Multiple sequence alignment - TraesCS7A01G316400

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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 TraesCS7A01G316400 chr7A 100.000 2513 0 0 1 2513 452019733 452022245 0 4641
1 TraesCS7A01G316400 chr7A 95.998 2524 81 8 1 2513 165281046 165283560 0 4084
2 TraesCS7A01G316400 chr1A 96.560 2529 65 13 1 2513 517446950 517444428 0 4169
3 TraesCS7A01G316400 chr1A 95.687 2527 78 17 3 2513 257591377 257588866 0 4034
4 TraesCS7A01G316400 chr4A 96.160 2500 73 11 3 2485 9466890 9469383 0 4063
5 TraesCS7A01G316400 chr4A 96.181 1152 31 4 1372 2513 246821742 246820594 0 1871
6 TraesCS7A01G316400 chr4A 94.127 664 23 4 1866 2513 45633295 45633958 0 996
7 TraesCS7A01G316400 chr2A 95.606 2526 86 12 1 2513 596742733 596740220 0 4026
8 TraesCS7A01G316400 chr2A 94.127 664 22 5 1866 2513 677263923 677264585 0 994
9 TraesCS7A01G316400 chr6A 95.604 2525 86 10 1 2513 357526638 357524127 0 4024
10 TraesCS7A01G316400 chr6A 95.642 2524 79 16 3 2513 468224303 468226808 0 4023
11 TraesCS7A01G316400 chr6A 95.525 2525 93 10 1 2513 251355324 251352808 0 4019
12 TraesCS7A01G316400 chr6A 95.134 2528 94 13 1 2513 509013987 509011474 0 3960
13 TraesCS7A01G316400 chr6A 95.797 2427 78 13 3 2415 356473981 356471565 0 3895
14 TraesCS7A01G316400 chr2B 95.444 2546 75 13 1 2513 143026812 143024275 0 4021
15 TraesCS7A01G316400 chr1B 95.169 2546 84 13 1 2513 592010706 592013245 0 3984
16 TraesCS7A01G316400 chr3B 95.008 2544 89 15 3 2513 577659244 577661782 0 3960


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 TraesCS7A01G316400 chr7A 452019733 452022245 2512 False 4641 4641 100.000 1 2513 1 chr7A.!!$F2 2512
1 TraesCS7A01G316400 chr7A 165281046 165283560 2514 False 4084 4084 95.998 1 2513 1 chr7A.!!$F1 2512
2 TraesCS7A01G316400 chr1A 517444428 517446950 2522 True 4169 4169 96.560 1 2513 1 chr1A.!!$R2 2512
3 TraesCS7A01G316400 chr1A 257588866 257591377 2511 True 4034 4034 95.687 3 2513 1 chr1A.!!$R1 2510
4 TraesCS7A01G316400 chr4A 9466890 9469383 2493 False 4063 4063 96.160 3 2485 1 chr4A.!!$F1 2482
5 TraesCS7A01G316400 chr4A 246820594 246821742 1148 True 1871 1871 96.181 1372 2513 1 chr4A.!!$R1 1141
6 TraesCS7A01G316400 chr4A 45633295 45633958 663 False 996 996 94.127 1866 2513 1 chr4A.!!$F2 647
7 TraesCS7A01G316400 chr2A 596740220 596742733 2513 True 4026 4026 95.606 1 2513 1 chr2A.!!$R1 2512
8 TraesCS7A01G316400 chr2A 677263923 677264585 662 False 994 994 94.127 1866 2513 1 chr2A.!!$F1 647
9 TraesCS7A01G316400 chr6A 357524127 357526638 2511 True 4024 4024 95.604 1 2513 1 chr6A.!!$R3 2512
10 TraesCS7A01G316400 chr6A 468224303 468226808 2505 False 4023 4023 95.642 3 2513 1 chr6A.!!$F1 2510
11 TraesCS7A01G316400 chr6A 251352808 251355324 2516 True 4019 4019 95.525 1 2513 1 chr6A.!!$R1 2512
12 TraesCS7A01G316400 chr6A 509011474 509013987 2513 True 3960 3960 95.134 1 2513 1 chr6A.!!$R4 2512
13 TraesCS7A01G316400 chr6A 356471565 356473981 2416 True 3895 3895 95.797 3 2415 1 chr6A.!!$R2 2412
14 TraesCS7A01G316400 chr2B 143024275 143026812 2537 True 4021 4021 95.444 1 2513 1 chr2B.!!$R1 2512
15 TraesCS7A01G316400 chr1B 592010706 592013245 2539 False 3984 3984 95.169 1 2513 1 chr1B.!!$F1 2512
16 TraesCS7A01G316400 chr3B 577659244 577661782 2538 False 3960 3960 95.008 3 2513 1 chr3B.!!$F1 2510

