Multiple sequence alignment - TraesCS1A01G064300

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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 TraesCS1A01G064300 chr1A 100.000 3405 0 0 1 3405 46203413 46200009 0.000000e+00 6288.0
1 TraesCS1A01G064300 chr1A 95.914 1811 36 9 1627 3405 46295091 46293287 0.000000e+00 2900.0
2 TraesCS1A01G064300 chr1A 98.241 1649 27 2 133 1781 46297240 46295594 0.000000e+00 2883.0
3 TraesCS1A01G064300 chr1A 91.811 1209 61 17 595 1787 45858405 45857219 0.000000e+00 1650.0
4 TraesCS1A01G064300 chr1A 88.335 1003 81 12 1463 2454 45857386 45856409 0.000000e+00 1171.0
5 TraesCS1A01G064300 chr1A 86.288 598 66 9 979 1571 46310430 46309844 1.330000e-178 636.0
6 TraesCS1A01G064300 chr1A 85.597 611 54 13 1783 2386 46309101 46308518 8.080000e-171 610.0
7 TraesCS1A01G064300 chr1A 85.434 611 55 12 1783 2386 46256794 46256211 3.760000e-169 604.0
8 TraesCS1A01G064300 chr1A 97.167 353 6 2 3056 3405 46252651 46252300 8.140000e-166 593.0
9 TraesCS1A01G064300 chr1A 98.571 210 3 0 1 210 46297450 46297241 4.150000e-99 372.0
10 TraesCS1A01G064300 chr1A 79.024 410 44 16 68 467 45859733 45859356 3.390000e-60 243.0
11 TraesCS1A01G064300 chr1A 77.460 315 60 9 2431 2741 46254469 46254162 9.710000e-41 178.0
12 TraesCS1A01G064300 chr1A 77.338 278 54 7 2431 2706 46305585 46305315 4.550000e-34 156.0
13 TraesCS1A01G064300 chr1A 93.478 46 3 0 496 541 46209455 46209410 6.100000e-08 69.4
14 TraesCS1A01G064300 chr1A 93.478 46 3 0 496 541 46258623 46258578 6.100000e-08 69.4
15 TraesCS1A01G064300 chr1A 93.478 46 3 0 496 541 46310909 46310864 6.100000e-08 69.4
16 TraesCS1A01G064300 chr1B 91.130 2875 162 52 588 3403 66376763 66373923 0.000000e+00 3810.0
17 TraesCS1A01G064300 chr1B 89.192 1906 131 36 596 2472 66125023 66123164 0.000000e+00 2309.0
18 TraesCS1A01G064300 chr1B 95.314 1195 51 4 588 1781 66501110 66499920 0.000000e+00 1892.0
19 TraesCS1A01G064300 chr1B 92.117 685 52 2 1459 2143 66499929 66499247 0.000000e+00 965.0
20 TraesCS1A01G064300 chr1B 94.636 522 25 3 2187 2707 66499248 66498729 0.000000e+00 806.0
21 TraesCS1A01G064300 chr1B 94.186 516 26 1 68 579 66501900 66501385 0.000000e+00 784.0
22 TraesCS1A01G064300 chr1B 93.407 364 18 1 222 579 66377401 66377038 5.000000e-148 534.0
23 TraesCS1A01G064300 chr1B 91.411 326 27 1 1459 1784 66500085 66499761 2.410000e-121 446.0
24 TraesCS1A01G064300 chr1B 87.569 362 19 12 2826 3184 66498672 66498334 2.460000e-106 396.0
25 TraesCS1A01G064300 chr1B 94.872 156 8 0 68 223 66377639 66377484 9.440000e-61 244.0
26 TraesCS1A01G064300 chr1B 79.508 366 38 15 109 468 66125513 66125179 3.420000e-55 226.0
27 TraesCS1A01G064300 chr1B 76.176 319 64 9 2428 2741 66510507 66510196 1.260000e-34 158.0
28 TraesCS1A01G064300 chr1B 90.667 75 5 2 1 73 47399611 47399537 7.780000e-17 99.0
29 TraesCS1A01G064300 chr1B 89.130 46 5 0 496 541 66515648 66515603 1.320000e-04 58.4
30 TraesCS1A01G064300 chr1D 91.275 1914 91 26 1538 3405 46449547 46447664 0.000000e+00 2540.0
31 TraesCS1A01G064300 chr1D 94.444 1602 70 10 68 1668 46451496 46449913 0.000000e+00 2447.0
32 TraesCS1A01G064300 chr1D 91.970 1208 59 19 596 1787 46397962 46396777 0.000000e+00 1659.0
33 TraesCS1A01G064300 chr1D 88.235 1003 83 11 1463 2454 46396944 46395966 0.000000e+00 1166.0
34 TraesCS1A01G064300 chr1D 85.574 610 58 11 1783 2386 46462567 46461982 2.250000e-171 612.0
35 TraesCS1A01G064300 chr1D 86.847 517 55 6 976 1488 46464091 46463584 1.770000e-157 566.0
36 TraesCS1A01G064300 chrUn 95.522 67 3 0 1 67 360089079 360089145 1.290000e-19 108.0
37 TraesCS1A01G064300 chrUn 95.522 67 3 0 1 67 416058131 416058197 1.290000e-19 108.0
38 TraesCS1A01G064300 chr7D 94.203 69 4 0 1 69 39202885 39202953 4.650000e-19 106.0
39 TraesCS1A01G064300 chr5D 92.105 76 3 1 1 76 474212348 474212276 1.670000e-18 104.0
40 TraesCS1A01G064300 chr4D 94.030 67 4 0 1 67 20231984 20231918 6.010000e-18 102.0
41 TraesCS1A01G064300 chr3A 94.030 67 4 0 1 67 421766983 421766917 6.010000e-18 102.0
42 TraesCS1A01G064300 chr2A 94.030 67 4 0 1 67 20199016 20198950 6.010000e-18 102.0


