Multiple sequence alignment - TraesCS5A01G154500

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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 TraesCS5A01G154500 chr5A 100.000 2538 0 0 1 2538 331888995 331886458 0.000000e+00 4687
1 TraesCS5A01G154500 chr1A 96.706 1973 61 3 567 2538 155144503 155142534 0.000000e+00 3280
2 TraesCS5A01G154500 chr5D 92.897 535 20 11 1 528 249086782 249086259 0.000000e+00 761
3 TraesCS5A01G154500 chr5B 92.885 506 18 8 1 488 282011245 282010740 0.000000e+00 719
4 TraesCS5A01G154500 chr2A 89.508 305 32 0 568 872 771550634 771550330 1.100000e-103 387
5 TraesCS5A01G154500 chr2A 85.644 202 29 0 2 203 750581204 750581003 1.980000e-51 213
6 TraesCS5A01G154500 chr2A 85.644 202 29 0 2 203 750617249 750617048 1.980000e-51 213
7 TraesCS5A01G154500 chr6B 90.071 282 28 0 570 851 567602840 567602559 1.430000e-97 366
8 TraesCS5A01G154500 chr7A 88.197 305 36 0 568 872 624884118 624883814 5.160000e-97 364
9 TraesCS5A01G154500 chr2B 88.119 202 24 0 2 203 758389829 758389628 9.070000e-60 241
10 TraesCS5A01G154500 chr2B 87.624 202 25 0 2 203 758147463 758147262 4.220000e-58 235
11 TraesCS5A01G154500 chr2D 87.129 202 26 0 2 203 619426437 619426236 1.960000e-56 230
12 TraesCS5A01G154500 chr2D 86.207 203 28 0 2 204 585861049 585861251 1.180000e-53 220
13 TraesCS5A01G154500 chr2D 85.644 202 29 0 2 203 619436494 619436293 1.980000e-51 213


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 TraesCS5A01G154500 chr5A 331886458 331888995 2537 True 4687 4687 100.000 1 2538 1 chr5A.!!$R1 2537
1 TraesCS5A01G154500 chr1A 155142534 155144503 1969 True 3280 3280 96.706 567 2538 1 chr1A.!!$R1 1971
2 TraesCS5A01G154500 chr5D 249086259 249086782 523 True 761 761 92.897 1 528 1 chr5D.!!$R1 527
3 TraesCS5A01G154500 chr5B 282010740 282011245 505 True 719 719 92.885 1 488 1 chr5B.!!$R1 487

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
647 671 0.325933 ATCTAGCAGCTGCACCAACA 59.674 50.0 38.24 17.05 45.16 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1802 0.316841 TCAACATTTTTCCGCTGGCC 59.683 50.0 0.0 0.0 0.0 5.36 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
134 135 2.358737 GTGCTACTGCCTTGGCGT 60.359 61.111 7.18 10.11 38.71 5.68
205 206 1.739562 CGGAGGTGCAGCTGAAGTC 60.740 63.158 25.60 8.44 0.00 3.01
