Multiple sequence alignment - TraesCS3D01G214800

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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 TraesCS3D01G214800 chr3D 100.000 6919 0 0 1 6919 290135238 290142156 0.000000e+00 12778.0
1 TraesCS3D01G214800 chr3D 97.276 257 6 1 1 256 100150514 100150258 1.070000e-117 435.0
2 TraesCS3D01G214800 chr3D 97.619 252 5 1 1 251 558280259 558280510 1.380000e-116 431.0
3 TraesCS3D01G214800 chr3D 80.870 460 53 16 5765 6200 525324718 525325166 5.170000e-86 329.0
4 TraesCS3D01G214800 chr3D 87.931 58 4 2 6864 6919 9759664 9759608 1.610000e-06 65.8
5 TraesCS3D01G214800 chr3D 92.683 41 2 1 6779 6818 525326677 525326717 2.700000e-04 58.4
6 TraesCS3D01G214800 chr3B 98.081 4482 68 13 1 4478 382655777 382660244 0.000000e+00 7784.0
7 TraesCS3D01G214800 chr3B 97.887 2461 35 6 4476 6919 382660582 382663042 0.000000e+00 4241.0
8 TraesCS3D01G214800 chr3B 89.855 138 14 0 5476 5613 692958883 692959020 1.980000e-40 178.0
9 TraesCS3D01G214800 chr3B 78.859 298 31 10 5765 6033 692959056 692959350 9.230000e-39 172.0
10 TraesCS3D01G214800 chr3A 94.759 4503 96 41 251 4679 382142674 382147110 0.000000e+00 6879.0
11 TraesCS3D01G214800 chr3A 93.361 979 32 11 5464 6431 382149237 382150193 0.000000e+00 1417.0
12 TraesCS3D01G214800 chr3A 96.452 620 19 3 4266 4883 168225412 168224794 0.000000e+00 1020.0
13 TraesCS3D01G214800 chr3A 97.878 377 7 1 5055 5430 382148547 382148923 0.000000e+00 651.0
14 TraesCS3D01G214800 chr3A 89.372 414 17 8 6423 6816 382150513 382150919 4.820000e-136 496.0
15 TraesCS3D01G214800 chr3A 94.389 303 15 2 4672 4973 382147946 382148247 1.360000e-126 464.0
16 TraesCS3D01G214800 chr3A 92.282 298 16 6 3854 4146 168225737 168225442 3.860000e-112 416.0
17 TraesCS3D01G214800 chr3A 93.458 214 12 2 5160 5372 659515356 659515568 4.030000e-82 316.0
18 TraesCS3D01G214800 chr3A 100.000 53 0 0 4181 4233 168225463 168225411 1.590000e-16 99.0
19 TraesCS3D01G214800 chr3A 92.683 41 2 1 6779 6818 659518433 659518473 2.700000e-04 58.4
20 TraesCS3D01G214800 chr5D 96.262 1311 32 11 4149 5448 484657129 484655825 0.000000e+00 2134.0
21 TraesCS3D01G214800 chr5D 99.099 111 1 0 5464 5574 484655839 484655729 4.230000e-47 200.0
22 TraesCS3D01G214800 chr5D 89.831 59 3 2 6863 6919 445179204 445179261 9.630000e-09 73.1
23 TraesCS3D01G214800 chr4B 95.270 1036 41 7 3854 4883 77643311 77644344 0.000000e+00 1635.0
24 TraesCS3D01G214800 chr4B 95.833 264 8 3 1 262 445002570 445002832 2.310000e-114 424.0
25 TraesCS3D01G214800 chr2B 94.603 982 33 7 3880 4858 384671068 384672032 0.000000e+00 1502.0
26 TraesCS3D01G214800 chr2B 95.522 201 6 3 4684 4883 384672031 384672229 1.120000e-82 318.0
