Multiple sequence alignment - TraesCS6A01G127100

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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 TraesCS6A01G127100 chr6A 100.000 2656 0 0 1 2656 100259036 100256381 0.000000e+00 4905
1 TraesCS6A01G127100 chr1A 94.907 1669 71 8 1 1668 530705469 530703814 0.000000e+00 2599
2 TraesCS6A01G127100 chr1A 96.579 994 30 4 1666 2656 551701646 551702638 0.000000e+00 1644
3 TraesCS6A01G127100 chr1A 96.281 995 30 6 1665 2656 39381308 39382298 0.000000e+00 1626
4 TraesCS6A01G127100 chr6B 94.787 1669 75 4 1 1668 471169169 471167512 0.000000e+00 2590
5 TraesCS6A01G127100 chr7A 96.973 991 26 4 1668 2656 20074616 20075604 0.000000e+00 1661
6 TraesCS6A01G127100 chr7A 96.784 995 26 5 1666 2656 20083118 20084110 0.000000e+00 1655
7 TraesCS6A01G127100 chr2A 96.562 989 30 3 1666 2653 725924055 725925040 0.000000e+00 1635
8 TraesCS6A01G127100 chr2A 96.162 990 34 3 1668 2656 573099354 573098368 0.000000e+00 1615
9 TraesCS6A01G127100 chr2A 95.591 998 35 9 1663 2656 556099539 556100531 0.000000e+00 1591
10 TraesCS6A01G127100 chr2A 82.890 263 40 5 1385 1645 705790779 705791038 5.720000e-57 231
11 TraesCS6A01G127100 chr3A 95.951 988 36 4 1671 2656 566844113 566843128 0.000000e+00 1600
12 TraesCS6A01G127100 chr3A 95.859 990 38 3 1668 2656 83273829 83272842 0.000000e+00 1598
13 TraesCS6A01G127100 chr7B 82.617 1605 244 29 86 1668 673520519 673522110 0.000000e+00 1386
14 TraesCS6A01G127100 chr2B 81.491 1556 234 36 125 1651 793163824 793162294 0.000000e+00 1229
15 TraesCS6A01G127100 chr5A 79.161 1550 264 47 131 1647 603381294 603379771 0.000000e+00 1018
16 TraesCS6A01G127100 chr4B 79.083 1549 267 45 131 1647 127722145 127720622 0.000000e+00 1013


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 TraesCS6A01G127100 chr6A 100256381 100259036 2655 True 4905 4905 100.000 1 2656 1 chr6A.!!$R1 2655
1 TraesCS6A01G127100 chr1A 530703814 530705469 1655 True 2599 2599 94.907 1 1668 1 chr1A.!!$R1 1667
2 TraesCS6A01G127100 chr1A 551701646 551702638 992 False 1644 1644 96.579 1666 2656 1 chr1A.!!$F2 990
3 TraesCS6A01G127100 chr1A 39381308 39382298 990 False 1626 1626 96.281 1665 2656 1 chr1A.!!$F1 991
4 TraesCS6A01G127100 chr6B 471167512 471169169 1657 True 2590 2590 94.787 1 1668 1 chr6B.!!$R1 1667
5 TraesCS6A01G127100 chr7A 20074616 20075604 988 False 1661 1661 96.973 1668 2656 1 chr7A.!!$F1 988
6 TraesCS6A01G127100 chr7A 20083118 20084110 992 False 1655 1655 96.784 1666 2656 1 chr7A.!!$F2 990
7 TraesCS6A01G127100 chr2A 725924055 725925040 985 False 1635 1635 96.562 1666 2653 1 chr2A.!!$F3 987
8 TraesCS6A01G127100 chr2A 573098368 573099354 986 True 1615 1615 96.162 1668 2656 1 chr2A.!!$R1 988
9 TraesCS6A01G127100 chr2A 556099539 556100531 992 False 1591 1591 95.591 1663 2656 1 chr2A.!!$F1 993
10 TraesCS6A01G127100 chr3A 566843128 566844113 985 True 1600 1600 95.951 1671 2656 1 chr3A.!!$R2 985
11 TraesCS6A01G127100 chr3A 83272842 83273829 987 True 1598 1598 95.859 1668 2656 1 chr3A.!!$R1 988
12 TraesCS6A01G127100 chr7B 673520519 673522110 1591 False 1386 1386 82.617 86 1668 1 chr7B.!!$F1 1582
13 TraesCS6A01G127100 chr2B 793162294 793163824 1530 True 1229 1229 81.491 125 1651 1 chr2B.!!$R1 1526
14 TraesCS6A01G127100 chr5A 603379771 603381294 1523 True 1018 1018 79.161 131 1647 1 chr5A.!!$R1 1516
15 TraesCS6A01G127100 chr4B 127720622 127722145 1523 True 1013 1013 79.083 131 1647 1 chr4B.!!$R1 1516