342 361 0.671472 TGCCGTGCATTGTGAGAGAG 60.671 55.000 0.00 0.00 31.71 3.20
369 388 5.106948 CGTGCGATTGCCAAGATAGAATATT 60.107 40.000 1.50 0.00 41.78 1.28
499 523 4.021894 GCTCACATGTTCGGTATATCTCCT 60.022 45.833 0.00 0.00 0.00 3.69
513 537 1.018148 TCTCCTTTGCACGCGAAAAA 58.982 45.000 15.93 9.25 0.00 1.94
528 552 5.410439 ACGCGAAAAAGTGTTCCATATAAGT 59.590 36.000 15.93 0.00 0.00 2.24
529 553 6.591062 ACGCGAAAAAGTGTTCCATATAAGTA 59.409 34.615 15.93 0.00 0.00 2.24
530 554 7.279313 ACGCGAAAAAGTGTTCCATATAAGTAT 59.721 33.333 15.93 0.00 0.00 2.12
531 555 7.792508 CGCGAAAAAGTGTTCCATATAAGTATC 59.207 37.037 0.00 0.00 0.00 2.24
532 556 8.827677 GCGAAAAAGTGTTCCATATAAGTATCT 58.172 33.333 0.00 0.00 0.00 1.98
539 563 9.830186 AGTGTTCCATATAAGTATCTCATACCT 57.170 33.333 0.00 0.00 36.40 3.08
594 618 2.048127 GTTTGGCGGACGAGCTCT 60.048 61.111 12.85 0.00 37.29 4.09
620 644 2.632028 AGCTCGGTATCCTAGTCGTCTA 59.368 50.000 0.00 0.00 0.00 2.59
647 671 0.325933 ATCTAGCAGCTGCACCAACA 59.674 50.000 38.24 17.05 45.16 3.33
667 691 7.967854 ACCAACACATTTAATGACATGTATTCG 59.032 33.333 12.28 0.00 32.16 3.34
672 696 7.585210 CACATTTAATGACATGTATTCGAGCTG 59.415 37.037 12.28 0.00 32.16 4.24
700 724 5.955959 AGGATATATGCCACACCGTATTCTA 59.044 40.000 0.00 0.00 0.00 2.10
710 734 6.563381 GCCACACCGTATTCTATATTTTCGTG 60.563 42.308 0.00 0.00 0.00 4.35
750 774 0.740149 CGAAAATGCATGGCAGGCTA 59.260 50.000 25.44 11.95 43.65 3.93
845 869 1.078848 AGCTCACGCTCCCATGTTC 60.079 57.895 0.00 0.00 45.15 3.18
866 890 4.145052 TCAGAGATAAGCCGATGAGCTAA 58.855 43.478 0.00 0.00 44.11 3.09
867 891 4.769488 TCAGAGATAAGCCGATGAGCTAAT 59.231 41.667 0.00 0.00 44.11 1.73
951 975 1.293924 CGGAGAACAGCAGCCTAATG 58.706 55.000 0.00 0.00 0.00 1.90
992 1016 6.244552 TCTCATCAGTGAATAGCTTGGAAT 57.755 37.500 0.00 0.00 33.05 3.01
1104 1128 1.168714 GGGTGGAGACAAACATCTGC 58.831 55.000 0.00 0.00 46.06 4.26
1144 1168 1.597461 GGGAGGCGCTTCTACAAGT 59.403 57.895 19.65 0.00 31.45 3.16
1152 1176 1.739067 GCTTCTACAAGTGCCCGATT 58.261 50.000 0.00 0.00 31.45 3.34
1172 1196 6.073276 CCGATTGACAGTGTAAGTTTTCATCA 60.073 38.462 0.00 0.00 0.00 3.07
1222 1246 9.778993 AAAATCGATAAATGAAGTCTCACATTG 57.221 29.630 0.00 0.00 36.92 2.82
1233 1257 5.643379 AGTCTCACATTGTTGTTTGTGTT 57.357 34.783 3.30 0.00 42.95 3.32
1234 1258 6.024552 AGTCTCACATTGTTGTTTGTGTTT 57.975 33.333 3.30 0.00 42.95 2.83
