Multiple sequence alignment - TraesCS3D01G373400

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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 TraesCS3D01G373400 chr3D 100.000 4298 0 0 1 4298 487117335 487121632 0.000000e+00 7938.0
1 TraesCS3D01G373400 chr3A 96.677 2558 72 6 752 3302 630767914 630770465 0.000000e+00 4241.0
2 TraesCS3D01G373400 chr3A 86.053 2323 266 30 1005 3298 630760598 630762891 0.000000e+00 2442.0
3 TraesCS3D01G373400 chr3B 96.275 2550 90 3 752 3299 650055902 650058448 0.000000e+00 4178.0
4 TraesCS3D01G373400 chr3B 85.241 2324 290 29 1005 3299 649997089 649999388 0.000000e+00 2342.0
5 TraesCS3D01G373400 chr3B 93.955 579 23 7 3467 4044 79278701 79279268 0.000000e+00 865.0
6 TraesCS3D01G373400 chr3B 83.508 861 141 1 1761 2620 567457246 567458106 0.000000e+00 802.0
7 TraesCS3D01G373400 chr3B 82.269 908 142 13 874 1765 567404481 567405385 0.000000e+00 767.0
8 TraesCS3D01G373400 chr3B 81.322 696 103 14 2612 3299 567458568 567459244 1.360000e-149 540.0
9 TraesCS3D01G373400 chr3B 96.648 179 6 0 3302 3480 79278498 79278676 9.040000e-77 298.0
10 TraesCS3D01G373400 chr3B 92.391 184 12 1 4117 4298 79279266 79279449 1.190000e-65 261.0
11 TraesCS3D01G373400 chr7D 98.354 790 7 3 3304 4092 16699664 16700448 0.000000e+00 1382.0
12 TraesCS3D01G373400 chr7D 88.645 775 60 20 1 751 26209213 26208443 0.000000e+00 918.0
13 TraesCS3D01G373400 chr7D 88.701 770 60 17 1 750 433887560 433888322 0.000000e+00 915.0
14 TraesCS3D01G373400 chr5D 97.662 770 12 2 3302 4070 432160050 432159286 0.000000e+00 1317.0
15 TraesCS3D01G373400 chr5D 96.067 178 7 0 3303 3480 495784669 495784492 1.510000e-74 291.0
16 TraesCS3D01G373400 chr5D 98.125 160 3 0 4139 4298 432158872 432158713 3.270000e-71 279.0
17 TraesCS3D01G373400 chr2D 90.183 764 54 14 1 748 483759712 483758954 0.000000e+00 976.0
18 TraesCS3D01G373400 chr6D 88.475 833 42 17 3469 4298 413374626 413375407 0.000000e+00 957.0
19 TraesCS3D01G373400 chr6D 88.351 764 68 16 1 746 368138558 368139318 0.000000e+00 898.0
20 TraesCS3D01G373400 chr1B 89.474 760 52 16 1 745 562513381 562514127 0.000000e+00 935.0
21 TraesCS3D01G373400 chr6B 88.802 768 63 17 2 749 134485175 134485939 0.000000e+00 920.0
22 TraesCS3D01G373400 chr6B 78.219 831 166 13 1247 2068 184364237 184363413 6.370000e-143 518.0
23 TraesCS3D01G373400 chr6B 77.035 897 174 17 2363 3252 184363091 184362220 1.800000e-133 486.0
24 TraesCS3D01G373400 chr6B 88.679 53 4 2 2823 2874 643545181 643545232 3.590000e-06 63.9
25 TraesCS3D01G373400 chr7A 88.672 768 55 24 1 748 546062880 546062125 0.000000e+00 907.0
26 TraesCS3D01G373400 chr5B 88.512 766 65 16 2 748 56914768 56915529 0.000000e+00 905.0
27 TraesCS3D01G373400 chr5B 93.085 564 28 4 3482 4044 617615694 617616247 0.000000e+00 815.0
28 TraesCS3D01G373400 chr5B 96.610 177 6 0 3304 3480 617615479 617615655 1.170000e-75 294.0
29 TraesCS3D01G373400 chr5B 91.848 184 13 1 4117 4298 617616245 617616428 5.520000e-64 255.0
30 TraesCS3D01G373400 chr5B 96.875 32 1 0 3125 3156 338961569 338961600 2.000000e-03 54.7
31 TraesCS3D01G373400 chr5B 96.875 32 1 0 3125 3156 338967073 338967104 2.000000e-03 54.7