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
47 48 0.036294 GCAGGTACTCTCCACCCAAC 60.036 60.0 0.0 0.0 34.60 3.77 F
311 314 0.610232 AAAAGCGAGCAAGGGCAGAT 60.610 50.0 0.0 0.0 44.61 2.90 F
1354 1392 1.006832 AATGCCGACGCTTGACATAC 58.993 50.0 0.0 0.0 35.36 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1060 1.069668 AGCAACCGGTAAAGTTCGTCT 59.930 47.619 8.00 0.0 0.00 4.18 R
1522 1560 1.202417 CGTCATGTATCTTGTCGGCCT 60.202 52.381 0.00 0.0 0.00 5.19 R
2333 2388 0.250234 CGGCCATCAGGAGAGTTTCA 59.750 55.000 2.24 0.0 36.89 2.69 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
42 43 0.037232 GTGGTGCAGGTACTCTCCAC 60.037 60.000 14.05 14.05 40.17 4.02
43 44 1.192146 TGGTGCAGGTACTCTCCACC 61.192 60.000 14.35 14.35 44.43 4.61
44 45 1.597461 GTGCAGGTACTCTCCACCC 59.403 63.158 0.00 0.00 34.60 4.61
45 46 1.157513 TGCAGGTACTCTCCACCCA 59.842 57.895 0.00 0.00 34.60 4.51
46 47 0.472925 TGCAGGTACTCTCCACCCAA 60.473 55.000 0.00 0.00 34.60 4.12
47 48 0.036294 GCAGGTACTCTCCACCCAAC 60.036 60.000 0.00 0.00 34.60 3.77
48 49 0.613777 CAGGTACTCTCCACCCAACC 59.386 60.000 0.00 0.00 34.60 3.77
189 192 3.684788 ACTCGCACATCAAATAGTTGGAC 59.315 43.478 2.65 0.00 35.29 4.02
228 231 2.398554 CCATCCTTGACGCCCGTTG 61.399 63.158 0.00 0.00 0.00 4.10
311 314 0.610232 AAAAGCGAGCAAGGGCAGAT 60.610 50.000 0.00 0.00 44.61 2.90
449 461 5.759763 CCATCATTCGAATTGGACATAGACA 59.240 40.000 19.90 0.00 0.00 3.41
845 875 3.118592 GCACCCAGTAGATTAAGCTGACT 60.119 47.826 2.82 0.62 32.39 3.41
963 994 3.057596 GCGATTGTTCTGAATTGGACCAA 60.058 43.478 9.92 9.92 0.00 3.67
988 1019 2.356780 GGGTCCTTGATCGTCCGGT 61.357 63.158 0.00 0.00 0.00 5.28
1038 1069 2.032681 GCCAGCCCAGACGAACTT 59.967 61.111 0.00 0.00 0.00 2.66
1053 1084 2.501261 GAACTTTACCGGTTGCTCCTT 58.499 47.619 15.04 0.00 0.00 3.36
1121 1153 6.173339 CCACTTTCTTGCCATAGTTCTAGAA 58.827 40.000 0.00 0.00 0.00 2.10
1130 1162 9.646427 CTTGCCATAGTTCTAGAAATATCCTAC 57.354 37.037 19.79 11.39 30.21 3.18
1275 1308 2.959030 TCGGATGGTAATGTCTCCAGAG 59.041 50.000 0.00 0.00 37.14 3.35
1343 1381 1.212751 GAACCCAAGCAATGCCGAC 59.787 57.895 0.00 0.00 0.00 4.79
1354 1392 1.006832 AATGCCGACGCTTGACATAC 58.993 50.000 0.00 0.00 35.36 2.39
1368 1406 4.054780 TGACATACGCCTAACTTCCATC 57.945 45.455 0.00 0.00 0.00 3.51
1500 1538 1.837439 ACCAGACAGAGGACACAACAA 59.163 47.619 0.00 0.00 0.00 2.83
1522 1560 4.901868 AGGAAAACTTGCCTTATGTACGA 58.098 39.130 0.00 0.00 0.00 3.43
