Multiple sequence alignment - TraesCS2A01G360900

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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 TraesCS2A01G360900 chr2A 100.000 3752 0 0 1 3752 605129592 605125841 0.000000e+00 6929
1 TraesCS2A01G360900 chr2A 86.107 2764 339 34 1 2739 605398769 605401512 0.000000e+00 2935
2 TraesCS2A01G360900 chr2A 86.842 1786 203 16 1 1774 605188354 605186589 0.000000e+00 1967
3 TraesCS2A01G360900 chr2A 98.387 744 12 0 3009 3752 77190697 77191440 0.000000e+00 1308
4 TraesCS2A01G360900 chr2A 85.495 717 95 9 1 711 605171133 605170420 0.000000e+00 739
5 TraesCS2A01G360900 chr2A 81.358 692 110 15 2069 2752 605355066 605354386 2.550000e-151 545
6 TraesCS2A01G360900 chr2A 82.149 577 87 13 2069 2637 605355834 605355266 7.290000e-132 481
7 TraesCS2A01G360900 chr3A 98.540 3013 44 0 1 3013 727469673 727472685 0.000000e+00 5321
8 TraesCS2A01G360900 chr3A 87.032 2244 266 20 1 2236 727397792 727400018 0.000000e+00 2508
9 TraesCS2A01G360900 chr3D 94.702 3020 147 6 1 3012 597486949 597489963 0.000000e+00 4678
10 TraesCS2A01G360900 chr3D 85.305 1953 255 23 788 2729 597295750 597297681 0.000000e+00 1988
11 TraesCS2A01G360900 chr3D 86.623 1211 157 5 754 1961 597409428 597410636 0.000000e+00 1334
12 TraesCS2A01G360900 chr3D 87.607 702 82 4 1 699 597477796 597478495 0.000000e+00 809
13 TraesCS2A01G360900 chr3B 94.345 3024 152 10 1 3010 804237967 804240985 0.000000e+00 4619
14 TraesCS2A01G360900 chr3B 85.293 2781 357 42 1 2750 804130310 804133069 0.000000e+00 2822
15 TraesCS2A01G360900 chr3B 85.686 1998 262 16 744 2729 804228291 804230276 0.000000e+00 2084
16 TraesCS2A01G360900 chr3B 84.837 2051 280 26 709 2739 804170642 804172681 0.000000e+00 2036
17 TraesCS2A01G360900 chr3B 98.785 741 9 0 3012 3752 581686111 581685371 0.000000e+00 1319
18 TraesCS2A01G360900 chr3B 98.238 738 13 0 3015 3752 814705520 814704783 0.000000e+00 1291
19 TraesCS2A01G360900 chr3B 86.416 692 90 4 1 690 804168117 804168806 0.000000e+00 754
20 TraesCS2A01G360900 chr4A 98.789 743 8 1 3010 3752 543416599 543415858 0.000000e+00 1321
21 TraesCS2A01G360900 chr4A 98.255 745 13 0 3008 3752 597181342 597180598 0.000000e+00 1304
22 TraesCS2A01G360900 chr1A 98.649 740 8 1 3013 3752 50136872 50136135 0.000000e+00 1310
23 TraesCS2A01G360900 chr6B 98.507 737 11 0 3016 3752 279181213 279181949 0.000000e+00 1301
24 TraesCS2A01G360900 chr7A 98.374 738 12 0 3015 3752 652989376 652990113 0.000000e+00 1297
25 TraesCS2A01G360900 chr7A 98.113 742 13 1 3011 3752 27353717 27352977 0.000000e+00 1291


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 TraesCS2A01G360900 chr2A 605125841 605129592 3751 True 6929 6929 100.0000 1 3752 1 chr2A.!!$R1 3751
1 TraesCS2A01G360900 chr2A 605398769 605401512 2743 False 2935 2935 86.1070 1 2739 1 chr2A.!!$F2 2738
2 TraesCS2A01G360900 chr2A 605186589 605188354 1765 True 1967 1967 86.8420 1 1774 1 chr2A.!!$R3 1773
