Multiple sequence alignment - TraesCS3B01G587500

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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 TraesCS3B01G587500 chr3B 100.000 3445 0 0 1 3445 813958675 813955231 0.000000e+00 6362
1 TraesCS3B01G587500 chr3B 99.634 3277 12 0 169 3445 829116459 829119735 0.000000e+00 5986
2 TraesCS3B01G587500 chr7B 99.604 3280 13 0 166 3445 204002751 204006030 0.000000e+00 5986
3 TraesCS3B01G587500 chr2A 99.086 3284 30 0 162 3445 713923483 713926766 0.000000e+00 5899
4 TraesCS3B01G587500 chr2A 98.897 2630 29 0 816 3445 39363907 39361278 0.000000e+00 4697
5 TraesCS3B01G587500 chr3A 99.085 3277 29 1 169 3445 610424330 610421055 0.000000e+00 5884
6 TraesCS3B01G587500 chr3A 98.214 168 3 0 169 336 212122665 212122832 9.350000e-76 294
7 TraesCS3B01G587500 chr4A 98.627 3277 44 1 169 3445 586088076 586084801 0.000000e+00 5801
8 TraesCS3B01G587500 chr7D 97.412 3052 77 2 395 3445 237548457 237551507 0.000000e+00 5197
9 TraesCS3B01G587500 chr7D 96.316 190 7 0 166 355 237548279 237548468 2.580000e-81 313
10 TraesCS3B01G587500 chr5B 98.335 2523 41 1 924 3445 599616903 599614381 0.000000e+00 4425
11 TraesCS3B01G587500 chr5B 92.958 213 11 2 169 377 531864099 531864311 1.200000e-79 307
12 TraesCS3B01G587500 chr5B 91.781 73 6 0 858 930 531864453 531864525 6.080000e-18 102
13 TraesCS3B01G587500 chr3D 95.353 2518 116 1 929 3445 511280668 511278151 0.000000e+00 4000
14 TraesCS3B01G587500 chr3D 93.897 213 9 2 169 377 511281792 511281580 5.550000e-83 318
15 TraesCS3B01G587500 chrUn 93.452 168 7 2 1 167 46223971 46223807 2.660000e-61 246


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 TraesCS3B01G587500 chr3B 813955231 813958675 3444 True 6362 6362 100.000 1 3445 1 chr3B.!!$R1 3444
1 TraesCS3B01G587500 chr3B 829116459 829119735 3276 False 5986 5986 99.634 169 3445 1 chr3B.!!$F1 3276
2 TraesCS3B01G587500 chr7B 204002751 204006030 3279 False 5986 5986 99.604 166 3445 1 chr7B.!!$F1 3279
3 TraesCS3B01G587500 chr2A 713923483 713926766 3283 False 5899 5899 99.086 162 3445 1 chr2A.!!$F1 3283
4 TraesCS3B01G587500 chr2A 39361278 39363907 2629 True 4697 4697 98.897 816 3445 1 chr2A.!!$R1 2629
5 TraesCS3B01G587500 chr3A 610421055 610424330 3275 True 5884 5884 99.085 169 3445 1 chr3A.!!$R1 3276
6 TraesCS3B01G587500 chr4A 586084801 586088076 3275 True 5801 5801 98.627 169 3445 1 chr4A.!!$R1 3276
7 TraesCS3B01G587500 chr7D 237548279 237551507 3228 False 2755 5197 96.864 166 3445 2 chr7D.!!$F1 3279
8 TraesCS3B01G587500 chr5B 599614381 599616903 2522 True 4425 4425 98.335 924 3445 1 chr5B.!!$R1 2521