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
966 991 0.969409 CGACCTCCTCGTTAACCCCT 60.969 60.0 0.0 0.0 37.64 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2468 2557 2.55567 CCCGAGCTAGCTACCCTATCTT 60.556 54.545 19.38 0.0 0.0 2.4 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
105 106 5.809001 ACTCACTCCAAAATGAAGCTATGA 58.191 37.500 0.00 0.00 0.00 2.15
109 110 6.372659 TCACTCCAAAATGAAGCTATGAAGAC 59.627 38.462 0.00 0.00 0.00 3.01
120 121 8.627208 TGAAGCTATGAAGACTTTTCTGATTT 57.373 30.769 0.00 0.00 29.98 2.17
121 122 9.071276 TGAAGCTATGAAGACTTTTCTGATTTT 57.929 29.630 0.00 0.00 29.98 1.82
210 215 5.528690 TGTTCATAGGTGATAGCTCATTTGC 59.471 40.000 0.00 0.00 33.56 3.68
288 298 7.657354 TCATAACCTTGTCACATATGATGCTAC 59.343 37.037 10.38 0.76 37.14 3.58
314 325 5.750547 TGCGCAAGAATTACAACATTTTGAA 59.249 32.000 8.16 0.00 43.02 2.69
315 326 6.423302 TGCGCAAGAATTACAACATTTTGAAT 59.577 30.769 8.16 0.00 43.02 2.57
718 742 5.575157 TCTGCCCCACTTTACATATGAAAA 58.425 37.500 10.38 0.29 0.00 2.29
799 823 7.651304 TCAAACTACAAAATACAATGTGGCAAG 59.349 33.333 0.00 0.00 31.91 4.01
894 918 5.045578 CCTCTGTTTCTTTCCCCATCTTCTA 60.046 44.000 0.00 0.00 0.00 2.10
903 927 7.189794 TCTTTCCCCATCTTCTAGTTCTTCTA 58.810 38.462 0.00 0.00 0.00 2.10
913 937 5.680594 TCTAGTTCTTCTACCTCTCGAGT 57.319 43.478 13.13 0.00 0.00 4.18
923 948 6.003859 TCTACCTCTCGAGTAATTCCTCTT 57.996 41.667 13.13 0.00 0.00 2.85
961 986 4.825546 GATATGTCGACCTCCTCGTTAA 57.174 45.455 14.12 0.00 43.45 2.01
966 991 0.969409 CGACCTCCTCGTTAACCCCT 60.969 60.000 0.00 0.00 37.64 4.79
1028 1053 2.665000 CACTGACTGCCCACGGAT 59.335 61.111 0.00 0.00 0.00 4.18
1130 1155 1.501582 GAGGGGCAGGTTAGATCTGT 58.498 55.000 5.18 0.00 34.89 3.41
2098 2133 8.602424 TCATGATTAGAAAAAGAGGTCTAACCA 58.398 33.333 0.00 0.00 41.95 3.67
2110 2155 7.939784 AGAGGTCTAACCAATAATTCAAACC 57.060 36.000 0.00 0.00 41.95 3.27
2232 2311 6.566197 AAAATACAGAGCTCTCAAACCAAG 57.434 37.500 14.96 2.23 0.00 3.61
2234 2313 1.771255 ACAGAGCTCTCAAACCAAGGT 59.229 47.619 14.96 2.14 0.00 3.50
2235 2314 2.173569 ACAGAGCTCTCAAACCAAGGTT 59.826 45.455 14.96 0.00 40.45 3.50
2290 2369 9.679661 TTTAGAAGGCATCTATAAACACATCAA 57.320 29.630 0.00 0.00 40.32 2.57
2502 2591 1.817520 CTCGGGCAACACACACACA 60.818 57.895 0.00 0.00 39.74 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
210 215 6.917477 TCATTTTCATGGAAAAAGTCTTCACG 59.083 34.615 2.57 0.0 43.32 4.35
288 298 2.308347 TGTTGTAATTCTTGCGCACG 57.692 45.000 11.12 9.2 0.00 5.34
718 742 4.380444 GGTGGTCATGTGCGAAAAATACAT 60.380 41.667 0.00 0.0 35.56 2.29
799 823 4.039366 AGAAGGGGAAGCTATATTGACGAC 59.961 45.833 0.00 0.0 0.00 4.34
894 918 6.319405 GGAATTACTCGAGAGGTAGAAGAACT 59.681 42.308 21.68 0.0 0.00 3.01
903 927 6.211785 AGAAAAAGAGGAATTACTCGAGAGGT 59.788 38.462 21.68 0.0 42.31 3.85
959 984 0.616371 CCACATGGAACGAGGGGTTA 59.384 55.000 0.00 0.0 39.50 2.85
961 986 3.077907 CCACATGGAACGAGGGGT 58.922 61.111 0.00 0.0 37.39 4.95
966 991 3.632080 ACCGGCCACATGGAACGA 61.632 61.111 14.60 0.0 38.71 3.85
1034 1059 1.610038 TCGAAGTCAACCGCTTCAGTA 59.390 47.619 5.99 0.0 41.61 2.74
1130 1155 4.843728 AGATAAAGGATGCGAGGAAAACA 58.156 39.130 0.00 0.0 0.00 2.83
1838 1866 4.091939 GGGCCCGCGAACTAGGTT 62.092 66.667 5.69 0.0 0.00 3.50
2043 2077 5.484715 TGGTTCGCTAGGCATAATAATACC 58.515 41.667 0.00 0.0 0.00 2.73
2468 2557 2.555670 CCCGAGCTAGCTACCCTATCTT 60.556 54.545 19.38 0.0 0.00 2.40


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

AutoCloner maintained by Alex Coulton.