Multiple sequence alignment - TraesCS3D01G242800

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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 TraesCS3D01G242800 chr3D 100.000 5222 0 0 1 5222 338313969 338319190 0.000000e+00 9644.0
1 TraesCS3D01G242800 chr3D 89.965 578 17 9 4668 5219 338318848 338319410 0.000000e+00 708.0
2 TraesCS3D01G242800 chr3D 90.300 433 15 12 4687 5095 338319066 338319495 4.600000e-150 542.0
3 TraesCS3D01G242800 chr3D 90.223 358 10 6 4880 5222 338318636 338318983 1.330000e-120 444.0
4 TraesCS3D01G242800 chr3D 81.250 496 64 18 471 949 550664130 550663647 1.780000e-99 374.0
5 TraesCS3D01G242800 chr3D 90.308 227 9 5 4668 4881 338319269 338319495 8.560000e-73 285.0
6 TraesCS3D01G242800 chr3D 88.889 126 2 6 5098 5222 338318655 338318769 1.520000e-30 145.0
7 TraesCS3D01G242800 chr3D 85.185 108 3 1 2073 2167 338315942 338316049 1.200000e-16 99.0
8 TraesCS3D01G242800 chr3D 85.185 108 3 1 1974 2081 338316041 338316135 1.200000e-16 99.0
9 TraesCS3D01G242800 chr3D 97.917 48 1 0 286 333 338314222 338314269 3.350000e-12 84.2
10 TraesCS3D01G242800 chr3D 97.917 48 1 0 254 301 338314254 338314301 3.350000e-12 84.2
11 TraesCS3D01G242800 chr3A 92.690 1751 96 14 2653 4397 456445431 456447155 0.000000e+00 2495.0
12 TraesCS3D01G242800 chr3A 90.305 1836 89 41 501 2296 456442730 456444516 0.000000e+00 2322.0
13 TraesCS3D01G242800 chr3A 93.919 444 13 4 1487 1930 456444819 456445248 0.000000e+00 658.0
14 TraesCS3D01G242800 chr3A 93.116 276 12 3 1 276 456442328 456442596 1.050000e-106 398.0
15 TraesCS3D01G242800 chr3A 96.154 234 9 0 2296 2529 456444544 456444777 2.950000e-102 383.0
16 TraesCS3D01G242800 chr3A 89.493 276 24 5 484 756 687616710 687616437 1.390000e-90 344.0
17 TraesCS3D01G242800 chr3A 83.245 376 22 12 4412 4758 456447141 456447504 1.830000e-79 307.0
18 TraesCS3D01G242800 chr3A 79.822 337 42 14 4883 5202 456447663 456447990 6.810000e-54 222.0
19 TraesCS3D01G242800 chr3A 84.793 217 20 3 4671 4875 456449732 456449947 6.850000e-49 206.0
20 TraesCS3D01G242800 chr3A 84.332 217 22 2 4671 4875 456447991 456448207 8.870000e-48 202.0
21 TraesCS3D01G242800 chr3A 92.188 128 8 2 5097 5222 456448006 456448133 4.150000e-41 180.0
22 TraesCS3D01G242800 chr3A 87.342 158 14 3 2471 2623 456445278 456445434 5.370000e-40 176.0
23 TraesCS3D01G242800 chr3A 96.939 98 3 0 1974 2071 456444291 456444388 1.160000e-36 165.0
24 TraesCS3D01G242800 chr3A 92.308 117 7 2 5097 5211 456447678 456447794 1.160000e-36 165.0
25 TraesCS3D01G242800 chr3A 92.661 109 5 3 5097 5202 456448753 456448861 2.520000e-33 154.0
26 TraesCS3D01G242800 chr3A 93.333 105 4 2 2068 2169 456444208 456444312 9.060000e-33 152.0
27 TraesCS3D01G242800 chr3A 79.915 234 23 15 4973 5202 456449518 456449731 3.260000e-32 150.0
28 TraesCS3D01G242800 chr3A 88.889 117 11 1 4759 4875 456448371 456448485 5.450000e-30 143.0
