Multiple sequence alignment - TraesCS3D01G216600

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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 TraesCS3D01G216600 chr3D 100.000 3992 0 0 1 3992 293814057 293810066 0.000000e+00 7372.0
1 TraesCS3D01G216600 chr3D 92.770 816 35 5 1 814 100469209 100470002 0.000000e+00 1158.0
2 TraesCS3D01G216600 chr3D 89.939 815 31 6 1 814 560364602 560363838 0.000000e+00 1003.0
3 TraesCS3D01G216600 chr3D 90.184 163 8 3 3534 3696 293810429 293810275 5.230000e-49 206.0
4 TraesCS3D01G216600 chr3D 90.184 163 8 3 3629 3783 293810524 293810362 5.230000e-49 206.0
5 TraesCS3D01G216600 chr3A 97.509 3091 45 3 902 3992 388098206 388095148 0.000000e+00 5252.0
6 TraesCS3D01G216600 chr3A 90.798 163 7 3 3534 3696 388095487 388095333 1.120000e-50 211.0
7 TraesCS3D01G216600 chr3A 87.117 163 8 2 3629 3783 388095577 388095420 5.300000e-39 172.0
8 TraesCS3D01G216600 chr3A 93.258 89 2 3 820 906 388098334 388098248 1.160000e-25 128.0
9 TraesCS3D01G216600 chr3B 97.368 2888 53 2 902 3768 387436793 387433908 0.000000e+00 4891.0
10 TraesCS3D01G216600 chr3B 91.429 210 16 2 3766 3973 387432831 387432622 1.820000e-73 287.0
11 TraesCS3D01G216600 chr3B 87.730 163 12 1 3629 3783 387434142 387433980 2.450000e-42 183.0
12 TraesCS3D01G216600 chr3B 95.402 87 2 2 820 906 387436916 387436832 1.930000e-28 137.0
13 TraesCS3D01G216600 chr3B 82.353 102 10 5 3434 3535 636436089 636436182 9.190000e-12 82.4
14 TraesCS3D01G216600 chr6D 92.421 818 40 5 1 816 270581525 270582322 0.000000e+00 1147.0
15 TraesCS3D01G216600 chr2D 92.430 819 35 7 1 814 36580519 36579723 0.000000e+00 1144.0
16 TraesCS3D01G216600 chr2D 91.892 777 41 6 1 774 573907145 573907902 0.000000e+00 1066.0
17 TraesCS3D01G216600 chr2D 91.262 103 8 1 3433 3535 568192397 568192296 5.380000e-29 139.0
18 TraesCS3D01G216600 chr4D 91.187 817 49 5 1 813 477373836 477373039 0.000000e+00 1088.0
19 TraesCS3D01G216600 chr4D 91.203 773 47 14 1 770 426869260 426870014 0.000000e+00 1031.0
20 TraesCS3D01G216600 chr6B 91.087 819 47 8 1 814 4465995 4466792 0.000000e+00 1085.0
21 TraesCS3D01G216600 chr6B 90.842 819 49 8 1 814 4462961 4463758 0.000000e+00 1074.0
22 TraesCS3D01G216600 chr6A 91.288 815 40 4 1 813 9363203 9363988 0.000000e+00 1083.0
23 TraesCS3D01G216600 chr7D 91.010 812 41 4 1 811 458371031 458370251 0.000000e+00 1066.0
24 TraesCS3D01G216600 chr7D 90.436 826 33 8 1 821 50094412 50093628 0.000000e+00 1046.0
25 TraesCS3D01G216600 chr1D 91.699 783 42 3 1 782 332922468 332921708 0.000000e+00 1064.0
26 TraesCS3D01G216600 chr1D 84.615 104 8 5 3432 3535 256204827 256204922 3.280000e-16 97.1
27 TraesCS3D01G216600 chr5D 92.286 713 34 3 100 811 133506732 133507424 0.000000e+00 992.0
28 TraesCS3D01G216600 chr2A 88.739 817 56 10 1 813 779163388 779164172 0.000000e+00 966.0
