Multiple sequence alignment - TraesCS7A01G057300

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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 TraesCS7A01G057300 chr7A 100.000 2909 0 0 1 2909 27539221 27542129 0.000000e+00 5373
1 TraesCS7A01G057300 chr7A 96.788 2273 63 4 646 2909 10616600 10614329 0.000000e+00 3784
2 TraesCS7A01G057300 chr7A 96.600 647 21 1 1 646 683022419 683021773 0.000000e+00 1072
3 TraesCS7A01G057300 chr6A 94.849 2291 67 11 646 2909 36425327 36423061 0.000000e+00 3530
4 TraesCS7A01G057300 chr6A 93.524 2131 74 19 811 2909 21289920 21287822 0.000000e+00 3112
5 TraesCS7A01G057300 chr6A 96.451 648 21 2 1 646 181456227 181455580 0.000000e+00 1068
6 TraesCS7A01G057300 chr6A 96.451 648 20 3 1 646 337682741 337682095 0.000000e+00 1066
7 TraesCS7A01G057300 chr3A 96.009 2180 65 7 646 2816 584282762 584284928 0.000000e+00 3524
8 TraesCS7A01G057300 chr3A 92.681 2309 97 22 646 2909 15355104 15357385 0.000000e+00 3262
9 TraesCS7A01G057300 chr3A 96.605 648 20 2 1 646 623765283 623764636 0.000000e+00 1074
10 TraesCS7A01G057300 chr3A 96.451 648 21 2 1 646 443708554 443709201 0.000000e+00 1068
11 TraesCS7A01G057300 chr3A 96.302 649 20 4 1 646 97463325 97462678 0.000000e+00 1062
12 TraesCS7A01G057300 chr4B 95.404 2154 75 7 646 2791 567645753 567647890 0.000000e+00 3408
13 TraesCS7A01G057300 chr5B 92.012 2316 108 27 646 2909 643322850 643320560 0.000000e+00 3181
14 TraesCS7A01G057300 chr5B 92.857 1498 65 8 1437 2908 607183674 607185155 0.000000e+00 2135
15 TraesCS7A01G057300 chr5B 88.642 810 63 20 646 1442 607064462 607065255 0.000000e+00 959
16 TraesCS7A01G057300 chr5B 88.272 810 66 19 646 1442 607119632 607120425 0.000000e+00 942
17 TraesCS7A01G057300 chr1D 91.029 2207 130 34 646 2821 78108614 78106445 0.000000e+00 2916
18 TraesCS7A01G057300 chr7D 91.971 2105 103 29 649 2724 35845991 35843924 0.000000e+00 2891
19 TraesCS7A01G057300 chr5A 96.560 1628 38 5 971 2592 44145593 44147208 0.000000e+00 2680
20 TraesCS7A01G057300 chr5A 96.600 647 21 1 1 646 697799112 697798466 0.000000e+00 1072
21 TraesCS7A01G057300 chr5A 89.943 348 12 4 2585 2909 44155993 44156340 7.450000e-116 427
22 TraesCS7A01G057300 chr4A 94.554 1726 58 7 1210 2909 707776348 707778063 0.000000e+00 2634
23 TraesCS7A01G057300 chr4A 96.319 652 21 3 1 650 12372373 12371723 0.000000e+00 1068
24 TraesCS7A01G057300 chr4A 95.874 509 18 1 646 1151 707775842 707776350 0.000000e+00 821
25 TraesCS7A01G057300 chr3B 93.732 1420 50 10 1513 2909 774142999 774141596 0.000000e+00 2093
26 TraesCS7A01G057300 chr1A 96.605 648 20 2 1 646 543612487 543611840 0.000000e+00 1074


