Multiple sequence alignment - TraesCS3B01G226700

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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 TraesCS3B01G226700 chr3B 100.000 3044 0 0 1 3044 317616047 317619090 0.000000e+00 5622
1 TraesCS3B01G226700 chr3B 95.975 2534 84 5 529 3044 195343862 195346395 0.000000e+00 4098
2 TraesCS3B01G226700 chr3B 95.589 2539 89 7 529 3044 203647852 203650390 0.000000e+00 4047
3 TraesCS3B01G226700 chr3B 95.539 2533 95 5 530 3044 368101098 368098566 0.000000e+00 4036
4 TraesCS3B01G226700 chr3B 95.366 2525 105 4 529 3044 707434620 707437141 0.000000e+00 4004
5 TraesCS3B01G226700 chr7B 95.975 2534 84 6 529 3044 257658962 257661495 0.000000e+00 4098
6 TraesCS3B01G226700 chr7B 90.943 530 34 4 4 520 658404777 658404249 0.000000e+00 701
7 TraesCS3B01G226700 chr2B 95.856 2534 87 5 529 3044 614910399 614912932 0.000000e+00 4082
8 TraesCS3B01G226700 chr2B 95.422 2534 97 6 529 3044 146974188 146976720 0.000000e+00 4019
9 TraesCS3B01G226700 chr2B 94.216 536 15 2 1 520 614909538 614910073 0.000000e+00 804
10 TraesCS3B01G226700 chr1B 95.817 2534 84 7 529 3044 452747452 452744923 0.000000e+00 4072
11 TraesCS3B01G226700 chr1B 95.432 1620 53 7 529 2130 161548130 161546514 0.000000e+00 2562
12 TraesCS3B01G226700 chr1B 94.860 856 30 4 529 1370 328125222 328124367 0.000000e+00 1325
13 TraesCS3B01G226700 chr1B 94.216 536 15 2 1 520 143632863 143633398 0.000000e+00 804
14 TraesCS3B01G226700 chr1B 93.494 538 19 2 4 525 524297713 524298250 0.000000e+00 785
15 TraesCS3B01G226700 chr1B 91.887 530 30 6 4 520 585899388 585899917 0.000000e+00 728
16 TraesCS3B01G226700 chr1B 91.103 517 35 2 4 518 451916914 451916407 0.000000e+00 689
17 TraesCS3B01G226700 chr4B 95.817 2534 78 7 529 3044 522691258 522693781 0.000000e+00 4067
18 TraesCS3B01G226700 chr4B 81.853 529 60 14 4 524 559865819 559865319 2.180000e-111 412
19 TraesCS3B01G226700 chr6B 95.656 2532 92 5 529 3042 240330063 240327532 0.000000e+00 4050
20 TraesCS3B01G226700 chr6B 95.494 2530 100 5 529 3044 637030073 637032602 0.000000e+00 4028
21 TraesCS3B01G226700 chr6B 94.270 541 15 2 1 525 240330939 240330399 0.000000e+00 813
22 TraesCS3B01G226700 chr6B 90.943 530 35 8 4 520 646219676 646219147 0.000000e+00 701
23 TraesCS3B01G226700 chr5A 90.433 2540 223 9 524 3044 457884673 457887211 0.000000e+00 3326
24 TraesCS3B01G226700 chrUn 93.962 530 21 4 1 523 119054314 119053789 0.000000e+00 791


