Multiple sequence alignment - TraesCS3D01G190300

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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 TraesCS3D01G190300 chr3D 100.000 3596 0 0 1 3596 178594247 178590652 0.000000e+00 6641.0
1 TraesCS3D01G190300 chr3B 95.490 3614 115 24 1 3596 257040086 257036503 0.000000e+00 5727.0
2 TraesCS3D01G190300 chr3A 95.012 3007 110 20 1 3002 220889680 220886709 0.000000e+00 4686.0
3 TraesCS3D01G190300 chr3A 94.754 610 22 5 2992 3594 220886637 220886031 0.000000e+00 941.0
4 TraesCS3D01G190300 chr3A 100.000 33 0 0 3333 3365 220886258 220886226 1.080000e-05 62.1
5 TraesCS3D01G190300 chr4B 87.179 78 8 2 3367 3443 421725725 421725649 1.780000e-13 87.9
6 TraesCS3D01G190300 chr5B 86.111 72 8 2 3367 3437 461494076 461494146 3.850000e-10 76.8
7 TraesCS3D01G190300 chr2D 100.000 28 0 0 620 647 602667556 602667529 6.000000e-03 52.8


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 TraesCS3D01G190300 chr3D 178590652 178594247 3595 True 6641.000000 6641 100.000000 1 3596 1 chr3D.!!$R1 3595
1 TraesCS3D01G190300 chr3B 257036503 257040086 3583 True 5727.000000 5727 95.490000 1 3596 1 chr3B.!!$R1 3595
2 TraesCS3D01G190300 chr3A 220886031 220889680 3649 True 1896.366667 4686 96.588667 1 3594 3 chr3A.!!$R1 3593

