Multiple sequence alignment - TraesCS1B01G476200

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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 TraesCS1B01G476200 chr1B 100.000 2549 0 0 1 2549 684835444 684832896 0 4708
1 TraesCS1B01G476200 chr1B 97.632 1985 42 5 567 2549 7851071 7853052 0 3400
2 TraesCS1B01G476200 chr3A 97.880 1981 37 5 571 2549 54951916 54953893 0 3421
3 TraesCS1B01G476200 chr6A 97.877 1978 41 1 573 2549 617222869 617220892 0 3419
4 TraesCS1B01G476200 chr3B 97.828 1980 38 5 572 2549 702857655 702855679 0 3413
5 TraesCS1B01G476200 chr3B 97.780 1982 38 6 571 2549 20305086 20307064 0 3411
6 TraesCS1B01G476200 chr3B 96.196 552 19 2 20 569 81718507 81719058 0 902
7 TraesCS1B01G476200 chr2B 97.779 1981 38 5 572 2549 776222961 776224938 0 3410
8 TraesCS1B01G476200 chr2B 97.492 1994 44 6 559 2549 781094227 781096217 0 3400
9 TraesCS1B01G476200 chr4A 97.728 1981 43 2 571 2549 36562911 36564891 0 3408
10 TraesCS1B01G476200 chr7B 97.778 1980 37 6 572 2549 202776915 202778889 0 3406
11 TraesCS1B01G476200 chr5B 96.390 554 19 1 20 572 611458986 611458433 0 911
12 TraesCS1B01G476200 chr5B 95.848 554 22 1 20 572 604568182 604567629 0 894
13 TraesCS1B01G476200 chr6B 95.856 555 20 3 20 572 678484526 678483973 0 894
14 TraesCS1B01G476200 chr6B 95.495 555 23 2 20 572 13988871 13989425 0 885
15 TraesCS1B01G476200 chr6B 95.495 555 23 2 20 572 13994918 13995472 0 885
16 TraesCS1B01G476200 chr6B 95.644 551 23 1 20 569 8952433 8952983 0 883
17 TraesCS1B01G476200 chr4B 95.644 551 22 2 20 569 24221589 24222138 0 883
18 TraesCS1B01G476200 chr4B 95.487 554 24 1 20 572 410948276 410948829 0 883


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 TraesCS1B01G476200 chr1B 684832896 684835444 2548 True 4708 4708 100.000 1 2549 1 chr1B.!!$R1 2548
1 TraesCS1B01G476200 chr1B 7851071 7853052 1981 False 3400 3400 97.632 567 2549 1 chr1B.!!$F1 1982
2 TraesCS1B01G476200 chr3A 54951916 54953893 1977 False 3421 3421 97.880 571 2549 1 chr3A.!!$F1 1978
3 TraesCS1B01G476200 chr6A 617220892 617222869 1977 True 3419 3419 97.877 573 2549 1 chr6A.!!$R1 1976
4 TraesCS1B01G476200 chr3B 702855679 702857655 1976 True 3413 3413 97.828 572 2549 1 chr3B.!!$R1 1977
5 TraesCS1B01G476200 chr3B 20305086 20307064 1978 False 3411 3411 97.780 571 2549 1 chr3B.!!$F1 1978
6 TraesCS1B01G476200 chr3B 81718507 81719058 551 False 902 902 96.196 20 569 1 chr3B.!!$F2 549
7 TraesCS1B01G476200 chr2B 776222961 776224938 1977 False 3410 3410 97.779 572 2549 1 chr2B.!!$F1 1977
8 TraesCS1B01G476200 chr2B 781094227 781096217 1990 False 3400 3400 97.492 559 2549 1 chr2B.!!$F2 1990
