Multiple sequence alignment - TraesCS3D01G132800

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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 TraesCS3D01G132800 chr3D 100.000 2942 0 0 1 2942 92360791 92357850 0.000000e+00 5433.0
1 TraesCS3D01G132800 chr3D 97.421 2404 29 12 550 2942 92125347 92122966 0.000000e+00 4065.0
2 TraesCS3D01G132800 chr3D 87.243 2093 209 29 576 2626 91802886 91800810 0.000000e+00 2333.0
3 TraesCS3D01G132800 chr3D 94.011 1319 54 8 1259 2558 92217228 92215916 0.000000e+00 1975.0
4 TraesCS3D01G132800 chr3D 88.575 1593 138 23 576 2129 91833478 91831891 0.000000e+00 1893.0
5 TraesCS3D01G132800 chr3D 89.319 1498 146 13 576 2065 92264255 92262764 0.000000e+00 1868.0
6 TraesCS3D01G132800 chr3D 93.820 178 8 1 191 365 92125826 92125649 6.250000e-67 265.0
7 TraesCS3D01G132800 chr3D 86.475 244 26 6 22 262 92128660 92128421 8.090000e-66 261.0
8 TraesCS3D01G132800 chr3D 96.732 153 4 1 404 556 92125567 92125416 1.350000e-63 254.0
9 TraesCS3D01G132800 chr3D 81.056 322 26 13 266 556 92224394 92224077 1.060000e-54 224.0
10 TraesCS3D01G132800 chr3D 89.326 178 17 2 1 177 92125989 92125813 3.820000e-54 222.0
11 TraesCS3D01G132800 chr3D 83.942 137 13 3 2806 2942 91800794 91800667 3.980000e-24 122.0
12 TraesCS3D01G132800 chr3D 83.673 98 16 0 455 552 91803635 91803538 3.120000e-15 93.5
13 TraesCS3D01G132800 chr3D 100.000 28 0 0 372 399 91803739 91803712 5.000000e-03 52.8
14 TraesCS3D01G132800 chr3B 96.750 1969 45 6 571 2523 141864534 141862569 0.000000e+00 3264.0
15 TraesCS3D01G132800 chr3B 87.351 2095 213 33 576 2622 141815814 141813724 0.000000e+00 2353.0
16 TraesCS3D01G132800 chr3B 89.238 1050 110 3 668 1715 141752483 141751435 0.000000e+00 1310.0
17 TraesCS3D01G132800 chr3B 86.878 945 92 19 1713 2626 141746089 141745146 0.000000e+00 1029.0
18 TraesCS3D01G132800 chr3B 96.214 449 6 4 2495 2942 141862568 141862130 0.000000e+00 725.0
19 TraesCS3D01G132800 chr3B 96.000 175 7 0 191 365 141865138 141864964 4.800000e-73 285.0
20 TraesCS3D01G132800 chr3B 96.753 154 5 0 403 556 141864860 141864707 1.050000e-64 257.0
21 TraesCS3D01G132800 chr3B 86.538 156 16 2 403 556 141752827 141752675 1.810000e-37 167.0
22 TraesCS3D01G132800 chr3B 87.324 142 12 4 2806 2942 141813617 141813477 1.090000e-34 158.0
23 TraesCS3D01G132800 chr3B 91.398 93 8 0 2818 2910 180277541 180277633 8.560000e-26 128.0
24 TraesCS3D01G132800 chr3B 90.323 93 6 3 1 91 141865723 141865632 5.150000e-23 119.0
25 TraesCS3D01G132800 chr3B 81.757 148 11 13 199 339 141753072 141752934 3.100000e-20 110.0
26 TraesCS3D01G132800 chr3B 86.869 99 12 1 2818 2916 250138437 250138340 3.100000e-20 110.0
27 TraesCS3D01G132800 chr3B 100.000 28 0 0 372 399 141864926 141864899 5.000000e-03 52.8
28 TraesCS3D01G132800 chr3A 87.162 2072 215 33 574 2626 545358703 545356664 0.000000e+00 2305.0
29 TraesCS3D01G132800 chr3A 93.773 1108 44 8 1469 2558 545891148 545890048 0.000000e+00 1640.0
