Multiple sequence alignment - TraesCS3B01G145600

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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 TraesCS3B01G145600 chr3B 100.000 7379 0 0 1 7379 134601977 134594599 0.000000e+00 13627.0
1 TraesCS3B01G145600 chr3B 99.371 6672 28 3 720 7379 135387382 135394051 0.000000e+00 12076.0
2 TraesCS3B01G145600 chr3B 98.617 723 10 0 1 723 135386387 135387109 0.000000e+00 1280.0
3 TraesCS3B01G145600 chr3B 83.127 403 64 4 6169 6571 131047899 131047501 1.510000e-96 364.0
4 TraesCS3B01G145600 chr5B 99.004 1807 16 2 1672 3476 476173293 476171487 0.000000e+00 3236.0
5 TraesCS3B01G145600 chr2B 95.077 1828 61 11 1672 3473 49594039 49595863 0.000000e+00 2850.0
6 TraesCS3B01G145600 chr2B 94.258 1846 62 12 1669 3473 677978661 677976819 0.000000e+00 2782.0
7 TraesCS3B01G145600 chr6B 93.315 1840 79 13 1673 3473 229145569 229143735 0.000000e+00 2676.0
8 TraesCS3B01G145600 chrUn 100.000 1447 0 0 1529 2975 399077327 399075881 0.000000e+00 2673.0
9 TraesCS3B01G145600 chrUn 94.289 1611 66 7 1673 3258 263441595 263443204 0.000000e+00 2442.0
10 TraesCS3B01G145600 chr6D 92.733 1844 89 13 1672 3474 76065445 76067284 0.000000e+00 2621.0
11 TraesCS3B01G145600 chr1B 92.579 1846 85 22 1676 3474 631823900 631822060 0.000000e+00 2603.0
12 TraesCS3B01G145600 chr1B 92.170 1839 74 22 1673 3474 408109642 408111447 0.000000e+00 2534.0
13 TraesCS3B01G145600 chr1B 88.095 126 11 3 284 408 629813149 629813271 5.970000e-31 147.0
14 TraesCS3B01G145600 chr7B 92.299 1844 81 28 1673 3475 25660536 25662359 0.000000e+00 2562.0
15 TraesCS3B01G145600 chr7B 92.391 1840 72 18 1673 3473 470292792 470294602 0.000000e+00 2560.0
16 TraesCS3B01G145600 chr7B 91.848 1840 79 25 1673 3473 470241808 470243615 0.000000e+00 2501.0
17 TraesCS3B01G145600 chr7B 88.000 125 14 1 287 410 699179744 699179868 5.970000e-31 147.0
18 TraesCS3B01G145600 chr7B 76.471 136 19 7 3865 3996 15002443 15002317 2.220000e-05 62.1
19 TraesCS3B01G145600 chr5D 91.820 1846 80 24 1672 3474 481152618 481150801 0.000000e+00 2507.0
20 TraesCS3B01G145600 chr2D 92.917 1680 88 13 1673 3324 521869085 521870761 0.000000e+00 2414.0
21 TraesCS3B01G145600 chr2D 84.247 146 19 4 285 428 623756918 623756775 9.980000e-29 139.0
22 TraesCS3B01G145600 chr4D 90.351 114 10 1 291 403 51798062 51798175 1.660000e-31 148.0
23 TraesCS3B01G145600 chr3A 86.131 137 16 3 269 404 720229636 720229502 2.150000e-30 145.0
24 TraesCS3B01G145600 chr4B 87.302 126 15 1 286 410 392367905 392368030 7.720000e-30 143.0
25 TraesCS3B01G145600 chr4B 87.705 122 12 3 284 403 178355890 178356010 9.980000e-29 139.0
26 TraesCS3B01G145600 chr1A 85.821 134 16 2 273 403 32469659 32469792 9.980000e-29 139.0


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 TraesCS3B01G145600 chr3B 134594599 134601977 7378 True 13627 13627 100.000 1 7379 1 chr3B.!!$R2 7378
