Multiple sequence alignment - TraesCS3A01G297900

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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 TraesCS3A01G297900 chr3A 100.000 2771 0 0 1 2771 532455813 532453043 0.000000e+00 5118
1 TraesCS3A01G297900 chr3A 95.153 1011 27 5 1 989 532465850 532464840 0.000000e+00 1576
2 TraesCS3A01G297900 chr3D 98.038 1784 35 0 988 2771 418722565 418724348 0.000000e+00 3101
3 TraesCS3A01G297900 chr3B 97.699 1782 41 0 990 2771 545061584 545063365 0.000000e+00 3064
4 TraesCS3A01G297900 chr2A 94.867 1013 28 5 1 989 158968671 158967659 0.000000e+00 1561
5 TraesCS3A01G297900 chr2A 92.826 683 28 3 1 662 158957936 158957254 0.000000e+00 970
6 TraesCS3A01G297900 chr7A 94.560 1011 33 5 1 989 228055548 228056558 0.000000e+00 1543
7 TraesCS3A01G297900 chr7A 92.913 1030 29 14 1 989 612324275 612323249 0.000000e+00 1458
8 TraesCS3A01G297900 chr7A 92.163 1008 55 7 1 987 66388694 66389698 0.000000e+00 1402
9 TraesCS3A01G297900 chr7A 91.774 1009 56 11 1 987 164966854 164965851 0.000000e+00 1378
10 TraesCS3A01G297900 chr7A 91.502 1012 56 12 1 988 370598080 370599085 0.000000e+00 1365
11 TraesCS3A01G297900 chr7A 89.204 565 37 6 447 989 370587836 370588398 0.000000e+00 684
12 TraesCS3A01G297900 chr7A 73.029 1598 374 42 1093 2659 91647380 91648951 6.850000e-141 510
13 TraesCS3A01G297900 chr6A 93.301 1030 28 2 1 989 25756792 25755763 0.000000e+00 1482
14 TraesCS3A01G297900 chr6A 89.120 1011 43 21 1 987 7221766 7222733 0.000000e+00 1195
15 TraesCS3A01G297900 chr6A 92.888 689 26 5 1 667 272853498 272854185 0.000000e+00 979
16 TraesCS3A01G297900 chr6A 91.272 676 41 14 1 667 7206508 7207174 0.000000e+00 905
17 TraesCS3A01G297900 chr1A 93.093 1028 29 5 1 987 113335157 113334131 0.000000e+00 1467
18 TraesCS3A01G297900 chr1A 93.003 1029 29 13 1 987 492686275 492687302 0.000000e+00 1461
19 TraesCS3A01G297900 chr1A 93.891 884 30 5 128 989 113345310 113344429 0.000000e+00 1312
20 TraesCS3A01G297900 chr1A 91.948 919 46 17 93 987 312849072 312849986 0.000000e+00 1262
21 TraesCS3A01G297900 chr2B 71.491 691 178 16 1976 2658 132518320 132518999 1.710000e-37 167
22 TraesCS3A01G297900 chr2D 72.519 524 135 7 2070 2590 80834731 80835248 7.940000e-36 161
23 TraesCS3A01G297900 chr2D 71.033 687 182 14 1988 2667 80783156 80782480 1.720000e-32 150


