Multiple sequence alignment - TraesCS6B01G080400

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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 TraesCS6B01G080400 chr6B 100.000 4832 0 0 1 4832 56427999 56432830 0.000000e+00 8924.0
1 TraesCS6B01G080400 chr6B 98.131 4708 57 9 125 4832 195188168 195192844 0.000000e+00 8178.0
2 TraesCS6B01G080400 chr6B 97.890 4739 64 3 125 4832 18581659 18576926 0.000000e+00 8165.0
3 TraesCS6B01G080400 chr6B 96.689 3836 113 9 122 3956 645758393 645762215 0.000000e+00 6368.0
4 TraesCS6B01G080400 chr6B 84.211 95 8 5 1 88 56313954 56314048 8.620000e-13 86.1
5 TraesCS6B01G080400 chr3A 98.726 4708 60 0 125 4832 684729031 684724324 0.000000e+00 8362.0
6 TraesCS6B01G080400 chr5B 98.556 4709 64 4 125 4832 371292296 371297001 0.000000e+00 8316.0
7 TraesCS6B01G080400 chr5B 98.153 4711 52 24 125 4832 264914596 264919274 0.000000e+00 8185.0
8 TraesCS6B01G080400 chr2A 98.260 4713 52 4 121 4832 61495402 61500085 0.000000e+00 8222.0
9 TraesCS6B01G080400 chr5A 98.114 4720 53 24 119 4832 613968276 613972965 0.000000e+00 8191.0
10 TraesCS6B01G080400 chr4A 97.258 4121 89 13 735 4832 731440816 731444935 0.000000e+00 6962.0
11 TraesCS6B01G080400 chr4A 97.015 938 28 0 3895 4832 674544313 674543376 0.000000e+00 1578.0
12 TraesCS6B01G080400 chr4B 96.439 3932 131 7 125 4054 103860489 103864413 0.000000e+00 6477.0


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 TraesCS6B01G080400 chr6B 56427999 56432830 4831 False 8924 8924 100.000 1 4832 1 chr6B.!!$F2 4831
1 TraesCS6B01G080400 chr6B 195188168 195192844 4676 False 8178 8178 98.131 125 4832 1 chr6B.!!$F3 4707
2 TraesCS6B01G080400 chr6B 18576926 18581659 4733 True 8165 8165 97.890 125 4832 1 chr6B.!!$R1 4707
3 TraesCS6B01G080400 chr6B 645758393 645762215 3822 False 6368 6368 96.689 122 3956 1 chr6B.!!$F4 3834
4 TraesCS6B01G080400 chr3A 684724324 684729031 4707 True 8362 8362 98.726 125 4832 1 chr3A.!!$R1 4707
5 TraesCS6B01G080400 chr5B 371292296 371297001 4705 False 8316 8316 98.556 125 4832 1 chr5B.!!$F2 4707
6 TraesCS6B01G080400 chr5B 264914596 264919274 4678 False 8185 8185 98.153 125 4832 1 chr5B.!!$F1 4707
7 TraesCS6B01G080400 chr2A 61495402 61500085 4683 False 8222 8222 98.260 121 4832 1 chr2A.!!$F1 4711
8 TraesCS6B01G080400 chr5A 613968276 613972965 4689 False 8191 8191 98.114 119 4832 1 chr5A.!!$F1 4713
9 TraesCS6B01G080400 chr4A 731440816 731444935 4119 False 6962 6962 97.258 735 4832 1 chr4A.!!$F1 4097
10 TraesCS6B01G080400 chr4A 674543376 674544313 937 True 1578 1578 97.015 3895 4832 1 chr4A.!!$R1 937
11 TraesCS6B01G080400 chr4B 103860489 103864413 3924 False 6477 6477 96.439 125 4054 1 chr4B.!!$F1 3929