3 TraesCS2A01G360900 chr2A 77190697 77191440 743 False 1308 1308 98.3870 3009 3752 1 chr2A.!!$F1 743
4 TraesCS2A01G360900 chr2A 605170420 605171133 713 True 739 739 85.4950 1 711 1 chr2A.!!$R2 710
5 TraesCS2A01G360900 chr2A 605354386 605355834 1448 True 513 545 81.7535 2069 2752 2 chr2A.!!$R4 683
6 TraesCS2A01G360900 chr3A 727469673 727472685 3012 False 5321 5321 98.5400 1 3013 1 chr3A.!!$F2 3012
7 TraesCS2A01G360900 chr3A 727397792 727400018 2226 False 2508 2508 87.0320 1 2236 1 chr3A.!!$F1 2235
8 TraesCS2A01G360900 chr3D 597486949 597489963 3014 False 4678 4678 94.7020 1 3012 1 chr3D.!!$F4 3011
9 TraesCS2A01G360900 chr3D 597295750 597297681 1931 False 1988 1988 85.3050 788 2729 1 chr3D.!!$F1 1941
10 TraesCS2A01G360900 chr3D 597409428 597410636 1208 False 1334 1334 86.6230 754 1961 1 chr3D.!!$F2 1207
11 TraesCS2A01G360900 chr3D 597477796 597478495 699 False 809 809 87.6070 1 699 1 chr3D.!!$F3 698
12 TraesCS2A01G360900 chr3B 804237967 804240985 3018 False 4619 4619 94.3450 1 3010 1 chr3B.!!$F3 3009
13 TraesCS2A01G360900 chr3B 804130310 804133069 2759 False 2822 2822 85.2930 1 2750 1 chr3B.!!$F1 2749
14 TraesCS2A01G360900 chr3B 804228291 804230276 1985 False 2084 2084 85.6860 744 2729 1 chr3B.!!$F2 1985
15 TraesCS2A01G360900 chr3B 804168117 804172681 4564 False 1395 2036 85.6265 1 2739 2 chr3B.!!$F4 2738
16 TraesCS2A01G360900 chr3B 581685371 581686111 740 True 1319 1319 98.7850 3012 3752 1 chr3B.!!$R1 740
17 TraesCS2A01G360900 chr3B 814704783 814705520 737 True 1291 1291 98.2380 3015 3752 1 chr3B.!!$R2 737
18 TraesCS2A01G360900 chr4A 543415858 543416599 741 True 1321 1321 98.7890 3010 3752 1 chr4A.!!$R1 742
19 TraesCS2A01G360900 chr4A 597180598 597181342 744 True 1304 1304 98.2550 3008 3752 1 chr4A.!!$R2 744
20 TraesCS2A01G360900 chr1A 50136135 50136872 737 True 1310 1310 98.6490 3013 3752 1 chr1A.!!$R1 739
21 TraesCS2A01G360900 chr6B 279181213 279181949 736 False 1301 1301 98.5070 3016 3752 1 chr6B.!!$F1 736
22 TraesCS2A01G360900 chr7A 652989376 652990113 737 False 1297 1297 98.3740 3015 3752 1 chr7A.!!$F1 737
23 TraesCS2A01G360900 chr7A 27352977 27353717 740 True 1291 1291 98.1130 3011 3752 1 chr7A.!!$R1 741

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
212 213 0.105593 TCAGATCGCTGGGCAGATTC 59.894 55.000 0.0 0.0 42.53 2.52 F
988 2835 2.011222 GTTGTTTTGGTCACCACGAGA 58.989 47.619 0.0 0.0 30.78 4.04 F
1963 3816 0.179150 GCTGCCGTGTTTGTTGTCAA 60.179 50.000 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 3797 0.179150 TTGACAACAAACACGGCAGC 60.179 50.000 0.0 0.0 32.73 5.25 R
2294 4162 0.259938 ATGGAGTTCCCCAATCCAGC 59.740 55.000 0.0 0.0 45.89 4.85 R
3230 5900 1.901464 GGTGTTGATTGGTGCCGGT 60.901 57.895 1.9 0.0 0.00 5.28 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
120 121 4.145876 TCGATGACTTCATGTGCAAAAC 57.854 40.909 0.00 0.00 36.57 2.43