29 TraesCS3D01G216600 chr2A 89.286 84 8 1 3452 3535 691607484 691607402 1.960000e-18 104.0
30 TraesCS3D01G216600 chr7A 88.501 774 54 22 43 811 107597384 107598127 0.000000e+00 904.0
31 TraesCS3D01G216600 chr4A 90.476 105 9 1 3431 3535 727051492 727051389 1.930000e-28 137.0
32 TraesCS3D01G216600 chr4A 100.000 31 0 0 3433 3463 688614729 688614759 1.550000e-04 58.4
33 TraesCS3D01G216600 chrUn 96.774 31 1 0 3433 3463 7178537 7178507 7.000000e-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 TraesCS3D01G216600 chr3D 293810066 293814057 3991 True 2594.666667 7372 93.45600 1 3992 3 chr3D.!!$R2 3991
1 TraesCS3D01G216600 chr3D 100469209 100470002 793 False 1158.000000 1158 92.77000 1 814 1 chr3D.!!$F1 813
2 TraesCS3D01G216600 chr3D 560363838 560364602 764 True 1003.000000 1003 89.93900 1 814 1 chr3D.!!$R1 813
3 TraesCS3D01G216600 chr3A 388095148 388098334 3186 True 1440.750000 5252 92.17050 820 3992 4 chr3A.!!$R1 3172
4 TraesCS3D01G216600 chr3B 387432622 387436916 4294 True 1374.500000 4891 92.98225 820 3973 4 chr3B.!!$R1 3153
5 TraesCS3D01G216600 chr6D 270581525 270582322 797 False 1147.000000 1147 92.42100 1 816 1 chr6D.!!$F1 815
6 TraesCS3D01G216600 chr2D 36579723 36580519 796 True 1144.000000 1144 92.43000 1 814 1 chr2D.!!$R1 813
7 TraesCS3D01G216600 chr2D 573907145 573907902 757 False 1066.000000 1066 91.89200 1 774 1 chr2D.!!$F1 773
8 TraesCS3D01G216600 chr4D 477373039 477373836 797 True 1088.000000 1088 91.18700 1 813 1 chr4D.!!$R1 812
9 TraesCS3D01G216600 chr4D 426869260 426870014 754 False 1031.000000 1031 91.20300 1 770 1 chr4D.!!$F1 769
10 TraesCS3D01G216600 chr6B 4462961 4466792 3831 False 1079.500000 1085 90.96450 1 814 2 chr6B.!!$F1 813
11 TraesCS3D01G216600 chr6A 9363203 9363988 785 False 1083.000000 1083 91.28800 1 813 1 chr6A.!!$F1 812
12 TraesCS3D01G216600 chr7D 458370251 458371031 780 True 1066.000000 1066 91.01000 1 811 1 chr7D.!!$R2 810
13 TraesCS3D01G216600 chr7D 50093628 50094412 784 True 1046.000000 1046 90.43600 1 821 1 chr7D.!!$R1 820
14 TraesCS3D01G216600 chr1D 332921708 332922468 760 True 1064.000000 1064 91.69900 1 782 1 chr1D.!!$R1 781
15 TraesCS3D01G216600 chr5D 133506732 133507424 692 False 992.000000 992 92.28600 100 811 1 chr5D.!!$F1 711
16 TraesCS3D01G216600 chr2A 779163388 779164172 784 False 966.000000 966 88.73900 1 813 1 chr2A.!!$F1 812
17 TraesCS3D01G216600 chr7A 107597384 107598127 743 False 904.000000 904 88.50100 43 811 1 chr7A.!!$F1 768

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
900 3979 1.530183 GGATCTTGCCCAGCCCATC 60.530 63.158 0.0 0.0 0.00 3.51 F
1626 4770 0.320683 CATATCGCATCCTTGCCCGA 60.321 55.000 0.0 0.0 46.57 5.14 F
1725 4869 1.205460 ACCCCCAGGTCTATGCGTTT 61.205 55.000 0.0 0.0 46.45 3.60 F
2326 5470 2.102070 TAATGTGGATGACGCCGTTT 57.898 45.000 0.0 0.0 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 5283 0.803117 CATCTGGTGTGCAGCTCTTG 59.197 55.000 0.00 0.00 0.00 3.02 R