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
121 122 0.613260 ACAATACGAAGCTGGCTCCA 59.387 50.000 0.00 0.0 0.0 3.86 F
123 124 1.134699 CAATACGAAGCTGGCTCCAGA 60.135 52.381 19.45 0.0 46.3 3.86 F
2722 2729 0.538977 ATGCAAGCAGAGCCAACAGT 60.539 50.000 0.00 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 2620 2.594303 CACCACCGGCTCTGCAAA 60.594 61.111 0.00 0.00 0.0 3.68 R
2757 2764 3.927142 CACGGACCTGCTTCTTAGTAAAG 59.073 47.826 0.00 0.00 0.0 1.85 R
4112 4259 0.861837 CCGGTGCTTTCTATCGATGC 59.138 55.000 8.54 2.63 0.0 3.91 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
17 18 4.625800 GGTCAAGCAGTAGCAGGG 57.374 61.111 0.00 0.00 45.49 4.45
18 19 1.746991 GGTCAAGCAGTAGCAGGGC 60.747 63.158 0.00 0.00 45.49 5.19
19 20 1.003355 GTCAAGCAGTAGCAGGGCA 60.003 57.895 0.00 0.00 45.49 5.36
20 21 1.003355 TCAAGCAGTAGCAGGGCAC 60.003 57.895 0.00 0.00 45.49 5.01
21 22 2.046892 AAGCAGTAGCAGGGCACG 60.047 61.111 0.00 0.00 45.49 5.34
22 23 3.612247 AAGCAGTAGCAGGGCACGG 62.612 63.158 0.00 0.00 45.49 4.94
23 24 4.394712 GCAGTAGCAGGGCACGGT 62.395 66.667 0.00 0.00 41.58 4.83
24 25 2.434884 CAGTAGCAGGGCACGGTG 60.435 66.667 3.15 3.15 0.00 4.94
25 26 4.394712 AGTAGCAGGGCACGGTGC 62.395 66.667 24.43 24.43 44.08 5.01
32 33 2.904866 GGGCACGGTGCACTCAAA 60.905 61.111 31.74 0.00 45.01 2.69
33 34 2.485795 GGGCACGGTGCACTCAAAA 61.486 57.895 31.74 0.00 45.01 2.44
34 35 2.010582 GGGCACGGTGCACTCAAAAA 62.011 55.000 31.74 0.00 45.01 1.94
35 36 3.293062 GGGCACGGTGCACTCAAAAAT 62.293 52.381 31.74 0.00 45.01 1.82
36 37 1.408422 GCACGGTGCACTCAAAAATC 58.592 50.000 27.10 0.00 44.26 2.17
37 38 1.268999 GCACGGTGCACTCAAAAATCA 60.269 47.619 27.10 0.00 44.26 2.57
38 39 2.607771 GCACGGTGCACTCAAAAATCAT 60.608 45.455 27.10 0.00 44.26 2.45
39 40 3.365868 GCACGGTGCACTCAAAAATCATA 60.366 43.478 27.10 0.00 44.26 2.15
40 41 4.158384 CACGGTGCACTCAAAAATCATAC 58.842 43.478 17.98 0.00 0.00 2.39
41 42 3.818210 ACGGTGCACTCAAAAATCATACA 59.182 39.130 17.98 0.00 0.00 2.29
42 43 4.083324 ACGGTGCACTCAAAAATCATACAG 60.083 41.667 17.98 0.00 0.00 2.74
43 44 4.154015 CGGTGCACTCAAAAATCATACAGA 59.846 41.667 17.98 0.00 0.00 3.41
44 45 5.634896 GGTGCACTCAAAAATCATACAGAG 58.365 41.667 17.98 0.00 0.00 3.35
45 46 5.392380 GGTGCACTCAAAAATCATACAGAGG 60.392 44.000 17.98 0.00 0.00 3.69
46 47 4.156556 TGCACTCAAAAATCATACAGAGGC 59.843 41.667 0.00 0.00 0.00 4.70
47 48 4.397417 GCACTCAAAAATCATACAGAGGCT 59.603 41.667 0.00 0.00 0.00 4.58
48 49 5.586243 GCACTCAAAAATCATACAGAGGCTA 59.414 40.000 0.00 0.00 0.00 3.93
49 50 6.238320 GCACTCAAAAATCATACAGAGGCTAG 60.238 42.308 0.00 0.00 0.00 3.42
50 51 7.044181 CACTCAAAAATCATACAGAGGCTAGA 58.956 38.462 0.00 0.00 0.00 2.43
