Multiple sequence alignment - TraesCS4A01G152500

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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 TraesCS4A01G152500 chr4A 100.000 2744 0 0 1 2744 309449062 309446319 0 5068
1 TraesCS4A01G152500 chr5D 96.299 2756 86 7 1 2744 6255938 6253187 0 4510
2 TraesCS4A01G152500 chr5D 95.792 2733 87 8 35 2744 503336802 503339529 0 4385
3 TraesCS4A01G152500 chr5D 95.303 2768 98 9 1 2744 503310832 503313591 0 4362
4 TraesCS4A01G152500 chr5D 94.581 2768 100 12 1 2744 329128559 329125818 0 4235
5 TraesCS4A01G152500 chr5D 95.908 1613 44 3 1 1592 481592288 481593899 0 2593
6 TraesCS4A01G152500 chr5D 95.749 1341 35 5 1 1320 503333452 503334791 0 2141
7 TraesCS4A01G152500 chr3A 95.921 2770 84 7 1 2744 105559634 105556868 0 4462
8 TraesCS4A01G152500 chr1B 95.764 2762 94 8 1 2744 633714304 633717060 0 4431
9 TraesCS4A01G152500 chr1D 96.167 2713 88 9 35 2744 254456798 254459497 0 4420
10 TraesCS4A01G152500 chr1D 94.899 2764 111 10 1 2744 51834624 51831871 0 4296
11 TraesCS4A01G152500 chr1D 96.092 1612 42 3 1 1592 254453963 254455573 0 2608
12 TraesCS4A01G152500 chr1A 95.567 2504 85 7 1 2481 554479583 554482083 0 3986
13 TraesCS4A01G152500 chr3B 95.664 2214 73 5 552 2744 101922754 101924965 0 3535
14 TraesCS4A01G152500 chr7B 95.350 2129 81 3 632 2744 662757072 662754946 0 3367


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 TraesCS4A01G152500 chr4A 309446319 309449062 2743 True 5068 5068 100.0000 1 2744 1 chr4A.!!$R1 2743
1 TraesCS4A01G152500 chr5D 6253187 6255938 2751 True 4510 4510 96.2990 1 2744 1 chr5D.!!$R1 2743
2 TraesCS4A01G152500 chr5D 503310832 503313591 2759 False 4362 4362 95.3030 1 2744 1 chr5D.!!$F2 2743
3 TraesCS4A01G152500 chr5D 329125818 329128559 2741 True 4235 4235 94.5810 1 2744 1 chr5D.!!$R2 2743
4 TraesCS4A01G152500 chr5D 503333452 503339529 6077 False 3263 4385 95.7705 1 2744 2 chr5D.!!$F3 2743
5 TraesCS4A01G152500 chr5D 481592288 481593899 1611 False 2593 2593 95.9080 1 1592 1 chr5D.!!$F1 1591
6 TraesCS4A01G152500 chr3A 105556868 105559634 2766 True 4462 4462 95.9210 1 2744 1 chr3A.!!$R1 2743
7 TraesCS4A01G152500 chr1B 633714304 633717060 2756 False 4431 4431 95.7640 1 2744 1 chr1B.!!$F1 2743
8 TraesCS4A01G152500 chr1D 51831871 51834624 2753 True 4296 4296 94.8990 1 2744 1 chr1D.!!$R1 2743
9 TraesCS4A01G152500 chr1D 254453963 254459497 5534 False 3514 4420 96.1295 1 2744 2 chr1D.!!$F1 2743
