Multiple sequence alignment - TraesCS3B01G430800

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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 TraesCS3B01G430800 chr3B 100.000 2489 0 0 1 2489 669904714 669907202 0.000000e+00 4597
1 TraesCS3B01G430800 chr6B 96.225 2490 91 3 1 2489 388136401 388138888 0.000000e+00 4074
2 TraesCS3B01G430800 chr6B 95.705 2491 102 5 1 2489 264980153 264977666 0.000000e+00 4002
3 TraesCS3B01G430800 chr6B 98.283 1747 30 0 1 1747 128897085 128895339 0.000000e+00 3061
4 TraesCS3B01G430800 chr6B 91.314 472 39 2 2016 2486 606986488 606986958 0.000000e+00 643
5 TraesCS3B01G430800 chr2B 96.222 2488 89 3 1 2488 526494336 526491854 0.000000e+00 4069
6 TraesCS3B01G430800 chr2B 96.066 2491 95 3 1 2489 357333381 357335870 0.000000e+00 4054
7 TraesCS3B01G430800 chr2B 94.730 721 31 2 1770 2489 391176537 391177251 0.000000e+00 1114
8 TraesCS3B01G430800 chr7A 98.226 1747 31 0 1 1747 200014076 200012330 0.000000e+00 3055
9 TraesCS3B01G430800 chr7B 98.111 1747 33 0 1 1747 742930383 742932129 0.000000e+00 3044
10 TraesCS3B01G430800 chr7B 98.054 1747 33 1 1 1747 698133712 698131967 0.000000e+00 3037
11 TraesCS3B01G430800 chrUn 98.055 1748 33 1 1 1747 246704098 246702351 0.000000e+00 3038
12 TraesCS3B01G430800 chr6A 93.974 780 39 3 1711 2489 597223374 597224146 0.000000e+00 1173
13 TraesCS3B01G430800 chr4D 83.071 762 97 23 1738 2489 450896753 450896014 0.000000e+00 664
14 TraesCS3B01G430800 chr3D 90.526 475 40 3 2016 2489 308556938 308556468 7.560000e-175 623
15 TraesCS3B01G430800 chr3D 83.916 143 21 2 1738 1880 308557205 308557065 4.320000e-28 135
16 TraesCS3B01G430800 chr6D 84.286 140 21 1 1738 1877 370023945 370024083 4.320000e-28 135
17 TraesCS3B01G430800 chr2D 83.688 141 21 2 1738 1877 39658053 39658192 5.590000e-27 132


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 TraesCS3B01G430800 chr3B 669904714 669907202 2488 False 4597 4597 100.000 1 2489 1 chr3B.!!$F1 2488
1 TraesCS3B01G430800 chr6B 388136401 388138888 2487 False 4074 4074 96.225 1 2489 1 chr6B.!!$F1 2488
2 TraesCS3B01G430800 chr6B 264977666 264980153 2487 True 4002 4002 95.705 1 2489 1 chr6B.!!$R2 2488
3 TraesCS3B01G430800 chr6B 128895339 128897085 1746 True 3061 3061 98.283 1 1747 1 chr6B.!!$R1 1746
4 TraesCS3B01G430800 chr2B 526491854 526494336 2482 True 4069 4069 96.222 1 2488 1 chr2B.!!$R1 2487
5 TraesCS3B01G430800 chr2B 357333381 357335870 2489 False 4054 4054 96.066 1 2489 1 chr2B.!!$F1 2488
6 TraesCS3B01G430800 chr2B 391176537 391177251 714 False 1114 1114 94.730 1770 2489 1 chr2B.!!$F2 719
7 TraesCS3B01G430800 chr7A 200012330 200014076 1746 True 3055 3055 98.226 1 1747 1 chr7A.!!$R1 1746
8 TraesCS3B01G430800 chr7B 742930383 742932129 1746 False 3044 3044 98.111 1 1747 1 chr7B.!!$F1 1746
9 TraesCS3B01G430800 chr7B 698131967 698133712 1745 True 3037 3037 98.054 1 1747 1 chr7B.!!$R1 1746
10 TraesCS3B01G430800 chrUn 246702351 246704098 1747 True 3038 3038 98.055 1 1747 1 chrUn.!!$R1 1746
11 TraesCS3B01G430800 chr6A 597223374 597224146 772 False 1173 1173 93.974 1711 2489 1 chr6A.!!$F1 778
12 TraesCS3B01G430800 chr4D 450896014 450896753 739 True 664 664 83.071 1738 2489 1 chr4D.!!$R1 751
13 TraesCS3B01G430800 chr3D 308556468 308557205 737 True 379 623 87.221 1738 2489 2 chr3D.!!$R1 751