32 TraesCS3D01G373400 chr5A 88.568 761 56 18 4 747 467582932 467583678 0.000000e+00 894.0
33 TraesCS3D01G373400 chr5A 91.367 556 42 2 3467 4022 78470653 78470104 0.000000e+00 756.0
34 TraesCS3D01G373400 chr5A 96.089 179 7 0 3302 3480 78470856 78470678 4.200000e-75 292.0
35 TraesCS3D01G373400 chr5A 90.556 180 12 2 4119 4298 78470104 78469930 2.580000e-57 233.0
36 TraesCS3D01G373400 chr2B 93.794 564 29 4 3482 4044 624289662 624290220 0.000000e+00 843.0
37 TraesCS3D01G373400 chr2B 97.191 178 5 0 3303 3480 624289446 624289623 6.980000e-78 302.0
38 TraesCS3D01G373400 chr2B 92.391 184 12 1 4117 4298 624290218 624290401 1.190000e-65 261.0
39 TraesCS3D01G373400 chr6A 91.727 556 40 2 3467 4022 30140484 30139935 0.000000e+00 767.0
40 TraesCS3D01G373400 chr6A 77.700 852 171 17 1228 2068 119791766 119790923 1.780000e-138 503.0
41 TraesCS3D01G373400 chr6A 77.363 857 163 21 2402 3252 119790562 119789731 3.010000e-131 479.0
42 TraesCS3D01G373400 chr6A 90.556 180 12 2 4119 4298 30139935 30139761 2.580000e-57 233.0
43 TraesCS3D01G373400 chr2A 90.827 556 44 3 3467 4022 711661707 711661159 0.000000e+00 737.0
44 TraesCS3D01G373400 chr2A 79.957 928 116 37 3297 4201 14715076 14715956 1.700000e-173 619.0
45 TraesCS3D01G373400 chr2A 89.944 179 13 2 4119 4297 711661159 711660986 4.320000e-55 226.0
46 TraesCS3D01G373400 chr4D 96.648 179 2 1 3303 3481 472216572 472216398 1.170000e-75 294.0
47 TraesCS3D01G373400 chr4D 95.455 176 4 1 4123 4298 472215084 472214913 1.180000e-70 278.0
48 TraesCS3D01G373400 chr4D 89.583 48 5 0 2845 2892 387756748 387756795 1.290000e-05 62.1


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 TraesCS3D01G373400 chr3D 487117335 487121632 4297 False 7938.000000 7938 100.000000 1 4298 1 chr3D.!!$F1 4297
1 TraesCS3D01G373400 chr3A 630767914 630770465 2551 False 4241.000000 4241 96.677000 752 3302 1 chr3A.!!$F2 2550
2 TraesCS3D01G373400 chr3A 630760598 630762891 2293 False 2442.000000 2442 86.053000 1005 3298 1 chr3A.!!$F1 2293
3 TraesCS3D01G373400 chr3B 650055902 650058448 2546 False 4178.000000 4178 96.275000 752 3299 1 chr3B.!!$F3 2547
4 TraesCS3D01G373400 chr3B 649997089 649999388 2299 False 2342.000000 2342 85.241000 1005 3299 1 chr3B.!!$F2 2294
5 TraesCS3D01G373400 chr3B 567404481 567405385 904 False 767.000000 767 82.269000 874 1765 1 chr3B.!!$F1 891
6 TraesCS3D01G373400 chr3B 567457246 567459244 1998 False 671.000000 802 82.415000 1761 3299 2 chr3B.!!$F5 1538
7 TraesCS3D01G373400 chr3B 79278498 79279449 951 False 474.666667 865 94.331333 3302 4298 3 chr3B.!!$F4 996
8 TraesCS3D01G373400 chr7D 16699664 16700448 784 False 1382.000000 1382 98.354000 3304 4092 1 chr7D.!!$F1 788
9 TraesCS3D01G373400 chr7D 26208443 26209213 770 True 918.000000 918 88.645000 1 751 1 chr7D.!!$R1 750
10 TraesCS3D01G373400 chr7D 433887560 433888322 762 False 915.000000 915 88.701000 1 750 1 chr7D.!!$F2 749
11 TraesCS3D01G373400 chr5D 432158713 432160050 1337 True 798.000000 1317 97.893500 3302 4298 2 chr5D.!!$R2 996
12 TraesCS3D01G373400 chr2D 483758954 483759712 758 True 976.000000 976 90.183000 1 748 1 chr2D.!!$R1 747
13 TraesCS3D01G373400 chr6D 413374626 413375407 781 False 957.000000 957 88.475000 3469 4298 1 chr6D.!!$F2 829
