Multiple sequence alignment - TraesCS7D01G317600

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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 TraesCS7D01G317600 chr7D 100.000 3850 0 0 1 3850 404061517 404065366 0.000000e+00 7110.0
1 TraesCS7D01G317600 chr7B 93.196 3498 120 42 427 3850 413578624 413582077 0.000000e+00 5033.0
2 TraesCS7D01G317600 chr7B 91.917 433 16 7 1 424 413578161 413578583 4.280000e-164 588.0
3 TraesCS7D01G317600 chr7A 94.715 2895 87 20 988 3844 462984530 462987396 0.000000e+00 4438.0
4 TraesCS7D01G317600 chr7A 93.523 386 19 4 46 430 462983314 462983694 1.550000e-158 569.0
5 TraesCS7D01G317600 chr7A 87.306 386 18 10 439 793 462983736 462984121 2.770000e-111 412.0
6 TraesCS7D01G317600 chr3D 78.988 257 45 7 1330 1580 496406624 496406371 2.380000e-37 167.0
7 TraesCS7D01G317600 chr3B 76.562 256 53 5 1330 1580 655422580 655422327 2.410000e-27 134.0
8 TraesCS7D01G317600 chr1A 97.403 77 1 1 3563 3638 432732279 432732355 3.120000e-26 130.0
9 TraesCS7D01G317600 chr4A 96.104 77 2 1 3563 3638 304839163 304839087 1.450000e-24 124.0
10 TraesCS7D01G317600 chr6D 81.579 76 10 3 3549 3623 24850117 24850189 4.150000e-05 60.2


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 TraesCS7D01G317600 chr7D 404061517 404065366 3849 False 7110.000000 7110 100.0000 1 3850 1 chr7D.!!$F1 3849
1 TraesCS7D01G317600 chr7B 413578161 413582077 3916 False 2810.500000 5033 92.5565 1 3850 2 chr7B.!!$F1 3849
2 TraesCS7D01G317600 chr7A 462983314 462987396 4082 False 1806.333333 4438 91.8480 46 3844 3 chr7A.!!$F1 3798

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
810 898 0.031616 TGTCCACCCTTGGCCTTTTT 60.032 50.0 3.32 0.0 43.56 1.94 F
1585 1906 0.106149 CCCCAGCGAGGTACCATAAC 59.894 60.0 15.94 0.0 34.66 1.89 F
1705 2060 0.109132 GCTTGCGGAGAATTTGTGGG 60.109 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 2050 0.037975 CAGCCACAGCCCACAAATTC 60.038 55.0 0.00 0.0 41.25 2.17 R
2699 3059 0.321564 TGGCCTTGATGAAGTCCACG 60.322 55.0 3.32 0.0 32.12 4.94 R
3586 3957 0.752658 GCCAATTAAGCATGTCCCCC 59.247 55.0 0.00 0.0 0.00 5.40 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
39 40 0.336048 CCACCCCCACTCATCCAAAT 59.664 55.000 0.00 0.00 0.00 2.32
57 58 2.217429 ATCAACCAACGGCACAAAAC 57.783 45.000 0.00 0.00 0.00 2.43
340 349 4.586884 CCTGTCAGACACACCTAGTACTA 58.413 47.826 0.00 1.89 0.00 1.82
355 364 5.231147 CCTAGTACTACGAGTTACGAGTCAC 59.769 48.000 0.00 0.00 45.77 3.67
546 606 3.318922 AAGACGAGGAGGGGGAGGG 62.319 68.421 0.00 0.00 0.00 4.30