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 TraesCS7A01G057300 chr7A 27539221 27542129 2908 False 5373.0 5373 100.000 1 2909 1 chr7A.!!$F1 2908
1 TraesCS7A01G057300 chr7A 10614329 10616600 2271 True 3784.0 3784 96.788 646 2909 1 chr7A.!!$R1 2263
2 TraesCS7A01G057300 chr7A 683021773 683022419 646 True 1072.0 1072 96.600 1 646 1 chr7A.!!$R2 645
3 TraesCS7A01G057300 chr6A 36423061 36425327 2266 True 3530.0 3530 94.849 646 2909 1 chr6A.!!$R2 2263
4 TraesCS7A01G057300 chr6A 21287822 21289920 2098 True 3112.0 3112 93.524 811 2909 1 chr6A.!!$R1 2098
5 TraesCS7A01G057300 chr6A 181455580 181456227 647 True 1068.0 1068 96.451 1 646 1 chr6A.!!$R3 645
6 TraesCS7A01G057300 chr6A 337682095 337682741 646 True 1066.0 1066 96.451 1 646 1 chr6A.!!$R4 645
7 TraesCS7A01G057300 chr3A 584282762 584284928 2166 False 3524.0 3524 96.009 646 2816 1 chr3A.!!$F3 2170
8 TraesCS7A01G057300 chr3A 15355104 15357385 2281 False 3262.0 3262 92.681 646 2909 1 chr3A.!!$F1 2263
9 TraesCS7A01G057300 chr3A 623764636 623765283 647 True 1074.0 1074 96.605 1 646 1 chr3A.!!$R2 645
10 TraesCS7A01G057300 chr3A 443708554 443709201 647 False 1068.0 1068 96.451 1 646 1 chr3A.!!$F2 645
11 TraesCS7A01G057300 chr3A 97462678 97463325 647 True 1062.0 1062 96.302 1 646 1 chr3A.!!$R1 645
12 TraesCS7A01G057300 chr4B 567645753 567647890 2137 False 3408.0 3408 95.404 646 2791 1 chr4B.!!$F1 2145
13 TraesCS7A01G057300 chr5B 643320560 643322850 2290 True 3181.0 3181 92.012 646 2909 1 chr5B.!!$R1 2263
14 TraesCS7A01G057300 chr5B 607183674 607185155 1481 False 2135.0 2135 92.857 1437 2908 1 chr5B.!!$F3 1471
15 TraesCS7A01G057300 chr5B 607064462 607065255 793 False 959.0 959 88.642 646 1442 1 chr5B.!!$F1 796
16 TraesCS7A01G057300 chr5B 607119632 607120425 793 False 942.0 942 88.272 646 1442 1 chr5B.!!$F2 796
17 TraesCS7A01G057300 chr1D 78106445 78108614 2169 True 2916.0 2916 91.029 646 2821 1 chr1D.!!$R1 2175
18 TraesCS7A01G057300 chr7D 35843924 35845991 2067 True 2891.0 2891 91.971 649 2724 1 chr7D.!!$R1 2075
19 TraesCS7A01G057300 chr5A 44145593 44147208 1615 False 2680.0 2680 96.560 971 2592 1 chr5A.!!$F1 1621
20 TraesCS7A01G057300 chr5A 697798466 697799112 646 True 1072.0 1072 96.600 1 646 1 chr5A.!!$R1 645
21 TraesCS7A01G057300 chr4A 707775842 707778063 2221 False 1727.5 2634 95.214 646 2909 2 chr4A.!!$F1 2263
22 TraesCS7A01G057300 chr4A 12371723 12372373 650 True 1068.0 1068 96.319 1 650 1 chr4A.!!$R1 649
23 TraesCS7A01G057300 chr3B 774141596 774142999 1403 True 2093.0 2093 93.732 1513 2909 1 chr3B.!!$R1 1396
24 TraesCS7A01G057300 chr1A 543611840 543612487 647 True 1074.0 1074 96.605 1 646 1 chr1A.!!$R1 645

