Multiple sequence alignment - TraesCS5D01G091400

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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 TraesCS5D01G091400 chr5D 100.000 2459 0 0 1 2459 98665399 98662941 0.000000e+00 4542.0
1 TraesCS5D01G091400 chr5D 94.452 1568 58 5 2 1540 495795850 495794283 0.000000e+00 2386.0
2 TraesCS5D01G091400 chr1D 94.444 1962 72 12 1 1938 278102091 278100143 0.000000e+00 2985.0
3 TraesCS5D01G091400 chr1D 94.079 1959 73 14 1 1929 430108871 430110816 0.000000e+00 2935.0
4 TraesCS5D01G091400 chr4D 94.382 1958 71 10 1 1930 502108439 502106493 0.000000e+00 2970.0
5 TraesCS5D01G091400 chr4D 94.163 1953 71 14 1 1928 481887411 481889345 0.000000e+00 2935.0
6 TraesCS5D01G091400 chr6D 94.094 1964 80 11 1 1930 449137679 449135718 0.000000e+00 2952.0
7 TraesCS5D01G091400 chr5A 94.034 1961 78 9 1 1929 619775013 619773060 0.000000e+00 2937.0
8 TraesCS5D01G091400 chr5A 93.734 399 24 1 1930 2327 104237308 104237706 4.530000e-167 597.0
9 TraesCS5D01G091400 chr5A 95.556 135 6 0 2320 2454 104253110 104253244 1.480000e-52 217.0
10 TraesCS5D01G091400 chr3D 93.904 1952 83 14 1 1922 553936974 553935029 0.000000e+00 2913.0
11 TraesCS5D01G091400 chr3D 93.076 1892 110 16 1 1888 162857135 162855261 0.000000e+00 2748.0
12 TraesCS5D01G091400 chr3D 94.172 1630 55 9 329 1929 431337548 431339166 0.000000e+00 2447.0
13 TraesCS5D01G091400 chr3D 94.040 604 25 5 1336 1929 132230871 132231473 0.000000e+00 905.0
14 TraesCS5D01G091400 chr7B 93.423 1931 88 12 28 1929 424148863 424146943 0.000000e+00 2826.0
15 TraesCS5D01G091400 chr2D 92.785 1968 96 24 1 1930 603142777 603144736 0.000000e+00 2806.0
16 TraesCS5D01G091400 chr7D 94.505 1383 42 6 567 1925 39012869 39011497 0.000000e+00 2102.0
17 TraesCS5D01G091400 chr2B 92.321 1133 54 4 821 1929 394127986 394126863 0.000000e+00 1580.0
18 TraesCS5D01G091400 chr2B 93.413 1002 40 3 952 1929 236519561 236520560 0.000000e+00 1461.0
19 TraesCS5D01G091400 chr5B 95.872 533 17 3 1930 2459 107906537 107906007 0.000000e+00 857.0
20 TraesCS5D01G091400 chr5B 96.825 126 4 0 1930 2055 107905594 107905469 6.890000e-51 211.0
21 TraesCS5D01G091400 chr5B 100.000 28 0 0 2154 2181 78424774 78424801 4.000000e-03 52.8


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 TraesCS5D01G091400 chr5D 98662941 98665399 2458 True 4542 4542 100.0000 1 2459 1 chr5D.!!$R1 2458
1 TraesCS5D01G091400 chr5D 495794283 495795850 1567 True 2386 2386 94.4520 2 1540 1 chr5D.!!$R2 1538
