Multiple sequence alignment - TraesCS1D01G123000

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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 TraesCS1D01G123000 chr1D 100.000 2567 0 0 1 2567 124102973 124105539 0.000000e+00 4741
1 TraesCS1D01G123000 chr1D 98.221 787 14 0 1 787 378301193 378300407 0.000000e+00 1376
2 TraesCS1D01G123000 chr1D 98.219 786 14 0 1 786 494178089 494177304 0.000000e+00 1375
3 TraesCS1D01G123000 chr1D 98.096 788 14 1 1 787 300053447 300052660 0.000000e+00 1371
4 TraesCS1D01G123000 chr1D 98.092 786 15 0 1 786 378294359 378293574 0.000000e+00 1369
5 TraesCS1D01G123000 chr1D 98.092 786 15 0 1 786 433858099 433858884 0.000000e+00 1369
6 TraesCS1D01G123000 chr1D 97.967 787 16 0 1 787 124096174 124096960 0.000000e+00 1365
7 TraesCS1D01G123000 chr3D 98.516 1011 14 1 1558 2567 495983823 495982813 0.000000e+00 1783
8 TraesCS1D01G123000 chr3D 98.408 1005 15 1 1564 2567 280541414 280540410 0.000000e+00 1766
9 TraesCS1D01G123000 chr3D 98.220 1011 15 3 1559 2567 253587210 253586201 0.000000e+00 1764
10 TraesCS1D01G123000 chr3D 97.833 1015 20 2 1555 2567 342470960 342469946 0.000000e+00 1751
11 TraesCS1D01G123000 chr5D 98.221 1012 16 2 1558 2567 564812520 564813531 0.000000e+00 1768
12 TraesCS1D01G123000 chr5D 98.406 1004 15 1 1565 2567 196885130 196886133 0.000000e+00 1764
13 TraesCS1D01G123000 chr5D 98.406 1004 13 2 1565 2567 88506471 88505470 0.000000e+00 1762
14 TraesCS1D01G123000 chr5D 89.896 772 76 2 794 1565 424050101 424050870 0.000000e+00 992
15 TraesCS1D01G123000 chr7D 98.408 1005 15 1 1564 2567 289331179 289332183 0.000000e+00 1766
16 TraesCS1D01G123000 chr7D 98.213 1007 17 1 1562 2567 23606604 23607610 0.000000e+00 1759
17 TraesCS1D01G123000 chr6D 98.348 787 13 0 1 787 10182856 10182070 0.000000e+00 1382
18 TraesCS1D01G123000 chr2D 98.092 786 15 0 1 786 571119342 571120127 0.000000e+00 1369
19 TraesCS1D01G123000 chr2D 97.848 790 17 0 1 790 526361761 526360972 0.000000e+00 1365
20 TraesCS1D01G123000 chr5A 89.419 775 77 3 794 1565 17624995 17624223 0.000000e+00 972
21 TraesCS1D01G123000 chr3A 89.003 782 79 4 787 1565 746538942 746539719 0.000000e+00 961
22 TraesCS1D01G123000 chr3A 81.562 781 116 14 789 1559 36882766 36883528 1.010000e-173 619
23 TraesCS1D01G123000 chr2A 88.531 776 81 6 794 1565 423771005 423770234 0.000000e+00 933
24 TraesCS1D01G123000 chr2A 84.319 778 108 6 788 1553 654865284 654864509 0.000000e+00 749