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 TraesCS1A01G064300 chr1A 46200009 46203413 3404 True 6288.000000 6288 100.000000 1 3405 1 chr1A.!!$R1 3404
1 TraesCS1A01G064300 chr1A 46293287 46297450 4163 True 2051.666667 2900 97.575333 1 3405 3 chr1A.!!$R5 3404
2 TraesCS1A01G064300 chr1A 45856409 45859733 3324 True 1021.333333 1650 86.390000 68 2454 3 chr1A.!!$R3 2386
3 TraesCS1A01G064300 chr1A 46305315 46310909 5594 True 367.850000 636 85.675250 496 2706 4 chr1A.!!$R6 2210
4 TraesCS1A01G064300 chr1A 46252300 46258623 6323 True 361.100000 604 88.384750 496 3405 4 chr1A.!!$R4 2909
5 TraesCS1A01G064300 chr1B 66373923 66377639 3716 True 1529.333333 3810 93.136333 68 3403 3 chr1B.!!$R5 3335
6 TraesCS1A01G064300 chr1B 66123164 66125513 2349 True 1267.500000 2309 84.350000 109 2472 2 chr1B.!!$R4 2363
7 TraesCS1A01G064300 chr1B 66498334 66501900 3566 True 881.500000 1892 92.538833 68 3184 6 chr1B.!!$R6 3116
8 TraesCS1A01G064300 chr1D 46447664 46451496 3832 True 2493.500000 2540 92.859500 68 3405 2 chr1D.!!$R2 3337
9 TraesCS1A01G064300 chr1D 46395966 46397962 1996 True 1412.500000 1659 90.102500 596 2454 2 chr1D.!!$R1 1858
10 TraesCS1A01G064300 chr1D 46461982 46464091 2109 True 589.000000 612 86.210500 976 2386 2 chr1D.!!$R3 1410

