Multiple sequence alignment - TraesCS3A01G165800

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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 TraesCS3A01G165800 chr3A 100.000 3268 0 0 1 3268 170782633 170785900 0.000000e+00 6035.0
1 TraesCS3A01G165800 chr3A 91.280 1078 50 8 957 2004 437464005 437462942 0.000000e+00 1430.0
2 TraesCS3A01G165800 chr3A 91.681 589 34 5 2692 3265 73919762 73919174 0.000000e+00 802.0
3 TraesCS3A01G165800 chr3A 92.789 527 34 2 2037 2559 437462947 437462421 0.000000e+00 760.0
4 TraesCS3A01G165800 chr3A 89.779 362 35 2 65 425 437464459 437464099 2.300000e-126 462.0
5 TraesCS3A01G165800 chr3A 82.000 400 60 8 451 848 587700437 587700826 2.430000e-86 329.0
6 TraesCS3A01G165800 chr3A 91.333 150 10 3 2554 2701 437462320 437462172 5.530000e-48 202.0
7 TraesCS3A01G165800 chr3A 89.720 107 7 1 2560 2666 437462089 437461987 2.050000e-27 134.0
8 TraesCS3A01G165800 chr3A 93.333 75 4 1 2692 2766 597317366 597317293 3.450000e-20 110.0
9 TraesCS3A01G165800 chr3A 81.169 154 10 9 1500 1653 312723387 312723253 4.460000e-19 106.0
10 TraesCS3A01G165800 chr3A 96.000 50 2 0 537 586 587700582 587700631 7.520000e-12 82.4
11 TraesCS3A01G165800 chr5A 96.754 2403 60 7 300 2701 63667272 63664887 0.000000e+00 3989.0
12 TraesCS3A01G165800 chr5A 85.580 319 41 4 530 846 52011907 52011592 2.430000e-86 329.0
13 TraesCS3A01G165800 chr5A 96.875 192 6 0 1 192 63668012 63667821 4.070000e-84 322.0
14 TraesCS3A01G165800 chr5A 85.405 185 16 3 1001 1179 660330987 660330808 7.200000e-42 182.0
15 TraesCS3A01G165800 chr5A 95.000 60 2 1 2846 2905 34853007 34852949 3.470000e-15 93.5
16 TraesCS3A01G165800 chr4A 95.195 2331 73 12 3 2331 475596629 475594336 0.000000e+00 3648.0
17 TraesCS3A01G165800 chr4A 96.718 579 16 3 2692 3268 101364375 101363798 0.000000e+00 961.0
18 TraesCS3A01G165800 chr4A 85.818 550 58 11 1936 2474 29176812 29177352 1.700000e-157 566.0
19 TraesCS3A01G165800 chr4A 85.946 185 14 4 1001 1179 612690792 612690614 1.550000e-43 187.0
20 TraesCS3A01G165800 chr4A 96.386 83 2 1 2619 2701 475594337 475594256 5.690000e-28 135.0
21 TraesCS3A01G165800 chr4A 93.333 75 3 2 2692 2766 636011242 636011314 3.450000e-20 110.0
22 TraesCS3A01G165800 chr6A 92.689 807 57 2 142 947 592320553 592321358 0.000000e+00 1162.0
23 TraesCS3A01G165800 chr6A 93.567 684 27 5 949 1629 592321721 592322390 0.000000e+00 1003.0
24 TraesCS3A01G165800 chr6A 92.789 527 33 3 2037 2559 592322462 592322987 0.000000e+00 758.0
25 TraesCS3A01G165800 chr6A 94.667 150 5 3 2554 2701 592323088 592323236 2.540000e-56 230.0
26 TraesCS3A01G165800 chr6A 94.355 124 5 2 1801 1922 12894615 12894492 4.300000e-44 189.0
27 TraesCS3A01G165800 chr6A 88.652 141 11 2 2560 2700 592323319 592323454 2.020000e-37 167.0
28 TraesCS3A01G165800 chr6A 94.805 77 4 0 1928 2004 592322391 592322467 1.590000e-23 121.0
29 TraesCS3A01G165800 chr6A 92.208 77 6 0 2690 2766 503953791 503953867 3.450000e-20 110.0
30 TraesCS3A01G165800 chr7A 96.021 578 21 2 2692 3268 291021967 291021391 0.000000e+00 939.0
31 TraesCS3A01G165800 chr7A 94.355 124 5 2 1801 1922 651088815 651088938 4.300000e-44 189.0