25 TraesCS1D01G123000 chr1B 86.061 782 102 4 787 1565 676249965 676250742 0.000000e+00 833
26 TraesCS1D01G123000 chr4B 83.592 774 116 5 789 1553 656869280 656868509 0.000000e+00 715
27 TraesCS1D01G123000 chr7A 84.032 739 109 4 828 1557 65494220 65493482 0.000000e+00 702


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 TraesCS1D01G123000 chr1D 124102973 124105539 2566 False 4741 4741 100.000 1 2567 1 chr1D.!!$F2 2566
1 TraesCS1D01G123000 chr1D 378300407 378301193 786 True 1376 1376 98.221 1 787 1 chr1D.!!$R3 786
2 TraesCS1D01G123000 chr1D 494177304 494178089 785 True 1375 1375 98.219 1 786 1 chr1D.!!$R4 785
3 TraesCS1D01G123000 chr1D 300052660 300053447 787 True 1371 1371 98.096 1 787 1 chr1D.!!$R1 786
4 TraesCS1D01G123000 chr1D 378293574 378294359 785 True 1369 1369 98.092 1 786 1 chr1D.!!$R2 785
5 TraesCS1D01G123000 chr1D 433858099 433858884 785 False 1369 1369 98.092 1 786 1 chr1D.!!$F3 785
6 TraesCS1D01G123000 chr1D 124096174 124096960 786 False 1365 1365 97.967 1 787 1 chr1D.!!$F1 786
7 TraesCS1D01G123000 chr3D 495982813 495983823 1010 True 1783 1783 98.516 1558 2567 1 chr3D.!!$R4 1009
8 TraesCS1D01G123000 chr3D 280540410 280541414 1004 True 1766 1766 98.408 1564 2567 1 chr3D.!!$R2 1003
9 TraesCS1D01G123000 chr3D 253586201 253587210 1009 True 1764 1764 98.220 1559 2567 1 chr3D.!!$R1 1008
10 TraesCS1D01G123000 chr3D 342469946 342470960 1014 True 1751 1751 97.833 1555 2567 1 chr3D.!!$R3 1012
11 TraesCS1D01G123000 chr5D 564812520 564813531 1011 False 1768 1768 98.221 1558 2567 1 chr5D.!!$F3 1009
12 TraesCS1D01G123000 chr5D 196885130 196886133 1003 False 1764 1764 98.406 1565 2567 1 chr5D.!!$F1 1002
13 TraesCS1D01G123000 chr5D 88505470 88506471 1001 True 1762 1762 98.406 1565 2567 1 chr5D.!!$R1 1002
14 TraesCS1D01G123000 chr5D 424050101 424050870 769 False 992 992 89.896 794 1565 1 chr5D.!!$F2 771
15 TraesCS1D01G123000 chr7D 289331179 289332183 1004 False 1766 1766 98.408 1564 2567 1 chr7D.!!$F2 1003
16 TraesCS1D01G123000 chr7D 23606604 23607610 1006 False 1759 1759 98.213 1562 2567 1 chr7D.!!$F1 1005
17 TraesCS1D01G123000 chr6D 10182070 10182856 786 True 1382 1382 98.348 1 787 1 chr6D.!!$R1 786
18 TraesCS1D01G123000 chr2D 571119342 571120127 785 False 1369 1369 98.092 1 786 1 chr2D.!!$F1 785
19 TraesCS1D01G123000 chr2D 526360972 526361761 789 True 1365 1365 97.848 1 790 1 chr2D.!!$R1 789
20 TraesCS1D01G123000 chr5A 17624223 17624995 772 True 972 972 89.419 794 1565 1 chr5A.!!$R1 771