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
874 2215 3.007506 TCAACATCCGCTTGAACCTTCTA 59.992 43.478 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2634 9256 1.042003 TTGCTCTTGTTTGCTGCCCA 61.042 50.0 0.0 0.0 0.0 5.36 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
143 144 9.515020 CATAATTATTACACGGCAACTGAAAAT 57.485 29.630 0.00 0.00 0.00 1.82
299 463 3.947834 TCTCGAGATATGCTCACTGAACA 59.052 43.478 12.08 0.00 44.15 3.18
874 2215 3.007506 TCAACATCCGCTTGAACCTTCTA 59.992 43.478 0.00 0.00 0.00 2.10
957 2316 6.915300 CCGTATGTCTTTGTTGATTCAAAACA 59.085 34.615 0.00 2.23 36.96 2.83
1202 2590 0.309612 GGTGACAACCATTTTCGCGT 59.690 50.000 5.77 0.00 46.75 6.01
1602 3844 3.608796 TGGAGAATCATCGCATGAACAA 58.391 40.909 0.00 0.00 43.50 2.83
1739 4908 5.012458 CAGATCTATACCAAGAGGCCAATGA 59.988 44.000 5.01 0.00 39.06 2.57
1749 4918 4.515028 AGAGGCCAATGAAGAATCATCA 57.485 40.909 5.01 0.00 45.60 3.07
1751 4920 3.949754 GAGGCCAATGAAGAATCATCACA 59.050 43.478 5.01 0.00 45.60 3.58
1956 5143 6.627395 ATCCGTGTTCAAACAAGTCAAATA 57.373 33.333 7.79 0.00 41.21 1.40
2057 5244 7.063898 CGAAGTATATGATTATCAGCCAACCTG 59.936 40.741 0.29 0.00 43.17 4.00
2542 9163 9.518906 GAATTTGATGTGATGCATACAAATACA 57.481 29.630 18.83 11.13 40.33 2.29
2634 9256 3.751518 AGTGCCGAGGAAACAACTTATT 58.248 40.909 0.00 0.00 0.00 1.40
2654 9276 0.598419 GGGCAGCAAACAAGAGCAAC 60.598 55.000 0.00 0.00 0.00 4.17
2665 9287 4.243007 ACAAGAGCAACCTAACAAATGC 57.757 40.909 0.00 0.00 39.06 3.56
2672 9294 5.181748 AGCAACCTAACAAATGCAAAACAA 58.818 33.333 0.00 0.00 41.18 2.83
2676 9298 7.487509 GCAACCTAACAAATGCAAAACAAAAAT 59.512 29.630 0.00 0.00 38.63 1.82
2907 9559 0.381801 CCCACACAACACAAGCAGAC 59.618 55.000 0.00 0.00 0.00 3.51
2984 9638 2.285969 AGAGCAGCCATGGGGAGT 60.286 61.111 15.13 0.00 35.59 3.85
2985 9639 1.919600 GAGAGCAGCCATGGGGAGTT 61.920 60.000 15.13 0.00 35.59 3.01
3063 10980 3.973206 TGAAATGGGACTACGATGTGT 57.027 42.857 0.00 0.00 0.00 3.72
3064 10981 3.595173 TGAAATGGGACTACGATGTGTG 58.405 45.455 0.00 0.00 0.00 3.82
3142 11059 6.998074 TGTGAGAAAGAACATAGGTGAAATGT 59.002 34.615 0.00 0.00 39.22 2.71
3331 11270 3.009714 ACGCCCCTCTCTTTCCCC 61.010 66.667 0.00 0.00 0.00 4.81
3337 11276 0.043334 CCCTCTCTTTCCCCTCTCCA 59.957 60.000 0.00 0.00 0.00 3.86
3376 11319 0.185901 TCTCTTGTTTGCCCTGCCTT 59.814 50.000 0.00 0.00 0.00 4.35
3380 11323 2.203625 GTTTGCCCTGCCTTCCCA 60.204 61.111 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 5.106317 GGTGTAAAGCAATCCTCGAATCAAA 60.106 40.000 0.00 0.00 0.00 2.69
755 2092 2.656947 TACTCATTAATGGCAGCCCC 57.343 50.000 15.36 0.00 0.00 5.80
874 2215 8.633561 GGGCTTGCTTATCATTTAAGTAAATCT 58.366 33.333 0.00 0.00 33.88 2.40
957 2316 5.482175 ACAGGAGTGTATAGAAGAGTTGCTT 59.518 40.000 0.00 0.00 35.53 3.91
1045 2433 5.287226 ACGAAAGAACAACACTCGAAGTAT 58.713 37.500 0.00 0.00 33.81 2.12
1202 2590 7.820044 AAACGTTTTGCAGAAGAAACAATTA 57.180 28.000 7.96 0.00 35.93 1.40
1739 4908 7.614583 AGGAATCTGTTCATTGTGATGATTCTT 59.385 33.333 18.65 13.77 41.71 2.52
1749 4918 6.703607 CGAGCTATTAGGAATCTGTTCATTGT 59.296 38.462 0.00 0.00 36.01 2.71
1751 4920 6.183361 ACCGAGCTATTAGGAATCTGTTCATT 60.183 38.462 4.31 0.00 36.01 2.57
1850 5037 2.858745 TGGTAAGAAGGTGTTTCTGCC 58.141 47.619 0.00 0.00 45.41 4.85
1956 5143 2.575279 ACTTGAGCCTTCTCCATGACAT 59.425 45.455 0.00 0.00 38.58 3.06
2057 5244 1.673626 CCAGCAATGTGACCAAATGGC 60.674 52.381 0.00 0.00 39.32 4.40
2542 9163 6.407202 ACTCAACGAGCCTATTGTCTAAAAT 58.593 36.000 0.00 0.00 32.04 1.82
2634 9256 1.042003 TTGCTCTTGTTTGCTGCCCA 61.042 50.000 0.00 0.00 0.00 5.36
2654 9276 7.305304 CGCAATTTTTGTTTTGCATTTGTTAGG 60.305 33.333 8.20 0.00 46.66 2.69
2665 9287 4.273274 CAAGCTCCGCAATTTTTGTTTTG 58.727 39.130 0.00 0.00 0.00 2.44
2672 9294 1.541588 GTCTCCAAGCTCCGCAATTTT 59.458 47.619 0.00 0.00 0.00 1.82
2676 9298 2.048222 CGTCTCCAAGCTCCGCAA 60.048 61.111 0.00 0.00 0.00 4.85
2984 9638 4.279671 ACTTCTTCGCTTTCTCTCTCTCAA 59.720 41.667 0.00 0.00 0.00 3.02
2985 9639 3.823873 ACTTCTTCGCTTTCTCTCTCTCA 59.176 43.478 0.00 0.00 0.00 3.27
3063 10980 1.406751 CCTTCCTCACACACACACACA 60.407 52.381 0.00 0.00 0.00 3.72
3064 10981 1.299541 CCTTCCTCACACACACACAC 58.700 55.000 0.00 0.00 0.00 3.82
3142 11059 1.485124 TGGCGCATTCTCTCTCCTTA 58.515 50.000 10.83 0.00 0.00 2.69
3331 11270 3.775654 GGGCGGGTCACTGGAGAG 61.776 72.222 0.00 0.00 0.00 3.20
3380 11323 1.050988 CCACATGGAGATCCCGGAGT 61.051 60.000 0.73 0.00 37.93 3.85


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

AutoCloner maintained by Alex Coulton.