32 TraesCS3A01G165800 chr7A 94.565 92 4 1 2555 2646 13604335 13604245 1.220000e-29 141.0
33 TraesCS3A01G165800 chr7A 88.776 98 8 1 1708 1802 510625408 510625311 2.060000e-22 117.0
34 TraesCS3A01G165800 chr7A 84.058 69 3 5 1836 1898 92633814 92633748 3.520000e-05 60.2
35 TraesCS3A01G165800 chr2A 93.169 527 32 2 2037 2559 362131238 362131764 0.000000e+00 771.0
36 TraesCS3A01G165800 chr2A 88.621 580 30 8 1452 2004 362130673 362131243 0.000000e+00 673.0
37 TraesCS3A01G165800 chr2A 79.615 520 70 18 2775 3267 652568508 652567998 1.120000e-89 340.0
38 TraesCS3A01G165800 chr2A 94.667 150 5 3 2554 2701 362131865 362132013 2.540000e-56 230.0
39 TraesCS3A01G165800 chr2A 87.943 141 12 2 2560 2700 362132096 362132231 9.380000e-36 161.0
40 TraesCS3A01G165800 chr2A 90.099 101 4 3 1709 1806 78840669 78840572 3.420000e-25 126.0
41 TraesCS3A01G165800 chr2A 88.776 98 8 1 1708 1802 416281080 416281177 2.060000e-22 117.0
42 TraesCS3A01G165800 chr2A 81.169 154 10 8 1500 1653 333797410 333797544 4.460000e-19 106.0
43 TraesCS3A01G165800 chr4D 86.472 547 59 6 1936 2475 439867567 439868105 1.310000e-163 586.0
44 TraesCS3A01G165800 chr4B 85.923 547 62 6 1936 2475 545035683 545036221 1.320000e-158 569.0
45 TraesCS3A01G165800 chr4B 90.860 186 16 1 1216 1401 371686373 371686557 7.000000e-62 248.0
46 TraesCS3A01G165800 chr5B 79.507 527 66 27 2775 3267 341546899 341546381 1.450000e-88 337.0
47 TraesCS3A01G165800 chr5B 87.736 106 9 2 1700 1802 295217256 295217360 1.590000e-23 121.0
48 TraesCS3A01G165800 chr3D 81.108 397 61 10 2880 3267 24044099 24044490 4.100000e-79 305.0
49 TraesCS3A01G165800 chr3D 82.014 278 43 6 2989 3260 461429490 461429766 2.540000e-56 230.0
50 TraesCS3A01G165800 chr3D 86.905 84 7 3 2829 2910 25369991 25370072 1.250000e-14 91.6
51 TraesCS3A01G165800 chr5D 81.818 308 47 9 2956 3258 482435416 482435113 1.950000e-62 250.0
52 TraesCS3A01G165800 chr3B 90.860 186 16 1 1216 1401 313596176 313595992 7.000000e-62 248.0
53 TraesCS3A01G165800 chr3B 90.860 186 16 1 1216 1401 313618154 313617970 7.000000e-62 248.0
54 TraesCS3A01G165800 chr3B 82.182 275 43 6 2992 3262 491825881 491825609 7.050000e-57 231.0
55 TraesCS3A01G165800 chr3B 84.574 188 18 3 998 1179 160996693 160996875 3.350000e-40 176.0
56 TraesCS3A01G165800 chr3B 93.243 74 3 1 2692 2765 4980154 4980083 1.240000e-19 108.0
57 TraesCS3A01G165800 chr3B 91.892 74 4 1 2692 2765 4153345 4153274 5.770000e-18 102.0
58 TraesCS3A01G165800 chr2B 90.860 186 16 1 1216 1401 204160755 204160939 7.000000e-62 248.0
59 TraesCS3A01G165800 chr2B 90.860 186 16 1 1216 1401 754954620 754954804 7.000000e-62 248.0
60 TraesCS3A01G165800 chr6D 96.032 126 3 2 1801 1924 467789475 467789600 1.540000e-48 204.0
61 TraesCS3A01G165800 chr6D 81.102 254 20 9 1398 1651 467789168 467789393 9.320000e-41 178.0
62 TraesCS3A01G165800 chr6D 86.207 145 14 3 2556 2700 467789736 467789874 5.650000e-33 152.0
63 TraesCS3A01G165800 chr6D 93.939 66 4 0 1646 1711 467789412 467789477 2.070000e-17 100.0
64 TraesCS3A01G165800 chr2D 83.128 243 20 7 1414 1646 381240648 381240879 5.530000e-48 202.0
65 TraesCS3A01G165800 chr2D 84.574 188 18 3 998 1179 22874737 22874919 3.350000e-40 176.0