2 TraesCS5D01G091400 chr1D 278100143 278102091 1948 True 2985 2985 94.4440 1 1938 1 chr1D.!!$R1 1937
3 TraesCS5D01G091400 chr1D 430108871 430110816 1945 False 2935 2935 94.0790 1 1929 1 chr1D.!!$F1 1928
4 TraesCS5D01G091400 chr4D 502106493 502108439 1946 True 2970 2970 94.3820 1 1930 1 chr4D.!!$R1 1929
5 TraesCS5D01G091400 chr4D 481887411 481889345 1934 False 2935 2935 94.1630 1 1928 1 chr4D.!!$F1 1927
6 TraesCS5D01G091400 chr6D 449135718 449137679 1961 True 2952 2952 94.0940 1 1930 1 chr6D.!!$R1 1929
7 TraesCS5D01G091400 chr5A 619773060 619775013 1953 True 2937 2937 94.0340 1 1929 1 chr5A.!!$R1 1928
8 TraesCS5D01G091400 chr3D 553935029 553936974 1945 True 2913 2913 93.9040 1 1922 1 chr3D.!!$R2 1921
9 TraesCS5D01G091400 chr3D 162855261 162857135 1874 True 2748 2748 93.0760 1 1888 1 chr3D.!!$R1 1887
10 TraesCS5D01G091400 chr3D 431337548 431339166 1618 False 2447 2447 94.1720 329 1929 1 chr3D.!!$F2 1600
11 TraesCS5D01G091400 chr3D 132230871 132231473 602 False 905 905 94.0400 1336 1929 1 chr3D.!!$F1 593
12 TraesCS5D01G091400 chr7B 424146943 424148863 1920 True 2826 2826 93.4230 28 1929 1 chr7B.!!$R1 1901
13 TraesCS5D01G091400 chr2D 603142777 603144736 1959 False 2806 2806 92.7850 1 1930 1 chr2D.!!$F1 1929
14 TraesCS5D01G091400 chr7D 39011497 39012869 1372 True 2102 2102 94.5050 567 1925 1 chr7D.!!$R1 1358
15 TraesCS5D01G091400 chr2B 394126863 394127986 1123 True 1580 1580 92.3210 821 1929 1 chr2B.!!$R1 1108
16 TraesCS5D01G091400 chr2B 236519561 236520560 999 False 1461 1461 93.4130 952 1929 1 chr2B.!!$F1 977
17 TraesCS5D01G091400 chr5B 107905469 107906537 1068 True 534 857 96.3485 1930 2459 2 chr5B.!!$R1 529

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
155 160 0.323999 TAGCTCAGTGGTTAGGCCGA 60.324 55.0 0.0 0.0 41.21 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2171 0.250338 AGGCCGAACTCACCAACTTC 60.25 55.0 0.0 0.0 0.0 3.01 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
98 101 2.432300 CCCCTACGCCATCCTCGTT 61.432 63.158 0.00 0.00 40.89 3.85
155 160 0.323999 TAGCTCAGTGGTTAGGCCGA 60.324 55.000 0.00 0.00 41.21 5.54
160 165 2.693591 CTCAGTGGTTAGGCCGATAAGA 59.306 50.000 0.00 0.00 41.21 2.10
215 220 3.548745 TCGAGGTCGACTAGGTTATGA 57.451 47.619 16.46 0.06 44.22 2.15
243 248 2.641815 GGATGAGGCTGATAATCCAGGT 59.358 50.000 0.00 0.00 38.78 4.00
349 354 0.701731 ATGGTCCATTGTTTCCCCGA 59.298 50.000 0.00 0.00 0.00 5.14