14 TraesCS3D01G373400 chr6D 368138558 368139318 760 False 898.000000 898 88.351000 1 746 1 chr6D.!!$F1 745
15 TraesCS3D01G373400 chr1B 562513381 562514127 746 False 935.000000 935 89.474000 1 745 1 chr1B.!!$F1 744
16 TraesCS3D01G373400 chr6B 134485175 134485939 764 False 920.000000 920 88.802000 2 749 1 chr6B.!!$F1 747
17 TraesCS3D01G373400 chr6B 184362220 184364237 2017 True 502.000000 518 77.627000 1247 3252 2 chr6B.!!$R1 2005
18 TraesCS3D01G373400 chr7A 546062125 546062880 755 True 907.000000 907 88.672000 1 748 1 chr7A.!!$R1 747
19 TraesCS3D01G373400 chr5B 56914768 56915529 761 False 905.000000 905 88.512000 2 748 1 chr5B.!!$F1 746
20 TraesCS3D01G373400 chr5B 617615479 617616428 949 False 454.666667 815 93.847667 3304 4298 3 chr5B.!!$F4 994
21 TraesCS3D01G373400 chr5A 467582932 467583678 746 False 894.000000 894 88.568000 4 747 1 chr5A.!!$F1 743
22 TraesCS3D01G373400 chr5A 78469930 78470856 926 True 427.000000 756 92.670667 3302 4298 3 chr5A.!!$R1 996
23 TraesCS3D01G373400 chr2B 624289446 624290401 955 False 468.666667 843 94.458667 3303 4298 3 chr2B.!!$F1 995
24 TraesCS3D01G373400 chr6A 30139761 30140484 723 True 500.000000 767 91.141500 3467 4298 2 chr6A.!!$R1 831
25 TraesCS3D01G373400 chr6A 119789731 119791766 2035 True 491.000000 503 77.531500 1228 3252 2 chr6A.!!$R2 2024
26 TraesCS3D01G373400 chr2A 14715076 14715956 880 False 619.000000 619 79.957000 3297 4201 1 chr2A.!!$F1 904
27 TraesCS3D01G373400 chr2A 711660986 711661707 721 True 481.500000 737 90.385500 3467 4297 2 chr2A.!!$R1 830
28 TraesCS3D01G373400 chr4D 472214913 472216572 1659 True 286.000000 294 96.051500 3303 4298 2 chr4D.!!$R1 995

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
682 723 2.704572 AGTAGCACACATCTTGAAGCC 58.295 47.619 0.00 0.00 32.44 4.35 F
1095 1168 0.029035 ATCAGCGGACGTCGTACATC 59.971 55.000 9.92 0.00 41.72 3.06 F
1187 1260 1.218585 CTCTAGCAGCAGCAGCAGT 59.781 57.895 12.92 0.00 45.49 4.40 F
2080 2164 0.373370 CACCGTGTCATATGGCAACG 59.627 55.000 12.49 16.64 39.21 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2013 0.389391 CGAGGATACCGTGCTCCATT 59.611 55.000 5.14 0.0 41.86 3.16 R
2080 2164 0.648958 GTTATGGTGGTTAGCGTCGC 59.351 55.000 9.80 9.8 0.00 5.19 R
2240 2339 1.233285 GGTGTTCAGCTGCTCAGTGG 61.233 60.000 9.47 0.0 0.00 4.00 R
3463 4069 1.682394 CGTACCACTAGGAGACCTGCT 60.682 57.143 0.00 0.0 38.69 4.24 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
327 354 8.637281 TGTGCTTTCAATAATATGCAAGAATG 57.363 30.769 0.00 0.00 32.10 2.67
437 464 6.325849 AGTGCGTTTTTCACAAAATTACAC 57.674 33.333 0.00 0.00 36.93 2.90
592 624 4.651045 AGACTTCAGCCCAACAAGAAATTT 59.349 37.500 0.00 0.00 0.00 1.82
603 635 6.215845 CCAACAAGAAATTTACTGACCCAAG 58.784 40.000 6.10 0.00 0.00 3.61
609 641 6.122964 AGAAATTTACTGACCCAAGATAGGC 58.877 40.000 0.00 0.00 0.00 3.93
652 690 3.317711 CCAATAAAGCACACACAACAGGA 59.682 43.478 0.00 0.00 0.00 3.86
682 723 2.704572 AGTAGCACACATCTTGAAGCC 58.295 47.619 0.00 0.00 32.44 4.35
726 769 6.954944 TCGACTGATCCAAAAGTTAAAACTG 58.045 36.000 0.00 0.00 39.66 3.16
1068 1141 3.358118 CTCTCTCTTCCTTACTCCGGTT 58.642 50.000 0.00 0.00 0.00 4.44