29 TraesCS3D01G242800 chr3A 88.889 117 11 1 4973 5089 456450111 456450225 5.450000e-30 143.0
30 TraesCS3D01G242800 chr3A 88.034 117 12 1 4973 5089 456448371 456448485 2.540000e-28 137.0
31 TraesCS3D01G242800 chr3A 88.034 117 12 1 4759 4875 456450111 456450225 2.540000e-28 137.0
32 TraesCS3D01G242800 chr3A 90.909 88 6 2 5137 5222 456448326 456448413 3.300000e-22 117.0
33 TraesCS3D01G242800 chr3A 90.909 88 6 2 5137 5222 456450066 456450153 3.300000e-22 117.0
34 TraesCS3D01G242800 chr3A 85.714 112 13 3 4648 4758 456448717 456448826 1.190000e-21 115.0
35 TraesCS3D01G242800 chr3A 84.956 113 13 3 4648 4758 456449586 456449696 1.540000e-20 111.0
36 TraesCS3D01G242800 chr3A 87.356 87 7 4 4887 4972 456448743 456448826 4.300000e-16 97.1
37 TraesCS3D01G242800 chr3A 87.500 88 6 4 4887 4972 456449612 456449696 4.300000e-16 97.1
38 TraesCS3D01G242800 chr3B 90.932 1169 69 13 2471 3624 436559857 436561003 0.000000e+00 1537.0
39 TraesCS3D01G242800 chr3B 89.248 1051 82 19 339 1376 436557939 436558971 0.000000e+00 1286.0
40 TraesCS3D01G242800 chr3B 96.414 502 18 0 3896 4397 436562025 436562526 0.000000e+00 828.0
41 TraesCS3D01G242800 chr3B 89.897 485 35 6 3426 3896 436561021 436561505 3.460000e-171 612.0
42 TraesCS3D01G242800 chr3B 87.616 323 13 12 1 301 436557376 436557693 2.990000e-92 350.0
43 TraesCS3D01G242800 chr3B 82.353 425 35 12 1547 1939 436559420 436559836 3.010000e-87 333.0
44 TraesCS3D01G242800 chr3B 80.870 345 24 11 4412 4714 436562512 436562856 3.140000e-57 233.0
45 TraesCS3D01G242800 chr3B 85.106 141 11 4 4814 4945 436569537 436569676 9.120000e-28 135.0
46 TraesCS3D01G242800 chr3B 84.672 137 9 5 5098 5222 436569630 436569766 5.490000e-25 126.0
47 TraesCS3D01G242800 chr3B 92.941 85 6 0 4649 4733 436569592 436569676 1.970000e-24 124.0
48 TraesCS3D01G242800 chr3B 86.301 73 9 1 1960 2032 818302683 818302612 1.560000e-10 78.7
49 TraesCS3D01G242800 chr3B 81.188 101 3 5 4582 4666 526684565 526684665 3.370000e-07 67.6
50 TraesCS3D01G242800 chr2D 89.560 364 29 7 511 873 584841806 584841451 2.220000e-123 453.0
51 TraesCS3D01G242800 chr2D 88.571 70 2 3 904 967 584841396 584841327 4.330000e-11 80.5
52 TraesCS3D01G242800 chr2D 90.000 50 2 1 4577 4626 409599327 409599373 1.570000e-05 62.1
53 TraesCS3D01G242800 chr2B 88.172 372 32 10 509 878 705223031 705222670 2.890000e-117 433.0
54 TraesCS3D01G242800 chr2B 91.429 105 9 0 1968 2072 743334542 743334646 1.520000e-30 145.0
55 TraesCS3D01G242800 chr5A 81.818 407 38 17 2096 2470 395055618 395056020 5.080000e-80 309.0
56 TraesCS3D01G242800 chr5A 90.566 53 3 2 4576 4626 338577874 338577822 9.380000e-08 69.4
57 TraesCS3D01G242800 chr5A 97.222 36 0 1 4628 4663 588870465 588870499 5.650000e-05 60.2
58 TraesCS3D01G242800 chr5A 82.143 84 1 3 4595 4664 606890420 606890337 5.650000e-05 60.2