472 478 2.285668 CCTTCAGGAGCAGGGGGA 60.286 66.667 0.00 0.00 37.39 4.81
562 568 2.065799 ACCAGAGGTTCAGGGTCATTT 58.934 47.619 0.00 0.00 27.29 2.32
878 884 2.625737 GTCACAGTCTGCAGCATACAT 58.374 47.619 9.47 0.00 0.00 2.29
1155 1161 4.353777 ACTATCCTAAGACTGCACAGGAA 58.646 43.478 2.21 0.00 40.48 3.36
1178 1184 7.174946 GGAATTGTTTAATCTCAGACACTCCAA 59.825 37.037 0.00 0.00 0.00 3.53
1227 1233 4.744795 TGGAGCTCTGAAGAATAGGTTC 57.255 45.455 14.64 0.00 34.46 3.62
1369 1417 1.523938 GTTAGCTCCGGCCATGGTC 60.524 63.158 14.67 10.70 39.73 4.02
1489 1620 0.386985 GAACAAGAAGCAGCAGCAGC 60.387 55.000 3.17 0.46 45.49 5.25
1507 1641 2.625375 CAGCAGAAGCAGCAACAGA 58.375 52.632 0.00 0.00 45.49 3.41
1508 1642 0.949397 CAGCAGAAGCAGCAACAGAA 59.051 50.000 0.00 0.00 45.49 3.02
1509 1643 1.069159 CAGCAGAAGCAGCAACAGAAG 60.069 52.381 0.00 0.00 45.49 2.85
1510 1644 0.386985 GCAGAAGCAGCAACAGAAGC 60.387 55.000 0.00 0.00 41.58 3.86
1534 1710 6.129179 CAGAAGTAGAAGAGGAGAGGAAGAT 58.871 44.000 0.00 0.00 0.00 2.40
1576 1753 5.399991 ACACCGATGAACTATCCCCTATTA 58.600 41.667 0.00 0.00 31.82 0.98
1684 1861 5.188327 TCAGATTCTATGTGGTAAGCTCG 57.812 43.478 0.00 0.00 0.00 5.03
1982 2160 1.129251 CGTCTGGTTGATGCATGTGTC 59.871 52.381 2.46 0.00 0.00 3.67
2087 2265 4.247380 GCCGATCCCCTGCCTCTG 62.247 72.222 0.00 0.00 0.00 3.35
2246 2427 3.887621 ATTAGGCAGCTTGTCGTCTTA 57.112 42.857 0.00 0.00 0.00 2.10
2252 2433 2.222596 GCAGCTTGTCGTCTTATCAACG 60.223 50.000 0.00 0.00 41.39 4.10
2302 2483 1.304547 CTCGACACTCTCCACCCCT 60.305 63.158 0.00 0.00 0.00 4.79
2307 2488 1.122019 ACACTCTCCACCCCTGTGTC 61.122 60.000 0.00 0.00 41.09 3.67
2308 2489 1.121407 CACTCTCCACCCCTGTGTCA 61.121 60.000 0.00 0.00 41.09 3.58
2334 2515 2.119029 CGATTTCCTTTCCCCCGCC 61.119 63.158 0.00 0.00 0.00 6.13
2335 2516 2.044352 ATTTCCTTTCCCCCGCCG 60.044 61.111 0.00 0.00 0.00 6.46
2428 2609 0.321298 TCTTCACCGCTGCCTTAACC 60.321 55.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.441712 AACAGCAAGGGCAGCACCT 62.442 57.895 0.00 0.00 44.61 4.00
90 93 0.179073 CCGGCATCAGAAACGAGGAT 60.179 55.000 0.00 0.00 0.00 3.24
98 101 0.744414 GCTGCTTACCGGCATCAGAA 60.744 55.000 15.09 0.00 45.47 3.02
155 160 7.124448 GGGAAATCGATCCTACACCTATCTTAT 59.876 40.741 0.00 0.00 39.57 1.73
160 165 4.283722 GTGGGAAATCGATCCTACACCTAT 59.716 45.833 14.68 0.00 46.88 2.57
199 204 2.159338 TGCGTTCATAACCTAGTCGACC 60.159 50.000 13.01 0.00 0.00 4.79
215 220 2.244117 ATCAGCCTCATCCGTGCGTT 62.244 55.000 0.00 0.00 0.00 4.84