51 52 7.714377 CACTCAAAAATCATACAGAGGCTAGAT 59.286 37.037 0.00 0.00 0.00 1.98
52 53 8.928448 ACTCAAAAATCATACAGAGGCTAGATA 58.072 33.333 0.00 0.00 0.00 1.98
53 54 9.770097 CTCAAAAATCATACAGAGGCTAGATAA 57.230 33.333 0.00 0.00 0.00 1.75
96 97 8.815565 ACAGATATGATGTAGGAGTAGTATGG 57.184 38.462 0.00 0.00 0.00 2.74
97 98 8.615705 ACAGATATGATGTAGGAGTAGTATGGA 58.384 37.037 0.00 0.00 0.00 3.41
98 99 9.467796 CAGATATGATGTAGGAGTAGTATGGAA 57.532 37.037 0.00 0.00 0.00 3.53
99 100 9.469097 AGATATGATGTAGGAGTAGTATGGAAC 57.531 37.037 0.00 0.00 0.00 3.62
115 116 4.481930 TGGAACAAACAATACGAAGCTG 57.518 40.909 0.00 0.00 31.92 4.24
116 117 3.252215 TGGAACAAACAATACGAAGCTGG 59.748 43.478 0.00 0.00 31.92 4.85
117 118 2.989422 ACAAACAATACGAAGCTGGC 57.011 45.000 0.00 0.00 0.00 4.85
118 119 2.504367 ACAAACAATACGAAGCTGGCT 58.496 42.857 0.00 0.00 0.00 4.75
119 120 2.484264 ACAAACAATACGAAGCTGGCTC 59.516 45.455 0.00 0.00 0.00 4.70
120 121 1.739067 AACAATACGAAGCTGGCTCC 58.261 50.000 0.00 0.00 0.00 4.70
121 122 0.613260 ACAATACGAAGCTGGCTCCA 59.387 50.000 0.00 0.00 0.00 3.86
122 123 1.293924 CAATACGAAGCTGGCTCCAG 58.706 55.000 11.47 11.47 46.15 3.86
123 124 1.134699 CAATACGAAGCTGGCTCCAGA 60.135 52.381 19.45 0.00 46.30 3.86
2722 2729 0.538977 ATGCAAGCAGAGCCAACAGT 60.539 50.000 0.00 0.00 0.00 3.55
2730 2737 2.165030 GCAGAGCCAACAGTGCAAATAT 59.835 45.455 0.00 0.00 35.91 1.28
2832 2839 1.738346 TAGCAGCACTCATCGCGGAT 61.738 55.000 6.13 0.00 0.00 4.18
2962 2969 3.754965 CCTCCAGTGAATTGGTCTTTGA 58.245 45.455 0.00 0.00 39.35 2.69
3106 3113 5.122239 CACGGCACTTTGAGATATTTCAGAA 59.878 40.000 0.00 0.00 0.00 3.02
4044 4191 9.489084 TGTATTTGTAATATGTCAGGACTATGC 57.511 33.333 0.65 0.00 0.00 3.14
4112 4259 6.537301 TCTTTGTATCCGTTGCTTAATGGTAG 59.463 38.462 0.00 0.00 0.00 3.18
4134 4281 1.758936 TCGATAGAAAGCACCGGAGA 58.241 50.000 9.46 0.00 46.15 3.71
4184 4331 0.390124 GTGTTGGTCACTCGTACCCA 59.610 55.000 0.00 0.00 43.13 4.51
4297 4448 4.335594 ACTTTTCATAGCCGCTAACAATCC 59.664 41.667 3.73 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.746991 GCCCTGCTACTGCTTGACC 60.747 63.158 0.00 0.00 40.48 4.02
2 3 1.003355 GTGCCCTGCTACTGCTTGA 60.003 57.895 0.00 0.00 40.48 3.02
3 4 2.393768 CGTGCCCTGCTACTGCTTG 61.394 63.158 0.00 0.00 40.48 4.01
4 5 2.046892 CGTGCCCTGCTACTGCTT 60.047 61.111 0.00 0.00 40.48 3.91
6 7 4.394712 ACCGTGCCCTGCTACTGC 62.395 66.667 0.00 0.00 40.20 4.40
7 8 2.434884 CACCGTGCCCTGCTACTG 60.435 66.667 0.00 0.00 0.00 2.74
8 9 4.394712 GCACCGTGCCCTGCTACT 62.395 66.667 12.80 0.00 37.42 2.57
9 10 4.697756 TGCACCGTGCCCTGCTAC 62.698 66.667 20.67 0.00 44.23 3.58
10 11 4.697756 GTGCACCGTGCCCTGCTA 62.698 66.667 20.67 0.00 44.23 3.49
