Multiple sequence alignment - TraesCS5B01G141700

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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 TraesCS5B01G141700 chr5B 100.000 2850 0 0 1 2850 267416351 267419200 0.000000e+00 5264
1 TraesCS5B01G141700 chr5B 92.943 666 39 5 184 844 31323875 31324537 0.000000e+00 963
2 TraesCS5B01G141700 chr5B 92.943 666 39 5 184 844 382127271 382127933 0.000000e+00 963
3 TraesCS5B01G141700 chr5B 95.238 189 9 0 1 189 26293357 26293545 1.660000e-77 300
4 TraesCS5B01G141700 chr5D 94.400 1893 50 13 852 2744 238150649 238148813 0.000000e+00 2857
5 TraesCS5B01G141700 chr5D 97.248 109 3 0 2742 2850 238148664 238148556 4.850000e-43 185
6 TraesCS5B01G141700 chr5A 93.219 1976 66 22 852 2802 316659015 316660947 0.000000e+00 2844
7 TraesCS5B01G141700 chr1B 91.509 848 32 8 1 834 472964658 472963837 0.000000e+00 1131
8 TraesCS5B01G141700 chr1B 93.816 663 34 5 187 845 517915506 517914847 0.000000e+00 990
9 TraesCS5B01G141700 chr1B 94.333 547 26 5 184 726 612810546 612811091 0.000000e+00 833
10 TraesCS5B01G141700 chr1B 97.884 189 4 0 1 189 612810310 612810498 7.610000e-86 327
11 TraesCS5B01G141700 chr1B 97.354 189 5 0 1 189 659764751 659764563 3.540000e-84 322
12 TraesCS5B01G141700 chr1B 90.135 223 13 9 1 219 615210421 615210204 6.010000e-72 281
13 TraesCS5B01G141700 chr6B 93.835 665 35 4 184 844 154822551 154823213 0.000000e+00 996
14 TraesCS5B01G141700 chr6B 93.072 664 36 5 184 842 75959331 75959989 0.000000e+00 963
15 TraesCS5B01G141700 chr6B 96.791 187 6 0 1 187 188675483 188675297 2.130000e-81 313
16 TraesCS5B01G141700 chr6B 96.296 189 7 0 1 189 154822293 154822481 7.670000e-81 311
17 TraesCS5B01G141700 chr2B 93.976 664 31 4 187 844 223412859 223412199 0.000000e+00 996
18 TraesCS5B01G141700 chr7B 91.867 664 46 4 182 842 44813444 44812786 0.000000e+00 920
19 TraesCS5B01G141700 chr7B 90.376 665 32 7 184 844 368427001 368427637 0.000000e+00 845
20 TraesCS5B01G141700 chr7B 92.063 189 9 1 1 189 608403018 608403200 7.830000e-66 261
21 TraesCS5B01G141700 chr4A 88.795 473 49 2 1063 1531 469101957 469102429 6.850000e-161 577
22 TraesCS5B01G141700 chr4D 88.938 452 50 0 1080 1531 106739243 106738792 2.480000e-155 558
23 TraesCS5B01G141700 chr2A 83.294 425 42 13 1798 2218 56885096 56885495 5.800000e-97 364
24 TraesCS5B01G141700 chr2A 82.824 425 44 20 1798 2218 56882048 56881649 1.260000e-93 353
25 TraesCS5B01G141700 chr2A 83.616 177 14 12 2042 2218 56534227 56534388 4.920000e-33 152
26 TraesCS5B01G141700 chrUn 95.238 189 8 1 1 189 42102370 42102183 5.970000e-77 298


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 TraesCS5B01G141700 chr5B 267416351 267419200 2849 False 5264.0 5264 100.0000 1 2850 1 chr5B.!!$F3 2849
1 TraesCS5B01G141700 chr5B 31323875 31324537 662 False 963.0 963 92.9430 184 844 1 chr5B.!!$F2 660
2 TraesCS5B01G141700 chr5B 382127271 382127933 662 False 963.0 963 92.9430 184 844 1 chr5B.!!$F4 660
3 TraesCS5B01G141700 chr5D 238148556 238150649 2093 True 1521.0 2857 95.8240 852 2850 2 chr5D.!!$R1 1998
4 TraesCS5B01G141700 chr5A 316659015 316660947 1932 False 2844.0 2844 93.2190 852 2802 1 chr5A.!!$F1 1950
5 TraesCS5B01G141700 chr1B 472963837 472964658 821 True 1131.0 1131 91.5090 1 834 1 chr1B.!!$R1 833
6 TraesCS5B01G141700 chr1B 517914847 517915506 659 True 990.0 990 93.8160 187 845 1 chr1B.!!$R2 658
7 TraesCS5B01G141700 chr1B 612810310 612811091 781 False 580.0 833 96.1085 1 726 2 chr1B.!!$F1 725
8 TraesCS5B01G141700 chr6B 75959331 75959989 658 False 963.0 963 93.0720 184 842 1 chr6B.!!$F1 658
9 TraesCS5B01G141700 chr6B 154822293 154823213 920 False 653.5 996 95.0655 1 844 2 chr6B.!!$F2 843
10 TraesCS5B01G141700 chr2B 223412199 223412859 660 True 996.0 996 93.9760 187 844 1 chr2B.!!$R1 657
11 TraesCS5B01G141700 chr7B 44812786 44813444 658 True 920.0 920 91.8670 182 842 1 chr7B.!!$R1 660
12 TraesCS5B01G141700 chr7B 368427001 368427637 636 False 845.0 845 90.3760 184 844 1 chr7B.!!$F1 660

