.454795 CATTTTTGTATACAAGGCCACAAGT 58.545 36.000 17.36 3.52 37.15 3.16
3376 4035 5.699097 TTTTGTATACAAGGCCACAAGTC 57.301 39.130 17.36 0.00 37.15 3.01
3379 4038 2.200373 ATACAAGGCCACAAGTCCAC 57.800 50.000 5.01 0.00 0.00 4.02
3390 4049 4.000988 CCACAAGTCCACATTACAGGTAC 58.999 47.826 0.00 0.00 0.00 3.34
3395 4054 3.263425 AGTCCACATTACAGGTACCAAGG 59.737 47.826 15.94 4.02 0.00 3.61
3465 4124 5.079406 CCTCGTTTGACGTGTGAATTAATG 58.921 41.667 0.00 0.00 43.14 1.90
3477 4136 9.607285 ACGTGTGAATTAATGTGTATTTTTCTC 57.393 29.630 0.00 0.00 0.00 2.87
3486 4145 7.667043 AATGTGTATTTTTCTCTCTAACGCA 57.333 32.000 0.00 0.00 0.00 5.24
3494 4153 3.728076 TCTCTCTAACGCACAACAAGT 57.272 42.857 0.00 0.00 0.00 3.16
3506 4165 2.614057 CACAACAAGTCAACCCTCTCAC 59.386 50.000 0.00 0.00 0.00 3.51
3507 4166 2.505819 ACAACAAGTCAACCCTCTCACT 59.494 45.455 0.00 0.00 0.00 3.41
3508 4167 3.134458 CAACAAGTCAACCCTCTCACTC 58.866 50.000 0.00 0.00 0.00 3.51
3529 4188 5.359009 ACTCCTCATTGGTTGATTAATGCAG 59.641 40.000 0.00 0.00 34.96 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
334 338 2.443394 CGCCTGCTCCTCCCCATTA 61.443 63.158 0.00 0.00 0.00 1.90
343 347 4.803426 CACTCCGTCGCCTGCTCC 62.803 72.222 0.00 0.00 0.00 4.70
366 372 2.443016 CCCTCCTCCCTCCACTCG 60.443 72.222 0.00 0.00 0.00 4.18
405 414 0.325296 CCAGCCACCCCACTACTCTA 60.325 60.000 0.00 0.00 0.00 2.43
436 445 1.393487 TTCGGGTCGAAGGTGTGTCA 61.393 55.000 0.00 0.00 41.05 3.58
499 508 1.257936 CTCCGTATGATTGAAACGCCG 59.742 52.381 0.00 0.00 35.36 6.46
501 510 5.459110 TTAACTCCGTATGATTGAAACGC 57.541 39.130 0.00 0.00 35.36 4.84
502 511 5.808540 TCCTTAACTCCGTATGATTGAAACG 59.191 40.000 0.00 0.00 36.42 3.60
518 528 6.350445 GCAAAATGGTCATGATGTCCTTAACT 60.350 38.462 9.96 0.00 0.00 2.24
520 530 5.716228 AGCAAAATGGTCATGATGTCCTTAA 59.284 36.000 9.96 0.00 0.00 1.85
532 830 5.957842 ATCTAAACGAAGCAAAATGGTCA 57.042 34.783 0.00 0.00 0.00 4.02
536 834 9.065871 CCTAGAAAATCTAAACGAAGCAAAATG 57.934 33.333 0.00 0.00 0.00 2.32
643 970 1.066257 GCGGCGGCATTCATTCAAT 59.934 52.632 9.78 0.00 39.62 2.57
927 1254 1.072331 GATATGGCGGTGTTCCAGGAT 59.928 52.381 0.00 0.00 36.98 3.24
1122 1449 0.391661 CAGTACCAACGCAGGCATCT 60.392 55.000 0.00 0.00 0.00 2.90
1125 1452 2.031919 CCAGTACCAACGCAGGCA 59.968 61.111 0.00 0.00 0.00 4.75
1134 1461 3.181445 ACAGCTTGATGAAACCAGTACCA 60.181 43.478 0.00 0.00 0.00 3.25
1137 1464 4.242475 CGTACAGCTTGATGAAACCAGTA 58.758 43.478 0.00 0.00 0.00 2.74
1162 1489 2.192443 CTCCATCAGGCCCAGCTG 59.808 66.667 6.78 6.78 33.74 4.24
1250 1577 2.670148 GCTTCCCCGGACCTCACAT 61.670 63.158 0.73 0.00 0.00 3.21
1269 1596 3.821421 AACTCCTTCATACACGATCCC 57.179 47.619 0.00 0.00 0.00 3.85
1424 1751 6.661304 AAGAATTGCACAGAAAAAGATCCT 57.339 33.333 0.00 0.00 0.00 3.24
1941 2268 2.621526 CAGGACACCCACAAAAGTTACC 59.378 50.000 0.00 0.00 33.88 2.85
2114 2441 8.550376 CATGTTTGAAAGGTAAGTTTGAAATGG 58.450 33.333 0.00 0.00 27.58 3.16
2169 2496 3.243068 GGTTACCATATTTTCTGCAGCCG 60.243 47.826 9.47 0.00 0.00 5.52