13 14 4.624364 TGAGTGCACCGTGCCCTG 62.624 66.667 20.67 0.00 44.23 4.45
14 15 2.902423 TTTTGAGTGCACCGTGCCCT 62.902 55.000 20.67 14.87 44.23 5.19
15 16 2.010582 TTTTTGAGTGCACCGTGCCC 62.011 55.000 20.67 9.63 44.23 5.36
16 17 0.031994 ATTTTTGAGTGCACCGTGCC 59.968 50.000 20.67 11.83 44.23 5.01
17 18 1.268999 TGATTTTTGAGTGCACCGTGC 60.269 47.619 16.93 16.93 45.29 5.34
18 19 2.772568 TGATTTTTGAGTGCACCGTG 57.227 45.000 14.63 0.00 0.00 4.94
19 20 3.818210 TGTATGATTTTTGAGTGCACCGT 59.182 39.130 14.63 0.00 0.00 4.83
20 21 4.154015 TCTGTATGATTTTTGAGTGCACCG 59.846 41.667 14.63 0.00 0.00 4.94
21 22 5.392380 CCTCTGTATGATTTTTGAGTGCACC 60.392 44.000 14.63 5.76 0.00 5.01
22 23 5.634896 CCTCTGTATGATTTTTGAGTGCAC 58.365 41.667 9.40 9.40 0.00 4.57
23 24 4.156556 GCCTCTGTATGATTTTTGAGTGCA 59.843 41.667 0.00 0.00 0.00 4.57
24 25 4.397417 AGCCTCTGTATGATTTTTGAGTGC 59.603 41.667 0.00 0.00 0.00 4.40
25 26 7.044181 TCTAGCCTCTGTATGATTTTTGAGTG 58.956 38.462 0.00 0.00 0.00 3.51
26 27 7.187824 TCTAGCCTCTGTATGATTTTTGAGT 57.812 36.000 0.00 0.00 0.00 3.41
27 28 9.770097 TTATCTAGCCTCTGTATGATTTTTGAG 57.230 33.333 0.00 0.00 0.00 3.02
60 61 9.477484 CCTACATCATATCTGTAGTTTGGTTAC 57.523 37.037 15.77 0.00 42.90 2.50
61 62 9.429109 TCCTACATCATATCTGTAGTTTGGTTA 57.571 33.333 15.77 0.00 42.90 2.85
62 63 8.319057 TCCTACATCATATCTGTAGTTTGGTT 57.681 34.615 15.77 0.00 42.90 3.67
63 64 7.565398 ACTCCTACATCATATCTGTAGTTTGGT 59.435 37.037 15.77 9.07 42.90 3.67
64 65 7.957002 ACTCCTACATCATATCTGTAGTTTGG 58.043 38.462 15.77 6.50 42.90 3.28
66 67 9.869667 ACTACTCCTACATCATATCTGTAGTTT 57.130 33.333 15.77 6.75 42.90 2.66
70 71 9.907229 CCATACTACTCCTACATCATATCTGTA 57.093 37.037 0.00 0.00 0.00 2.74
71 72 8.615705 TCCATACTACTCCTACATCATATCTGT 58.384 37.037 0.00 0.00 0.00 3.41
72 73 9.467796 TTCCATACTACTCCTACATCATATCTG 57.532 37.037 0.00 0.00 0.00 2.90
73 74 9.469097 GTTCCATACTACTCCTACATCATATCT 57.531 37.037 0.00 0.00 0.00 1.98
74 75 9.244292 TGTTCCATACTACTCCTACATCATATC 57.756 37.037 0.00 0.00 0.00 1.63
75 76 9.601810 TTGTTCCATACTACTCCTACATCATAT 57.398 33.333 0.00 0.00 0.00 1.78
76 77 9.429109 TTTGTTCCATACTACTCCTACATCATA 57.571 33.333 0.00 0.00 0.00 2.15
77 78 7.914427 TTGTTCCATACTACTCCTACATCAT 57.086 36.000 0.00 0.00 0.00 2.45
78 79 7.179516 TGTTTGTTCCATACTACTCCTACATCA 59.820 37.037 0.00 0.00 0.00 3.07
79 80 7.553334 TGTTTGTTCCATACTACTCCTACATC 58.447 38.462 0.00 0.00 0.00 3.06
80 81 7.490657 TGTTTGTTCCATACTACTCCTACAT 57.509 36.000 0.00 0.00 0.00 2.29
81 82 6.921486 TGTTTGTTCCATACTACTCCTACA 57.079 37.500 0.00 0.00 0.00 2.74
82 83 9.310716 GTATTGTTTGTTCCATACTACTCCTAC 57.689 37.037 0.00 0.00 0.00 3.18
83 84 8.192774 CGTATTGTTTGTTCCATACTACTCCTA 58.807 37.037 0.00 0.00 0.00 2.94