568 628 1.882352 GCCAGCTCCCATAAATACCCG 60.882 57.143 0.00 0.00 0.00 5.28
606 672 1.578117 GTCGAGTCGAGTCGCTTCG 60.578 63.158 32.58 23.60 39.90 3.79
683 753 1.964933 GTATTTCCTCCTCCTCCTCCG 59.035 57.143 0.00 0.00 0.00 4.63
763 851 1.066918 CCGTCGCCGCTATAAAGGT 59.933 57.895 0.00 0.00 0.00 3.50
810 898 0.031616 TGTCCACCCTTGGCCTTTTT 60.032 50.000 3.32 0.00 43.56 1.94
823 911 1.767759 CCTTTTTCGCCTGGATCCAT 58.232 50.000 16.63 0.00 0.00 3.41
850 938 0.927029 GGTTAGGATTTCCCCTGCCT 59.073 55.000 0.00 0.00 37.10 4.75
910 998 2.899339 GCCCCATCTTGCTCGCTC 60.899 66.667 0.00 0.00 0.00 5.03
911 999 2.587194 CCCCATCTTGCTCGCTCG 60.587 66.667 0.00 0.00 0.00 5.03
912 1000 2.185350 CCCATCTTGCTCGCTCGT 59.815 61.111 0.00 0.00 0.00 4.18
913 1001 1.448540 CCCATCTTGCTCGCTCGTT 60.449 57.895 0.00 0.00 0.00 3.85
914 1002 1.424493 CCCATCTTGCTCGCTCGTTC 61.424 60.000 0.00 0.00 0.00 3.95
915 1003 1.424493 CCATCTTGCTCGCTCGTTCC 61.424 60.000 0.00 0.00 0.00 3.62
916 1004 1.153549 ATCTTGCTCGCTCGTTCCC 60.154 57.895 0.00 0.00 0.00 3.97
917 1005 1.608717 ATCTTGCTCGCTCGTTCCCT 61.609 55.000 0.00 0.00 0.00 4.20
918 1006 1.807573 CTTGCTCGCTCGTTCCCTC 60.808 63.158 0.00 0.00 0.00 4.30
919 1007 3.626680 TTGCTCGCTCGTTCCCTCG 62.627 63.158 0.00 0.00 0.00 4.63
971 1292 2.823829 GCCCGCGCTCGATTTGATT 61.824 57.895 5.56 0.00 38.10 2.57
983 1304 2.019984 GATTTGATTCTCGGCCTGCTT 58.980 47.619 0.00 0.00 0.00 3.91
1585 1906 0.106149 CCCCAGCGAGGTACCATAAC 59.894 60.000 15.94 0.00 34.66 1.89
1643 1998 6.256975 CCTTAATGATATTGAACGAACCGTGA 59.743 38.462 0.00 0.00 39.99 4.35
1684 2039 4.468095 AGTTGAACGAACTATGTTGTGC 57.532 40.909 0.00 0.00 43.54 4.57
1688 2043 2.169832 ACGAACTATGTTGTGCTGCT 57.830 45.000 0.00 0.00 0.00 4.24
1695 2050 1.859427 ATGTTGTGCTGCTTGCGGAG 61.859 55.000 5.52 0.00 46.63 4.63
1700 2055 0.242017 GTGCTGCTTGCGGAGAATTT 59.758 50.000 5.52 0.00 46.63 1.82
1701 2056 0.241749 TGCTGCTTGCGGAGAATTTG 59.758 50.000 5.52 0.00 46.63 2.32
1702 2057 0.242017 GCTGCTTGCGGAGAATTTGT 59.758 50.000 5.52 0.00 0.00 2.83
1703 2058 1.973138 CTGCTTGCGGAGAATTTGTG 58.027 50.000 0.00 0.00 0.00 3.33
1704 2059 0.597568 TGCTTGCGGAGAATTTGTGG 59.402 50.000 0.00 0.00 0.00 4.17
1705 2060 0.109132 GCTTGCGGAGAATTTGTGGG 60.109 55.000 0.00 0.00 0.00 4.61
1706 2061 0.109132 CTTGCGGAGAATTTGTGGGC 60.109 55.000 0.00 0.00 0.00 5.36
1818 2173 5.970317 TGATTCATGATTGGGATATGTGC 57.030 39.130 0.00 0.00 0.00 4.57
2032 2387 7.928706 TGGTTGGGAATTTGTTTATTTGTGTAG 59.071 33.333 0.00 0.00 0.00 2.74