1375 1399 1.073199 CCAAGGTTCGAGCCAAGGT 59.927 57.895 21.22 0.00 0.00 3.50
1434 1458 2.491621 CGAGATCGTCAGGCAGCA 59.508 61.111 0.00 0.00 34.11 4.41
1478 1502 3.444805 GAGGCCGCGACTGTCTCT 61.445 66.667 8.23 0.00 0.00 3.10
1480 1504 2.507324 GGCCGCGACTGTCTCTTC 60.507 66.667 8.23 0.00 0.00 2.87
1547 1571 0.532573 ACGGGTGTGATGAGCTACTG 59.467 55.000 0.00 0.00 0.00 2.74
1556 1580 2.275318 GATGAGCTACTGTCAAGCACC 58.725 52.381 5.45 0.00 42.62 5.01
1642 1666 1.005748 TTGCGAGTCACTGAGCCTG 60.006 57.895 0.00 0.00 0.00 4.85
1714 1738 8.717821 GTCAGTGTATGCTTCAAGTTTATGTTA 58.282 33.333 0.00 0.00 0.00 2.41
1778 1802 2.654749 TGGACACGCTAATCAGTCTG 57.345 50.000 0.00 0.00 0.00 3.51
1786 1810 0.531532 CTAATCAGTCTGGCCAGCGG 60.532 60.000 28.91 21.81 0.00 5.52
1831 1855 0.249868 GGCCCCACTTTTTGCTTGAC 60.250 55.000 0.00 0.00 0.00 3.18
1926 1950 1.805428 GCACACAACCACCATCACCC 61.805 60.000 0.00 0.00 0.00 4.61
1928 1952 0.260230 ACACAACCACCATCACCCAA 59.740 50.000 0.00 0.00 0.00 4.12
1945 1969 2.222953 CCCAACAGTAAATAGAACGCGC 60.223 50.000 5.73 0.00 0.00 6.86
1949 1973 0.921347 AGTAAATAGAACGCGCGCTG 59.079 50.000 32.58 23.88 0.00 5.18
1997 2021 2.042831 CCCCTGCTTTTCTGCCTCG 61.043 63.158 0.00 0.00 0.00 4.63
2055 2080 1.226323 CAGCGCTGAAGCTTGCATC 60.226 57.895 33.66 0.00 46.80 3.91
2132 2157 1.063183 AAGCAAGAAGAGGAGGCAGT 58.937 50.000 0.00 0.00 0.00 4.40
2133 2158 0.324285 AGCAAGAAGAGGAGGCAGTG 59.676 55.000 0.00 0.00 0.00 3.66
2171 2196 1.490910 AGGAGGCAGGTATGTAAAGGC 59.509 52.381 0.00 0.00 0.00 4.35
2200 2225 2.421775 ACTCTCTGTATCACACTCGCAG 59.578 50.000 0.00 0.00 0.00 5.18
2210 2235 1.583404 CACACTCGCAGTTGCAAAAAC 59.417 47.619 0.00 0.00 42.21 2.43
2220 2245 6.148645 TCGCAGTTGCAAAAACTATTCATCTA 59.851 34.615 0.00 0.00 42.21 1.98
2259 2284 5.756950 TTGAAATGCTCGAGTTTAGTACG 57.243 39.130 15.13 0.00 0.00 3.67
2304 2329 9.699410 TTTGATTTACCAGATCCATCTTGTATT 57.301 29.630 2.26 0.00 35.69 1.89
2322 2347 8.721478 TCTTGTATTTTCTGTTCAATCTGTAGC 58.279 33.333 0.00 0.00 0.00 3.58
2342 2367 2.528743 CGCACCTCATCACATCGGC 61.529 63.158 0.00 0.00 0.00 5.54
2346 2371 1.323271 ACCTCATCACATCGGCGTCT 61.323 55.000 6.85 0.00 0.00 4.18
2348 2373 1.203928 CTCATCACATCGGCGTCTTC 58.796 55.000 6.85 0.00 0.00 2.87
2460 2485 5.233050 CGCAGTTACATCTAGGATTTCAGTG 59.767 44.000 0.00 0.00 0.00 3.66