66 TraesCS3A01G165800 chr2D 90.099 101 4 3 1709 1806 78531528 78531431 3.420000e-25 126.0
67 TraesCS3A01G165800 chr7B 93.651 126 4 4 1801 1924 704542678 704542801 5.570000e-43 185.0
68 TraesCS3A01G165800 chr1A 84.574 188 18 3 998 1179 438025213 438025395 3.350000e-40 176.0
69 TraesCS3A01G165800 chr1A 92.000 75 4 2 2692 2766 408688679 408688607 1.600000e-18 104.0
70 TraesCS3A01G165800 chr7D 88.095 84 6 3 2829 2910 37826800 37826719 2.680000e-16 97.1
71 TraesCS3A01G165800 chr7D 84.524 84 8 4 2829 2910 487861287 487861367 9.720000e-11 78.7
72 TraesCS3A01G165800 chr7D 95.000 40 2 0 2010 2049 135442932 135442971 2.720000e-06 63.9


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 TraesCS3A01G165800 chr3A 170782633 170785900 3267 False 6035.00 6035 100.0000 1 3268 1 chr3A.!!$F1 3267
1 TraesCS3A01G165800 chr3A 73919174 73919762 588 True 802.00 802 91.6810 2692 3265 1 chr3A.!!$R1 573
2 TraesCS3A01G165800 chr3A 437461987 437464459 2472 True 597.60 1430 90.9802 65 2701 5 chr3A.!!$R4 2636
3 TraesCS3A01G165800 chr5A 63664887 63668012 3125 True 2155.50 3989 96.8145 1 2701 2 chr5A.!!$R4 2700
4 TraesCS3A01G165800 chr4A 475594256 475596629 2373 True 1891.50 3648 95.7905 3 2701 2 chr4A.!!$R3 2698
5 TraesCS3A01G165800 chr4A 101363798 101364375 577 True 961.00 961 96.7180 2692 3268 1 chr4A.!!$R1 576
6 TraesCS3A01G165800 chr4A 29176812 29177352 540 False 566.00 566 85.8180 1936 2474 1 chr4A.!!$F1 538
7 TraesCS3A01G165800 chr6A 592320553 592323454 2901 False 573.50 1162 92.8615 142 2701 6 chr6A.!!$F2 2559
8 TraesCS3A01G165800 chr7A 291021391 291021967 576 True 939.00 939 96.0210 2692 3268 1 chr7A.!!$R3 576
9 TraesCS3A01G165800 chr2A 362130673 362132231 1558 False 458.75 771 91.1000 1452 2701 4 chr2A.!!$F3 1249
10 TraesCS3A01G165800 chr2A 652567998 652568508 510 True 340.00 340 79.6150 2775 3267 1 chr2A.!!$R2 492
11 TraesCS3A01G165800 chr4D 439867567 439868105 538 False 586.00 586 86.4720 1936 2475 1 chr4D.!!$F1 539
12 TraesCS3A01G165800 chr4B 545035683 545036221 538 False 569.00 569 85.9230 1936 2475 1 chr4B.!!$F2 539
13 TraesCS3A01G165800 chr5B 341546381 341546899 518 True 337.00 337 79.5070 2775 3267 1 chr5B.!!$R1 492

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
535 979 2.099756 AGCAAACACAGGAAGTTTCTGC 59.900 45.455 11.34 0.0 37.10 4.26 F
910 1356 3.743521 AGTCATAACTGCTTCTTGTGCA 58.256 40.909 0.00 0.0 38.81 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2834 2.498481 CTCAATGTTGGTCCCATTGCAT 59.502 45.455 13.33 5.28 45.57 3.96 R
2427 3277 4.448210 ACTTTTTCTCTACCAGAACGCAA 58.552 39.130 0.00 0.00 41.13 4.85 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
345 789 4.467084 GCCGAGCCAATCCACCGA 62.467 66.667 0.00 0.00 0.00 4.69
418 862 3.741325 GCTTCCTCCCCCAAGCTA 58.259 61.111 0.00 0.00 41.61 3.32
535 979 2.099756 AGCAAACACAGGAAGTTTCTGC 59.900 45.455 11.34 0.00 37.10 4.26
750 1195 4.100189 AGCGCCCTTATATCATCAGTATCC 59.900 45.833 2.29 0.00 0.00 2.59
790 1235 8.847196 TGACCATCGTAGTAGATTATATATGGC 58.153 37.037 0.00 0.00 35.78 4.40
910 1356 3.743521 AGTCATAACTGCTTCTTGTGCA 58.256 40.909 0.00 0.00 38.81 4.57