30 TraesCS3D01G132800 chr3A 90.026 1153 107 7 550 1699 545892298 545891151 0.000000e+00 1485.0
31 TraesCS3D01G132800 chr3A 86.122 1297 136 22 1115 2372 545364841 545363550 0.000000e+00 1358.0
32 TraesCS3D01G132800 chr3A 84.681 235 26 9 1 227 545893546 545893314 2.950000e-55 226.0
33 TraesCS3D01G132800 chr3A 93.836 146 9 0 411 556 545892512 545892367 1.370000e-53 220.0
34 TraesCS3D01G132800 chr3A 87.324 142 12 4 2806 2942 545356648 545356508 1.090000e-34 158.0
35 TraesCS3D01G132800 chr2D 91.617 167 12 2 2622 2786 79056163 79056329 2.280000e-56 230.0
36 TraesCS3D01G132800 chr2A 90.395 177 13 4 2614 2786 79315991 79316167 2.280000e-56 230.0
37 TraesCS3D01G132800 chr4D 93.464 153 9 1 2625 2776 74079351 74079503 2.950000e-55 226.0
38 TraesCS3D01G132800 chr5D 93.421 152 8 1 2625 2776 528717278 528717427 1.060000e-54 224.0
39 TraesCS3D01G132800 chr5B 93.421 152 8 1 2625 2776 665744469 665744618 1.060000e-54 224.0
40 TraesCS3D01G132800 chr5A 93.421 152 8 1 2625 2776 656872285 656872434 1.060000e-54 224.0
41 TraesCS3D01G132800 chr7B 91.824 159 12 1 2625 2782 505937314 505937472 1.370000e-53 220.0
42 TraesCS3D01G132800 chr2B 90.323 93 9 0 2818 2910 399342041 399342133 3.980000e-24 122.0
43 TraesCS3D01G132800 chr6D 89.247 93 10 0 2818 2910 126868486 126868578 1.850000e-22 117.0


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 TraesCS3D01G132800 chr3D 92357850 92360791 2941 True 5433.000 5433 100.000000 1 2942 1 chr3D.!!$R5 2941
1 TraesCS3D01G132800 chr3D 92215916 92217228 1312 True 1975.000 1975 94.011000 1259 2558 1 chr3D.!!$R2 1299
2 TraesCS3D01G132800 chr3D 91831891 91833478 1587 True 1893.000 1893 88.575000 576 2129 1 chr3D.!!$R1 1553
3 TraesCS3D01G132800 chr3D 92262764 92264255 1491 True 1868.000 1868 89.319000 576 2065 1 chr3D.!!$R4 1489
4 TraesCS3D01G132800 chr3D 92122966 92128660 5694 True 1013.400 4065 92.754800 1 2942 5 chr3D.!!$R7 2941
5 TraesCS3D01G132800 chr3D 91800667 91803739 3072 True 650.325 2333 88.714500 372 2942 4 chr3D.!!$R6 2570
6 TraesCS3D01G132800 chr3B 141813477 141815814 2337 True 1255.500 2353 87.337500 576 2942 2 chr3B.!!$R4 2366
7 TraesCS3D01G132800 chr3B 141745146 141746089 943 True 1029.000 1029 86.878000 1713 2626 1 chr3B.!!$R1 913
8 TraesCS3D01G132800 chr3B 141862130 141865723 3593 True 783.800 3264 96.006667 1 2942 6 chr3B.!!$R5 2941
9 TraesCS3D01G132800 chr3B 141751435 141753072 1637 True 529.000 1310 85.844333 199 1715 3 chr3B.!!$R3 1516
10 TraesCS3D01G132800 chr3A 545363550 545364841 1291 True 1358.000 1358 86.122000 1115 2372 1 chr3A.!!$R1 1257
11 TraesCS3D01G132800 chr3A 545356508 545358703 2195 True 1231.500 2305 87.243000 574 2942 2 chr3A.!!$R2 2368
12 TraesCS3D01G132800 chr3A 545890048 545893546 3498 True 892.750 1640 90.579000 1 2558 4 chr3A.!!$R3 2557

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