27 TraesCS3D01G214800 chr2B 87.931 58 5 2 6863 6919 59264137 59264193 4.480000e-07 67.6
28 TraesCS3D01G214800 chr2B 87.931 58 4 2 6864 6919 699214759 699214815 1.610000e-06 65.8
29 TraesCS3D01G214800 chr2B 86.441 59 5 2 6863 6919 768619792 768619849 2.080000e-05 62.1
30 TraesCS3D01G214800 chr7A 97.667 300 7 0 3658 3957 610194184 610194483 3.700000e-142 516.0
31 TraesCS3D01G214800 chr7A 98.113 106 2 0 3852 3957 610194802 610194907 1.190000e-42 185.0
32 TraesCS3D01G214800 chr7A 87.719 57 4 2 6865 6919 15127578 15127523 5.790000e-06 63.9
33 TraesCS3D01G214800 chr7A 85.714 56 8 0 5369 5424 107598195 107598140 7.490000e-05 60.2
34 TraesCS3D01G214800 chr4A 97.638 254 5 1 1 253 163851852 163851599 1.070000e-117 435.0
35 TraesCS3D01G214800 chr4A 94.000 50 3 0 3353 3402 623362866 623362817 7.440000e-10 76.8
36 TraesCS3D01G214800 chr7D 97.619 252 5 1 1 251 438758027 438757776 1.380000e-116 431.0
37 TraesCS3D01G214800 chr7D 93.885 278 14 3 1 275 263987554 263987831 3.860000e-112 416.0
38 TraesCS3D01G214800 chr7D 88.136 59 4 3 6863 6919 223819653 223819710 4.480000e-07 67.6
39 TraesCS3D01G214800 chr4D 97.619 252 5 1 1 251 455840079 455839828 1.380000e-116 431.0
40 TraesCS3D01G214800 chr6B 94.545 275 11 4 1 271 199056184 199056458 8.300000e-114 422.0
41 TraesCS3D01G214800 chr1A 94.915 59 3 0 5369 5427 259180720 259180778 7.390000e-15 93.5
42 TraesCS3D01G214800 chr5B 92.000 50 2 1 6863 6910 510513756 510513805 1.250000e-07 69.4


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 TraesCS3D01G214800 chr3D 290135238 290142156 6918 False 12778.000000 12778 100.000000 1 6919 1 chr3D.!!$F1 6918
1 TraesCS3D01G214800 chr3B 382655777 382663042 7265 False 6012.500000 7784 97.984000 1 6919 2 chr3B.!!$F1 6918
2 TraesCS3D01G214800 chr3A 382142674 382150919 8245 False 1981.400000 6879 93.951800 251 6816 5 chr3A.!!$F1 6565
3 TraesCS3D01G214800 chr3A 168224794 168225737 943 True 511.666667 1020 96.244667 3854 4883 3 chr3A.!!$R1 1029
4 TraesCS3D01G214800 chr5D 484655729 484657129 1400 True 1167.000000 2134 97.680500 4149 5574 2 chr5D.!!$R1 1425
5 TraesCS3D01G214800 chr4B 77643311 77644344 1033 False 1635.000000 1635 95.270000 3854 4883 1 chr4B.!!$F1 1029
6 TraesCS3D01G214800 chr2B 384671068 384672229 1161 False 910.000000 1502 95.062500 3880 4883 2 chr2B.!!$F4 1003
7 TraesCS3D01G214800 chr7A 610194184 610194907 723 False 350.500000 516 97.890000 3658 3957 2 chr7A.!!$F1 299

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
558 561 1.134159 CCTTCCTTGCTCCTCCATCAG 60.134 57.143 0.00 0.00 0.00 2.90 F
1657 1684 0.865111 CAAACTCGATTGGCACACGA 59.135 50.000 13.07 13.07 39.29 4.35 F