2339 2699 1.675552 CGGTGTTCAACTTCCCAACT 58.324 50.000 0.00 0.00 0.00 3.16
2435 2795 1.702491 GCTACAACCGTCGAATGGCC 61.702 60.000 0.00 0.00 0.00 5.36
2453 2813 1.153289 CCCTCACATCTTGCCGGAG 60.153 63.158 5.05 0.00 0.00 4.63
2699 3059 4.641989 AGATATGGTGCTGGAAACATCAAC 59.358 41.667 0.00 0.00 44.36 3.18
2705 3065 1.069227 GCTGGAAACATCAACGTGGAC 60.069 52.381 0.00 0.00 41.51 4.02
2853 3213 1.676006 CGGTGTTGGACTTTTGAGCTT 59.324 47.619 0.00 0.00 0.00 3.74
2892 3253 9.853555 CATTATATTATCGAGCTATCTCCATCC 57.146 37.037 0.00 0.00 35.94 3.51
3090 3451 1.803334 TGGACGAATGGCACTACAAC 58.197 50.000 0.00 0.00 0.00 3.32
3196 3557 6.659242 CCCCCATATCACTTATTGTAATGACC 59.341 42.308 0.00 0.00 0.00 4.02
3248 3614 2.895404 ACTTGCTCAATCATTGCTTGGT 59.105 40.909 0.00 0.00 0.00 3.67
3309 3675 2.541346 CGCACTTGATACATAGCCACAG 59.459 50.000 0.00 0.00 0.00 3.66
3310 3676 2.874701 GCACTTGATACATAGCCACAGG 59.125 50.000 0.00 0.00 0.00 4.00
3585 3956 6.708054 GGCTGTGAGACTGCATAATAGTATTT 59.292 38.462 0.00 0.00 43.66 1.40
3586 3957 7.307632 GGCTGTGAGACTGCATAATAGTATTTG 60.308 40.741 0.00 1.43 43.66 2.32
3632 4003 0.461693 TTTGGCAGCTGCACAAAACC 60.462 50.000 33.87 21.47 44.36 3.27
3846 4247 7.547722 GTGTTTGTTTAGGATTTGTTCTGGTTT 59.452 33.333 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.366273 CCGTTGGTTGATTTGGATGAGTG 60.366 47.826 0.00 0.00 0.00 3.51
39 40 0.173708 GGTTTTGTGCCGTTGGTTGA 59.826 50.000 0.00 0.00 0.00 3.18
114 115 2.826128 AGAGCAAGAGGACACGTGATTA 59.174 45.455 25.01 0.00 0.00 1.75
320 329 3.999001 CGTAGTACTAGGTGTGTCTGACA 59.001 47.826 13.34 6.36 0.00 3.58
340 349 1.246737 GGGGGTGACTCGTAACTCGT 61.247 60.000 0.00 0.00 40.80 4.18
483 537 2.202810 GGCGAGAAGAAGAGGCCG 60.203 66.667 0.00 0.00 33.58 6.13
513 573 2.743126 TCGTCTTCTTCTTCTCCGAGTC 59.257 50.000 0.00 0.00 0.00 3.36
546 606 2.553247 GGGTATTTATGGGAGCTGGCTC 60.553 54.545 13.56 13.56 42.04 4.70
662 732 2.690026 CGGAGGAGGAGGAGGAAATACA 60.690 54.545 0.00 0.00 0.00 2.29
683 753 3.746940 TGTGTTTCTTAGTGGGTAAGGC 58.253 45.455 0.00 0.00 39.03 4.35
717 790 3.334054 GGCAAGGAGGAGGCTGGT 61.334 66.667 0.00 0.00 0.00 4.00
850 938 4.880426 GGGGAGCCCCGATCTGGA 62.880 72.222 9.24 0.00 46.66 3.86
1485 1806 1.026584 GGAGGTAGACGGAGAAGAGC 58.973 60.000 0.00 0.00 0.00 4.09
1585 1906 5.419239 AGGAAAGAAGAGACTGAGATTGG 57.581 43.478 0.00 0.00 0.00 3.16
1671 2026 2.589014 GCAAGCAGCACAACATAGTTC 58.411 47.619 0.00 0.00 44.79 3.01
1684 2039 1.401931 CCACAAATTCTCCGCAAGCAG 60.402 52.381 0.00 0.00 0.00 4.24