1 TraesCS3B01G145600 chr3B 135386387 135394051 7664 False 6678 12076 98.994 1 7379 2 chr3B.!!$F1 7378
2 TraesCS3B01G145600 chr5B 476171487 476173293 1806 True 3236 3236 99.004 1672 3476 1 chr5B.!!$R1 1804
3 TraesCS3B01G145600 chr2B 49594039 49595863 1824 False 2850 2850 95.077 1672 3473 1 chr2B.!!$F1 1801
4 TraesCS3B01G145600 chr2B 677976819 677978661 1842 True 2782 2782 94.258 1669 3473 1 chr2B.!!$R1 1804
5 TraesCS3B01G145600 chr6B 229143735 229145569 1834 True 2676 2676 93.315 1673 3473 1 chr6B.!!$R1 1800
6 TraesCS3B01G145600 chrUn 399075881 399077327 1446 True 2673 2673 100.000 1529 2975 1 chrUn.!!$R1 1446
7 TraesCS3B01G145600 chrUn 263441595 263443204 1609 False 2442 2442 94.289 1673 3258 1 chrUn.!!$F1 1585
8 TraesCS3B01G145600 chr6D 76065445 76067284 1839 False 2621 2621 92.733 1672 3474 1 chr6D.!!$F1 1802
9 TraesCS3B01G145600 chr1B 631822060 631823900 1840 True 2603 2603 92.579 1676 3474 1 chr1B.!!$R1 1798
10 TraesCS3B01G145600 chr1B 408109642 408111447 1805 False 2534 2534 92.170 1673 3474 1 chr1B.!!$F1 1801
11 TraesCS3B01G145600 chr7B 25660536 25662359 1823 False 2562 2562 92.299 1673 3475 1 chr7B.!!$F1 1802
12 TraesCS3B01G145600 chr7B 470292792 470294602 1810 False 2560 2560 92.391 1673 3473 1 chr7B.!!$F3 1800
13 TraesCS3B01G145600 chr7B 470241808 470243615 1807 False 2501 2501 91.848 1673 3473 1 chr7B.!!$F2 1800
14 TraesCS3B01G145600 chr5D 481150801 481152618 1817 True 2507 2507 91.820 1672 3474 1 chr5D.!!$R1 1802
15 TraesCS3B01G145600 chr2D 521869085 521870761 1676 False 2414 2414 92.917 1673 3324 1 chr2D.!!$F1 1651

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
312 313 1.167781 TCCGCCCGGAAAAACTTGTC 61.168 55.000 0.73 0.0 42.05 3.18 F
1237 1514 1.296715 GTCGACATGGACTTGGGCT 59.703 57.895 11.55 0.0 34.09 5.19 F
1321 1598 5.708736 TTGGATTATTGGGAGAGTTGCTA 57.291 39.130 0.00 0.0 0.00 3.49 F
3447 3785 1.603172 GGATTCGGCTCCTGTACATCG 60.603 57.143 0.00 0.0 32.18 3.84 F
3502 3840 1.226746 CCCTTCCAACAGTGAACGAC 58.773 55.000 0.00 0.0 0.00 4.34 F
4866 5204 3.217626 CTGCATTCTCAGGGGTTAATCC 58.782 50.000 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1258 1535 2.440247 CCTGGGATTTCACGGCCC 60.440 66.667 0.0 0.0 42.38 5.80 R
2975 3290 7.303634 TCCGAATATAGTTTTCTTTGTGAGC 57.696 36.000 0.0 0.0 0.00 4.26 R
3245 3562 6.496565 TCTCTCTCCTCTCTCTCAAACAAATT 59.503 38.462 0.0 0.0 0.00 1.82 R
4866 5204 1.269517 GCATAGAGAGAAGACGCCAGG 60.270 57.143 0.0 0.0 0.00 4.45 R
5516 5854 2.037902 TCTGCCAGGTACGTCAATGAAA 59.962 45.455 0.0 0.0 0.00 2.69 R
6864 7214 6.744537 CCAGAGAAATTAGAAATTCAGCAACG 59.255 38.462 0.0 0.0 0.00 4.10 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
237 238 5.923733 TCAAGTCTTCCCTCTGAATAGAC 57.076 43.478 0.00 0.0 31.53 2.59