162 163 4.142038 ACTGGTTTTATCCAAGACACCAC 58.858 43.478 0.00 0.00 37.01 4.16
212 213 0.105593 TCAGATCGCTGGGCAGATTC 59.894 55.000 0.00 0.00 42.53 2.52
611 616 6.513180 TGTGAGTTAAATGTTCTTCTCGACT 58.487 36.000 0.00 0.00 0.00 4.18
988 2835 2.011222 GTTGTTTTGGTCACCACGAGA 58.989 47.619 0.00 0.00 30.78 4.04
1070 2917 6.318396 AGGATATTTTGCTCTGAAGAAGCTTC 59.682 38.462 19.11 19.11 0.00 3.86
1126 2973 3.054728 TCTCAAGAAGTGTGGTGGTTTGA 60.055 43.478 0.00 0.00 0.00 2.69
1962 3815 1.029408 AGCTGCCGTGTTTGTTGTCA 61.029 50.000 0.00 0.00 0.00 3.58
1963 3816 0.179150 GCTGCCGTGTTTGTTGTCAA 60.179 50.000 0.00 0.00 0.00 3.18
2062 3918 1.071299 ACGCTGCACACCTCAATCA 59.929 52.632 0.00 0.00 0.00 2.57
2091 3947 1.075600 GGGCCTAGGAGAGCTCACT 60.076 63.158 17.77 15.75 0.00 3.41
2294 4162 1.074951 GAATATCCCGGGCCCCAAG 59.925 63.158 18.49 4.88 0.00 3.61
2347 4215 6.118170 AGCTTGCATATCACTGTTGATAAGT 58.882 36.000 0.00 0.00 45.83 2.24
2592 5240 2.022129 GAAGGACGACAGCACCACG 61.022 63.158 0.00 0.00 0.00 4.94
2700 5354 1.001293 TCAGCCATTAGGAGCGCTATG 59.999 52.381 11.50 10.78 36.89 2.23
2907 5576 5.650266 TCTTTTTGTTGTAGCAAGACTTCCA 59.350 36.000 0.00 0.00 0.00 3.53
3062 5732 1.408969 ACAAAGCAACCAACCGGATT 58.591 45.000 9.46 0.00 35.59 3.01
3230 5900 1.293498 GCTCCAAGACTCCGAAGCA 59.707 57.895 0.00 0.00 0.00 3.91
3700 6370 1.814169 CGTAAAGCTCCCGCCTTCC 60.814 63.158 0.00 0.00 36.60 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 3.548818 CCTTGAAGTTTTGAGGCGTTGAG 60.549 47.826 0.00 0.00 0.00 3.02
212 213 2.350772 GCACAAGTTTCTTGATGTCCCG 60.351 50.000 15.04 0.00 0.00 5.14
950 2797 4.415150 ATGCCCCAGCCACAGTCG 62.415 66.667 0.00 0.00 38.69 4.18
988 2835 8.606830 ACTAAGAGGTTCCATTTCAAGAATACT 58.393 33.333 0.00 0.00 0.00 2.12
1003 2850 6.334102 TGAGTCTTCTTCACTAAGAGGTTC 57.666 41.667 0.00 0.00 42.60 3.62
1070 2917 2.830923 ACATCTCTGAGTTGACCTGGAG 59.169 50.000 19.66 0.00 0.00 3.86
1126 2973 5.829391 TGGATATGCTAATGATTGCAAGTGT 59.171 36.000 4.94 0.00 42.74 3.55
1944 3797 0.179150 TTGACAACAAACACGGCAGC 60.179 50.000 0.00 0.00 32.73 5.25
1962 3815 3.195396 ACGGCAGGTGAAAAATATGCATT 59.805 39.130 3.54 0.00 38.63 3.56
1963 3816 2.760092 ACGGCAGGTGAAAAATATGCAT 59.240 40.909 3.79 3.79 38.63 3.96
2062 3918 3.041946 CTCCTAGGCCCTTGATACTGTT 58.958 50.000 2.96 0.00 0.00 3.16
2120 3976 7.065120 TCCATGTCCACATTTTCAGAAAAAT 57.935 32.000 12.38 1.53 44.12 1.82
2131 3987 6.248433 AGTTTAGAACATCCATGTCCACATT 58.752 36.000 0.00 0.00 40.80 2.71
2294 4162 0.259938 ATGGAGTTCCCCAATCCAGC 59.740 55.000 0.00 0.00 45.89 4.85
2347 4215 7.861629 AGAATACCAACATCATCCTTGTCTAA 58.138 34.615 0.00 0.00 0.00 2.10
2700 5354 0.387929 CATGGCCAGGATGCATGTTC 59.612 55.000 13.35 0.00 31.97 3.18
3062 5732 2.494627 CCCCAGCACCTATCCCTGTATA 60.495 54.545 0.00 0.00 0.00 1.47
3230 5900 1.901464 GGTGTTGATTGGTGCCGGT 60.901 57.895 1.90 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.