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
44 45 3.087253 TTCCCGGGCGATCACCAT 61.087 61.111 18.49 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 1954 0.387622 CAAGGTGTGCCGCATTTCTG 60.388 55.0 0.0 0.0 40.5 3.02 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
44 45 3.087253 TTCCCGGGCGATCACCAT 61.087 61.111 18.49 0.00 0.00 3.55
88 89 5.934402 AGAAATCAAGACCCGTACTACAT 57.066 39.130 0.00 0.00 0.00 2.29
172 173 3.838903 AGGGTACAGAGGAAGAACGAAAT 59.161 43.478 0.00 0.00 0.00 2.17
446 447 9.416284 TCAAGTTATTTTTACCAAAGAAGTCCT 57.584 29.630 0.00 0.00 0.00 3.85
974 983 7.726738 AGAGAAATTCATAGACCTAGGTAGGAC 59.273 40.741 16.29 1.70 46.63 3.85
997 1006 9.147732 GGACAGGAAAATTGATAAAGGGAATAT 57.852 33.333 0.00 0.00 0.00 1.28
1192 1201 4.322567 AGACATCTCTTTTCAACTGAGGC 58.677 43.478 0.00 0.00 0.00 4.70
1266 1275 5.365314 TCCATTAATAATGCCAAAAGGGGTC 59.635 40.000 7.45 0.00 37.57 4.46
1304 1313 4.291792 TGTTATTCTGGTCGATTAGGGGA 58.708 43.478 0.00 0.00 0.00 4.81
1386 1395 3.694566 ACCAGAAAAACGATTATGCTCCC 59.305 43.478 0.00 0.00 0.00 4.30
1474 1483 2.526432 AGGGACGTGCTATATCCGAAT 58.474 47.619 7.11 0.00 32.90 3.34
1480 1489 3.499537 ACGTGCTATATCCGAATCGTACA 59.500 43.478 0.82 0.00 0.00 2.90
1523 1532 1.613925 GCAGATGTAGTAGGGATCGCA 59.386 52.381 12.83 0.00 0.00 5.10
1527 1536 3.961408 AGATGTAGTAGGGATCGCAAACT 59.039 43.478 17.82 17.82 0.00 2.66
1586 1595 5.051816 CCAAAAGTTGTAGAGTTGGTCGTA 58.948 41.667 0.00 0.00 35.12 3.43
1611 1620 3.070015 TCATATCGAGCCATTGAAGCAGA 59.930 43.478 0.00 0.00 0.00 4.26
1833 1843 6.509418 AATAGTTATCATTGTGTTTGCGGT 57.491 33.333 0.00 0.00 0.00 5.68
1852 1862 4.622220 GCGGTTGTAGTTTTAGATCCCTCA 60.622 45.833 0.00 0.00 0.00 3.86
1943 1953 1.353022 ACATTCTACGGGCCCTTTTCA 59.647 47.619 22.43 0.45 0.00 2.69
1944 1954 1.743394 CATTCTACGGGCCCTTTTCAC 59.257 52.381 22.43 0.00 0.00 3.18
1976 1986 1.472662 CACCTTGAGTGGACGGGAGT 61.473 60.000 0.00 0.00 43.26 3.85
1989 2000 1.461461 GGGAGTGCTATGCCCCCTA 60.461 63.158 0.00 0.00 35.76 3.53
1999 2010 2.280308 ATGCCCCCTAGTAGGAACAA 57.720 50.000 18.43 1.08 37.67 2.83
2330 2342 4.708576 ACCAGTGTATCCGAGAGATCTA 57.291 45.455 0.00 0.00 36.33 1.98