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
842 854 0.240145 CGAGCTGACACCGTCTAACA 59.76 55.0 0.0 0.0 33.15 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2169 1.172175 CCTCTTTCTTTGCCAGCTCC 58.828 55.0 0.0 0.0 0.0 4.7 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
78 81 4.202264 ACACACGAGAACATCTCCTTCTTT 60.202 41.667 1.98 0.00 40.34 2.52
118 121 2.125912 CCTCGTCTCTTGCGGTGG 60.126 66.667 0.00 0.00 0.00 4.61
335 338 1.471287 CGAGTACGACTCCATCAACCA 59.529 52.381 8.73 0.00 42.12 3.67
404 408 1.153745 CTCTCCTTCCCTCGTTGCG 60.154 63.158 0.00 0.00 0.00 4.85
509 513 6.072618 GCTAGGTCTATGCGTAGTTTCTATGA 60.073 42.308 12.66 0.00 31.61 2.15
513 517 5.970023 GTCTATGCGTAGTTTCTATGAACGT 59.030 40.000 12.66 0.00 36.03 3.99
572 577 2.363788 TGCTTGCCGTTACTAGTCTG 57.636 50.000 0.00 0.00 0.00 3.51
651 656 0.532862 ACGTGAGACTGGTTTGCAGG 60.533 55.000 0.00 0.00 0.00 4.85
692 700 3.018423 AGGTTTGCAGGAAACACTCTT 57.982 42.857 18.24 0.00 45.15 2.85
693 701 2.952310 AGGTTTGCAGGAAACACTCTTC 59.048 45.455 18.24 1.13 45.15 2.87
694 702 2.952310 GGTTTGCAGGAAACACTCTTCT 59.048 45.455 18.24 0.00 45.15 2.85
776 787 1.197721 CTGTTCGGGCAGTTTAAGCAG 59.802 52.381 0.00 0.00 0.00 4.24
842 854 0.240145 CGAGCTGACACCGTCTAACA 59.760 55.000 0.00 0.00 33.15 2.41
864 876 2.913578 TACAGTGCGGACCGGTGT 60.914 61.111 14.63 3.89 0.00 4.16
919 941 2.419739 GCCCTCTCCTCTCGTCACC 61.420 68.421 0.00 0.00 0.00 4.02
941 963 2.172505 CTGCTCTCCTCTCCTCACTCTA 59.827 54.545 0.00 0.00 0.00 2.43
1171 1200 3.719268 TTATCTTTGCTTGCTCCTCCA 57.281 42.857 0.00 0.00 0.00 3.86
1333 1362 7.500992 TGTGCTAAGAAGGTATGATCCTTTAG 58.499 38.462 0.00 0.90 46.38 1.85
1351 1380 5.120830 CCTTTAGAAGTGAAGGTGTTCATCG 59.879 44.000 0.00 0.00 44.58 3.84
1400 1479 8.301720 GTTTGGTATTTCTTTACCTTTACCTGG 58.698 37.037 0.00 0.00 41.90 4.45
2046 2157 3.511934 CAGAGCTAGAAACTGTAGTGGGT 59.488 47.826 0.00 0.00 0.00 4.51
2058 2169 4.235360 CTGTAGTGGGTAACTTGAAGTCG 58.765 47.826 0.00 0.00 40.56 4.18
2084 2195 2.304180 TGGCAAAGAAAGAGGAGGAGAG 59.696 50.000 0.00 0.00 0.00 3.20
2284 2398 4.488770 AGAGGAGGAGAAGAAGAAGTTGT 58.511 43.478 0.00 0.00 0.00 3.32
2431 2548 6.017605 TCACATTTCTGAGCTTCAAAAGTCTC 60.018 38.462 0.00 0.00 34.43 3.36
2750 2867 7.373493 ACCTTCATGAATGTGAGTCAAATTTC 58.627 34.615 14.64 6.94 0.00 2.17
2871 3012 2.158249 TGGGGTTGGATCCAATTTGACA 60.158 45.455 29.37 19.76 38.28 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
404 408 8.592809 ACCAAGATCAATCTATGGAGTAATCTC 58.407 37.037 19.34 0.00 37.92 2.75
572 577 0.514691 GATGCCGCCGAATCAAGATC 59.485 55.000 0.00 0.00 0.00 2.75
651 656 3.733443 AAGCTGAAATGTGGTGGTTTC 57.267 42.857 0.00 0.00 35.45 2.78
692 700 4.142578 TGTTTTCTGCAGCAAAAACGTAGA 60.143 37.500 26.13 14.14 44.49 2.59
693 701 4.027702 GTGTTTTCTGCAGCAAAAACGTAG 60.028 41.667 26.13 5.08 44.49 3.51
694 702 3.854809 GTGTTTTCTGCAGCAAAAACGTA 59.145 39.130 26.13 14.89 44.49 3.57
776 787 3.046374 AGGGTCCCACCTGTCATAATAC 58.954 50.000 11.55 0.00 40.04 1.89
864 876 1.409064 CTGAGCTGGTTACTATCGGCA 59.591 52.381 0.00 0.00 37.71 5.69
873 885 2.222227 TGAGAGAGCTGAGCTGGTTA 57.778 50.000 13.71 0.00 39.88 2.85
919 941 0.033208 AGTGAGGAGAGGAGAGCAGG 60.033 60.000 0.00 0.00 0.00 4.85
941 963 2.732619 GGCGTCGGGGGAGAAGAAT 61.733 63.158 0.00 0.00 0.00 2.40
1333 1362 3.131396 ACACGATGAACACCTTCACTTC 58.869 45.455 0.00 0.00 39.28 3.01
1351 1380 3.293311 AGCACATTCAGCAATGAACAC 57.707 42.857 3.92 0.00 41.97 3.32
1400 1479 1.337071 CCATCTGATGACAAGGCATGC 59.663 52.381 18.92 9.90 0.00 4.06
1429 1508 8.807948 AGCTGTAATCACTAACCACAATAAAT 57.192 30.769 0.00 0.00 0.00 1.40
1451 1530 7.716612 AGCTTAACAACTTGATAAACAAAGCT 58.283 30.769 0.00 0.00 37.67 3.74
1511 1593 3.795688 ATGACAACCATCCACTCACTT 57.204 42.857 0.00 0.00 0.00 3.16
1626 1708 6.146184 CCATACTCCATAAGCTAACATGTTCG 59.854 42.308 15.85 10.31 0.00 3.95
2046 2157 1.337823 GCCAGCTCCGACTTCAAGTTA 60.338 52.381 0.00 0.00 0.00 2.24
2058 2169 1.172175 CCTCTTTCTTTGCCAGCTCC 58.828 55.000 0.00 0.00 0.00 4.70
2084 2195 5.657302 TCATAGTCCTCCTGTACTTTCTTCC 59.343 44.000 0.00 0.00 0.00 3.46
2284 2398 6.993079 TCACTAGAGTCTCATACTTTTGCAA 58.007 36.000 0.00 0.00 39.07 4.08


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

AutoCloner maintained by Alex Coulton.