1095 1168 0.029035 ATCAGCGGACGTCGTACATC 59.971 55.000 9.92 0.00 41.72 3.06
1187 1260 1.218585 CTCTAGCAGCAGCAGCAGT 59.781 57.895 12.92 0.00 45.49 4.40
1200 1273 3.371063 GCAGTCGACTCACCGGGA 61.371 66.667 16.96 0.00 0.00 5.14
1209 1282 3.438017 CTCACCGGGAGCTGCTAGC 62.438 68.421 8.10 8.10 42.84 3.42
1239 1312 1.783031 CGCGGCTCGTCTACACCTAT 61.783 60.000 0.00 0.00 0.00 2.57
2080 2164 0.373370 CACCGTGTCATATGGCAACG 59.627 55.000 12.49 16.64 39.21 4.10
2240 2339 1.808390 GTCGTGACACCGGGTATGC 60.808 63.158 6.32 0.00 0.00 3.14
2712 3313 1.605457 GCCATGATCAAGTCGGCGATA 60.605 52.381 14.79 0.00 32.14 2.92
2961 3562 2.817423 GAGGTCGTCGACGGCGTAT 61.817 63.158 33.93 23.13 46.26 3.06
3074 3678 2.264794 GGTGACCAGCGTCGGATT 59.735 61.111 0.00 0.00 42.37 3.01
3463 4069 1.955778 CAATCAGGCAGGTTCACACAA 59.044 47.619 0.00 0.00 0.00 3.33
3673 4764 2.867647 GCTTCCATGCAAAACTGTTCCC 60.868 50.000 0.00 0.00 0.00 3.97
3905 5009 0.530650 CACGGGTGGGATCGAAGATG 60.531 60.000 0.00 0.00 45.12 2.90
3906 5010 1.069765 CGGGTGGGATCGAAGATGG 59.930 63.158 0.00 0.00 45.12 3.51
3968 5072 2.027100 TCTCCTCGTCTCACTTCTGCTA 60.027 50.000 0.00 0.00 0.00 3.49
4099 5207 2.134287 GCCCGATGCTCCTGACCTA 61.134 63.158 0.00 0.00 36.87 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.965902 AATGTCACTAATTCATTCCTTCTTAGT 57.034 29.630 0.00 0.00 33.97 2.24
297 323 9.910511 CTTGCATATTATTGAAAGCACAATTTC 57.089 29.630 8.57 0.12 40.36 2.17
327 354 6.127758 TGTGAAAATTCCACTACCATATGCAC 60.128 38.462 0.00 0.00 35.66 4.57
592 624 2.029623 GACGCCTATCTTGGGTCAGTA 58.970 52.381 0.00 0.00 31.82 2.74
636 669 3.951775 TTTTTCCTGTTGTGTGTGCTT 57.048 38.095 0.00 0.00 0.00 3.91
659 699 3.669023 GCTTCAAGATGTGTGCTACTTGC 60.669 47.826 0.00 0.00 39.33 4.01
726 769 4.499183 ACACTTTAGCTACATGTCAGCTC 58.501 43.478 24.04 4.48 46.37 4.09
788 835 1.617947 GCAGGAGGAACCGAGGTCAT 61.618 60.000 0.00 0.00 44.74 3.06
1124 1197 2.032681 GGTGGTTGGAGAGCGCTT 59.967 61.111 13.26 0.58 36.53 4.68
1187 1260 3.062466 CAGCTCCCGGTGAGTCGA 61.062 66.667 17.79 0.00 43.48 4.20
1239 1312 4.794439 CCGTGGAGCGCATCGTCA 62.794 66.667 11.47 0.00 39.71 4.35
1932 2013 0.389391 CGAGGATACCGTGCTCCATT 59.611 55.000 5.14 0.00 41.86 3.16
2048 2132 1.346395 ACACGGTGCCAGAGAACATTA 59.654 47.619 8.30 0.00 0.00 1.90
2080 2164 0.648958 GTTATGGTGGTTAGCGTCGC 59.351 55.000 9.80 9.80 0.00 5.19
2240 2339 1.233285 GGTGTTCAGCTGCTCAGTGG 61.233 60.000 9.47 0.00 0.00 4.00
2691 3292 1.815003 CGCCGACTTGATCATGGCA 60.815 57.895 21.38 0.00 46.02 4.92
2712 3313 2.358247 GTGGTCGCGGTGGTCATT 60.358 61.111 6.13 0.00 0.00 2.57
2961 3562 1.919240 TGGACGAGAAGGAGCAGTTA 58.081 50.000 0.00 0.00 0.00 2.24
3172 3776 2.937149 TGATGTCTACCTCGAACGAGAG 59.063 50.000 22.96 14.25 44.53 3.20
3463 4069 1.682394 CGTACCACTAGGAGACCTGCT 60.682 57.143 0.00 0.00 38.69 4.24
3905 5009 3.472726 TACCCGCGTTCCCATCCC 61.473 66.667 4.92 0.00 0.00 3.85
3906 5010 2.202974 GTACCCGCGTTCCCATCC 60.203 66.667 4.92 0.00 0.00 3.51
4112 5220 0.179150 TTGAAACACAACACGCTGCC 60.179 50.000 0.00 0.00 33.18 4.85
4113 5221 3.320884 TTGAAACACAACACGCTGC 57.679 47.368 0.00 0.00 33.18 5.25


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

AutoCloner maintained by Alex Coulton.