2468 2493 3.758554 TCTAGGATTTCAGTGCAAAAGCC 59.241 43.478 8.30 8.30 41.42 4.35
2529 2554 6.151817 GGAAGTTGATAGCAGAGATTGGTTTT 59.848 38.462 0.00 0.00 38.70 2.43
2530 2555 6.506500 AGTTGATAGCAGAGATTGGTTTTG 57.493 37.500 0.00 0.00 38.70 2.44
2532 2557 6.716628 AGTTGATAGCAGAGATTGGTTTTGAA 59.283 34.615 0.00 0.00 38.70 2.69
2534 2559 5.649395 TGATAGCAGAGATTGGTTTTGAAGG 59.351 40.000 0.00 0.00 38.70 3.46
2535 2560 2.560105 AGCAGAGATTGGTTTTGAAGGC 59.440 45.455 0.00 0.00 32.47 4.35
2536 2561 2.669391 GCAGAGATTGGTTTTGAAGGCG 60.669 50.000 0.00 0.00 0.00 5.52
2537 2562 2.554032 CAGAGATTGGTTTTGAAGGCGT 59.446 45.455 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 206 4.988598 ACAGCCTTGTCGCCGTGG 62.989 66.667 0.00 0.00 29.46 4.94
233 234 1.656652 GTCCTGTTGTCGATGATGGG 58.343 55.000 0.00 0.00 0.00 4.00
259 260 6.677781 TCTTTGCCTTCAATAATTAGGTCG 57.322 37.500 0.00 0.00 31.33 4.79
342 361 2.257286 ATCTTGGCAATCGCACGCAC 62.257 55.000 0.00 0.00 41.24 5.34
369 388 8.840833 AACACACAGATACAAATACATACACA 57.159 30.769 0.00 0.00 0.00 3.72
399 418 6.109359 AGTACTTGTCATGTTGATAAGCTCC 58.891 40.000 12.23 3.29 45.69 4.70
448 472 3.938963 CACCTCAGTGTACCGCAAATATT 59.061 43.478 0.00 0.00 39.30 1.28
449 473 3.196901 TCACCTCAGTGTACCGCAAATAT 59.803 43.478 0.00 0.00 44.83 1.28
450 474 2.563620 TCACCTCAGTGTACCGCAAATA 59.436 45.455 0.00 0.00 44.83 1.40
451 475 1.346395 TCACCTCAGTGTACCGCAAAT 59.654 47.619 0.00 0.00 44.83 2.32
452 476 0.753867 TCACCTCAGTGTACCGCAAA 59.246 50.000 0.00 0.00 44.83 3.68
499 523 1.914700 GAACACTTTTTCGCGTGCAAA 59.085 42.857 5.77 1.06 34.58 3.68
513 537 9.830186 AGGTATGAGATACTTATATGGAACACT 57.170 33.333 0.00 0.00 37.21 3.55
545 569 8.983702 TTCGGTTATGGGCTAACTATTTAAAT 57.016 30.769 5.89 5.89 39.78 1.40
546 570 8.804912 TTTCGGTTATGGGCTAACTATTTAAA 57.195 30.769 0.00 0.00 39.78 1.52
547 571 8.804912 TTTTCGGTTATGGGCTAACTATTTAA 57.195 30.769 0.00 0.00 39.78 1.52
548 572 8.842280 CATTTTCGGTTATGGGCTAACTATTTA 58.158 33.333 0.00 0.00 39.78 1.40
549 573 7.683463 GCATTTTCGGTTATGGGCTAACTATTT 60.683 37.037 0.00 0.00 39.78 1.40
550 574 6.238925 GCATTTTCGGTTATGGGCTAACTATT 60.239 38.462 0.00 0.00 39.78 1.73
551 575 5.240844 GCATTTTCGGTTATGGGCTAACTAT 59.759 40.000 0.00 0.00 39.78 2.12
552 576 4.577283 GCATTTTCGGTTATGGGCTAACTA 59.423 41.667 0.00 0.00 39.78 2.24