2764 5908 1.488393 GGCAGCAGATTCCTCCTTAGT 59.512 52.381 0.00 0.00 0.00 2.24 R
2954 6098 1.565156 GACCTGCGACGTTGCATCAA 61.565 55.000 29.86 8.16 45.26 2.57 R
3838 8064 1.199615 TCATGGATGTAACGGCTCCA 58.800 50.000 0.00 0.00 42.95 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
349 3418 2.038007 AGGAGCTCGAAGCCCTCA 59.962 61.111 7.83 0.00 43.77 3.86
508 3580 3.923864 TGTCGTCCAGTTGCCGCT 61.924 61.111 0.00 0.00 0.00 5.52
541 3615 2.071372 TCAGATCCGGACCCCTAGTAT 58.929 52.381 6.12 0.00 0.00 2.12
621 3696 4.794248 TGCGATGAACAATGTAGTATGC 57.206 40.909 0.00 0.00 0.00 3.14
622 3697 3.245048 TGCGATGAACAATGTAGTATGCG 59.755 43.478 0.00 0.00 0.00 4.73
623 3698 3.489416 GCGATGAACAATGTAGTATGCGA 59.511 43.478 0.00 0.00 0.00 5.10
624 3699 4.150627 GCGATGAACAATGTAGTATGCGAT 59.849 41.667 0.00 0.00 0.00 4.58
625 3700 5.602516 CGATGAACAATGTAGTATGCGATG 58.397 41.667 0.00 0.00 0.00 3.84
626 3701 5.402270 CGATGAACAATGTAGTATGCGATGA 59.598 40.000 0.00 0.00 0.00 2.92
627 3702 6.074356 CGATGAACAATGTAGTATGCGATGAA 60.074 38.462 0.00 0.00 0.00 2.57
628 3703 6.344572 TGAACAATGTAGTATGCGATGAAC 57.655 37.500 0.00 0.00 0.00 3.18
629 3704 5.872070 TGAACAATGTAGTATGCGATGAACA 59.128 36.000 0.00 0.00 0.00 3.18
630 3705 6.370166 TGAACAATGTAGTATGCGATGAACAA 59.630 34.615 0.00 0.00 0.00 2.83
631 3706 6.925610 ACAATGTAGTATGCGATGAACAAT 57.074 33.333 0.00 0.00 0.00 2.71
632 3707 6.718388 ACAATGTAGTATGCGATGAACAATG 58.282 36.000 0.00 0.00 0.00 2.82
633 3708 6.316140 ACAATGTAGTATGCGATGAACAATGT 59.684 34.615 0.00 0.00 0.00 2.71
634 3709 7.494298 ACAATGTAGTATGCGATGAACAATGTA 59.506 33.333 0.00 0.00 31.22 2.29
635 3710 7.643528 ATGTAGTATGCGATGAACAATGTAG 57.356 36.000 0.00 0.00 0.00 2.74
636 3711 6.569780 TGTAGTATGCGATGAACAATGTAGT 58.430 36.000 0.00 0.00 0.00 2.73
637 3712 7.708998 TGTAGTATGCGATGAACAATGTAGTA 58.291 34.615 0.00 0.00 0.00 1.82
638 3713 8.357402 TGTAGTATGCGATGAACAATGTAGTAT 58.643 33.333 0.00 0.00 0.00 2.12
639 3714 7.643528 AGTATGCGATGAACAATGTAGTATG 57.356 36.000 0.00 0.00 0.00 2.39
664 3739 8.355913 TGTGATGAACTATGTTTGTGCAATTTA 58.644 29.630 0.00 0.00 0.00 1.40
666 3741 9.926158 TGATGAACTATGTTTGTGCAATTTATT 57.074 25.926 0.00 0.00 0.00 1.40
798 3875 1.808343 GTCTTATTTTTGCGGGTCCGT 59.192 47.619 11.25 0.00 42.09 4.69
828 3905 4.228317 GCTCTTAGAATCGTCGTTATCCC 58.772 47.826 0.00 0.00 0.00 3.85
899 3978 2.605299 GGATCTTGCCCAGCCCAT 59.395 61.111 0.00 0.00 0.00 4.00
900 3979 1.530183 GGATCTTGCCCAGCCCATC 60.530 63.158 0.00 0.00 0.00 3.51
1410 4554 1.336887 ACCTGCAACACAGTACTAGCG 60.337 52.381 0.00 0.00 45.68 4.26
1626 4770 0.320683 CATATCGCATCCTTGCCCGA 60.321 55.000 0.00 0.00 46.57 5.14
1725 4869 1.205460 ACCCCCAGGTCTATGCGTTT 61.205 55.000 0.00 0.00 46.45 3.60
2139 5283 2.209273 GTGTTTGGCAAAATGGGTGAC 58.791 47.619 15.29 0.53 0.00 3.67