1934 1961 9.190858 GTGAATATGTTGCAATAAAAGTTGTCA 57.809 29.630 0.59 0.00 0.00 3.58 F
3613 3687 0.804989 CTGACGATGGAAAAGGGTGC 59.195 55.000 0.00 0.00 0.00 5.01 F
5293 7037 2.756840 ACTACACCGGCTAAAGGTTC 57.243 50.000 0.00 0.00 40.59 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2972 3006 5.049405 GGTATGTTCCTGATTATCAAAGGCG 60.049 44.000 0.00 0.0 0.00 5.52 R
3298 3353 4.973168 ACTAAAGAAGCTGTGATCCAACA 58.027 39.130 0.00 0.0 0.00 3.33 R
4018 4120 5.118729 TGGTCTAACCACAAGGAAAAAGA 57.881 39.130 0.00 0.0 44.79 2.52 R
5804 7871 2.109126 GTCCGCCAGTGATGCCTTC 61.109 63.158 0.00 0.0 0.00 3.46 R
6475 8871 1.534163 GACAAAAGGTACCCACGAAGC 59.466 52.381 8.74 0.0 0.00 3.86 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
25 26 6.226052 TCATTCTTCTAATGATGTGATCCCG 58.774 40.000 0.00 0.00 32.21 5.14
37 38 3.684908 TGTGATCCCGTTCATCAAATGT 58.315 40.909 0.00 0.00 31.98 2.71
52 53 7.754625 TCATCAAATGTCAACACATGTCTATG 58.245 34.615 0.00 0.00 42.89 2.23
58 59 5.487433 TGTCAACACATGTCTATGGTTAGG 58.513 41.667 0.00 0.00 38.66 2.69
103 104 3.496884 CGAGCTAGTCTAGTAGAGGCTTG 59.503 52.174 17.68 16.90 36.38 4.01
163 165 8.795842 TGTATCAAGTTTCCGGTTAATACAAT 57.204 30.769 0.00 0.00 0.00 2.71
165 167 9.712359 GTATCAAGTTTCCGGTTAATACAATTC 57.288 33.333 0.00 0.00 0.00 2.17
453 456 7.550712 CCTTGCCAAAAGAGCTAGATTAAATT 58.449 34.615 0.00 0.00 35.46 1.82
475 478 6.669125 TTGTTCAAGATCATGGAAACCAAT 57.331 33.333 0.00 0.00 36.95 3.16
526 529 1.348064 CTCCTAGGACACCCAACACA 58.652 55.000 7.62 0.00 33.88 3.72
558 561 1.134159 CCTTCCTTGCTCCTCCATCAG 60.134 57.143 0.00 0.00 0.00 2.90
951 956 2.025898 CCTAGGGTTTCTCCGTCTCTC 58.974 57.143 0.00 0.00 37.00 3.20
952 957 2.357361 CCTAGGGTTTCTCCGTCTCTCT 60.357 54.545 0.00 0.00 37.00 3.10
1390 1417 4.331108 TGCCAATGTGCACATAGTTTAGA 58.669 39.130 31.55 10.20 36.04 2.10
1391 1418 4.764308 TGCCAATGTGCACATAGTTTAGAA 59.236 37.500 31.55 9.60 36.04 2.10
1657 1684 0.865111 CAAACTCGATTGGCACACGA 59.135 50.000 13.07 13.07 39.29 4.35
1934 1961 9.190858 GTGAATATGTTGCAATAAAAGTTGTCA 57.809 29.630 0.59 0.00 0.00 3.58
2972 3006 9.780186 ATAAAGCTGATAGATTTTGGTAGTACC 57.220 33.333 12.80 12.80 35.26 3.34
3298 3353 8.701895 TGTGTTATTTACTTAGCTAGTAGCCAT 58.298 33.333 18.65 3.79 43.77 4.40
3421 3477 9.241317 GTTTAGCACAATGATGGAAGATAAATG 57.759 33.333 0.00 0.00 0.00 2.32
3613 3687 0.804989 CTGACGATGGAAAAGGGTGC 59.195 55.000 0.00 0.00 0.00 5.01
3724 3798 3.633525 TGCCCTGAAGATTGCATTACATC 59.366 43.478 0.00 0.00 0.00 3.06
3870 3945 8.936864 GCATGAATAGTTATACAGTTGGGTATC 58.063 37.037 0.00 0.00 35.64 2.24
3951 4053 7.394016 TGATCCTCTTATTTTACTGTGCTGAA 58.606 34.615 0.00 0.00 0.00 3.02