10 TraesCS4A01G152500 chr1A 554479583 554482083 2500 False 3986 3986 95.5670 1 2481 1 chr1A.!!$F1 2480
11 TraesCS4A01G152500 chr3B 101922754 101924965 2211 False 3535 3535 95.6640 552 2744 1 chr3B.!!$F1 2192
12 TraesCS4A01G152500 chr7B 662754946 662757072 2126 True 3367 3367 95.3500 632 2744 1 chr7B.!!$R1 2112

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
782 786 0.314935 AATTCTTGGGCAACTGCGTG 59.685 50.0 0.0 0.0 43.26 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 8485 1.077787 CCTACGGCCAATCCAGCAA 60.078 57.895 2.24 0.0 34.01 3.91 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
309 312 0.620030 TCAGCTGCAATAAGGGCTCA 59.380 50.000 9.47 0.00 32.30 4.26
404 407 8.764524 TTCTCAATTTAGAGACTTAAGAGCAC 57.235 34.615 10.09 0.00 43.91 4.40
525 529 5.991933 ATATATGACGAGATTGCCAGACT 57.008 39.130 0.00 0.00 0.00 3.24
536 540 1.511850 TGCCAGACTTTGTGATCGTG 58.488 50.000 0.00 0.00 0.00 4.35
584 588 4.644685 GCTCTTAGGGAATGTGCCATTTTA 59.355 41.667 2.53 0.00 0.00 1.52
670 674 4.103627 TCCAGCCAATGATGACACTATGAT 59.896 41.667 0.00 0.00 0.00 2.45
719 723 9.533831 AAATTAGTATTTTCAATCTGTGAGGGT 57.466 29.630 0.00 0.00 37.61 4.34
731 735 2.680841 CTGTGAGGGTCGTTCTCTCTAG 59.319 54.545 10.43 6.37 43.66 2.43
742 746 7.013464 GGGTCGTTCTCTCTAGATAAGAAATCA 59.987 40.741 15.59 4.51 32.46 2.57
782 786 0.314935 AATTCTTGGGCAACTGCGTG 59.685 50.000 0.00 0.00 43.26 5.34
1035 1572 7.360113 ACCTTGTTCCATTAAAACACTCAAT 57.640 32.000 0.00 0.00 36.41 2.57
1053 1590 9.031537 ACACTCAATGGGTTATACGATATATCA 57.968 33.333 13.11 0.00 0.00 2.15
1093 1630 6.322201 CCAACACTTCTATTGGCAAATAGGAT 59.678 38.462 18.86 4.27 43.75 3.24
1193 1730 1.633432 TCGGAATCCACAAACCATCCT 59.367 47.619 0.00 0.00 0.00 3.24
1197 1734 3.562176 GGAATCCACAAACCATCCTGACT 60.562 47.826 0.00 0.00 0.00 3.41
1201 1738 2.487086 CCACAAACCATCCTGACTGACA 60.487 50.000 0.00 0.00 0.00 3.58
1276 1813 6.590068 ACTCAGATTGGAGAAGAATATGGTG 58.410 40.000 0.00 0.00 38.30 4.17
1443 1981 0.099968 TACTCACGTCAGCGGCATAC 59.900 55.000 1.45 0.00 43.45 2.39
1451 1989 2.607635 CGTCAGCGGCATACTTTTATGT 59.392 45.455 1.45 0.00 37.92 2.29
1547 2085 8.697507 AACATCCTAGAAGATTTCACAAAACT 57.302 30.769 0.00 0.00 0.00 2.66
1581 4918 4.332819 AGCTTTCGACTTTTCGGGAATATG 59.667 41.667 0.00 0.00 45.90 1.78
1608 7726 4.724036 GCGGATGAATTAGTCGTTGTTGTC 60.724 45.833 0.00 0.00 0.00 3.18
1679 7797 8.826710 TCTTGGATTATTTACAAGCAGTATTCG 58.173 33.333 0.00 0.00 40.93 3.34