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
717 726 0.042431 AGAGCTCCACCAGTCCATCT 59.958 55.0 10.93 0.0 0.00 2.9 F
718 727 0.177604 GAGCTCCACCAGTCCATCTG 59.822 60.0 0.87 0.0 43.27 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 2379 1.202582 GAGTCGCCAGCTTCAGTCTTA 59.797 52.381 0.0 0.0 0.00 2.10 R
2893 2907 3.968649 TCACATTCAAACAGAAAGCTGC 58.031 40.909 0.0 0.0 46.26 5.25 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 1.535444 ATCACCCCTGTCACCGTCA 60.535 57.895 0.00 0.00 0.00 4.35
34 35 1.518352 TCATGGTCGTCGCCAATCG 60.518 57.895 11.52 5.16 42.48 3.34
107 109 4.465512 CATTGCAGCCACGACCGC 62.466 66.667 0.00 0.00 0.00 5.68
133 135 1.671328 TCGTGTTCCGACAAATTGCAA 59.329 42.857 0.00 0.00 41.60 4.08
167 169 1.833606 TTGGAGTCGCTGGTTCCAA 59.166 52.632 1.27 1.27 45.95 3.53
235 240 2.526873 ACCTTGTGGTCTCCGCCT 60.527 61.111 0.00 0.00 44.78 5.52
242 248 4.767255 GGTCTCCGCCTGTGCCAG 62.767 72.222 0.00 0.00 0.00 4.85
351 358 0.179089 CTAGAGCTCTGCGGCATGTT 60.179 55.000 26.78 0.00 34.17 2.71
352 359 0.179100 TAGAGCTCTGCGGCATGTTC 60.179 55.000 26.78 7.45 34.17 3.18
357 364 3.725459 CTGCGGCATGTTCGTGCA 61.725 61.111 16.98 6.04 46.81 4.57
461 469 0.915364 AGTGATTGAGGGGAAGAGGC 59.085 55.000 0.00 0.00 0.00 4.70
478 486 4.488136 CCTATGCGTGGGGCTGCA 62.488 66.667 0.00 0.00 46.51 4.41
516 524 2.942804 TGAAGTTGATGGGTTCTGCAA 58.057 42.857 0.00 0.00 0.00 4.08
553 561 2.809174 CGACCGACGCAATGCTCA 60.809 61.111 2.94 0.00 34.51 4.26
558 566 2.789917 GACGCAATGCTCAGCCAG 59.210 61.111 2.94 0.00 0.00 4.85
578 586 6.992123 AGCCAGTTGATCGTATTGAATCATTA 59.008 34.615 0.00 0.00 0.00 1.90
579 587 7.041780 AGCCAGTTGATCGTATTGAATCATTAC 60.042 37.037 5.49 5.49 0.00 1.89
580 588 7.576236 CCAGTTGATCGTATTGAATCATTACC 58.424 38.462 9.02 0.00 0.00 2.85
581 589 7.283633 CAGTTGATCGTATTGAATCATTACCG 58.716 38.462 9.02 5.67 0.00 4.02
582 590 7.169140 CAGTTGATCGTATTGAATCATTACCGA 59.831 37.037 9.02 9.58 0.00 4.69
583 591 7.709182 AGTTGATCGTATTGAATCATTACCGAA 59.291 33.333 9.02 0.00 0.00 4.30
584 592 8.332464 GTTGATCGTATTGAATCATTACCGAAA 58.668 33.333 9.02 2.25 0.00 3.46
585 593 8.426881 TGATCGTATTGAATCATTACCGAAAA 57.573 30.769 9.02 2.61 0.00 2.29
586 594 9.051679 TGATCGTATTGAATCATTACCGAAAAT 57.948 29.630 9.02 0.00 0.00 1.82
595 603 9.621629 TGAATCATTACCGAAAATAATGTAGGT 57.378 29.630 5.02 0.00 39.83 3.08
647 655 8.521170 TTATATTATGAGACGGATGGAGTAGG 57.479 38.462 0.00 0.00 0.00 3.18
654 662 3.053842 AGACGGATGGAGTAGGTCTTACA 60.054 47.826 0.00 0.00 34.49 2.41
673 681 0.106918 ACGCACTTCCCAAACTTCCA 60.107 50.000 0.00 0.00 0.00 3.53
715 724 1.908340 GCAGAGCTCCACCAGTCCAT 61.908 60.000 10.93 0.00 0.00 3.41
716 725 0.177604 CAGAGCTCCACCAGTCCATC 59.822 60.000 10.93 0.00 0.00 3.51
717 726 0.042431 AGAGCTCCACCAGTCCATCT 59.958 55.000 10.93 0.00 0.00 2.90
718 727 0.177604 GAGCTCCACCAGTCCATCTG 59.822 60.000 0.87 0.00 43.27 2.90
1199 1211 2.203126 GCGGGAAGAGCAGGATGG 60.203 66.667 0.00 0.00 35.86 3.51
1302 1314 2.520904 GCTGATCAAGACGCTCGCC 61.521 63.158 0.00 0.00 0.00 5.54
2082 2094 1.078497 CGTAAGCAGGGCCATGTCA 60.078 57.895 20.22 1.12 0.00 3.58
2190 2202 7.147408 ACAATACCAGATAAGAAAGAGGAGCAT 60.147 37.037 0.00 0.00 0.00 3.79
2366 2378 3.177884 TGGCACTGGGCAGGAAGT 61.178 61.111 3.46 0.00 45.76 3.01
2367 2379 2.766925 TGGCACTGGGCAGGAAGTT 61.767 57.895 3.46 0.00 45.76 2.66
2649 2661 4.068599 AGTGCTCTAAAAAGCCTCAAGTC 58.931 43.478 0.00 0.00 41.77 3.01
2868 2882 3.414549 AACTTGTTTGCGGTTAGTGTG 57.585 42.857 0.00 0.00 0.00 3.82
2919 2933 6.580041 CAGCTTTCTGTTTGAATGTGATACAC 59.420 38.462 0.00 0.00 35.61 2.90
3078 3176 0.319405 ATTTGCAGTGCTTGAAGGCC 59.681 50.000 17.60 0.00 0.00 5.19
3262 3364 8.257602 TCAGTATAGGTAGCAATATTGGTTCA 57.742 34.615 24.01 5.76 39.88 3.18
3404 3508 3.123804 CGCTAGCAACCAAACTCGATAT 58.876 45.455 16.45 0.00 0.00 1.63
3408 3512 6.237996 CGCTAGCAACCAAACTCGATATAAAA 60.238 38.462 16.45 0.00 0.00 1.52