9 TraesCS3B01G587500 chr3D 511278151 511281792 3641 True 2159 4000 94.625 169 3445 2 chr3D.!!$R1 3276

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
100 101 0.114954 ACCCCTCAATGTGCCATTGT 59.885 50.0 20.38 5.46 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 3026 6.099557 TGTTTCCTTTTCTCCCATCATTGTTT 59.9 34.615 0.0 0.0 0.0 2.83 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
29 30 9.716507 CACCTAATTTTATTACGACATCTTTGG 57.283 33.333 0.00 0.00 0.00 3.28
30 31 9.675464 ACCTAATTTTATTACGACATCTTTGGA 57.325 29.630 0.00 0.00 0.00 3.53
34 35 9.634163 AATTTTATTACGACATCTTTGGAAACC 57.366 29.630 0.00 0.00 0.00 3.27
35 36 7.989416 TTTATTACGACATCTTTGGAAACCT 57.011 32.000 0.00 0.00 0.00 3.50
36 37 9.504708 TTTTATTACGACATCTTTGGAAACCTA 57.495 29.630 0.00 0.00 0.00 3.08
37 38 9.504708 TTTATTACGACATCTTTGGAAACCTAA 57.495 29.630 0.00 0.00 0.00 2.69
38 39 9.675464 TTATTACGACATCTTTGGAAACCTAAT 57.325 29.630 0.00 0.00 0.00 1.73
40 41 9.675464 ATTACGACATCTTTGGAAACCTAATAA 57.325 29.630 0.00 0.00 0.00 1.40
41 42 9.675464 TTACGACATCTTTGGAAACCTAATAAT 57.325 29.630 0.00 0.00 0.00 1.28
43 44 9.675464 ACGACATCTTTGGAAACCTAATAATAA 57.325 29.630 0.00 0.00 0.00 1.40
74 75 9.988815 ATGATAGTTCACAAGAGTATATTCCAC 57.011 33.333 0.00 0.00 33.85 4.02
75 76 9.201989 TGATAGTTCACAAGAGTATATTCCACT 57.798 33.333 0.00 0.00 0.00 4.00
79 80 9.574516 AGTTCACAAGAGTATATTCCACTTTTT 57.425 29.630 0.00 0.00 0.00 1.94
84 85 9.239551 ACAAGAGTATATTCCACTTTTTAACCC 57.760 33.333 0.00 0.00 0.00 4.11
85 86 8.683615 CAAGAGTATATTCCACTTTTTAACCCC 58.316 37.037 0.00 0.00 0.00 4.95
86 87 8.171337 AGAGTATATTCCACTTTTTAACCCCT 57.829 34.615 0.00 0.00 0.00 4.79
87 88 8.272889 AGAGTATATTCCACTTTTTAACCCCTC 58.727 37.037 0.00 0.00 0.00 4.30
88 89 7.935405 AGTATATTCCACTTTTTAACCCCTCA 58.065 34.615 0.00 0.00 0.00 3.86
89 90 8.395605 AGTATATTCCACTTTTTAACCCCTCAA 58.604 33.333 0.00 0.00 0.00 3.02
90 91 9.197306 GTATATTCCACTTTTTAACCCCTCAAT 57.803 33.333 0.00 0.00 0.00 2.57
91 92 5.799827 TTCCACTTTTTAACCCCTCAATG 57.200 39.130 0.00 0.00 0.00 2.82
92 93 4.810345 TCCACTTTTTAACCCCTCAATGT 58.190 39.130 0.00 0.00 0.00 2.71
93 94 4.586841 TCCACTTTTTAACCCCTCAATGTG 59.413 41.667 0.00 0.00 0.00 3.21
94 95 4.306600 CACTTTTTAACCCCTCAATGTGC 58.693 43.478 0.00 0.00 0.00 4.57
95 96 3.323691 ACTTTTTAACCCCTCAATGTGCC 59.676 43.478 0.00 0.00 0.00 5.01
96 97 2.685106 TTTAACCCCTCAATGTGCCA 57.315 45.000 0.00 0.00 0.00 4.92
97 98 2.917713 TTAACCCCTCAATGTGCCAT 57.082 45.000 0.00 0.00 0.00 4.40
98 99 2.917713 TAACCCCTCAATGTGCCATT 57.082 45.000 0.00 0.00 0.00 3.16
99 100 1.269012 AACCCCTCAATGTGCCATTG 58.731 50.000 17.09 17.09 0.00 2.82
100 101 0.114954 ACCCCTCAATGTGCCATTGT 59.885 50.000 20.38 5.46 0.00 2.71