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 TraesCS3A01G297900 chr3A 532453043 532455813 2770 True 5118 5118 100.000 1 2771 1 chr3A.!!$R1 2770
1 TraesCS3A01G297900 chr3A 532464840 532465850 1010 True 1576 1576 95.153 1 989 1 chr3A.!!$R2 988
2 TraesCS3A01G297900 chr3D 418722565 418724348 1783 False 3101 3101 98.038 988 2771 1 chr3D.!!$F1 1783
3 TraesCS3A01G297900 chr3B 545061584 545063365 1781 False 3064 3064 97.699 990 2771 1 chr3B.!!$F1 1781
4 TraesCS3A01G297900 chr2A 158967659 158968671 1012 True 1561 1561 94.867 1 989 1 chr2A.!!$R2 988
5 TraesCS3A01G297900 chr2A 158957254 158957936 682 True 970 970 92.826 1 662 1 chr2A.!!$R1 661
6 TraesCS3A01G297900 chr7A 228055548 228056558 1010 False 1543 1543 94.560 1 989 1 chr7A.!!$F3 988
7 TraesCS3A01G297900 chr7A 612323249 612324275 1026 True 1458 1458 92.913 1 989 1 chr7A.!!$R2 988
8 TraesCS3A01G297900 chr7A 66388694 66389698 1004 False 1402 1402 92.163 1 987 1 chr7A.!!$F1 986
9 TraesCS3A01G297900 chr7A 164965851 164966854 1003 True 1378 1378 91.774 1 987 1 chr7A.!!$R1 986
10 TraesCS3A01G297900 chr7A 370598080 370599085 1005 False 1365 1365 91.502 1 988 1 chr7A.!!$F5 987
11 TraesCS3A01G297900 chr7A 370587836 370588398 562 False 684 684 89.204 447 989 1 chr7A.!!$F4 542
12 TraesCS3A01G297900 chr7A 91647380 91648951 1571 False 510 510 73.029 1093 2659 1 chr7A.!!$F2 1566
13 TraesCS3A01G297900 chr6A 25755763 25756792 1029 True 1482 1482 93.301 1 989 1 chr6A.!!$R1 988
14 TraesCS3A01G297900 chr6A 7221766 7222733 967 False 1195 1195 89.120 1 987 1 chr6A.!!$F2 986
15 TraesCS3A01G297900 chr6A 272853498 272854185 687 False 979 979 92.888 1 667 1 chr6A.!!$F3 666
16 TraesCS3A01G297900 chr6A 7206508 7207174 666 False 905 905 91.272 1 667 1 chr6A.!!$F1 666
17 TraesCS3A01G297900 chr1A 113334131 113335157 1026 True 1467 1467 93.093 1 987 1 chr1A.!!$R1 986
18 TraesCS3A01G297900 chr1A 492686275 492687302 1027 False 1461 1461 93.003 1 987 1 chr1A.!!$F2 986
19 TraesCS3A01G297900 chr1A 113344429 113345310 881 True 1312 1312 93.891 128 989 1 chr1A.!!$R2 861
20 TraesCS3A01G297900 chr1A 312849072 312849986 914 False 1262 1262 91.948 93 987 1 chr1A.!!$F1 894