9 TraesCS1B01G476200 chr4A 36562911 36564891 1980 False 3408 3408 97.728 571 2549 1 chr4A.!!$F1 1978
10 TraesCS1B01G476200 chr7B 202776915 202778889 1974 False 3406 3406 97.778 572 2549 1 chr7B.!!$F1 1977
11 TraesCS1B01G476200 chr5B 611458433 611458986 553 True 911 911 96.390 20 572 1 chr5B.!!$R2 552
12 TraesCS1B01G476200 chr5B 604567629 604568182 553 True 894 894 95.848 20 572 1 chr5B.!!$R1 552
13 TraesCS1B01G476200 chr6B 678483973 678484526 553 True 894 894 95.856 20 572 1 chr6B.!!$R1 552
14 TraesCS1B01G476200 chr6B 13988871 13989425 554 False 885 885 95.495 20 572 1 chr6B.!!$F2 552
15 TraesCS1B01G476200 chr6B 13994918 13995472 554 False 885 885 95.495 20 572 1 chr6B.!!$F3 552
16 TraesCS1B01G476200 chr6B 8952433 8952983 550 False 883 883 95.644 20 569 1 chr6B.!!$F1 549
17 TraesCS1B01G476200 chr4B 24221589 24222138 549 False 883 883 95.644 20 569 1 chr4B.!!$F1 549
18 TraesCS1B01G476200 chr4B 410948276 410948829 553 False 883 883 95.487 20 572 1 chr4B.!!$F2 552

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
685 688 0.518636 CCGACTCGTTCCGTGAACTA 59.481 55.0 12.8 3.9 40.05 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1729 0.250467 TGGACAGAAAGGCAGAGCAC 60.25 55.0 0.0 0.0 0.0 4.4 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
18 19 3.532896 GAACGAAGATGTCCCTGCA 57.467 52.632 0.00 0.0 0.00 4.41
34 35 3.368013 CCCTGCAGTCATTTACTCGTGTA 60.368 47.826 13.81 0.0 35.76 2.90
402 403 3.797451 TTCAAACATGTTGAGCTTGCA 57.203 38.095 12.82 0.0 0.00 4.08
448 450 8.874744 AATATCTGTACTAAGCGGGAATACTA 57.125 34.615 0.00 0.0 0.00 1.82
480 482 5.459505 TCCAAATCCCTTGAACCAAGTTTA 58.540 37.500 6.04 0.0 39.58 2.01
619 622 2.362077 GGTGTCCATGTGCTCAGTTTTT 59.638 45.455 0.00 0.0 0.00 1.94
685 688 0.518636 CCGACTCGTTCCGTGAACTA 59.481 55.000 12.80 3.9 40.05 2.24
725 728 1.633945 ACCTTTTGACTCGGCCCTTAT 59.366 47.619 0.00 0.0 0.00 1.73
731 734 1.342674 TGACTCGGCCCTTATAGGTGT 60.343 52.381 0.00 0.0 31.93 4.16
878 881 2.182791 CACGGCGACAGAGAGCAT 59.817 61.111 16.62 0.0 34.54 3.79
907 910 1.453015 ACGGCGAGAGAGAGAGCAT 60.453 57.895 16.62 0.0 0.00 3.79
1135 1138 2.635915 ACACCAAGGAACCAGAATCGTA 59.364 45.455 0.00 0.0 0.00 3.43
1338 1341 3.725459 CGCATGCTGCCACGAACA 61.725 61.111 17.13 0.0 41.12 3.18
1431 1434 6.749923 ATTGAGCTTAGGATGTTGAAGAAC 57.250 37.500 0.00 0.0 0.00 3.01
1725 1729 4.632538 TGATCAATGAAATGCAGCTCTG 57.367 40.909 0.00 0.0 0.00 3.35
1744 1748 0.250467 GTGCTCTGCCTTTCTGTCCA 60.250 55.000 0.00 0.0 0.00 4.02
1793 1797 3.966215 GCGTAGAGCCAAGTGCAA 58.034 55.556 0.00 0.0 44.83 4.08