3952 4054 7.334421 TGATCCTCTTATTTTACTGTGCTGAAC 59.666 37.037 0.00 0.00 0.00 3.18
3953 4055 6.769512 TCCTCTTATTTTACTGTGCTGAACT 58.230 36.000 0.00 0.00 0.00 3.01
3954 4056 7.903145 TCCTCTTATTTTACTGTGCTGAACTA 58.097 34.615 0.00 0.00 0.00 2.24
3955 4057 7.817962 TCCTCTTATTTTACTGTGCTGAACTAC 59.182 37.037 0.00 0.00 0.00 2.73
3956 4058 7.064728 CCTCTTATTTTACTGTGCTGAACTACC 59.935 40.741 0.00 0.00 0.00 3.18
3957 4059 6.588756 TCTTATTTTACTGTGCTGAACTACCG 59.411 38.462 0.00 0.00 0.00 4.02
3958 4060 4.325028 TTTTACTGTGCTGAACTACCGA 57.675 40.909 0.00 0.00 0.00 4.69
3959 4061 4.530710 TTTACTGTGCTGAACTACCGAT 57.469 40.909 0.00 0.00 0.00 4.18
3960 4062 5.648178 TTTACTGTGCTGAACTACCGATA 57.352 39.130 0.00 0.00 0.00 2.92
3961 4063 5.648178 TTACTGTGCTGAACTACCGATAA 57.352 39.130 0.00 0.00 0.00 1.75
3962 4064 4.530710 ACTGTGCTGAACTACCGATAAA 57.469 40.909 0.00 0.00 0.00 1.40
3963 4065 5.086104 ACTGTGCTGAACTACCGATAAAT 57.914 39.130 0.00 0.00 0.00 1.40
3964 4066 6.216801 ACTGTGCTGAACTACCGATAAATA 57.783 37.500 0.00 0.00 0.00 1.40
3965 4067 6.817184 ACTGTGCTGAACTACCGATAAATAT 58.183 36.000 0.00 0.00 0.00 1.28
3966 4068 7.272978 ACTGTGCTGAACTACCGATAAATATT 58.727 34.615 0.00 0.00 0.00 1.28
3967 4069 7.224753 ACTGTGCTGAACTACCGATAAATATTG 59.775 37.037 0.00 0.00 0.00 1.90
3968 4070 7.269316 TGTGCTGAACTACCGATAAATATTGA 58.731 34.615 0.00 0.00 0.00 2.57
3969 4071 7.931407 TGTGCTGAACTACCGATAAATATTGAT 59.069 33.333 0.00 0.00 0.00 2.57
3970 4072 8.774586 GTGCTGAACTACCGATAAATATTGATT 58.225 33.333 0.00 0.00 0.00 2.57
3971 4073 9.990360 TGCTGAACTACCGATAAATATTGATTA 57.010 29.630 0.00 0.00 0.00 1.75
4104 4206 4.808414 TCCTGAGTTCTGATGTTACTGG 57.192 45.455 0.00 0.00 0.00 4.00
4704 6029 8.375506 TCTTTCTCCTTTGCACTAAATCTTCTA 58.624 33.333 0.00 0.00 0.00 2.10
4779 6104 7.254227 TCTTTTATTTTTACACGCAGTCACT 57.746 32.000 0.00 0.00 41.61 3.41
4783 6108 9.784680 TTTTATTTTTACACGCAGTCACTTTTA 57.215 25.926 0.00 0.00 41.61 1.52
5012 6756 9.528018 TGTTTCTGCTAATTCCACTTTAAAAAG 57.472 29.630 0.90 0.90 41.73 2.27
5293 7037 2.756840 ACTACACCGGCTAAAGGTTC 57.243 50.000 0.00 0.00 40.59 3.62
5315 7059 6.192970 TCTGATTCCCCTGATTATTCCTTC 57.807 41.667 0.00 0.00 0.00 3.46
5804 7871 1.267732 GCGAGAAATGCTGACCATTCG 60.268 52.381 0.00 0.00 43.22 3.34
5864 7931 1.257750 TTGAGCCTTCAGAGCGCCTA 61.258 55.000 2.29 0.00 34.15 3.93
6475 8871 2.011932 TTGATTGTTTGTTCGTCGCG 57.988 45.000 0.00 0.00 0.00 5.87
6898 9313 4.569719 AAACTACCACATTACAGGAGGG 57.430 45.455 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.441274 AGACATGTGTTGACATTTGATGAAC 58.559 36.000 1.15 0.00 41.12 3.18
37 38 6.367374 TTCCTAACCATAGACATGTGTTGA 57.633 37.500 1.15 0.00 31.85 3.18