3409 3513 7.126398 GCTAGCAACCAAACTCGATATAAAAG 58.874 38.462 10.63 0.00 0.00 2.27
3410 3514 7.201617 GCTAGCAACCAAACTCGATATAAAAGT 60.202 37.037 10.63 0.00 0.00 2.66
3412 3516 6.093633 AGCAACCAAACTCGATATAAAAGTCC 59.906 38.462 0.00 0.00 0.00 3.85
3414 3518 5.114081 ACCAAACTCGATATAAAAGTCCGG 58.886 41.667 0.00 0.00 0.00 5.14
3415 3519 4.025145 CCAAACTCGATATAAAAGTCCGGC 60.025 45.833 0.00 0.00 0.00 6.13
3416 3520 4.667519 AACTCGATATAAAAGTCCGGCT 57.332 40.909 0.00 0.00 0.00 5.52
3417 3521 4.240175 ACTCGATATAAAAGTCCGGCTC 57.760 45.455 0.00 0.00 0.00 4.70
3477 3581 1.068333 CCAAACTGCGCTAAAGCATGT 60.068 47.619 9.73 0.00 46.97 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.248907 CTACGATTGGCGACGACCAT 60.249 55.000 11.00 0.00 44.57 3.55
53 54 2.331194 AGCGATGCAATTTGCTTGAAC 58.669 42.857 21.19 8.09 45.31 3.18
96 97 4.388499 AAATCGGCGGTCGTGGCT 62.388 61.111 7.21 0.00 40.32 4.75
153 155 1.757682 TTTTGTTGGAACCAGCGACT 58.242 45.000 3.51 0.00 0.00 4.18
194 199 4.043200 GCTGCAACCACTTCGGCC 62.043 66.667 0.00 0.00 39.03 6.13
196 201 2.671177 CGAGCTGCAACCACTTCGG 61.671 63.158 1.02 0.00 42.50 4.30
199 204 3.349006 CGCGAGCTGCAACCACTT 61.349 61.111 0.00 0.00 46.97 3.16
235 240 1.900016 CTTGCAAGCTCCTGGCACA 60.900 57.895 14.65 0.00 40.47 4.57
287 293 2.125512 GCATCGTCGCTGGGAACT 60.126 61.111 0.00 0.00 0.00 3.01
351 358 4.631740 TCCTCCCCCACTGCACGA 62.632 66.667 0.00 0.00 0.00 4.35
352 359 4.087892 CTCCTCCCCCACTGCACG 62.088 72.222 0.00 0.00 0.00 5.34
357 364 2.540910 TCCTCCTCCTCCCCCACT 60.541 66.667 0.00 0.00 0.00 4.00
405 412 3.753797 GCCTCGTCTTTTCTTCTTTCCAT 59.246 43.478 0.00 0.00 0.00 3.41
461 469 3.993614 TTGCAGCCCCACGCATAGG 62.994 63.158 0.00 0.00 41.38 2.57
490 498 2.610438 ACCCATCAACTTCAAGGCAT 57.390 45.000 0.00 0.00 0.00 4.40
516 524 2.077801 CTTATGCATTCGTCGCGCGT 62.078 55.000 30.98 6.92 42.13 6.01
553 561 4.769688 TGATTCAATACGATCAACTGGCT 58.230 39.130 0.00 0.00 0.00 4.75
558 566 7.402811 TCGGTAATGATTCAATACGATCAAC 57.597 36.000 5.94 0.00 0.00 3.18
621 629 8.967918 CCTACTCCATCCGTCTCATAATATAAA 58.032 37.037 0.00 0.00 0.00 1.40
647 655 1.873698 TTGGGAAGTGCGTGTAAGAC 58.126 50.000 0.00 0.00 0.00 3.01
654 662 0.106918 TGGAAGTTTGGGAAGTGCGT 60.107 50.000 0.00 0.00 0.00 5.24
673 681 1.424638 CCTAACGGGTCTGGATCCAT 58.575 55.000 16.63 0.18 0.00 3.41
720 729 1.227943 TGCGATTAGGGCCAGATGC 60.228 57.895 6.18 3.32 40.16 3.91
721 730 0.886490 GGTGCGATTAGGGCCAGATG 60.886 60.000 6.18 0.00 0.00 2.90
722 731 1.451936 GGTGCGATTAGGGCCAGAT 59.548 57.895 6.18 0.00 0.00 2.90
723 732 2.908015 GGTGCGATTAGGGCCAGA 59.092 61.111 6.18 0.00 0.00 3.86
921 930 1.240256 GGCGTCAGGAGATAGATCGT 58.760 55.000 0.00 0.00 0.00 3.73
1215 1227 3.519973 CTCATCCGCTGCCGCCATA 62.520 63.158 0.00 0.00 0.00 2.74
1900 1912 7.414319 GCCTTCAATCTCATCTTTTCTCTCTTG 60.414 40.741 0.00 0.00 0.00 3.02
2082 2094 3.641906 TGAGTTCTTCCTCGTCTTCCTTT 59.358 43.478 0.00 0.00 34.04 3.11
2190 2202 2.730382 TGGCTAACAGACTCACCGATA 58.270 47.619 0.00 0.00 0.00 2.92
2366 2378 1.618837 AGTCGCCAGCTTCAGTCTTAA 59.381 47.619 0.00 0.00 0.00 1.85
2367 2379 1.202582 GAGTCGCCAGCTTCAGTCTTA 59.797 52.381 0.00 0.00 0.00 2.10
2893 2907 3.968649 TCACATTCAAACAGAAAGCTGC 58.031 40.909 0.00 0.00 46.26 5.25
3008 3105 5.071788 TGAACTCCAGTCAAGTTACCTTCAT 59.928 40.000 0.00 0.00 37.10 2.57
3404 3508 0.249398 GGAGCAGAGCCGGACTTTTA 59.751 55.000 5.05 0.00 0.00 1.52
3414 3518 1.294659 CTGTTTGGACGGAGCAGAGC 61.295 60.000 0.00 0.00 33.82 4.09
3415 3519 0.034059 ACTGTTTGGACGGAGCAGAG 59.966 55.000 0.00 0.00 36.01 3.35
3416 3520 0.249868 CACTGTTTGGACGGAGCAGA 60.250 55.000 0.00 0.00 36.01 4.26
3417 3521 2.238353 CACTGTTTGGACGGAGCAG 58.762 57.895 0.00 0.00 36.01 4.24
3477 3581 4.437794 CGTAGGACGTGTAATTCAGTAGCA 60.438 45.833 0.00 0.00 36.74 3.49


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

AutoCloner maintained by Alex Coulton.