101 102 0.533491 CCCCTCAATGTGCCATTGTG 59.467 55.000 20.38 18.38 0.00 3.33
102 103 1.548081 CCCTCAATGTGCCATTGTGA 58.452 50.000 21.40 9.14 0.00 3.58
103 104 1.203052 CCCTCAATGTGCCATTGTGAC 59.797 52.381 21.40 0.00 0.00 3.67
104 105 1.887854 CCTCAATGTGCCATTGTGACA 59.112 47.619 21.40 3.12 0.00 3.58
105 106 2.296752 CCTCAATGTGCCATTGTGACAA 59.703 45.455 21.40 0.00 0.00 3.18
106 107 3.311106 CTCAATGTGCCATTGTGACAAC 58.689 45.455 20.38 0.00 0.00 3.32
107 108 2.035704 TCAATGTGCCATTGTGACAACC 59.964 45.455 20.38 0.00 0.00 3.77
108 109 1.999648 ATGTGCCATTGTGACAACCT 58.000 45.000 0.00 0.00 0.00 3.50
109 110 1.774110 TGTGCCATTGTGACAACCTT 58.226 45.000 0.00 0.00 0.00 3.50
110 111 2.937519 TGTGCCATTGTGACAACCTTA 58.062 42.857 0.00 0.00 0.00 2.69
111 112 2.621055 TGTGCCATTGTGACAACCTTAC 59.379 45.455 0.00 0.00 0.00 2.34
112 113 2.030274 GTGCCATTGTGACAACCTTACC 60.030 50.000 0.00 0.00 0.00 2.85
113 114 1.199097 GCCATTGTGACAACCTTACCG 59.801 52.381 0.00 0.00 0.00 4.02
114 115 1.199097 CCATTGTGACAACCTTACCGC 59.801 52.381 0.00 0.00 0.00 5.68
115 116 1.876799 CATTGTGACAACCTTACCGCA 59.123 47.619 0.00 0.00 0.00 5.69
116 117 2.264005 TTGTGACAACCTTACCGCAT 57.736 45.000 0.00 0.00 0.00 4.73
117 118 2.264005 TGTGACAACCTTACCGCATT 57.736 45.000 0.00 0.00 0.00 3.56
118 119 2.577700 TGTGACAACCTTACCGCATTT 58.422 42.857 0.00 0.00 0.00 2.32
119 120 3.741249 TGTGACAACCTTACCGCATTTA 58.259 40.909 0.00 0.00 0.00 1.40
120 121 3.749088 TGTGACAACCTTACCGCATTTAG 59.251 43.478 0.00 0.00 0.00 1.85
121 122 3.998341 GTGACAACCTTACCGCATTTAGA 59.002 43.478 0.00 0.00 0.00 2.10
122 123 4.453136 GTGACAACCTTACCGCATTTAGAA 59.547 41.667 0.00 0.00 0.00 2.10
123 124 5.049267 GTGACAACCTTACCGCATTTAGAAA 60.049 40.000 0.00 0.00 0.00 2.52
124 125 5.531659 TGACAACCTTACCGCATTTAGAAAA 59.468 36.000 0.00 0.00 0.00 2.29
125 126 6.039493 TGACAACCTTACCGCATTTAGAAAAA 59.961 34.615 0.00 0.00 0.00 1.94
142 143 3.874392 AAAAATGATTCTGGGAAGCGG 57.126 42.857 0.00 0.00 0.00 5.52
143 144 2.806945 AAATGATTCTGGGAAGCGGA 57.193 45.000 0.00 0.00 0.00 5.54
144 145 3.303351 AAATGATTCTGGGAAGCGGAT 57.697 42.857 0.00 0.00 0.00 4.18
145 146 3.303351 AATGATTCTGGGAAGCGGATT 57.697 42.857 0.00 0.00 0.00 3.01
146 147 2.806945 TGATTCTGGGAAGCGGATTT 57.193 45.000 0.00 0.00 0.00 2.17
147 148 3.085952 TGATTCTGGGAAGCGGATTTT 57.914 42.857 0.00 0.00 0.00 1.82
148 149 3.430453 TGATTCTGGGAAGCGGATTTTT 58.570 40.909 0.00 0.00 0.00 1.94
167 168 1.436326 TTGTGTGGGGCTGTAACCTA 58.564 50.000 0.00 0.00 0.00 3.08
1900 2425 5.482878 GGATATAACCGAGGTGGATTAAGGA 59.517 44.000 0.00 0.00 42.00 3.36
2501 3026 2.086094 TGCGGTGTCTACGATGTTAGA 58.914 47.619 0.00 0.00 0.00 2.10