999 1807 8.614346 AGTAAACTTTCTTTTGTATGTTACGCA 58.386 29.630 0.00 0.00 0.00 5.24
1267 2078 4.431416 ACATGGTTAACTTGTGTCCAGA 57.569 40.909 5.42 0.00 36.25 3.86
1469 2280 7.341445 AGACTCTACCATGTAGAGAAATGAC 57.659 40.000 28.78 15.74 42.68 3.06
1563 2374 8.335532 TGTACATGAAGTATTTTAGCTTGCTT 57.664 30.769 0.00 0.00 34.67 3.91
1564 2375 8.236586 TGTACATGAAGTATTTTAGCTTGCTTG 58.763 33.333 0.00 0.00 34.67 4.01
1565 2376 7.219484 ACATGAAGTATTTTAGCTTGCTTGT 57.781 32.000 0.00 0.00 0.00 3.16
1566 2377 7.661040 ACATGAAGTATTTTAGCTTGCTTGTT 58.339 30.769 0.00 0.00 0.00 2.83
1609 2420 7.826744 TGTCAAAAGCCTTGGTTTATTTTTCTT 59.173 29.630 0.00 0.00 32.76 2.52
1629 2440 6.072112 TCTTGGCTAATTCAACTTGTTGTC 57.928 37.500 12.44 0.00 0.00 3.18
1996 2834 7.227711 GGGAGCAAAAATTAAAAGGCTTGTTTA 59.772 33.333 0.00 0.00 0.00 2.01
2345 3190 1.270839 ACACTGAATCCACAGGTTCCG 60.271 52.381 0.00 0.00 41.59 4.30
2427 3277 3.886123 AGAAGCACAACTAAACACCTGT 58.114 40.909 0.00 0.00 0.00 4.00
2933 3953 4.101448 AGAGGAATTGCCGCCGCT 62.101 61.111 0.00 0.00 43.43 5.52
2954 3987 1.304547 CCTCCTCAGTCCTCACGGT 60.305 63.158 0.00 0.00 0.00 4.83
3065 4098 0.468400 GGAGCTCGATGTAGGGAGGT 60.468 60.000 7.83 0.00 43.15 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.682136 TGACGGCGGAGGGATCAA 60.682 61.111 13.24 0.00 0.00 2.57
271 274 3.081554 CTCTGGAGTGGTTGGGGG 58.918 66.667 0.00 0.00 0.00 5.40
345 789 3.069318 GCGGAGGAGGAAGGTCGT 61.069 66.667 0.00 0.00 0.00 4.34
535 979 8.804743 CAGATCAATACAAGCAAAAATTAGCAG 58.195 33.333 0.00 0.00 0.00 4.24
615 1060 5.485353 AGACTCCCAACAGATGAATACAAGA 59.515 40.000 0.00 0.00 0.00 3.02
750 1195 3.062099 CGATGGTCACTATTGTTTCGGTG 59.938 47.826 0.00 0.00 0.00 4.94
790 1235 1.224069 CCAGACTGCAGTTGACACGG 61.224 60.000 22.65 11.27 0.00 4.94
910 1356 8.947055 ACATTGAAAATGAACAAAGTAAGCTT 57.053 26.923 3.48 3.48 36.30 3.74
999 1807 4.441913 GCTTGTAAGGCCATGCAATACATT 60.442 41.667 11.98 0.00 36.64 2.71
1267 2078 4.077822 CTGGAATCAGGAGCTCAAGTTTT 58.922 43.478 17.19 1.93 37.36 2.43
1469 2280 4.158949 TGTGAGCATGGAATCCAATGAAAG 59.841 41.667 5.89 0.00 36.95 2.62
1563 2374 7.072177 TGACAAACAAACAAACAAACAAACA 57.928 28.000 0.00 0.00 0.00 2.83
1564 2375 7.954906 TTGACAAACAAACAAACAAACAAAC 57.045 28.000 0.00 0.00 35.39 2.93
1565 2376 8.964420 TTTTGACAAACAAACAAACAAACAAA 57.036 23.077 0.00 0.00 46.32 2.83
1566 2377 7.218963 GCTTTTGACAAACAAACAAACAAACAA 59.781 29.630 0.00 0.00 46.32 2.83
1609 2420 4.211125 TGGACAACAAGTTGAATTAGCCA 58.789 39.130 18.90 12.05 42.93 4.75
1629 2440 4.651778 TGGTTCACTTTCCTACATCTTGG 58.348 43.478 0.00 0.00 0.00 3.61
1996 2834 2.498481 CTCAATGTTGGTCCCATTGCAT 59.502 45.455 13.33 5.28 45.57 3.96
2427 3277 4.448210 ACTTTTTCTCTACCAGAACGCAA 58.552 39.130 0.00 0.00 41.13 4.85
2933 3953 0.609406 CGTGAGGACTGAGGAGGTCA 60.609 60.000 0.00 0.00 35.61 4.02
2954 3987 3.611674 TGCAACCGCTCGAGGTCA 61.612 61.111 15.58 0.00 45.21 4.02
2979 4012 3.560025 CCACTGCTCCAGTCTAATTTGGT 60.560 47.826 0.00 0.00 43.43 3.67
3065 4098 2.490217 GGCGCTCTTGCTCGTCTA 59.510 61.111 7.64 0.00 36.97 2.59


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

AutoCloner maintained by Alex Coulton.