635 5115 0.108281 GGTTCGGAGCTACCCTTGTC 60.108 60.0 0.0 0.0 34.64 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 7026 0.98989 CAGTACTCGGTTAAGCGTGC 59.01 55.0 24.71 11.61 0.0 5.34 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
65 2739 3.629142 ACGATAAGGAAAACCAGAGGG 57.371 47.619 0.00 0.00 41.29 4.30
66 2740 2.238898 ACGATAAGGAAAACCAGAGGGG 59.761 50.000 0.00 0.00 44.81 4.79
67 2741 2.421529 CGATAAGGAAAACCAGAGGGGG 60.422 54.545 0.00 0.00 42.91 5.40
100 2807 0.248907 GTCGCAGCGCTAGTAATGGA 60.249 55.000 10.99 0.00 0.00 3.41
102 2809 0.249073 CGCAGCGCTAGTAATGGACT 60.249 55.000 10.99 0.00 42.69 3.85
105 2812 0.753262 AGCGCTAGTAATGGACTGGG 59.247 55.000 8.99 0.00 39.39 4.45
171 3266 0.878086 GGGCGAGACATAGCTCTTGC 60.878 60.000 4.66 4.66 44.29 4.01
177 3272 1.827969 AGACATAGCTCTTGCGAAGGT 59.172 47.619 0.00 0.00 45.42 3.50
178 3273 2.159170 AGACATAGCTCTTGCGAAGGTC 60.159 50.000 0.00 0.00 45.42 3.85
180 3275 2.234908 ACATAGCTCTTGCGAAGGTCTT 59.765 45.455 0.00 0.00 45.42 3.01
181 3276 2.656560 TAGCTCTTGCGAAGGTCTTC 57.343 50.000 0.00 0.85 45.42 2.87
182 3277 0.972883 AGCTCTTGCGAAGGTCTTCT 59.027 50.000 8.79 0.00 45.42 2.85
183 3278 2.171840 AGCTCTTGCGAAGGTCTTCTA 58.828 47.619 8.79 0.00 45.42 2.10
184 3279 2.563179 AGCTCTTGCGAAGGTCTTCTAA 59.437 45.455 8.79 3.95 45.42 2.10
251 3813 3.073735 CCTCCACCGCTCAGAGCT 61.074 66.667 20.39 0.00 39.60 4.09
399 4003 2.750350 CCGCACAACCCCTCTCTT 59.250 61.111 0.00 0.00 0.00 2.85
400 4004 1.550130 CCCGCACAACCCCTCTCTTA 61.550 60.000 0.00 0.00 0.00 2.10
401 4005 0.541863 CCGCACAACCCCTCTCTTAT 59.458 55.000 0.00 0.00 0.00 1.73
466 4184 0.671781 CAGTTCTGCCTCGACCCTTG 60.672 60.000 0.00 0.00 0.00 3.61
538 4256 0.601311 CCCGATTCATTCCTCTCCGC 60.601 60.000 0.00 0.00 0.00 5.54
563 4935 5.050702 CGAGTTGTTTCTTCTGAAAGTCCTC 60.051 44.000 0.00 0.00 42.15 3.71
623 5103 1.057851 ACCTTCCAGTTGGGTTCGGA 61.058 55.000 0.00 0.00 38.11 4.55
624 5104 0.321653 CCTTCCAGTTGGGTTCGGAG 60.322 60.000 0.00 0.00 38.11 4.63
625 5105 0.955919 CTTCCAGTTGGGTTCGGAGC 60.956 60.000 0.00 0.00 38.11 4.70
626 5106 1.415672 TTCCAGTTGGGTTCGGAGCT 61.416 55.000 0.00 0.00 38.11 4.09
627 5107 0.543410 TCCAGTTGGGTTCGGAGCTA 60.543 55.000 0.00 0.00 38.11 3.32
628 5108 0.391263 CCAGTTGGGTTCGGAGCTAC 60.391 60.000 0.00 0.00 0.00 3.58
629 5109 0.391263 CAGTTGGGTTCGGAGCTACC 60.391 60.000 0.00 0.00 0.00 3.18
632 5112 3.723245 GGGTTCGGAGCTACCCTT 58.277 61.111 14.30 0.00 44.91 3.95
633 5113 1.221021 GGGTTCGGAGCTACCCTTG 59.779 63.158 14.30 0.00 44.91 3.61
634 5114 1.551019 GGGTTCGGAGCTACCCTTGT 61.551 60.000 14.30 0.00 44.91 3.16
635 5115 0.108281 GGTTCGGAGCTACCCTTGTC 60.108 60.000 0.00 0.00 34.64 3.18
643 5123 3.770388 GGAGCTACCCTTGTCCCTATATC 59.230 52.174 0.00 0.00 0.00 1.63
648 5129 7.894561 AGCTACCCTTGTCCCTATATCATATA 58.105 38.462 0.00 0.00 0.00 0.86
649 5130 7.785506 AGCTACCCTTGTCCCTATATCATATAC 59.214 40.741 0.00 0.00 0.00 1.47
701 5208 1.214175 TGGACAAAGCTTCTGTTCCCA 59.786 47.619 0.00 8.43 0.00 4.37