52 53 7.754851 TCAAAGATGGTTAAGTTTCCTAACC 57.245 36.000 5.05 5.05 42.55 2.85
58 59 9.543018 CTCGTTAATCAAAGATGGTTAAGTTTC 57.457 33.333 0.00 0.00 41.55 2.78
73 74 7.441760 CCTCTACTAGACTAGCTCGTTAATCAA 59.558 40.741 9.52 0.00 0.00 2.57
103 104 3.467803 AGACAAAACACTGTGTCCTAGC 58.532 45.455 14.68 4.61 44.30 3.42
230 232 4.044308 TGGTGAAGGAAATATGCCCTAGA 58.956 43.478 0.00 0.00 31.36 2.43
244 246 8.537858 TGATATGAAGATATGAGATGGTGAAGG 58.462 37.037 0.00 0.00 0.00 3.46
453 456 7.835682 AGATATTGGTTTCCATGATCTTGAACA 59.164 33.333 10.07 0.00 34.00 3.18
526 529 3.008049 AGCAAGGAAGGTCAACGAATAGT 59.992 43.478 0.00 0.00 0.00 2.12
637 640 3.433343 TGATCAAATCAGTGGCACCATT 58.567 40.909 15.27 10.23 33.59 3.16
808 813 9.439537 GGATTTCGATTAATAAAGCTCAGTTTC 57.560 33.333 0.00 0.00 0.00 2.78
951 956 0.108585 CGGGGGAGAGAGAGAGAGAG 59.891 65.000 0.00 0.00 0.00 3.20
952 957 0.622154 ACGGGGGAGAGAGAGAGAGA 60.622 60.000 0.00 0.00 0.00 3.10
2972 3006 5.049405 GGTATGTTCCTGATTATCAAAGGCG 60.049 44.000 0.00 0.00 0.00 5.52
3077 3111 9.077885 ACATAAACATACACCTCAAACAAGATT 57.922 29.630 0.00 0.00 0.00 2.40
3298 3353 4.973168 ACTAAAGAAGCTGTGATCCAACA 58.027 39.130 0.00 0.00 0.00 3.33
3421 3477 6.631016 TCATTGGATGTCTGTAGAACTGTAC 58.369 40.000 0.00 0.00 0.00 2.90
3613 3687 8.500238 ACCCAGTAAATATACCCCTCTTAAAAG 58.500 37.037 0.00 0.00 32.08 2.27
3724 3798 5.188327 TCAGCTAGTACATCAATCCTTCG 57.812 43.478 0.00 0.00 0.00 3.79
3870 3945 6.312918 ACGCACTGTACAATTTAGACCAATAG 59.687 38.462 0.00 0.00 0.00 1.73
3969 4071 9.832445 ACAAAGAAAGAACAGAGTTCAGTATAA 57.168 29.630 11.92 0.00 0.00 0.98
3970 4072 9.832445 AACAAAGAAAGAACAGAGTTCAGTATA 57.168 29.630 11.92 0.00 0.00 1.47
3971 4073 8.616076 CAACAAAGAAAGAACAGAGTTCAGTAT 58.384 33.333 11.92 0.00 0.00 2.12
3972 4074 7.822334 TCAACAAAGAAAGAACAGAGTTCAGTA 59.178 33.333 11.92 0.00 0.00 2.74
3973 4075 6.655003 TCAACAAAGAAAGAACAGAGTTCAGT 59.345 34.615 11.92 0.00 0.00 3.41
3974 4076 7.076842 TCAACAAAGAAAGAACAGAGTTCAG 57.923 36.000 11.92 0.00 0.00 3.02
3975 4077 7.447374 TTCAACAAAGAAAGAACAGAGTTCA 57.553 32.000 11.92 0.00 0.00 3.18
4003 4105 9.591792 CAAGGAAAAAGAAGAAAAGATGAGTTT 57.408 29.630 0.00 0.00 0.00 2.66
4018 4120 5.118729 TGGTCTAACCACAAGGAAAAAGA 57.881 39.130 0.00 0.00 44.79 2.52
5158 6902 7.230108 ACTGCATATTCCAAGGAATACAATGAG 59.770 37.037 20.62 16.26 46.01 2.90
5293 7037 6.198237 AGAAGGAATAATCAGGGGAATCAG 57.802 41.667 0.00 0.00 0.00 2.90
5804 7871 2.109126 GTCCGCCAGTGATGCCTTC 61.109 63.158 0.00 0.00 0.00 3.46
6475 8871 1.534163 GACAAAAGGTACCCACGAAGC 59.466 52.381 8.74 0.00 0.00 3.86
6521 8917 6.384015 TGACAATGGGAAAGAGCTTAGAGATA 59.616 38.462 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.