553 577 3.380320 GCATTTTCGGTTATGGGCTAACT 59.620 43.478 0.00 0.00 39.78 2.24
554 578 3.490249 GGCATTTTCGGTTATGGGCTAAC 60.490 47.826 0.00 0.00 39.25 2.34
555 579 2.691011 GGCATTTTCGGTTATGGGCTAA 59.309 45.455 0.00 0.00 0.00 3.09
556 580 2.303175 GGCATTTTCGGTTATGGGCTA 58.697 47.619 0.00 0.00 0.00 3.93
557 581 1.111277 GGCATTTTCGGTTATGGGCT 58.889 50.000 0.00 0.00 0.00 5.19
558 582 0.248866 CGGCATTTTCGGTTATGGGC 60.249 55.000 0.00 0.00 0.00 5.36
559 583 1.099689 ACGGCATTTTCGGTTATGGG 58.900 50.000 0.00 0.00 0.00 4.00
560 584 2.920490 CAAACGGCATTTTCGGTTATGG 59.080 45.455 0.00 0.00 35.15 2.74
561 585 2.920490 CCAAACGGCATTTTCGGTTATG 59.080 45.455 0.00 0.00 35.15 1.90
562 586 3.224884 CCAAACGGCATTTTCGGTTAT 57.775 42.857 0.00 0.00 35.15 1.89
563 587 2.708386 CCAAACGGCATTTTCGGTTA 57.292 45.000 0.00 0.00 35.15 2.85
564 588 3.579066 CCAAACGGCATTTTCGGTT 57.421 47.368 0.00 0.00 38.12 4.44
594 618 3.082548 GACTAGGATACCGAGCTGCATA 58.917 50.000 1.02 0.00 29.11 3.14
647 671 7.254898 CCAGCTCGAATACATGTCATTAAATGT 60.255 37.037 0.00 0.00 40.13 2.71
710 734 0.179062 CAGTCCTGGGATGCTACTGC 60.179 60.000 0.00 0.00 40.20 4.40
720 744 0.804989 GCATTTTCGTCAGTCCTGGG 59.195 55.000 0.00 0.00 0.00 4.45
722 746 2.159476 CCATGCATTTTCGTCAGTCCTG 60.159 50.000 0.00 0.00 0.00 3.86
750 774 1.067212 GGATCGATGGCACGTCTAACT 59.933 52.381 0.54 0.00 34.70 2.24
845 869 4.511617 TTAGCTCATCGGCTTATCTCTG 57.488 45.455 0.00 0.00 42.97 3.35
866 890 2.088950 ACGTTCGGATTCCAAACGAT 57.911 45.000 30.13 14.77 46.42 3.73
867 891 1.527736 CAACGTTCGGATTCCAAACGA 59.472 47.619 30.13 7.23 46.42 3.85
951 975 0.746659 GAGCTGAGAGGAGGAGAAGC 59.253 60.000 0.00 0.00 0.00 3.86
957 981 1.958579 CTGATGAGAGCTGAGAGGAGG 59.041 57.143 0.00 0.00 0.00 4.30
1104 1128 1.581447 GTTCGGCCCTTCTTTGCTG 59.419 57.895 0.00 0.00 35.14 4.41
1144 1168 1.346395 ACTTACACTGTCAATCGGGCA 59.654 47.619 0.00 0.00 0.00 5.36
1152 1176 7.255104 GGACATTGATGAAAACTTACACTGTCA 60.255 37.037 1.65 0.00 40.38 3.58
1172 1196 3.828451 CCATGGAACTTCTTGTGGACATT 59.172 43.478 5.56 0.00 0.00 2.71
1241 1265 2.377810 CCTGCTCAGCCCCATACCA 61.378 63.158 0.00 0.00 0.00 3.25
1244 1268 3.492353 GCCCTGCTCAGCCCCATA 61.492 66.667 0.00 0.00 0.00 2.74
1375 1399 3.986970 CGTAGCATGTCCAGCCATA 57.013 52.632 0.00 0.00 0.00 2.74
1434 1458 0.882042 CTGTGCTTGTTCAGTCCGCT 60.882 55.000 0.00 0.00 0.00 5.52