1708 7826 2.515926 TTTTGCAACATTAGCCGCAA 57.484 40.000 0.00 0.00 42.29 4.85
1711 7829 1.175347 TGCAACATTAGCCGCAACCA 61.175 50.000 0.00 0.00 0.00 3.67
1991 8114 9.268282 TGTCTATAAGTGGAGTCCTCTTTTATT 57.732 33.333 26.93 14.45 38.19 1.40
1992 8115 9.535878 GTCTATAAGTGGAGTCCTCTTTTATTG 57.464 37.037 26.93 17.30 38.19 1.90
2007 8130 9.860898 CCTCTTTTATTGAGGTTTCCATTTTAG 57.139 33.333 0.00 0.00 44.42 1.85
2241 8378 3.922171 ACTTCTCCCCAATAGAGCTTG 57.078 47.619 0.00 0.00 0.00 4.01
2283 8420 7.893302 TGGTTGATTGTATCCTTAACCATTTCT 59.107 33.333 0.00 0.00 41.68 2.52
2310 8449 0.750249 TGACACGAGGAACTGCTCAA 59.250 50.000 0.00 0.00 41.55 3.02
2328 8467 5.711506 TGCTCAACATGAATCCACTAATTGT 59.288 36.000 0.00 0.00 0.00 2.71
2339 8478 7.446931 TGAATCCACTAATTGTTGTTGCTTCTA 59.553 33.333 0.00 0.00 0.00 2.10
2384 8523 2.172717 GGGCTTGCTTCTATTGGACCTA 59.827 50.000 0.00 0.00 0.00 3.08
2406 8545 1.768870 AGTTGGTCAAGGTACTGCTGT 59.231 47.619 0.66 0.66 40.86 4.40
2415 8554 2.890814 AGGTACTGCTGTAGGACAAGT 58.109 47.619 10.37 0.00 42.48 3.16
2527 8666 2.479566 ATGGACTAGTTGTGGCACTG 57.520 50.000 19.83 6.42 0.00 3.66
2529 8668 0.396811 GGACTAGTTGTGGCACTGGT 59.603 55.000 19.83 6.63 40.92 4.00
2721 8863 7.079700 TCAGGACAGATAATACCCCATTCTAA 58.920 38.462 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 84 5.255397 ACCATGACCAAAATGAACTCCTA 57.745 39.130 0.00 0.00 0.00 2.94
414 418 6.131904 TGGGAGATGGTGGAATTTTCCCAT 62.132 45.833 5.28 4.19 45.79 4.00
584 588 7.783596 TCGACTAAAGAAATAGTAGGAATCCCT 59.216 37.037 0.00 0.00 46.62 4.20
618 622 3.518998 CGCGAGATCCGGGTCACT 61.519 66.667 19.03 0.00 44.85 3.41
656 660 8.667076 ATCGAATTGAAATCATAGTGTCATCA 57.333 30.769 0.00 0.00 0.00 3.07
691 695 9.793252 CCTCACAGATTGAAAATACTAATTTGG 57.207 33.333 0.00 0.00 35.46 3.28
710 714 1.540267 AGAGAGAACGACCCTCACAG 58.460 55.000 0.00 0.00 33.25 3.66
719 723 9.958234 CAATGATTTCTTATCTAGAGAGAACGA 57.042 33.333 16.71 7.71 34.61 3.85
762 766 0.314935 ACGCAGTTGCCCAAGAATTG 59.685 50.000 0.00 0.00 43.33 2.32
1035 1572 8.330993 TCTACACCTGATATATCGTATAACCCA 58.669 37.037 8.19 0.00 0.00 4.51
1053 1590 2.302157 GTGTTGGCCTACTTCTACACCT 59.698 50.000 18.31 0.00 34.98 4.00
1093 1630 3.390639 ACTTGGGCATGAATTTGGAAACA 59.609 39.130 0.00 0.00 39.83 2.83
1197 1734 8.859090 ACATATTCCAAAAATTTCTGACTGTCA 58.141 29.630 10.50 10.50 0.00 3.58
1215 1752 7.494625 TCTCGAATAAACACAAGGACATATTCC 59.505 37.037 0.00 0.00 46.33 3.01
1229 1766 6.260050 AGTTTTGCTCAAGTCTCGAATAAACA 59.740 34.615 0.00 0.00 0.00 2.83