295 296 7.686434 ACAAATGGTATATACATACACCCTCC 58.314 38.462 14.70 0.0 39.09 4.30
297 298 3.765511 TGGTATATACATACACCCTCCGC 59.234 47.826 14.70 0.0 39.09 5.54
301 302 4.235762 CATACACCCTCCGCCCGG 62.236 72.222 0.00 0.0 0.00 5.73
312 313 1.167781 TCCGCCCGGAAAAACTTGTC 61.168 55.000 0.73 0.0 42.05 3.18
322 323 4.037446 CGGAAAAACTTGTCCCTCAAATGA 59.963 41.667 0.00 0.0 35.48 2.57
335 336 7.560991 TGTCCCTCAAATGAATGTATTTAGCAT 59.439 33.333 0.00 0.0 0.00 3.79
364 365 9.109393 GTTAGTGCTAGATACATCCATTTGAAA 57.891 33.333 0.00 0.0 0.00 2.69
864 1141 1.784358 ATAGCATGCATTTGTGCCCT 58.216 45.000 21.98 0.0 42.20 5.19
1237 1514 1.296715 GTCGACATGGACTTGGGCT 59.703 57.895 11.55 0.0 34.09 5.19
1321 1598 5.708736 TTGGATTATTGGGAGAGTTGCTA 57.291 39.130 0.00 0.0 0.00 3.49
3447 3785 1.603172 GGATTCGGCTCCTGTACATCG 60.603 57.143 0.00 0.0 32.18 3.84
3502 3840 1.226746 CCCTTCCAACAGTGAACGAC 58.773 55.000 0.00 0.0 0.00 4.34
3855 4193 5.500234 CCTTGGTTTTGATCAGGATGTCTA 58.500 41.667 0.00 0.0 37.40 2.59
4866 5204 3.217626 CTGCATTCTCAGGGGTTAATCC 58.782 50.000 0.00 0.0 0.00 3.01
5516 5854 5.263599 TGTAACCATTGCAGATTCAGGAAT 58.736 37.500 0.00 0.0 0.00 3.01
5593 5931 3.897141 TGGCGATGTACCTTGTCATTA 57.103 42.857 0.00 0.0 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 238 2.057316 CTCAGAGATAATCAAGCCGCG 58.943 52.381 0.00 0.00 0.00 6.46
295 296 1.284715 GGACAAGTTTTTCCGGGCG 59.715 57.895 0.00 0.00 0.00 6.13
297 298 1.244816 GAGGGACAAGTTTTTCCGGG 58.755 55.000 0.00 0.00 32.00 5.73
301 302 6.986231 ACATTCATTTGAGGGACAAGTTTTTC 59.014 34.615 0.00 0.00 39.77 2.29
312 313 9.903682 CTTATGCTAAATACATTCATTTGAGGG 57.096 33.333 0.00 0.00 30.84 4.30
335 336 9.764363 CAAATGGATGTATCTAGCACTAACTTA 57.236 33.333 0.00 0.00 0.00 2.24
364 365 4.414337 AAGACTTGTCTCAAGCTTGTCT 57.586 40.909 25.19 15.70 35.20 3.41
661 662 3.782443 GGAGGACGAACCGGGCAT 61.782 66.667 6.32 0.00 44.74 4.40
799 1076 0.604243 ACATAAGCACACCCGCGAAA 60.604 50.000 8.23 0.00 36.85 3.46
864 1141 1.532078 TGTAGCCACAGACGGGTGA 60.532 57.895 5.81 0.00 41.32 4.02
1237 1514 3.475494 ACACCACTGCCACGACCA 61.475 61.111 0.00 0.00 0.00 4.02
1258 1535 2.440247 CCTGGGATTTCACGGCCC 60.440 66.667 0.00 0.00 42.38 5.80
2975 3290 7.303634 TCCGAATATAGTTTTCTTTGTGAGC 57.696 36.000 0.00 0.00 0.00 4.26
3245 3562 6.496565 TCTCTCTCCTCTCTCTCAAACAAATT 59.503 38.462 0.00 0.00 0.00 1.82
3502 3840 8.031277 ACGAGTGTACCTGGTAAAAATTACTAG 58.969 37.037 8.40 8.91 29.28 2.57
3855 4193 2.128771 AAAATAGGACATGGCGCACT 57.871 45.000 10.83 0.00 0.00 4.40
4866 5204 1.269517 GCATAGAGAGAAGACGCCAGG 60.270 57.143 0.00 0.00 0.00 4.45
5516 5854 2.037902 TCTGCCAGGTACGTCAATGAAA 59.962 45.455 0.00 0.00 0.00 2.69
5593 5931 5.832539 ATACTGCTGATTATAGCCAAGGT 57.167 39.130 0.00 0.00 43.02 3.50
6864 7214 6.744537 CCAGAGAAATTAGAAATTCAGCAACG 59.255 38.462 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.