1951 1991 3.966665 GGAGGAGAGGTTGATGAAGATCT 59.033 47.826 0.00 0.00 0.00 2.75
2065 2106 2.035442 GCGCCAAGACTCAAGGGTC 61.035 63.158 0.00 0.00 36.56 4.46
2248 2302 1.386772 TTCCCCACCCCACTTCAGT 60.387 57.895 0.00 0.00 0.00 3.41
2333 2388 1.197812 GTACAATACCGGTGACCCCT 58.802 55.000 19.93 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.036294 GTTGGGTGGAGAGTACCTGC 60.036 60.000 0.00 0.00 38.30 4.85
63 64 4.386951 TCATCACGGCCGGGTGTG 62.387 66.667 29.71 25.94 39.00 3.82
64 65 4.388499 GTCATCACGGCCGGGTGT 62.388 66.667 29.71 15.24 39.00 4.16
176 179 3.334691 CAGCCTTCGTCCAACTATTTGA 58.665 45.455 0.00 0.00 34.24 2.69
189 192 1.066573 AGATGACAACTCCAGCCTTCG 60.067 52.381 0.00 0.00 0.00 3.79
228 231 2.051345 CACTGGTTTGGCGCGTTC 60.051 61.111 8.43 0.58 0.00 3.95
311 314 1.324740 ACCTATTACCTGGCGCGTCA 61.325 55.000 14.98 14.98 0.00 4.35
360 369 4.263462 TGCATGGACAACCTATGAGAACTT 60.263 41.667 0.00 0.00 37.04 2.66
449 461 1.602165 CGTACTGGCTTCGTTGTGTCT 60.602 52.381 0.00 0.00 0.00 3.41
672 684 2.280797 GCACCAGACGGTTGCTCA 60.281 61.111 0.00 0.00 46.31 4.26
818 848 0.906066 TAATCTACTGGGTGCGGCAA 59.094 50.000 3.23 0.00 0.00 4.52
825 855 4.532521 ACAAGTCAGCTTAATCTACTGGGT 59.467 41.667 0.00 0.00 32.87 4.51
963 994 0.539051 CGATCAAGGACCCAAGCTCT 59.461 55.000 0.00 0.00 0.00 4.09
988 1019 3.327464 TGTGACTCCATCTGTCCAATTCA 59.673 43.478 0.00 0.00 33.83 2.57
1029 1060 1.069668 AGCAACCGGTAAAGTTCGTCT 59.930 47.619 8.00 0.00 0.00 4.18
1038 1069 3.927555 CTCAAGGAGCAACCGGTAA 57.072 52.632 8.00 0.00 44.74 2.85
1053 1084 2.016318 CATACCGCAAAATCAGGCTCA 58.984 47.619 0.00 0.00 0.00 4.26
1059 1090 5.635417 TGTGATTTCATACCGCAAAATCA 57.365 34.783 5.82 5.82 43.48 2.57
1101 1132 9.561069 GGATATTTCTAGAACTATGGCAAGAAA 57.439 33.333 17.40 9.85 37.36 2.52
1275 1308 8.424274 AACAGAGAAATTTGGATGAAAACAAC 57.576 30.769 0.00 0.00 0.00 3.32
1343 1381 1.922570 AGTTAGGCGTATGTCAAGCG 58.077 50.000 0.00 0.00 31.59 4.68
1354 1392 3.619038 GTGAGAAAGATGGAAGTTAGGCG 59.381 47.826 0.00 0.00 0.00 5.52
1368 1406 5.422214 ACCTGTTACATAGGGTGAGAAAG 57.578 43.478 0.00 0.00 39.71 2.62
1500 1538 4.901868 TCGTACATAAGGCAAGTTTTCCT 58.098 39.130 0.00 0.00 0.00 3.36
1522 1560 1.202417 CGTCATGTATCTTGTCGGCCT 60.202 52.381 0.00 0.00 0.00 5.19
2236 2290 1.500783 CCCATGGACTGAAGTGGGGT 61.501 60.000 15.22 0.00 46.08 4.95
2333 2388 0.250234 CGGCCATCAGGAGAGTTTCA 59.750 55.000 2.24 0.00 36.89 2.69


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

AutoCloner maintained by Alex Coulton.