2326 5470 2.102070 TAATGTGGATGACGCCGTTT 57.898 45.000 0.00 0.00 0.00 3.60
2398 5542 5.709966 CCTTTAACAAAGTCATAAGTGGCC 58.290 41.667 0.00 0.00 36.77 5.36
2764 5908 2.826488 AGAAGAAGGCTGAGGCTAAGA 58.174 47.619 9.60 0.00 37.50 2.10
2954 6098 4.590647 TGATGACCAGAAGAAAGAGTCTGT 59.409 41.667 0.00 0.00 39.76 3.41
3315 6459 3.728845 TCTCCTGCAAGTGTAAAGTGAC 58.271 45.455 0.00 0.00 0.00 3.67
3415 6562 5.467035 TCACCTTTTCTTATTTGCCCTTG 57.533 39.130 0.00 0.00 0.00 3.61
3555 6702 9.941664 CTTCATTTAGCTTTACCATCATGTAAG 57.058 33.333 0.00 0.00 32.63 2.34
3613 6760 9.516314 GTAATTACCTTCAACTGGAAAATATGC 57.484 33.333 4.11 0.00 34.44 3.14
3634 6781 4.819630 TGCGACTTACCTTCAAAATTGAGT 59.180 37.500 0.00 0.00 38.61 3.41
3836 8062 8.193953 ACATTCAAAATTTCTTGACCACCTAT 57.806 30.769 0.00 0.00 35.07 2.57
3837 8063 9.308000 ACATTCAAAATTTCTTGACCACCTATA 57.692 29.630 0.00 0.00 35.07 1.31
3840 8066 8.292444 TCAAAATTTCTTGACCACCTATATGG 57.708 34.615 0.00 0.00 46.10 2.74
3841 8067 8.112822 TCAAAATTTCTTGACCACCTATATGGA 58.887 33.333 0.00 0.00 43.37 3.41
3842 8068 8.408601 CAAAATTTCTTGACCACCTATATGGAG 58.591 37.037 0.00 0.00 43.02 3.86
3843 8069 4.689612 TTCTTGACCACCTATATGGAGC 57.310 45.455 0.00 0.00 43.02 4.70
3844 8070 2.972713 TCTTGACCACCTATATGGAGCC 59.027 50.000 0.00 0.00 43.02 4.70
3845 8071 1.338107 TGACCACCTATATGGAGCCG 58.662 55.000 0.00 0.00 43.02 5.52
3846 8072 1.339097 GACCACCTATATGGAGCCGT 58.661 55.000 0.00 0.00 43.02 5.68
3847 8073 1.692519 GACCACCTATATGGAGCCGTT 59.307 52.381 0.00 0.00 43.02 4.44
3848 8074 2.895404 GACCACCTATATGGAGCCGTTA 59.105 50.000 0.00 0.00 43.02 3.18
3849 8075 2.631545 ACCACCTATATGGAGCCGTTAC 59.368 50.000 0.00 0.00 43.02 2.50
3850 8076 2.631062 CCACCTATATGGAGCCGTTACA 59.369 50.000 0.00 0.00 43.02 2.41
3851 8077 3.260884 CCACCTATATGGAGCCGTTACAT 59.739 47.826 0.00 0.00 43.02 2.29
3852 8078 4.495422 CACCTATATGGAGCCGTTACATC 58.505 47.826 0.00 0.00 39.71 3.06
3853 8079 3.514309 ACCTATATGGAGCCGTTACATCC 59.486 47.826 0.00 0.00 39.71 3.51
3854 8080 3.513912 CCTATATGGAGCCGTTACATCCA 59.486 47.826 3.90 3.90 46.69 3.41
3856 8082 3.778619 TGGAGCCGTTACATCCATG 57.221 52.632 0.00 0.00 38.19 3.66
3857 8083 1.199615 TGGAGCCGTTACATCCATGA 58.800 50.000 0.00 0.00 38.19 3.07
3858 8084 1.557371 TGGAGCCGTTACATCCATGAA 59.443 47.619 0.00 0.00 38.19 2.57
3859 8085 1.940613 GGAGCCGTTACATCCATGAAC 59.059 52.381 0.00 0.00 33.08 3.18
3941 8191 4.020128 ACAAGTACTCCCTAGCTTCTTTGG 60.020 45.833 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.807538 TACTCCACCGTCTCGCGC 61.808 66.667 0.00 0.00 39.71 6.86
53 54 3.574445 CGGAGGAGATCGACGCGT 61.574 66.667 13.85 13.85 0.00 6.01
530 3603 8.226819 ACTACGTTAAACTAATACTAGGGGTC 57.773 38.462 0.00 0.00 0.00 4.46
621 3696 7.698836 TCATCACATACTACATTGTTCATCG 57.301 36.000 0.00 0.00 0.00 3.84
622 3697 9.102757 AGTTCATCACATACTACATTGTTCATC 57.897 33.333 0.00 0.00 0.00 2.92