21 TraesCS1D01G123000 chr3A 746538942 746539719 777 False 961 961 89.003 787 1565 1 chr3A.!!$F2 778
22 TraesCS1D01G123000 chr3A 36882766 36883528 762 False 619 619 81.562 789 1559 1 chr3A.!!$F1 770
23 TraesCS1D01G123000 chr2A 423770234 423771005 771 True 933 933 88.531 794 1565 1 chr2A.!!$R1 771
24 TraesCS1D01G123000 chr2A 654864509 654865284 775 True 749 749 84.319 788 1553 1 chr2A.!!$R2 765
25 TraesCS1D01G123000 chr1B 676249965 676250742 777 False 833 833 86.061 787 1565 1 chr1B.!!$F1 778
26 TraesCS1D01G123000 chr4B 656868509 656869280 771 True 715 715 83.592 789 1553 1 chr4B.!!$R1 764
27 TraesCS1D01G123000 chr7A 65493482 65494220 738 True 702 702 84.032 828 1557 1 chr7A.!!$R1 729

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
797 799 0.693049 TTCCTTCAGGCACTTCTCCC 59.307 55.0 0.0 0.0 34.6 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 1887 0.3199 CCGATCCAATGCCTACGAGG 60.32 60.0 0.0 0.0 38.8 4.63 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
154 155 3.604065 TTCGATCGTCGGTATCTCAAG 57.396 47.619 15.94 0.00 40.88 3.02
247 249 1.962807 AGTTACAATGCTTGCAAGGCA 59.037 42.857 27.10 23.46 44.05 4.75
375 377 6.958767 ACACCTGTAGAGCACCTTTATAATT 58.041 36.000 0.00 0.00 0.00 1.40
427 429 3.818773 CACAAAGTGTTCCTCCGGTAAAT 59.181 43.478 0.00 0.00 0.00 1.40
548 550 5.220548 GGTCAAGTCAATCACATCATTCTCG 60.221 44.000 0.00 0.00 0.00 4.04
787 789 4.263243 CCTCTAGGGCATATTTCCTTCAGG 60.263 50.000 0.00 2.64 34.75 3.86
790 792 1.683385 GGGCATATTTCCTTCAGGCAC 59.317 52.381 0.00 0.00 34.44 5.01
791 793 2.659428 GGCATATTTCCTTCAGGCACT 58.341 47.619 0.00 0.00 43.88 4.40
792 794 3.026694 GGCATATTTCCTTCAGGCACTT 58.973 45.455 0.00 0.00 34.60 3.16
793 795 3.067320 GGCATATTTCCTTCAGGCACTTC 59.933 47.826 0.00 0.00 34.60 3.01
794 796 3.950395 GCATATTTCCTTCAGGCACTTCT 59.050 43.478 0.00 0.00 34.60 2.85
795 797 4.036144 GCATATTTCCTTCAGGCACTTCTC 59.964 45.833 0.00 0.00 34.60 2.87
796 798 2.568623 TTTCCTTCAGGCACTTCTCC 57.431 50.000 0.00 0.00 34.60 3.71
797 799 0.693049 TTCCTTCAGGCACTTCTCCC 59.307 55.000 0.00 0.00 34.60 4.30
798 800 1.201429 TCCTTCAGGCACTTCTCCCC 61.201 60.000 0.00 0.00 34.60 4.81
799 801 1.204113 CCTTCAGGCACTTCTCCCCT 61.204 60.000 0.00 0.00 34.60 4.79
812 814 2.348472 TCTCCCCTGTTCATCTTTGGT 58.652 47.619 0.00 0.00 0.00 3.67
818 820 4.256920 CCCTGTTCATCTTTGGTACTCTG 58.743 47.826 0.00 0.00 0.00 3.35
821 823 3.072330 TGTTCATCTTTGGTACTCTGCCA 59.928 43.478 0.00 0.00 0.00 4.92