1444 1468 4.290622 CCCCTGGCCTGTGCTTGT 62.291 66.667 3.32 0.00 37.74 3.16
1474 1498 2.169978 CACCATGAGGCAGATGAAGAGA 59.830 50.000 0.00 0.00 39.06 3.10
1478 1502 2.506644 TGATCACCATGAGGCAGATGAA 59.493 45.455 0.00 0.00 39.06 2.57
1480 1504 2.617308 GTTGATCACCATGAGGCAGATG 59.383 50.000 0.00 0.00 39.06 2.90
1547 1571 1.207329 AGAACGGATAGGGTGCTTGAC 59.793 52.381 0.00 0.00 0.00 3.18
1556 1580 5.936686 TGTCTACGATTAGAACGGATAGG 57.063 43.478 0.00 0.00 36.03 2.57
1642 1666 5.180271 TGACCCATTAACGACCTAATCAAC 58.820 41.667 0.00 0.00 0.00 3.18
1746 1770 1.224075 GTGTCCATCCGATGATGCAG 58.776 55.000 10.12 0.00 45.86 4.41
1778 1802 0.316841 TCAACATTTTTCCGCTGGCC 59.683 50.000 0.00 0.00 0.00 5.36
1786 1810 8.539770 TCTCTCTGACTATGTCAACATTTTTC 57.460 34.615 0.20 0.00 42.26 2.29
1831 1855 4.626042 GTCCAGCAAGTAGATATCACCAG 58.374 47.826 5.32 0.00 0.00 4.00
1926 1950 2.678705 CGCGCGTTCTATTTACTGTTG 58.321 47.619 24.19 0.00 0.00 3.33
1928 1952 0.643820 GCGCGCGTTCTATTTACTGT 59.356 50.000 32.35 0.00 0.00 3.55
1945 1969 1.646189 GCTCCCTTCTAGTTTCAGCG 58.354 55.000 0.00 0.00 0.00 5.18
1949 1973 2.007547 GCACCGCTCCCTTCTAGTTTC 61.008 57.143 0.00 0.00 0.00 2.78
2055 2080 3.736483 GCTGGTGCCATGGATACG 58.264 61.111 18.40 3.21 42.51 3.06
2100 2125 3.238108 TCTTGCTTGAATCCTCGACTC 57.762 47.619 0.00 0.00 0.00 3.36
2132 2157 3.072915 TCCTGTTCTTGCTTGAATCCTCA 59.927 43.478 0.00 0.00 0.00 3.86
2133 2158 3.679389 TCCTGTTCTTGCTTGAATCCTC 58.321 45.455 0.00 0.00 0.00 3.71
2171 2196 6.169094 AGTGTGATACAGAGAGTTGGATTTG 58.831 40.000 0.00 0.00 0.00 2.32
2200 2225 9.443283 CTGCTATAGATGAATAGTTTTTGCAAC 57.557 33.333 3.21 0.00 32.89 4.17
2210 2235 7.782168 TGGATCCCTACTGCTATAGATGAATAG 59.218 40.741 9.90 0.00 33.37 1.73
2220 2245 5.912149 TTTCAATGGATCCCTACTGCTAT 57.088 39.130 9.90 0.00 0.00 2.97
2304 2329 2.411748 CGCGCTACAGATTGAACAGAAA 59.588 45.455 5.56 0.00 0.00 2.52
2322 2347 2.863853 CGATGTGATGAGGTGCGCG 61.864 63.158 0.00 0.00 0.00 6.86
2346 2371 2.749839 CTTTCCATGCCGGCCGAA 60.750 61.111 30.73 19.62 33.14 4.30
2438 2463 6.108687 TGCACTGAAATCCTAGATGTAACTG 58.891 40.000 0.00 0.00 0.00 3.16
2460 2485 1.994916 ATATGTTGCACGGCTTTTGC 58.005 45.000 0.00 0.00 46.64 3.68
2468 2493 2.632377 ACTGGGAGAATATGTTGCACG 58.368 47.619 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.