1688 2043 0.539438 AGCCCACAAATTCTCCGCAA 60.539 50.000 0.00 0.00 0.00 4.85
1695 2050 0.037975 CAGCCACAGCCCACAAATTC 60.038 55.000 0.00 0.00 41.25 2.17
1700 2055 1.604308 CAATCAGCCACAGCCCACA 60.604 57.895 0.00 0.00 41.25 4.17
1701 2056 0.682209 ATCAATCAGCCACAGCCCAC 60.682 55.000 0.00 0.00 41.25 4.61
1702 2057 0.040058 AATCAATCAGCCACAGCCCA 59.960 50.000 0.00 0.00 41.25 5.36
1703 2058 0.743097 GAATCAATCAGCCACAGCCC 59.257 55.000 0.00 0.00 41.25 5.19
1704 2059 0.379669 CGAATCAATCAGCCACAGCC 59.620 55.000 0.00 0.00 41.25 4.85
1705 2060 1.089920 ACGAATCAATCAGCCACAGC 58.910 50.000 0.00 0.00 40.32 4.40
1706 2061 3.242543 GCTAACGAATCAATCAGCCACAG 60.243 47.826 0.00 0.00 0.00 3.66
1818 2173 5.477510 CCTAGAGGCTAGAGCAAATACATG 58.522 45.833 3.54 0.00 44.36 3.21
2267 2627 4.613622 CGCTCGTTTGAGAAATCCAACAAT 60.614 41.667 0.00 0.00 45.57 2.71
2435 2795 1.153289 CTCCGGCAAGATGTGAGGG 60.153 63.158 0.00 0.00 0.00 4.30
2453 2813 1.004745 TCTGACCCTTTCCTCCATTGC 59.995 52.381 0.00 0.00 0.00 3.56
2645 3005 0.462759 GGCCTCCTCTTGACCAATCG 60.463 60.000 0.00 0.00 0.00 3.34
2675 3035 4.454678 TGATGTTTCCAGCACCATATCTC 58.545 43.478 0.00 0.00 30.62 2.75
2699 3059 0.321564 TGGCCTTGATGAAGTCCACG 60.322 55.000 3.32 0.00 32.12 4.94
2705 3065 2.686915 GTTCCTGATGGCCTTGATGAAG 59.313 50.000 3.32 0.00 0.00 3.02
2810 3170 3.007940 TCGAAGTGAGGTTCATCAATGGT 59.992 43.478 0.00 0.00 0.00 3.55
2853 3213 6.095300 CGATAATATAATGCCAATGGAAGCCA 59.905 38.462 2.05 0.00 38.19 4.75
3054 3415 1.416401 TCCATTACTCGGGAATCAGCC 59.584 52.381 0.00 0.00 0.00 4.85
3196 3557 6.543465 TCACATAAAATTAGCATCCTGACCAG 59.457 38.462 0.00 0.00 0.00 4.00
3310 3676 4.616143 GCTTAAAGGTTTTGAGGCTGTAGC 60.616 45.833 0.00 0.00 41.14 3.58
3311 3677 4.518970 TGCTTAAAGGTTTTGAGGCTGTAG 59.481 41.667 0.00 0.00 0.00 2.74
3312 3678 4.465886 TGCTTAAAGGTTTTGAGGCTGTA 58.534 39.130 0.00 0.00 0.00 2.74
3313 3679 3.295973 TGCTTAAAGGTTTTGAGGCTGT 58.704 40.909 0.00 0.00 0.00 4.40
3314 3680 4.051237 GTTGCTTAAAGGTTTTGAGGCTG 58.949 43.478 0.00 0.00 0.00 4.85
3315 3681 3.704061 TGTTGCTTAAAGGTTTTGAGGCT 59.296 39.130 0.00 0.00 0.00 4.58
3450 3821 3.386768 TCTTCCTTTCTTGTGGAGACG 57.613 47.619 0.00 0.00 33.02 4.18
3585 3956 1.964344 GCCAATTAAGCATGTCCCCCA 60.964 52.381 0.00 0.00 0.00 4.96
3586 3957 0.752658 GCCAATTAAGCATGTCCCCC 59.247 55.000 0.00 0.00 0.00 5.40
3632 4003 2.428171 CCATGTTAGCCAACCAATCCTG 59.572 50.000 0.00 0.00 33.41 3.86


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

AutoCloner maintained by Alex Coulton.