626 3701 9.890629 ACATAGTTCATCACATACTACATTGTT 57.109 29.630 0.00 0.00 0.00 2.83
627 3702 9.890629 AACATAGTTCATCACATACTACATTGT 57.109 29.630 0.00 0.00 0.00 2.71
630 3705 9.890629 ACAAACATAGTTCATCACATACTACAT 57.109 29.630 0.00 0.00 0.00 2.29
631 3706 9.150348 CACAAACATAGTTCATCACATACTACA 57.850 33.333 0.00 0.00 0.00 2.74
632 3707 8.116753 GCACAAACATAGTTCATCACATACTAC 58.883 37.037 0.00 0.00 0.00 2.73
633 3708 7.821846 TGCACAAACATAGTTCATCACATACTA 59.178 33.333 0.00 0.00 0.00 1.82
634 3709 6.654582 TGCACAAACATAGTTCATCACATACT 59.345 34.615 0.00 0.00 0.00 2.12
635 3710 6.841119 TGCACAAACATAGTTCATCACATAC 58.159 36.000 0.00 0.00 0.00 2.39
636 3711 7.446001 TTGCACAAACATAGTTCATCACATA 57.554 32.000 0.00 0.00 0.00 2.29
637 3712 5.963176 TGCACAAACATAGTTCATCACAT 57.037 34.783 0.00 0.00 0.00 3.21
638 3713 5.764487 TTGCACAAACATAGTTCATCACA 57.236 34.783 0.00 0.00 0.00 3.58
639 3714 7.642071 AAATTGCACAAACATAGTTCATCAC 57.358 32.000 0.00 0.00 0.00 3.06
781 3857 3.672808 TCTAACGGACCCGCAAAAATAA 58.327 40.909 8.55 0.00 44.19 1.40
798 3875 5.123502 ACGACGATTCTAAGAGCAACTCTAA 59.876 40.000 0.00 0.00 40.28 2.10
915 4038 0.246086 TGGAAATGGCAAATGGCGAC 59.754 50.000 0.00 0.00 46.16 5.19
1725 4869 2.428890 GTTGACAAAACCACCCATGACA 59.571 45.455 0.00 0.00 0.00 3.58
1851 4995 7.344871 TCCTTCTCCATACCCTTTAGAAAGTAG 59.655 40.741 1.56 0.00 34.20 2.57
2139 5283 0.803117 CATCTGGTGTGCAGCTCTTG 59.197 55.000 0.00 0.00 0.00 3.02
2398 5542 4.878397 GTCAATCCTATCAACCTTCACCAG 59.122 45.833 0.00 0.00 0.00 4.00
2764 5908 1.488393 GGCAGCAGATTCCTCCTTAGT 59.512 52.381 0.00 0.00 0.00 2.24
2954 6098 1.565156 GACCTGCGACGTTGCATCAA 61.565 55.000 29.86 8.16 45.26 2.57
3285 6429 3.388024 ACACTTGCAGGAGAAAGAGTGTA 59.612 43.478 13.42 0.00 44.02 2.90
3315 6459 9.076596 GCAATACTTAAGTAAATGAAAAGCTGG 57.923 33.333 24.82 6.00 33.76 4.85
3606 6753 8.519526 TCAATTTTGAAGGTAAGTCGCATATTT 58.480 29.630 0.00 0.00 33.55 1.40
3613 6760 9.166126 GTAAAACTCAATTTTGAAGGTAAGTCG 57.834 33.333 0.00 0.00 40.80 4.18
3634 6781 8.449397 GCAAATTGCATTTACATGATGGTAAAA 58.551 29.630 13.73 0.00 44.26 1.52
3836 8062 2.969262 TCATGGATGTAACGGCTCCATA 59.031 45.455 3.65 0.00 45.75 2.74
3838 8064 1.199615 TCATGGATGTAACGGCTCCA 58.800 50.000 0.00 0.00 42.95 3.86
3839 8065 1.940613 GTTCATGGATGTAACGGCTCC 59.059 52.381 0.00 0.00 0.00 4.70
3840 8066 2.906354 AGTTCATGGATGTAACGGCTC 58.094 47.619 0.00 0.00 0.00 4.70
3841 8067 4.481368 TTAGTTCATGGATGTAACGGCT 57.519 40.909 0.00 0.00 0.00 5.52
3842 8068 6.073222 CCTTATTAGTTCATGGATGTAACGGC 60.073 42.308 0.00 0.00 0.00 5.68
3843 8069 6.990349 ACCTTATTAGTTCATGGATGTAACGG 59.010 38.462 0.00 0.00 0.00 4.44
3844 8070 9.706691 ATACCTTATTAGTTCATGGATGTAACG 57.293 33.333 0.00 0.00 0.00 3.18
3941 8191 2.363788 TGACTGTGACCGAATACTGC 57.636 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.