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
443 455 0.550914 TCCGGCATAATTGGAAGGCT 59.449 50.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 2296 1.392589 CGGCCCATGCTAACAATCTT 58.607 50.0 0.0 0.0 37.74 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
136 137 5.684704 TCACTTGATTGGACAACTTCTCTT 58.315 37.500 0.00 0.00 0.00 2.85
285 295 3.641434 AGTGTGAGCTCAAATATGGCT 57.359 42.857 20.19 2.72 36.28 4.75
307 317 0.753867 TGTAGTGCAAGTGAACGGGA 59.246 50.000 0.00 0.00 0.00 5.14
378 390 5.127031 ACTTAAAGAGCAAGGCAGAAAACAA 59.873 36.000 0.00 0.00 0.00 2.83
443 455 0.550914 TCCGGCATAATTGGAAGGCT 59.449 50.000 0.00 0.00 0.00 4.58
942 1043 7.504926 TTGTTAGTCCCCTACATGTAGATTT 57.495 36.000 30.41 14.82 35.21 2.17
1197 1302 4.335400 AACAAATGGCACCTTTAACCTG 57.665 40.909 0.00 0.00 0.00 4.00
1238 1343 1.853963 ACTCCTCTACACTTCCGCAT 58.146 50.000 0.00 0.00 0.00 4.73
1256 1361 1.867233 CATGTCGCCTAGTGGTTATGC 59.133 52.381 0.00 0.00 35.27 3.14
1359 1464 5.237344 CGTCACCAGAAACAAGAATTTCTCT 59.763 40.000 0.00 0.00 45.19 3.10
1438 1543 3.980646 GCAACCATATATTTGCGGTGA 57.019 42.857 6.41 0.00 38.86 4.02
1537 1642 2.173143 TCTGTGCAATCCCATGATGCTA 59.827 45.455 0.00 0.00 0.00 3.49
1548 1653 3.314635 CCCATGATGCTAGCTTCTTTGAC 59.685 47.826 25.75 5.24 0.00 3.18
1691 1799 2.162681 GCCTGCAAGACCATTACTGTT 58.837 47.619 0.00 0.00 34.07 3.16
1729 1837 3.591023 TCAACAGTTTTCACAGACACGA 58.409 40.909 0.00 0.00 0.00 4.35
1769 1877 1.462283 CGCAACTGGAGTCATCAACTG 59.538 52.381 0.00 0.00 38.74 3.16
1820 1928 0.034670 ATGGGAAAGACTGCTCCTGC 60.035 55.000 4.31 0.00 40.20 4.85
1941 2049 8.945195 TCATCCTTATTGCTGGAATTATCATT 57.055 30.769 0.00 0.00 35.81 2.57
1973 2081 5.316167 TGCTCGAAGGAAATTGGCATATAT 58.684 37.500 0.00 0.00 0.00 0.86
2148 2256 3.078837 GGAGGTTGCGGTGAAGAAATTA 58.921 45.455 0.00 0.00 0.00 1.40
2188 2296 6.377146 GCAGGGAACAAAGGAATTCATTACTA 59.623 38.462 5.67 0.00 28.79 1.82
2385 2502 2.655090 TCAAAGGAGTTGCATGTGGA 57.345 45.000 0.00 0.00 37.13 4.02
2492 2609 2.184533 TGGGCGACTAGGAGATTTTGA 58.815 47.619 0.00 0.00 0.00 2.69
2603 2720 2.170187 CAGGCAAGCTGTCTCCTCTTAT 59.830 50.000 0.00 0.00 23.66 1.73
2742 2859 4.157289 CAGAAAGGAACAATGGTGGAGATG 59.843 45.833 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 3.359033 CCAAGGGATTTGAGAGCATTCA 58.641 45.455 0.00 0.0 39.21 2.57
285 295 1.937223 CCGTTCACTTGCACTACAACA 59.063 47.619 0.00 0.0 33.68 3.33
378 390 1.075659 GCCCCTCTGTTTCCTGCTT 59.924 57.895 0.00 0.0 0.00 3.91
435 447 3.309582 GGATGTCCGAGCCTTCCA 58.690 61.111 0.00 0.0 0.00 3.53
1197 1302 2.106511 TGGGTATAGAGCATGGCCTTTC 59.893 50.000 3.32 0.0 0.00 2.62
1238 1343 0.899019 TGCATAACCACTAGGCGACA 59.101 50.000 0.00 0.0 40.27 4.35
1256 1361 7.543868 AGACGAAGATGATAGAAAAAGACTGTG 59.456 37.037 0.00 0.0 0.00 3.66
1359 1464 3.899981 CTGGGCTGGCAACGCACTA 62.900 63.158 3.28 0.0 39.69 2.74
1438 1543 6.265196 TCACTATTTTCATTGGTGTCAAGCTT 59.735 34.615 0.00 0.0 36.19 3.74
1453 1558 6.173339 TGATGTCCTGGAACTCACTATTTTC 58.827 40.000 0.00 0.0 0.00 2.29
1503 1608 3.876274 TGCACAGAGTGGAGACTATTC 57.124 47.619 0.00 0.0 33.64 1.75
1537 1642 3.065371 CCAGTTTTGTCGTCAAAGAAGCT 59.935 43.478 7.82 3.7 43.17 3.74
1548 1653 5.666969 TCTTGAACATACCAGTTTTGTCG 57.333 39.130 0.00 0.0 0.00 4.35
1691 1799 7.904558 ACTGTTGAGAGATCATAGATGGTTA 57.095 36.000 0.00 0.0 0.00 2.85
1729 1837 2.738643 CGGACGAGAAGCCAATGTATGT 60.739 50.000 0.00 0.0 0.00 2.29
1769 1877 6.406692 TCCAGCCAAGTATGTAGTATCTTC 57.593 41.667 0.00 0.0 0.00 2.87
1820 1928 1.664016 GCAGCTTGGTTGTGTCAATCG 60.664 52.381 0.00 0.0 0.00 3.34
1941 2049 7.491048 GCCAATTTCCTTCGAGCAAATAAAATA 59.509 33.333 0.00 0.0 0.00 1.40
1973 2081 1.819288 CCCAGTCTTCTTGTAGCTCGA 59.181 52.381 0.00 0.0 0.00 4.04
2078 2186 2.829023 ACACCTTTCCGAATCCTCCTA 58.171 47.619 0.00 0.0 0.00 2.94
2148 2256 3.972133 TCCCTGCTTTGAATCATGTGAT 58.028 40.909 0.00 0.0 36.07 3.06
2188 2296 1.392589 CGGCCCATGCTAACAATCTT 58.607 50.000 0.00 0.0 37.74 2.40
2385 2502 2.836636 TCTCATGGAGGTAGAGCAGT 57.163 50.000 0.00 0.0 0.00 4.40
2492 2609 5.221106 CCATGATCATACGATTTTGCAAGGT 60.221 40.000 8.15 0.0 29.66 3.50
2742 2859 1.691434 CCTTGGAGCCTCTGGTCTATC 59.309 57.143 0.00 0.0 39.02 2.08


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

AutoCloner maintained by Alex Coulton.