349 354 5.486775 TCAGATTTTGGATCTCTCCTGTTCT 59.513 40.000 0.00 0.00 42.59 3.01
472 478 6.179756 TGGTGTTGATGCTATCTTGTAACAT 58.820 36.000 0.00 0.00 0.00 2.71
562 568 4.594123 TTGATCTCCTGAACGTGTTGTA 57.406 40.909 0.00 0.00 0.00 2.41
878 884 0.472925 TGTGTAGTGCTTCCTCCCCA 60.473 55.000 0.00 0.00 0.00 4.96
1142 1148 6.006449 AGATTAAACAATTCCTGTGCAGTCT 58.994 36.000 0.00 0.00 38.67 3.24
1155 1161 6.431234 GGTTGGAGTGTCTGAGATTAAACAAT 59.569 38.462 0.00 0.00 0.00 2.71
1178 1184 4.773149 CCCTCTCAACAGTTACTCTAAGGT 59.227 45.833 0.00 0.00 0.00 3.50
1227 1233 2.172082 TGGCTTCTGATCCAGGATCTTG 59.828 50.000 26.94 19.69 39.56 3.02
1369 1417 2.159476 CGTCATTGTCAAATGCCTCCAG 60.159 50.000 0.00 0.00 42.55 3.86
1489 1620 0.949397 TTCTGTTGCTGCTTCTGCTG 59.051 50.000 0.00 0.00 40.48 4.41
1502 1636 4.835615 TCCTCTTCTACTTCTGCTTCTGTT 59.164 41.667 0.00 0.00 0.00 3.16
1503 1637 4.411927 TCCTCTTCTACTTCTGCTTCTGT 58.588 43.478 0.00 0.00 0.00 3.41
1504 1638 4.704540 TCTCCTCTTCTACTTCTGCTTCTG 59.295 45.833 0.00 0.00 0.00 3.02
1505 1639 4.929479 TCTCCTCTTCTACTTCTGCTTCT 58.071 43.478 0.00 0.00 0.00 2.85
1506 1640 4.097892 CCTCTCCTCTTCTACTTCTGCTTC 59.902 50.000 0.00 0.00 0.00 3.86
1507 1641 4.023291 CCTCTCCTCTTCTACTTCTGCTT 58.977 47.826 0.00 0.00 0.00 3.91
1508 1642 3.268334 TCCTCTCCTCTTCTACTTCTGCT 59.732 47.826 0.00 0.00 0.00 4.24
1509 1643 3.626930 TCCTCTCCTCTTCTACTTCTGC 58.373 50.000 0.00 0.00 0.00 4.26
1510 1644 5.505780 TCTTCCTCTCCTCTTCTACTTCTG 58.494 45.833 0.00 0.00 0.00 3.02
1534 1710 2.302733 TGTTGCTGCTACCAGATCTTCA 59.697 45.455 11.51 0.00 41.77 3.02
1982 2160 3.726517 CAACTTCGCCAGGGCACG 61.727 66.667 11.42 0.17 42.06 5.34
1993 2171 0.250338 AGGCCGAACTCACCAACTTC 60.250 55.000 0.00 0.00 0.00 3.01
2019 2197 5.354513 GCCAAGGTAGATAGGAAACTTCAAC 59.645 44.000 0.00 0.00 43.67 3.18
2087 2265 2.047179 GAAGGCCACGGAGTCCAC 60.047 66.667 10.49 0.00 41.61 4.02
2246 2427 3.617263 GCACGAGAGGTATTTTCGTTGAT 59.383 43.478 0.00 0.00 44.30 2.57
2252 2433 0.651031 GCCGCACGAGAGGTATTTTC 59.349 55.000 4.38 0.00 37.01 2.29
2302 2483 0.249120 AAATCGGCGGAGATGACACA 59.751 50.000 7.21 0.00 0.00 3.72
2307 2488 1.599542 GAAAGGAAATCGGCGGAGATG 59.400 52.381 7.21 0.00 0.00 2.90
2308 2489 1.475213 GGAAAGGAAATCGGCGGAGAT 60.475 52.381 7.21 0.00 0.00 2.75
2342 2523 2.125350 CCCAAGAGGAGCGAGTGC 60.125 66.667 0.00 0.00 38.24 4.40
2390 2571 2.054799 GATATGGGGTGGTTCTGGCTA 58.945 52.381 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.