2536 3061 6.041637 GGGAGAAAAGGAAACAAAGGTAATGT 59.958 38.462 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.716507 CCAAAGATGTCGTAATAAAATTAGGTG 57.283 33.333 0.0 0.0 0.00 4.00
4 5 9.675464 TCCAAAGATGTCGTAATAAAATTAGGT 57.325 29.630 0.0 0.0 0.00 3.08
8 9 9.634163 GGTTTCCAAAGATGTCGTAATAAAATT 57.366 29.630 0.0 0.0 0.00 1.82
9 10 9.020731 AGGTTTCCAAAGATGTCGTAATAAAAT 57.979 29.630 0.0 0.0 0.00 1.82
10 11 8.398878 AGGTTTCCAAAGATGTCGTAATAAAA 57.601 30.769 0.0 0.0 0.00 1.52
11 12 7.989416 AGGTTTCCAAAGATGTCGTAATAAA 57.011 32.000 0.0 0.0 0.00 1.40
12 13 9.675464 ATTAGGTTTCCAAAGATGTCGTAATAA 57.325 29.630 0.0 0.0 0.00 1.40
14 15 9.675464 TTATTAGGTTTCCAAAGATGTCGTAAT 57.325 29.630 0.0 0.0 0.00 1.89
15 16 9.675464 ATTATTAGGTTTCCAAAGATGTCGTAA 57.325 29.630 0.0 0.0 0.00 3.18
17 18 9.675464 TTATTATTAGGTTTCCAAAGATGTCGT 57.325 29.630 0.0 0.0 0.00 4.34
48 49 9.988815 GTGGAATATACTCTTGTGAACTATCAT 57.011 33.333 0.0 0.0 38.01 2.45
49 50 9.201989 AGTGGAATATACTCTTGTGAACTATCA 57.798 33.333 0.0 0.0 0.00 2.15
53 54 9.574516 AAAAAGTGGAATATACTCTTGTGAACT 57.425 29.630 0.0 0.0 0.00 3.01
58 59 9.239551 GGGTTAAAAAGTGGAATATACTCTTGT 57.760 33.333 0.0 0.0 0.00 3.16
59 60 8.683615 GGGGTTAAAAAGTGGAATATACTCTTG 58.316 37.037 0.0 0.0 0.00 3.02
60 61 8.621073 AGGGGTTAAAAAGTGGAATATACTCTT 58.379 33.333 0.0 0.0 0.00 2.85
61 62 8.171337 AGGGGTTAAAAAGTGGAATATACTCT 57.829 34.615 0.0 0.0 0.00 3.24
62 63 8.050930 TGAGGGGTTAAAAAGTGGAATATACTC 58.949 37.037 0.0 0.0 0.00 2.59
63 64 7.935405 TGAGGGGTTAAAAAGTGGAATATACT 58.065 34.615 0.0 0.0 0.00 2.12
64 65 8.584063 TTGAGGGGTTAAAAAGTGGAATATAC 57.416 34.615 0.0 0.0 0.00 1.47
65 66 9.196139 CATTGAGGGGTTAAAAAGTGGAATATA 57.804 33.333 0.0 0.0 0.00 0.86
66 67 7.678171 ACATTGAGGGGTTAAAAAGTGGAATAT 59.322 33.333 0.0 0.0 0.00 1.28
67 68 7.013834 ACATTGAGGGGTTAAAAAGTGGAATA 58.986 34.615 0.0 0.0 0.00 1.75
68 69 5.843969 ACATTGAGGGGTTAAAAAGTGGAAT 59.156 36.000 0.0 0.0 0.00 3.01
69 70 5.069781 CACATTGAGGGGTTAAAAAGTGGAA 59.930 40.000 0.0 0.0 0.00 3.53
70 71 4.586841 CACATTGAGGGGTTAAAAAGTGGA 59.413 41.667 0.0 0.0 0.00 4.02
71 72 4.799255 GCACATTGAGGGGTTAAAAAGTGG 60.799 45.833 0.0 0.0 0.00 4.00
72 73 4.306600 GCACATTGAGGGGTTAAAAAGTG 58.693 43.478 0.0 0.0 0.00 3.16
73 74 3.323691 GGCACATTGAGGGGTTAAAAAGT 59.676 43.478 0.0 0.0 0.00 2.66
74 75 3.323403 TGGCACATTGAGGGGTTAAAAAG 59.677 43.478 0.0 0.0 0.00 2.27
75 76 3.309296 TGGCACATTGAGGGGTTAAAAA 58.691 40.909 0.0 0.0 0.00 1.94
76 77 2.964209 TGGCACATTGAGGGGTTAAAA 58.036 42.857 0.0 0.0 0.00 1.52
77 78 2.685106 TGGCACATTGAGGGGTTAAA 57.315 45.000 0.0 0.0 0.00 1.52
91 92 2.030274 GGTAAGGTTGTCACAATGGCAC 60.030 50.000 0.0 0.0 28.02 5.01