59 TraesCS3D01G242800 chr7A 89.431 246 20 6 509 750 85958098 85957855 6.570000e-79 305.0
60 TraesCS3D01G242800 chr7A 83.436 163 16 8 2097 2258 155303463 155303311 1.960000e-29 141.0
61 TraesCS3D01G242800 chr7A 86.207 58 5 3 4572 4626 291339 291282 5.650000e-05 60.2
62 TraesCS3D01G242800 chr7D 86.905 252 29 4 501 750 84796422 84796173 3.980000e-71 279.0
63 TraesCS3D01G242800 chr7D 94.118 68 4 0 2397 2464 628721650 628721583 2.570000e-18 104.0
64 TraesCS3D01G242800 chr7B 87.059 255 19 13 509 755 186974035 186974283 5.150000e-70 276.0
65 TraesCS3D01G242800 chr5B 87.200 250 22 6 2054 2295 576276696 576276943 5.150000e-70 276.0
66 TraesCS3D01G242800 chr5B 94.737 76 4 0 2395 2470 300394528 300394453 9.190000e-23 119.0
67 TraesCS3D01G242800 chr4A 78.436 422 58 15 2068 2470 578536657 578537064 1.450000e-60 244.0
68 TraesCS3D01G242800 chr4A 90.265 113 10 1 1960 2072 13761665 13761554 4.210000e-31 147.0
69 TraesCS3D01G242800 chr4A 88.496 113 12 1 1960 2072 13762940 13762829 9.120000e-28 135.0
70 TraesCS3D01G242800 chr4A 95.455 44 2 0 2029 2072 13776511 13776468 2.610000e-08 71.3
71 TraesCS3D01G242800 chr5D 83.600 250 19 12 2054 2296 82951141 82951375 1.140000e-51 215.0
72 TraesCS3D01G242800 chr5D 97.436 39 1 0 4588 4626 255507861 255507823 3.370000e-07 67.6
73 TraesCS3D01G242800 chr5D 82.759 87 2 2 4591 4664 486160786 486160700 1.210000e-06 65.8
74 TraesCS3D01G242800 chr4D 93.103 87 6 0 1986 2072 453314934 453315020 1.530000e-25 128.0
75 TraesCS3D01G242800 chr4D 79.474 190 17 13 2298 2470 23422869 23422685 1.190000e-21 115.0
76 TraesCS3D01G242800 chr4D 88.732 71 8 0 1986 2056 453317472 453317542 2.590000e-13 87.9
77 TraesCS3D01G242800 chr4D 82.927 82 1 2 4591 4659 473822387 473822468 1.570000e-05 62.1
78 TraesCS3D01G242800 chr4B 79.365 189 19 13 2298 2470 35522958 35522774 1.190000e-21 115.0
79 TraesCS3D01G242800 chr6B 96.875 64 2 0 2394 2457 185660851 185660914 1.990000e-19 108.0
80 TraesCS3D01G242800 chr6B 100.000 32 0 0 4595 4626 54775761 54775792 5.650000e-05 60.2
81 TraesCS3D01G242800 chr6B 100.000 32 0 0 4595 4626 54899073 54899042 5.650000e-05 60.2
82 TraesCS3D01G242800 chr6A 83.607 122 10 6 2336 2457 121888533 121888644 7.150000e-19 106.0
83 TraesCS3D01G242800 chr6A 82.222 90 1 4 4595 4670 28894310 28894398 4.370000e-06 63.9
84 TraesCS3D01G242800 chr1B 97.561 41 0 1 4587 4626 22073990 22073950 9.380000e-08 69.4
85 TraesCS3D01G242800 chr2A 90.000 50 2 1 4577 4626 578159656 578159702 1.570000e-05 62.1


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 TraesCS3D01G242800 chr3D 338313969 338319190 5221 False 9644.000000 9644 100.000000 1 5222 1 chr3D.!!$F1 5221
1 TraesCS3D01G242800 chr3D 338314222 338319495 5273 False 276.711111 708 90.654333 254 5222 9 chr3D.!!$F2 4968
2 TraesCS3D01G242800 chr3A 456442328 456450225 7897 False 367.276923 2495 89.009692 1 5222 26 chr3A.!!$F1 5221