1945 1949 4.082463 TGAATTATTCCGGAGCCAAACAAC 60.082 41.667 3.34 0.0 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.338200 ACTGCAGGGACATCTTCGTTC 60.338 52.381 19.93 0.00 0.00 3.95
4 5 2.706339 ATGACTGCAGGGACATCTTC 57.294 50.000 19.93 4.13 0.00 2.87
5 6 3.446442 AAATGACTGCAGGGACATCTT 57.554 42.857 19.93 13.00 0.00 2.40
6 7 3.521126 AGTAAATGACTGCAGGGACATCT 59.479 43.478 19.93 9.85 36.87 2.90
7 8 3.873952 GAGTAAATGACTGCAGGGACATC 59.126 47.826 19.93 6.49 39.06 3.06
8 9 3.679917 CGAGTAAATGACTGCAGGGACAT 60.680 47.826 19.93 16.60 39.06 3.06
9 10 2.353704 CGAGTAAATGACTGCAGGGACA 60.354 50.000 19.93 15.05 39.06 4.02
10 11 2.271800 CGAGTAAATGACTGCAGGGAC 58.728 52.381 19.93 9.63 39.06 4.46
12 13 2.002586 CACGAGTAAATGACTGCAGGG 58.997 52.381 19.93 0.00 39.06 4.45
13 14 2.688507 ACACGAGTAAATGACTGCAGG 58.311 47.619 19.93 0.00 39.06 4.85
14 15 4.486090 AGTACACGAGTAAATGACTGCAG 58.514 43.478 13.48 13.48 39.06 4.41
15 16 4.514781 AGTACACGAGTAAATGACTGCA 57.485 40.909 0.00 0.00 39.06 4.41
16 17 4.921515 TGAAGTACACGAGTAAATGACTGC 59.078 41.667 0.00 0.00 39.06 4.40
17 18 6.377406 GTGAAGTACACGAGTAAATGACTG 57.623 41.667 0.00 0.00 37.94 3.51
167 168 7.341769 TGACCAATATAATGCTTGCTAACCTTT 59.658 33.333 0.00 0.00 0.00 3.11
184 185 8.014070 TCATGAATTGCTCAAATGACCAATAT 57.986 30.769 0.00 0.00 37.67 1.28
402 403 1.010795 AGGCTAGCAAAGGGGGAAAT 58.989 50.000 18.24 0.00 0.00 2.17
448 450 2.564062 CAAGGGATTTGGATGCACAAGT 59.436 45.455 0.00 0.00 32.95 3.16
480 482 3.117888 GGTATGGTGGACACTCATGGAAT 60.118 47.826 13.23 0.00 0.00 3.01
619 622 2.013563 GCACAATTCGCATCTGAGGGA 61.014 52.381 0.00 0.00 0.00 4.20
725 728 3.702048 GCCGCCTGGTCACACCTA 61.702 66.667 0.00 0.00 39.58 3.08
731 734 2.281484 GTTTCTGCCGCCTGGTCA 60.281 61.111 0.00 0.00 37.67 4.02
804 807 0.392193 CCAACGGCTCTCTGCTCAAT 60.392 55.000 0.00 0.00 42.39 2.57
843 846 4.664677 GTCACCACCGCTGTCGCT 62.665 66.667 0.00 0.00 0.00 4.93
1092 1095 3.323691 TCTGAGAAACCCTTCGATCAACA 59.676 43.478 0.00 0.00 36.61 3.33
1223 1226 2.100584 GTCACCTGCATGAACACCAAAA 59.899 45.455 0.00 0.00 0.00 2.44
1227 1230 1.200716 CATGTCACCTGCATGAACACC 59.799 52.381 0.00 0.00 44.60 4.16
1431 1434 5.248640 TGATCTTCAAGCTTCCTAACCTTG 58.751 41.667 0.00 0.00 37.80 3.61
1462 1465 7.390162 CCAAAAGTATTTGCAAATGGGTATTGT 59.610 33.333 30.43 12.40 43.73 2.71
1725 1729 0.250467 TGGACAGAAAGGCAGAGCAC 60.250 55.000 0.00 0.00 0.00 4.40
1793 1797 2.171448 CAGTTGGCCCATTAGTCTAGCT 59.829 50.000 0.00 0.00 0.00 3.32
2165 2170 1.609794 GTCCTGGGTTCGAGTCCCT 60.610 63.158 22.42 0.00 44.84 4.20
2298 2305 6.128391 GCAAACATTCACGGTCTCACTATTTA 60.128 38.462 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.