92 93 2.235016 GGTAAGGTTGTCACAATGGCA 58.765 47.619 0.0 0.0 0.00 4.92
93 94 1.199097 CGGTAAGGTTGTCACAATGGC 59.801 52.381 0.0 0.0 0.00 4.40
94 95 1.199097 GCGGTAAGGTTGTCACAATGG 59.801 52.381 0.0 0.0 0.00 3.16
95 96 1.876799 TGCGGTAAGGTTGTCACAATG 59.123 47.619 0.0 0.0 0.00 2.82
96 97 2.264005 TGCGGTAAGGTTGTCACAAT 57.736 45.000 0.0 0.0 0.00 2.71
97 98 2.264005 ATGCGGTAAGGTTGTCACAA 57.736 45.000 0.0 0.0 0.00 3.33
98 99 2.264005 AATGCGGTAAGGTTGTCACA 57.736 45.000 0.0 0.0 0.00 3.58
99 100 3.998341 TCTAAATGCGGTAAGGTTGTCAC 59.002 43.478 0.0 0.0 0.00 3.67
100 101 4.274602 TCTAAATGCGGTAAGGTTGTCA 57.725 40.909 0.0 0.0 0.00 3.58
101 102 5.616488 TTTCTAAATGCGGTAAGGTTGTC 57.384 39.130 0.0 0.0 0.00 3.18
102 103 6.394025 TTTTTCTAAATGCGGTAAGGTTGT 57.606 33.333 0.0 0.0 0.00 3.32
122 123 3.430453 TCCGCTTCCCAGAATCATTTTT 58.570 40.909 0.0 0.0 0.00 1.94
123 124 3.085952 TCCGCTTCCCAGAATCATTTT 57.914 42.857 0.0 0.0 0.00 1.82
124 125 2.806945 TCCGCTTCCCAGAATCATTT 57.193 45.000 0.0 0.0 0.00 2.32
125 126 3.303351 AATCCGCTTCCCAGAATCATT 57.697 42.857 0.0 0.0 0.00 2.57
126 127 3.303351 AAATCCGCTTCCCAGAATCAT 57.697 42.857 0.0 0.0 0.00 2.45
127 128 2.806945 AAATCCGCTTCCCAGAATCA 57.193 45.000 0.0 0.0 0.00 2.57
145 146 1.757699 GGTTACAGCCCCACACAAAAA 59.242 47.619 0.0 0.0 0.00 1.94
146 147 1.063567 AGGTTACAGCCCCACACAAAA 60.064 47.619 0.0 0.0 0.00 2.44
147 148 0.553819 AGGTTACAGCCCCACACAAA 59.446 50.000 0.0 0.0 0.00 2.83
148 149 1.436326 TAGGTTACAGCCCCACACAA 58.564 50.000 0.0 0.0 0.00 3.33
149 150 1.663911 ATAGGTTACAGCCCCACACA 58.336 50.000 0.0 0.0 0.00 3.72
150 151 2.365582 CAATAGGTTACAGCCCCACAC 58.634 52.381 0.0 0.0 0.00 3.82
151 152 1.283613 CCAATAGGTTACAGCCCCACA 59.716 52.381 0.0 0.0 0.00 4.17
152 153 1.409661 CCCAATAGGTTACAGCCCCAC 60.410 57.143 0.0 0.0 0.00 4.61
153 154 0.923358 CCCAATAGGTTACAGCCCCA 59.077 55.000 0.0 0.0 0.00 4.96
154 155 0.467474 GCCCAATAGGTTACAGCCCC 60.467 60.000 0.0 0.0 38.26 5.80
155 156 0.551396 AGCCCAATAGGTTACAGCCC 59.449 55.000 0.0 0.0 38.26 5.19
156 157 1.064685 ACAGCCCAATAGGTTACAGCC 60.065 52.381 0.0 0.0 38.26 4.85
157 158 2.420058 ACAGCCCAATAGGTTACAGC 57.580 50.000 0.0 0.0 38.26 4.40
158 159 6.650807 CACATATACAGCCCAATAGGTTACAG 59.349 42.308 0.0 0.0 38.26 2.74
159 160 6.100569 ACACATATACAGCCCAATAGGTTACA 59.899 38.462 0.0 0.0 38.26 2.41
160 161 6.426937 CACACATATACAGCCCAATAGGTTAC 59.573 42.308 0.0 0.0 38.26 2.50
167 168 5.766670 CAGATTCACACATATACAGCCCAAT 59.233 40.000 0.0 0.0 0.00 3.16
2501 3026 6.099557 TGTTTCCTTTTCTCCCATCATTGTTT 59.900 34.615 0.0 0.0 0.00 2.83


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

AutoCloner maintained by Alex Coulton.