84 85 7.039882 CGTATTGTTTGTTCCATACTACTCCT 58.960 38.462 0.00 0.00 0.00 3.69
85 86 7.037438 TCGTATTGTTTGTTCCATACTACTCC 58.963 38.462 0.00 0.00 0.00 3.85
86 87 8.470040 TTCGTATTGTTTGTTCCATACTACTC 57.530 34.615 0.00 0.00 0.00 2.59
87 88 7.064253 GCTTCGTATTGTTTGTTCCATACTACT 59.936 37.037 0.00 0.00 0.00 2.57
88 89 7.064253 AGCTTCGTATTGTTTGTTCCATACTAC 59.936 37.037 0.00 0.00 0.00 2.73
89 90 7.064134 CAGCTTCGTATTGTTTGTTCCATACTA 59.936 37.037 0.00 0.00 0.00 1.82
90 91 5.938125 AGCTTCGTATTGTTTGTTCCATACT 59.062 36.000 0.00 0.00 0.00 2.12
91 92 6.021596 CAGCTTCGTATTGTTTGTTCCATAC 58.978 40.000 0.00 0.00 0.00 2.39
92 93 5.123186 CCAGCTTCGTATTGTTTGTTCCATA 59.877 40.000 0.00 0.00 0.00 2.74
93 94 4.082787 CCAGCTTCGTATTGTTTGTTCCAT 60.083 41.667 0.00 0.00 0.00 3.41
94 95 3.252215 CCAGCTTCGTATTGTTTGTTCCA 59.748 43.478 0.00 0.00 0.00 3.53
95 96 3.821841 CCAGCTTCGTATTGTTTGTTCC 58.178 45.455 0.00 0.00 0.00 3.62
96 97 3.058224 AGCCAGCTTCGTATTGTTTGTTC 60.058 43.478 0.00 0.00 0.00 3.18
97 98 2.884639 AGCCAGCTTCGTATTGTTTGTT 59.115 40.909 0.00 0.00 0.00 2.83
98 99 2.484264 GAGCCAGCTTCGTATTGTTTGT 59.516 45.455 0.00 0.00 0.00 2.83
99 100 2.159517 GGAGCCAGCTTCGTATTGTTTG 60.160 50.000 0.00 0.00 0.00 2.93
100 101 2.084546 GGAGCCAGCTTCGTATTGTTT 58.915 47.619 0.00 0.00 0.00 2.83
101 102 1.003118 TGGAGCCAGCTTCGTATTGTT 59.997 47.619 0.00 0.00 0.00 2.83
102 103 0.613260 TGGAGCCAGCTTCGTATTGT 59.387 50.000 0.00 0.00 0.00 2.71
103 104 1.134699 TCTGGAGCCAGCTTCGTATTG 60.135 52.381 11.68 0.00 43.31 1.90
104 105 1.195115 TCTGGAGCCAGCTTCGTATT 58.805 50.000 11.68 0.00 43.31 1.89
105 106 1.418334 ATCTGGAGCCAGCTTCGTAT 58.582 50.000 11.68 0.00 43.31 3.06
106 107 1.195115 AATCTGGAGCCAGCTTCGTA 58.805 50.000 11.68 0.00 43.31 3.43
107 108 0.326264 AAATCTGGAGCCAGCTTCGT 59.674 50.000 11.68 0.00 43.31 3.85
108 109 1.457346 AAAATCTGGAGCCAGCTTCG 58.543 50.000 11.68 0.00 43.31 3.79
2613 2620 2.594303 CACCACCGGCTCTGCAAA 60.594 61.111 0.00 0.00 0.00 3.68
2757 2764 3.927142 CACGGACCTGCTTCTTAGTAAAG 59.073 47.826 0.00 0.00 0.00 1.85
2832 2839 4.544564 AAGACCTATTGGCTCCTCTAGA 57.455 45.455 0.00 0.00 36.63 2.43
3106 3113 3.211045 TCTTTGCTAACTCGTGCCTTTT 58.789 40.909 0.00 0.00 0.00 2.27
4044 4191 6.017400 ACAAATCTCAGGTGCAAATACAAG 57.983 37.500 0.00 0.00 0.00 3.16
4112 4259 0.861837 CCGGTGCTTTCTATCGATGC 59.138 55.000 8.54 2.63 0.00 3.91
4132 4279 1.700042 CCCGCTTCCAATAGGGCTCT 61.700 60.000 0.00 0.00 37.07 4.09
4134 4281 2.919043 CCCGCTTCCAATAGGGCT 59.081 61.111 0.00 0.00 37.07 5.19
4184 4331 4.929808 CGTGTATCAGCCAGTTAGTCTTTT 59.070 41.667 0.00 0.00 0.00 2.27
4297 4448 7.039993 AGCCCAACTTAACCTACAAAATAACAG 60.040 37.037 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.