1323 1861 1.995376 AAAGAGCACCCGACCAAATT 58.005 45.000 0.00 0.00 0.00 1.82
1547 2085 7.766219 AAAAGTCGAAAGCTAAGCGATAATA 57.234 32.000 8.42 0.00 36.37 0.98
1581 4918 2.277084 ACGACTAATTCATCCGCCAAC 58.723 47.619 0.00 0.00 0.00 3.77
1608 7726 5.877491 ACTAAGGGGACTAAAGAAACAAGG 58.123 41.667 0.00 0.00 42.68 3.61
1679 7797 6.254373 GGCTAATGTTGCAAAAATAAGAGCTC 59.746 38.462 5.27 5.27 29.43 4.09
1708 7826 5.014544 CCTCCATGGATTCACCTATATTGGT 59.985 44.000 16.63 2.68 38.41 3.67
1711 7829 5.173246 ACCCTCCATGGATTCACCTATATT 58.827 41.667 16.63 0.00 39.86 1.28
1775 7898 4.202121 CCATGCATGAATTGAGCTAAGCTT 60.202 41.667 28.31 3.48 39.88 3.74
1838 7961 7.932335 ACTCTAGGCTATATATTCATACGCAC 58.068 38.462 0.00 0.00 0.00 5.34
1905 8028 7.770897 CCACCCTCCTTAATGCATATATACTTC 59.229 40.741 0.00 0.00 0.00 3.01
1991 8114 5.083122 TCATTGCCTAAAATGGAAACCTCA 58.917 37.500 0.00 0.00 37.98 3.86
1992 8115 5.659440 TCATTGCCTAAAATGGAAACCTC 57.341 39.130 0.00 0.00 37.98 3.85
2002 8125 8.287439 TCGGATTCTAAAATCATTGCCTAAAA 57.713 30.769 1.05 0.00 42.66 1.52
2007 8130 6.738114 TGAATCGGATTCTAAAATCATTGCC 58.262 36.000 26.15 1.74 42.66 4.52
2129 8266 7.845537 AAGGGAATTCCATATCCATATACCA 57.154 36.000 25.67 0.00 37.46 3.25
2155 8292 5.801350 ATGTGAATTGTCCGAACTACATG 57.199 39.130 0.00 0.00 0.00 3.21
2213 8350 6.098552 GCTCTATTGGGGAGAAGTAAAGTAGT 59.901 42.308 0.00 0.00 33.03 2.73
2214 8351 6.325286 AGCTCTATTGGGGAGAAGTAAAGTAG 59.675 42.308 0.00 0.00 33.03 2.57
2305 8444 6.199937 ACAATTAGTGGATTCATGTTGAGC 57.800 37.500 0.00 0.00 0.00 4.26
2310 8449 6.015180 AGCAACAACAATTAGTGGATTCATGT 60.015 34.615 0.00 0.00 0.00 3.21
2328 8467 6.208402 TCCAGCAACAATAATAGAAGCAACAA 59.792 34.615 0.00 0.00 0.00 2.83
2339 8478 2.101249 CGGCCAATCCAGCAACAATAAT 59.899 45.455 2.24 0.00 34.01 1.28
2346 8485 1.077787 CCTACGGCCAATCCAGCAA 60.078 57.895 2.24 0.00 34.01 3.91
2384 8523 2.037772 CAGCAGTACCTTGACCAACTCT 59.962 50.000 0.00 0.00 0.00 3.24
2406 8545 6.403878 GCAATACCTTCTACAACTTGTCCTA 58.596 40.000 0.00 0.00 0.00 2.94
2415 8554 4.744570 CTGTCTCGCAATACCTTCTACAA 58.255 43.478 0.00 0.00 0.00 2.41
2446 8585 9.605275 AATAAAGTACCTCGTATTTTACCTTCC 57.395 33.333 2.74 0.00 34.66 3.46
2527 8666 2.029380 AGGGTTCGCAAATAAAAGCACC 60.029 45.455 0.00 0.00 0.00 5.01
2529 8668 4.329462 AAAGGGTTCGCAAATAAAAGCA 57.671 36.364 0.00 0.00 0.00 3.91
2698 8840 7.313731 TCTTAGAATGGGGTATTATCTGTCCT 58.686 38.462 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.