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 TraesCS3B01G226700 chr3B 317616047 317619090 3043 False 5622.0 5622 100.000 1 3044 1 chr3B.!!$F3 3043
1 TraesCS3B01G226700 chr3B 195343862 195346395 2533 False 4098.0 4098 95.975 529 3044 1 chr3B.!!$F1 2515
2 TraesCS3B01G226700 chr3B 203647852 203650390 2538 False 4047.0 4047 95.589 529 3044 1 chr3B.!!$F2 2515
3 TraesCS3B01G226700 chr3B 368098566 368101098 2532 True 4036.0 4036 95.539 530 3044 1 chr3B.!!$R1 2514
4 TraesCS3B01G226700 chr3B 707434620 707437141 2521 False 4004.0 4004 95.366 529 3044 1 chr3B.!!$F4 2515
5 TraesCS3B01G226700 chr7B 257658962 257661495 2533 False 4098.0 4098 95.975 529 3044 1 chr7B.!!$F1 2515
6 TraesCS3B01G226700 chr7B 658404249 658404777 528 True 701.0 701 90.943 4 520 1 chr7B.!!$R1 516
7 TraesCS3B01G226700 chr2B 146974188 146976720 2532 False 4019.0 4019 95.422 529 3044 1 chr2B.!!$F1 2515
8 TraesCS3B01G226700 chr2B 614909538 614912932 3394 False 2443.0 4082 95.036 1 3044 2 chr2B.!!$F2 3043
9 TraesCS3B01G226700 chr1B 452744923 452747452 2529 True 4072.0 4072 95.817 529 3044 1 chr1B.!!$R4 2515
10 TraesCS3B01G226700 chr1B 161546514 161548130 1616 True 2562.0 2562 95.432 529 2130 1 chr1B.!!$R1 1601
11 TraesCS3B01G226700 chr1B 328124367 328125222 855 True 1325.0 1325 94.860 529 1370 1 chr1B.!!$R2 841
12 TraesCS3B01G226700 chr1B 143632863 143633398 535 False 804.0 804 94.216 1 520 1 chr1B.!!$F1 519
13 TraesCS3B01G226700 chr1B 524297713 524298250 537 False 785.0 785 93.494 4 525 1 chr1B.!!$F2 521
14 TraesCS3B01G226700 chr1B 585899388 585899917 529 False 728.0 728 91.887 4 520 1 chr1B.!!$F3 516
15 TraesCS3B01G226700 chr1B 451916407 451916914 507 True 689.0 689 91.103 4 518 1 chr1B.!!$R3 514
16 TraesCS3B01G226700 chr4B 522691258 522693781 2523 False 4067.0 4067 95.817 529 3044 1 chr4B.!!$F1 2515
17 TraesCS3B01G226700 chr4B 559865319 559865819 500 True 412.0 412 81.853 4 524 1 chr4B.!!$R1 520
18 TraesCS3B01G226700 chr6B 637030073 637032602 2529 False 4028.0 4028 95.494 529 3044 1 chr6B.!!$F1 2515
19 TraesCS3B01G226700 chr6B 240327532 240330939 3407 True 2431.5 4050 94.963 1 3042 2 chr6B.!!$R2 3041
20 TraesCS3B01G226700 chr6B 646219147 646219676 529 True 701.0 701 90.943 4 520 1 chr6B.!!$R1 516
21 TraesCS3B01G226700 chr5A 457884673 457887211 2538 False 3326.0 3326 90.433 524 3044 1 chr5A.!!$F1 2520
22 TraesCS3B01G226700 chrUn 119053789 119054314 525 True 791.0 791 93.962 1 523 1 chrUn.!!$R1 522