1068 5576 3.982516 TCTCATACTAGTGAACCCTGCT 58.017 45.455 5.39 0.00 0.00 4.24
1135 5645 3.243602 TGTTAGACTGCGCTACACTGAAA 60.244 43.478 9.73 0.00 0.00 2.69
2203 7026 5.452078 TTGCTATGGTTGTTTTCAAGGAG 57.548 39.130 0.00 0.00 40.74 3.69
2303 7133 6.419116 GCTTAAATGCTTAGCCTTTTATGCTC 59.581 38.462 23.86 9.80 40.23 4.26
2479 7313 6.920569 ATTGTTTCATTCGTATGTCCCTAC 57.079 37.500 1.75 0.00 33.34 3.18
2914 7783 5.584649 GGCTAAAAGGCTTTGTTGTTTTTCT 59.415 36.000 14.19 0.00 37.85 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 2681 4.202253 GCAGAGGTTTTCATTGGTTTTCCT 60.202 41.667 0.00 0.00 41.38 3.36
10 2683 4.692228 TGCAGAGGTTTTCATTGGTTTTC 58.308 39.130 0.00 0.00 0.00 2.29
65 2739 1.060465 GACGCGCGAGATTTTTCCC 59.940 57.895 39.36 7.68 0.00 3.97
66 2740 1.295930 CGACGCGCGAGATTTTTCC 60.296 57.895 39.36 11.63 44.57 3.13
67 2741 1.923614 GCGACGCGCGAGATTTTTC 60.924 57.895 39.36 20.47 44.55 2.29
127 3222 3.536548 AGACGTAGCTCAGTCTCGT 57.463 52.632 15.72 7.27 43.52 4.18
251 3813 1.816863 GAGGAGCACGAGGGTTGTGA 61.817 60.000 0.00 0.00 39.73 3.58
538 4256 4.024809 GGACTTTCAGAAGAAACAACTCGG 60.025 45.833 0.00 0.00 38.76 4.63
563 4935 4.377431 GGACTTTCAGAAATACTGTGCACG 60.377 45.833 13.13 9.67 45.86 5.34
623 5103 4.487282 TGATATAGGGACAAGGGTAGCT 57.513 45.455 0.00 0.00 0.00 3.32
624 5104 7.785506 AGTATATGATATAGGGACAAGGGTAGC 59.214 40.741 0.00 0.00 0.00 3.58
627 5107 8.630091 TGTAGTATATGATATAGGGACAAGGGT 58.370 37.037 0.00 0.00 0.00 4.34
628 5108 8.915036 GTGTAGTATATGATATAGGGACAAGGG 58.085 40.741 0.00 0.00 0.00 3.95
629 5109 9.475620 TGTGTAGTATATGATATAGGGACAAGG 57.524 37.037 0.00 0.00 0.00 3.61
631 5111 9.816787 TGTGTGTAGTATATGATATAGGGACAA 57.183 33.333 0.00 0.00 0.00 3.18
632 5112 9.816787 TTGTGTGTAGTATATGATATAGGGACA 57.183 33.333 0.00 0.00 0.00 4.02
701 5208 3.698040 GTGCTCCAATCTGGTGAATCATT 59.302 43.478 0.00 0.00 39.03 2.57
1135 5645 4.234550 TCATATCCATCTAGCACACCCTT 58.765 43.478 0.00 0.00 0.00 3.95
2203 7026 0.989890 CAGTACTCGGTTAAGCGTGC 59.010 55.000 24.71 11.61 0.00 5.34
2303 7133 4.758773 ATTTGGTTTGGCCTCCATAATG 57.241 40.909 3.32 0.00 38.35 1.90
2801 7665 5.220835 GCACGTGGACATATTCAATGATTCA 60.221 40.000 18.88 0.00 0.00 2.57
2802 7666 5.207768 GCACGTGGACATATTCAATGATTC 58.792 41.667 18.88 0.00 0.00 2.52
2803 7667 4.036734 GGCACGTGGACATATTCAATGATT 59.963 41.667 18.88 0.00 0.00 2.57
2804 7668 3.565482 GGCACGTGGACATATTCAATGAT 59.435 43.478 18.88 0.00 0.00 2.45
2805 7669 2.942376 GGCACGTGGACATATTCAATGA 59.058 45.455 18.88 0.00 0.00 2.57
2806 7670 2.682352 TGGCACGTGGACATATTCAATG 59.318 45.455 18.88 0.00 0.00 2.82
2807 7671 2.945008 CTGGCACGTGGACATATTCAAT 59.055 45.455 18.88 0.00 30.67 2.57
2808 7672 2.027653 TCTGGCACGTGGACATATTCAA 60.028 45.455 18.88 0.00 30.67 2.69
2914 7783 8.422577 ACCAGCTAGTTGATCATACATGTATA 57.577 34.615 17.86 7.59 0.00 1.47


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

AutoCloner maintained by Alex Coulton.