2445 2457 4.863548 TCAAGCTTCATTTCCAGGATGAT 58.136 39.130 0.00 0.00 39.69 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.367159 TCTTGTCTTGTTTTCGTTTTAGTCA 57.633 32.000 0.00 0.0 0.00 3.41
128 129 1.734465 GCTTGAATGAAGACACCCGAG 59.266 52.381 0.00 0.0 32.82 4.63
172 173 3.003173 CCCCGGCCTCTCACTTCA 61.003 66.667 0.00 0.0 0.00 3.02
463 464 6.070136 GGAGGGTCCTTTTTAGTAGATGACTT 60.070 42.308 0.00 0.0 34.94 3.01
693 695 1.407258 CGGGCCAAACACTTTTTCTCA 59.593 47.619 4.39 0.0 0.00 3.27
1037 1046 7.701924 CGTTCAAATAAGAGTTGTACCCGTATA 59.298 37.037 0.00 0.0 0.00 1.47
1038 1047 6.532657 CGTTCAAATAAGAGTTGTACCCGTAT 59.467 38.462 0.00 0.0 0.00 3.06
1192 1201 5.106197 TGGAACGAAATGAGATTGGATTGTG 60.106 40.000 0.00 0.0 0.00 3.33
1266 1275 6.365247 CAGAATAACAAATACGTATCCCCTCG 59.635 42.308 8.86 0.0 0.00 4.63
1304 1313 4.672587 TCAGTTCTAGCTATTTCCGCAT 57.327 40.909 0.00 0.0 0.00 4.73
1386 1395 4.202326 CGTTACGAGTAGATACTTCTGCG 58.798 47.826 0.00 0.0 39.36 5.18
1518 1527 2.290008 TGTGTACCATCCAGTTTGCGAT 60.290 45.455 0.00 0.0 0.00 4.58
1523 1532 3.888930 CCAAGTTGTGTACCATCCAGTTT 59.111 43.478 1.45 0.0 0.00 2.66
1527 1536 3.586470 AACCAAGTTGTGTACCATCCA 57.414 42.857 1.45 0.0 0.00 3.41
1586 1595 4.823442 TGCTTCAATGGCTCGATATGAAAT 59.177 37.500 0.00 0.0 30.37 2.17
1628 1637 4.375272 CTCATAGCACGATGGAATTGTCT 58.625 43.478 0.00 0.0 39.48 3.41
1807 1817 8.682710 ACCGCAAACACAATGATAACTATTATT 58.317 29.630 0.00 0.0 0.00 1.40
1826 1836 4.456566 GGGATCTAAAACTACAACCGCAAA 59.543 41.667 0.00 0.0 0.00 3.68
1833 1843 7.710907 CGATCAATGAGGGATCTAAAACTACAA 59.289 37.037 0.00 0.0 39.17 2.41
1943 1953 0.823356 AAGGTGTGCCGCATTTCTGT 60.823 50.000 0.00 0.0 40.50 3.41
1944 1954 0.387622 CAAGGTGTGCCGCATTTCTG 60.388 55.000 0.00 0.0 40.50 3.02
1976 1986 0.864659 TCCTACTAGGGGGCATAGCA 59.135 55.000 2.04 0.0 35.59 3.49
1989 2000 1.884067 GCCAGCAGCTTTGTTCCTACT 60.884 52.381 0.00 0.0 38.99 2.57
2050 2062 4.005650 AGCATTAGATGAATGTATGCCGG 58.994 43.478 0.00 0.0 45.88 6.13
2330 2342 3.817647 GTCTGTTGCATGAAAGTTCTCCT 59.182 43.478 0.00 0.0 0.00 3.69
2445 2457 4.536090 AGTTCAGGTGGGATCTTATCAACA 59.464 41.667 0.00 0.0 0.00 3.33


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

AutoCloner maintained by Alex Coulton.