824 826 2.024176 TCTTTGGTACTCTGCCAGGA 57.976 50.000 0.00 0.00 37.31 3.86
846 848 3.774528 CCTAGCGCCACTGCTCCA 61.775 66.667 2.29 0.00 45.87 3.86
861 863 1.618074 GCTCCAGCTTCCTCCCAATTT 60.618 52.381 0.00 0.00 38.21 1.82
960 983 4.768968 CACATCAAATTCCTTCTCAACCCT 59.231 41.667 0.00 0.00 0.00 4.34
1014 1038 1.860641 TCCTTATGGTCCTGCTTCGA 58.139 50.000 0.00 0.00 34.23 3.71
1042 1066 3.304324 CGTCATGTATCTGATCGAGCACT 60.304 47.826 0.00 0.00 0.00 4.40
1051 1075 1.107114 GATCGAGCACTCTCCTCCAA 58.893 55.000 0.00 0.00 35.94 3.53
1053 1077 0.251386 TCGAGCACTCTCCTCCAACT 60.251 55.000 0.00 0.00 35.94 3.16
1064 1088 1.349688 TCCTCCAACTAACGCCAACAT 59.650 47.619 0.00 0.00 0.00 2.71
1086 1110 1.542030 CAGTACCTTGAGCTCGACACT 59.458 52.381 9.64 5.83 0.00 3.55
1110 1134 2.111878 GCCCTCGCCATGTATGCT 59.888 61.111 0.00 0.00 0.00 3.79
1129 1153 2.815963 GCTACCCTCTCCGATCAGATCA 60.816 54.545 11.12 0.00 0.00 2.92
1138 1162 2.765699 TCCGATCAGATCATTGACCACA 59.234 45.455 11.12 0.00 0.00 4.17
1146 1170 3.470709 GATCATTGACCACATGATCGGT 58.529 45.455 0.00 2.38 40.56 4.69
1195 1219 3.024547 CAGATTCGGGACTACTTCCTCA 58.975 50.000 0.00 0.00 45.09 3.86
1205 1229 2.029290 ACTACTTCCTCACAAATCGCGT 60.029 45.455 5.77 0.00 0.00 6.01
1208 1232 0.953471 TTCCTCACAAATCGCGTGGG 60.953 55.000 5.77 0.00 35.03 4.61
1251 1275 4.377943 CGTCAATATCGCAACCTCAAACAA 60.378 41.667 0.00 0.00 0.00 2.83
1252 1276 5.640732 GTCAATATCGCAACCTCAAACAAT 58.359 37.500 0.00 0.00 0.00 2.71
1282 1306 4.815293 TCGACGAATACGCGCGCA 62.815 61.111 32.58 20.08 43.96 6.09
1313 1337 4.657824 CACCGCGGGTCTCGTGTT 62.658 66.667 31.76 0.57 46.86 3.32
1445 1469 1.329599 GTTTGAGACCGTGTTTTCGCT 59.670 47.619 0.00 0.00 0.00 4.93
1929 1954 6.845782 CGGTTCATCATGTAACAATCATAACG 59.154 38.462 0.00 0.00 0.00 3.18
2424 2449 8.249638 CGATTACATGATAGATCTCATCCAACT 58.750 37.037 0.00 0.00 33.59 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 3.181482 TGACAAAGGGAACAACGTACGTA 60.181 43.478 23.12 0.00 0.00 3.57
92 93 3.120786 CGATGACAAAGGGAACAACGTAC 60.121 47.826 0.00 0.00 0.00 3.67
247 249 5.987953 CACTCAGTAATGCACAGCACTATAT 59.012 40.000 0.00 0.00 43.04 0.86
255 257 1.089920 GCCCACTCAGTAATGCACAG 58.910 55.000 0.00 0.00 0.00 3.66
375 377 2.420628 CGTCACAACGTAACTGGGTA 57.579 50.000 0.00 0.00 43.94 3.69
427 429 5.366477 TGACTATGAGATTATGCAACTCCCA 59.634 40.000 0.00 0.00 0.00 4.37
548 550 7.490962 TTGATTAACGGGATCACATCATTAC 57.509 36.000 0.00 0.00 33.51 1.89
787 789 1.280421 AGATGAACAGGGGAGAAGTGC 59.720 52.381 0.00 0.00 0.00 4.40