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
632 982 2.494918 GCCACATACGACGGCTCT 59.505 61.111 0.0 0.0 42.78 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 2594 0.036952 CATGTGCCGTCTGACTTCCT 60.037 55.0 6.21 0.0 0.0 3.36 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
632 982 2.494918 GCCACATACGACGGCTCT 59.505 61.111 0.00 0.00 42.78 4.09
1126 1481 4.767255 CCCAGCTGTCTCCGGCAC 62.767 72.222 13.81 0.00 45.95 5.01
1127 1482 3.699894 CCAGCTGTCTCCGGCACT 61.700 66.667 13.81 0.00 45.95 4.40
1198 1562 1.668294 CTCACTCAGGCCGAACAGT 59.332 57.895 0.00 0.00 0.00 3.55
1290 1654 2.096174 CCTCTTCTACTTGGAGACGACG 59.904 54.545 0.00 0.00 0.00 5.12
1305 1669 1.296755 CGACGGACGAGACTGAGGAA 61.297 60.000 0.00 0.00 45.77 3.36
1308 1672 0.448593 CGGACGAGACTGAGGAAGAC 59.551 60.000 0.00 0.00 0.00 3.01
1742 2196 4.831155 TCCTATTCTATGGGATTTCGACGT 59.169 41.667 0.00 0.00 34.71 4.34
1882 2336 1.685421 GAGAGCCTCCTCCAGCAGT 60.685 63.158 0.00 0.00 38.96 4.40
2016 2516 1.980765 TGCAGAAGGATGAGTTGGAGT 59.019 47.619 0.00 0.00 0.00 3.85
2048 2548 1.006220 CATGCTCGCGGTAGGCATA 60.006 57.895 21.51 4.05 43.62 3.14
2094 2594 4.717629 CGCCGGTGCTTCTCGTCA 62.718 66.667 0.00 0.00 34.43 4.35
2322 2822 2.049433 ACGGCCACTTCGAGTTCG 60.049 61.111 2.24 0.00 41.45 3.95
2431 2931 5.927030 TGTGCTCGTTTTCTTTGATGATAC 58.073 37.500 0.00 0.00 0.00 2.24
2619 3119 3.825160 GACAAGGTGGCAGCCGTCA 62.825 63.158 23.95 0.00 0.00 4.35
2928 3428 2.664081 CCCCTCGCCTTCTTCAGCT 61.664 63.158 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
520 538 1.377202 GATGATGGTGCACCGTGGT 60.377 57.895 34.99 21.90 39.43 4.16
525 543 3.211963 GGCGGATGATGGTGCACC 61.212 66.667 29.67 29.67 0.00 5.01
632 982 1.290955 CCAGTTAAGCGGGTCGTCA 59.709 57.895 0.00 0.00 0.00 4.35
698 1048 0.537371 AAGCCAGCCAAGTACGCTTT 60.537 50.000 0.00 0.00 36.40 3.51
699 1049 0.955919 GAAGCCAGCCAAGTACGCTT 60.956 55.000 2.14 2.14 42.25 4.68
1091 1446 4.115199 GAAGCTGTCGGCCCCCAT 62.115 66.667 0.00 0.00 43.05 4.00
1115 1470 2.523168 TGGACAGTGCCGGAGACA 60.523 61.111 5.05 0.00 0.00 3.41
1191 1555 2.549282 CGGCGTTCCAACTGTTCG 59.451 61.111 0.00 0.00 0.00 3.95
1290 1654 1.200484 GTGTCTTCCTCAGTCTCGTCC 59.800 57.143 0.00 0.00 0.00 4.79
1305 1669 1.557269 GGCCATCCTCCAGTGTGTCT 61.557 60.000 0.00 0.00 0.00 3.41
1308 1672 3.408229 AGGCCATCCTCCAGTGTG 58.592 61.111 5.01 0.00 38.72 3.82
1742 2196 0.247460 CCAGAAGGTCATCGTCAGCA 59.753 55.000 0.00 0.00 0.00 4.41
1780 2234 4.358841 CCCAATGCCGTCCCACCA 62.359 66.667 0.00 0.00 0.00 4.17
1882 2336 1.138036 CGGTGAAGATGTCCGCGTA 59.862 57.895 4.92 0.00 37.90 4.42
2016 2516 3.051479 CATGAGCGCACACTGCCA 61.051 61.111 10.42 0.00 41.12 4.92
2041 2541 1.267121 GGAGAGCCGGATTATGCCTA 58.733 55.000 5.05 0.00 0.00 3.93
2048 2548 1.517832 CGAAGTGGAGAGCCGGATT 59.482 57.895 5.05 0.00 36.79 3.01
2094 2594 0.036952 CATGTGCCGTCTGACTTCCT 60.037 55.000 6.21 0.00 0.00 3.36
2431 2931 4.355437 CCAAGACGCACTGTAGATTAGAG 58.645 47.826 0.00 0.00 0.00 2.43
2534 3034 1.227263 CATCGAAGGCGTCCCGAAT 60.227 57.895 6.22 0.00 38.98 3.34


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

AutoCloner maintained by Alex Coulton.