3 TraesCS3D01G242800 chr3B 436557376 436562856 5480 False 739.857143 1537 88.190000 1 4714 7 chr3B.!!$F2 4713

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
235 241 0.179073 CCCGCGGATCTGAGAAACAT 60.179 55.0 30.73 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4889 8378 6.921307 ACCCAGAATACAAAATTTGAACGAAC 59.079 34.615 13.19 0.0 0.0 3.95 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
33 35 3.438434 GTGCTCTCAGGTCCTTGAAAATC 59.562 47.826 0.00 0.00 0.00 2.17
140 146 7.165154 CAGCGATTTAGAAACGAAAACTGAAAA 59.835 33.333 0.00 0.00 0.00 2.29
141 147 7.698970 AGCGATTTAGAAACGAAAACTGAAAAA 59.301 29.630 0.00 0.00 0.00 1.94
235 241 0.179073 CCCGCGGATCTGAGAAACAT 60.179 55.000 30.73 0.00 0.00 2.71
236 242 1.068588 CCCGCGGATCTGAGAAACATA 59.931 52.381 30.73 0.00 0.00 2.29
237 243 2.398498 CCGCGGATCTGAGAAACATAG 58.602 52.381 24.07 0.00 0.00 2.23
242 248 4.979197 GCGGATCTGAGAAACATAGTAGTG 59.021 45.833 5.48 0.00 0.00 2.74
4889 8378 3.325870 TGCTGTCCTCGATACAGTTTTG 58.674 45.455 22.11 5.36 45.01 2.44
4897 8386 4.446385 CCTCGATACAGTTTTGTTCGTTCA 59.554 41.667 0.00 0.00 38.17 3.18
4923 8412 2.422597 TGTATTCTGGGTGCAGTTTCG 58.577 47.619 0.00 0.00 0.00 3.46
4934 8423 4.261867 GGGTGCAGTTTCGTTCCTAAAAAT 60.262 41.667 0.00 0.00 0.00 1.82
5075 8576 4.738124 TGTGCAAATCAAAAACTTCACGA 58.262 34.783 0.00 0.00 0.00 4.35
5133 9172 4.261867 GGGTGCAGTTTCGTTCCTAAAAAT 60.262 41.667 0.00 0.00 0.00 1.82
5212 9660 5.883673 CCTTCCGGTTGAGGTTATGAATAAA 59.116 40.000 0.00 0.00 0.00 1.40
5215 9663 9.116067 CTTCCGGTTGAGGTTATGAATAAAATA 57.884 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 241 5.012664 TCTCAAACTGGAATTGGCACTACTA 59.987 40.000 0.00 0.00 0.00 1.82
236 242 4.074970 CTCAAACTGGAATTGGCACTACT 58.925 43.478 0.00 0.00 0.00 2.57
237 243 4.072131 TCTCAAACTGGAATTGGCACTAC 58.928 43.478 0.00 0.00 0.00 2.73
242 248 2.297033 TGCTTCTCAAACTGGAATTGGC 59.703 45.455 0.00 0.00 0.00 4.52
4889 8378 6.921307 ACCCAGAATACAAAATTTGAACGAAC 59.079 34.615 13.19 0.00 0.00 3.95
4897 8386 5.806654 ACTGCACCCAGAATACAAAATTT 57.193 34.783 0.00 0.00 41.77 1.82
4909 8398 0.535102 AGGAACGAAACTGCACCCAG 60.535 55.000 0.00 0.00 44.80 4.45
4955 8444 3.951037 AGCGTCATGGCAATGGTATAAAA 59.049 39.130 0.00 0.00 34.30 1.52
4961 8450 1.472480 GTTAAGCGTCATGGCAATGGT 59.528 47.619 0.00 0.00 34.30 3.55
5157 9321 5.008415 GCCATCATATAGTAGATGCAATGGC 59.992 44.000 23.83 23.83 42.60 4.40
5158 9322 5.235831 CGCCATCATATAGTAGATGCAATGG 59.764 44.000 16.04 16.04 40.15 3.16
5160 9324 4.813161 GCGCCATCATATAGTAGATGCAAT 59.187 41.667 0.00 0.00 40.15 3.56
5161 9325 4.081476 AGCGCCATCATATAGTAGATGCAA 60.081 41.667 2.29 0.00 40.15 4.08
5163 9327 4.052159 AGCGCCATCATATAGTAGATGC 57.948 45.455 2.29 0.00 40.15 3.91


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

AutoCloner maintained by Alex Coulton.