790 792 3.245052 ACCAAAGATGAACAGGGGAGAAG 60.245 47.826 0.00 0.00 0.00 2.85
791 793 2.716424 ACCAAAGATGAACAGGGGAGAA 59.284 45.455 0.00 0.00 0.00 2.87
792 794 2.348472 ACCAAAGATGAACAGGGGAGA 58.652 47.619 0.00 0.00 0.00 3.71
793 795 2.887151 ACCAAAGATGAACAGGGGAG 57.113 50.000 0.00 0.00 0.00 4.30
794 796 3.256704 AGTACCAAAGATGAACAGGGGA 58.743 45.455 0.00 0.00 0.00 4.81
795 797 3.264450 AGAGTACCAAAGATGAACAGGGG 59.736 47.826 0.00 0.00 0.00 4.79
796 798 4.256920 CAGAGTACCAAAGATGAACAGGG 58.743 47.826 0.00 0.00 0.00 4.45
797 799 3.686726 GCAGAGTACCAAAGATGAACAGG 59.313 47.826 0.00 0.00 0.00 4.00
798 800 3.686726 GGCAGAGTACCAAAGATGAACAG 59.313 47.826 0.00 0.00 0.00 3.16
799 801 3.072330 TGGCAGAGTACCAAAGATGAACA 59.928 43.478 0.00 0.00 33.12 3.18
812 814 2.868964 AGGGTTATCCTGGCAGAGTA 57.131 50.000 17.94 5.37 46.07 2.59
824 826 1.146263 GCAGTGGCGCTAGGGTTAT 59.854 57.895 7.64 0.00 0.00 1.89
846 848 1.618074 GGAGCAAATTGGGAGGAAGCT 60.618 52.381 0.00 0.00 0.00 3.74
861 863 1.613630 GGAGGTGAAGAGGGGAGCA 60.614 63.158 0.00 0.00 0.00 4.26
960 983 3.068560 GTTGTGGTAATTGTGCTCGGTA 58.931 45.455 0.00 0.00 0.00 4.02
1014 1038 3.426292 CGATCAGATACATGACGCCGTAT 60.426 47.826 0.00 0.00 30.46 3.06
1042 1066 1.001633 GTTGGCGTTAGTTGGAGGAGA 59.998 52.381 0.00 0.00 0.00 3.71
1051 1075 2.354403 GGTACTGGATGTTGGCGTTAGT 60.354 50.000 0.00 0.00 0.00 2.24
1053 1077 1.903860 AGGTACTGGATGTTGGCGTTA 59.096 47.619 0.00 0.00 37.18 3.18
1064 1088 1.174783 GTCGAGCTCAAGGTACTGGA 58.825 55.000 15.40 0.00 40.86 3.86
1110 1134 3.816398 ATGATCTGATCGGAGAGGGTA 57.184 47.619 10.61 0.00 43.63 3.69
1129 1153 1.382522 GCACCGATCATGTGGTCAAT 58.617 50.000 12.75 0.00 35.96 2.57
1138 1162 2.272146 GGTGGTGGCACCGATCAT 59.728 61.111 30.14 0.00 42.58 2.45
1146 1170 0.605319 GATCGAAAGTGGTGGTGGCA 60.605 55.000 0.00 0.00 0.00 4.92
1195 1219 2.157305 TACCGACCCACGCGATTTGT 62.157 55.000 15.93 3.74 41.07 2.83
1205 1229 0.464036 GAGCATCATGTACCGACCCA 59.536 55.000 0.00 0.00 33.17 4.51
1251 1275 1.649815 GTCGACGGAGAGATCGCAT 59.350 57.895 0.00 0.00 38.24 4.73
1252 1276 2.810012 CGTCGACGGAGAGATCGCA 61.810 63.158 29.70 0.00 38.24 5.10
1445 1469 1.532604 TTCTTCGGCGAGCTTCAGGA 61.533 55.000 10.46 0.00 0.00 3.86
1862 1887 0.319900 CCGATCCAATGCCTACGAGG 60.320 60.000 0.00 0.00 38.80 4.63
1929 1954 2.826725 AGCTAGTTCTGTGTCACCCTAC 59.173 50.000 0.00 0.00 0.00 3.18
2424 2449 1.375908 GCTTGCTGGACGGTGATGA 60.376 57.895 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.