2309 2636 2.261430 AATCGCAGCATCCCTCAGCA 62.261 55.000 0.00 0.00 0.00 4.41
2439 2766 3.405170 AACTGAAGTTGTTGCAGAACG 57.595 42.857 0.00 0.00 36.80 3.95
2626 2954 4.206609 GCATAAGTAACTAACCTTCTCGCG 59.793 45.833 0.00 0.00 0.00 5.87
2655 2983 4.034279 GTGAGTCGACTGATGTAGTAGGTC 59.966 50.000 25.58 4.13 40.53 3.85
2863 3191 3.004524 CGTTGGAAAACCGGAAATACCAA 59.995 43.478 9.46 14.05 38.90 3.67
2873 3201 3.824414 AAGAATAGCGTTGGAAAACCG 57.176 42.857 0.00 0.00 0.00 4.44
2883 3211 5.339008 TCATACCACTGAAAGAATAGCGT 57.661 39.130 0.00 0.00 37.43 5.07
2942 3270 8.865090 ACTGAACCGATAGATCTTAAGATTGAT 58.135 33.333 18.88 14.43 34.37 2.57
2950 3278 7.502561 TCTCAATGACTGAACCGATAGATCTTA 59.497 37.037 0.00 0.00 32.50 2.10
2970 3298 4.408270 CGATATCCCCATGAGGATCTCAAT 59.592 45.833 12.72 0.15 43.48 2.57
2971 3299 3.771479 CGATATCCCCATGAGGATCTCAA 59.229 47.826 12.72 0.00 43.48 3.02
3015 3345 3.460825 TCTAGCCCTACCACCTGAAATT 58.539 45.455 0.00 0.00 0.00 1.82
3112 3447 1.670811 CGAAATGGTCCCTCGATTTGG 59.329 52.381 0.00 0.00 35.26 3.28
3211 3548 4.369182 ACAGTCTTCTGGTTAACAACTCG 58.631 43.478 8.10 0.00 45.14 4.18
3237 3578 3.067833 GCTTACTGAAACTCCGAGCTTT 58.932 45.455 0.00 0.00 0.00 3.51
3243 3584 1.079503 GCTGGCTTACTGAAACTCCG 58.920 55.000 0.00 0.00 0.00 4.63
3294 3635 0.318614 GTCCAACACATTTGGGTGCG 60.319 55.000 3.25 0.00 42.55 5.34
3326 3668 6.884836 GGAGGAAGTAATTCCACATGTAAGTT 59.115 38.462 23.06 0.00 43.54 2.66
3347 4006 4.709397 TGGCCTTGTATACAAAAATGGAGG 59.291 41.667 20.31 16.09 35.15 4.30
3350 4009 5.398603 TGTGGCCTTGTATACAAAAATGG 57.601 39.130 18.55 16.25 35.15 3.16
3361 4020 0.840617 TGTGGACTTGTGGCCTTGTA 59.159 50.000 3.32 0.00 0.00 2.41
3363 4022 1.331214 AATGTGGACTTGTGGCCTTG 58.669 50.000 3.32 0.00 0.00 3.61
3374 4033 3.008704 ACCTTGGTACCTGTAATGTGGAC 59.991 47.826 14.36 0.00 0.00 4.02
3375 4034 3.253220 ACCTTGGTACCTGTAATGTGGA 58.747 45.455 14.36 0.00 0.00 4.02
3376 4035 3.713826 ACCTTGGTACCTGTAATGTGG 57.286 47.619 14.36 6.07 0.00 4.17
3390 4049 7.619964 AAACCGACACTAATATTTACCTTGG 57.380 36.000 0.00 0.00 0.00 3.61
3395 4054 8.200364 TGGCTTAAACCGACACTAATATTTAC 57.800 34.615 0.00 0.00 0.00 2.01
3405 4064 3.003897 TCAACATTGGCTTAAACCGACAC 59.996 43.478 0.00 0.00 0.00 3.67
3440 4099 2.296831 TTCACACGTCAAACGAGGAA 57.703 45.000 6.48 4.24 46.05 3.36
3465 4124 6.462073 TGTGCGTTAGAGAGAAAAATACAC 57.538 37.500 0.00 0.00 0.00 2.90
3477 4136 3.303132 GGTTGACTTGTTGTGCGTTAGAG 60.303 47.826 0.00 0.00 0.00 2.43
3480 4139 1.671845 GGGTTGACTTGTTGTGCGTTA 59.328 47.619 0.00 0.00 0.00 3.18
3486 4145 2.505819 AGTGAGAGGGTTGACTTGTTGT 59.494 45.455 0.00 0.00 0.00 3.32
3494 4153 2.568956 CAATGAGGAGTGAGAGGGTTGA 59.431 50.000 0.00 0.00 0.00 3.18
3506 4165 5.828747 CTGCATTAATCAACCAATGAGGAG 58.171 41.667 0.00 0.00 42.53 3.69
3507 4166 5.840243 CTGCATTAATCAACCAATGAGGA 57.160 39.130 0.00 0.00 42.53 3.71


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

AutoCloner maintained by Alex Coulton.