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
845 941 0.108041 CTTAAGGCGCCGTTTAGGGA 60.108 55.0 22.74 0.0 41.48 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2150 3.983988 CCGATATCCTCAAACATCTCACG 59.016 47.826 0.0 0.0 0.0 4.35 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
294 371 5.113383 TCACAAAATGTTCAGTACGTGTCT 58.887 37.500 0.00 0.00 0.00 3.41
376 455 5.620654 CGATGAACTCCTTTTGAATGCATGT 60.621 40.000 0.00 0.00 0.00 3.21
434 513 8.858003 TTATACGCACTGAACATTTTTCAAAA 57.142 26.923 0.00 0.00 0.00 2.44
610 706 5.890424 AAAACTCTTTCCACGAAAACAGA 57.110 34.783 0.00 0.00 30.84 3.41
644 740 5.117355 GGTTAAAAGCCTGTCAGTTAACC 57.883 43.478 19.33 19.33 43.68 2.85
845 941 0.108041 CTTAAGGCGCCGTTTAGGGA 60.108 55.000 22.74 0.00 41.48 4.20
846 942 0.324285 TTAAGGCGCCGTTTAGGGAA 59.676 50.000 22.74 4.29 41.48 3.97
847 943 0.542805 TAAGGCGCCGTTTAGGGAAT 59.457 50.000 22.74 0.00 41.48 3.01
848 944 1.029947 AAGGCGCCGTTTAGGGAATG 61.030 55.000 23.20 0.00 41.48 2.67
849 945 2.407616 GCGCCGTTTAGGGAATGC 59.592 61.111 0.00 0.00 41.48 3.56
850 946 3.107447 CGCCGTTTAGGGAATGCC 58.893 61.111 0.00 0.00 41.48 4.40
870 966 1.232621 GCTTGGCGGTCGGTAGTTTT 61.233 55.000 0.00 0.00 0.00 2.43
871 967 0.794473 CTTGGCGGTCGGTAGTTTTC 59.206 55.000 0.00 0.00 0.00 2.29
888 984 7.281549 GGTAGTTTTCTTTCTAACACAAGGACA 59.718 37.037 0.00 0.00 0.00 4.02
923 1019 4.263068 CCGAGAGAAGGCCCAACATATTAT 60.263 45.833 0.00 0.00 0.00 1.28
926 1022 6.521527 AGAGAAGGCCCAACATATTATCTT 57.478 37.500 0.00 0.00 0.00 2.40
969 1069 2.175035 TAAACCCCAACGCCTCCGAG 62.175 60.000 0.00 0.00 38.29 4.63
1307 1416 2.833582 ATGAGGATCCGCGTCCGT 60.834 61.111 11.16 0.00 43.27 4.69
1548 1657 1.630126 ATTGGCCTGCAGGATCGTCT 61.630 55.000 37.21 11.85 37.39 4.18
1645 1754 5.994054 AGATATTGTGGTATGATGTGCTGTC 59.006 40.000 0.00 0.00 0.00 3.51
1683 1793 4.275810 ACTACTGGGTAGTTGCTCGATTA 58.724 43.478 4.72 0.00 45.68 1.75
1740 1850 0.874390 ATGGTTGCGTACTTGCACTG 59.126 50.000 0.00 0.00 46.25 3.66
1756 1866 7.697691 ACTTGCACTGTATTTTATGCTATGTC 58.302 34.615 0.00 0.00 38.90 3.06
1757 1867 6.618287 TGCACTGTATTTTATGCTATGTCC 57.382 37.500 0.00 0.00 38.90 4.02
1763 1875 7.338449 ACTGTATTTTATGCTATGTCCGGTTTT 59.662 33.333 0.00 0.00 0.00 2.43
1769 1881 4.409718 TGCTATGTCCGGTTTTATGCTA 57.590 40.909 0.00 0.00 0.00 3.49
1860 1972 8.954350 CAATCACTTTGATCTTCTAGGAAATGT 58.046 33.333 0.00 0.00 35.76 2.71
1895 2007 6.429692 TCTTTATTCTTTGCATCTTCCGTTGA 59.570 34.615 0.00 0.00 0.00 3.18
2038 2150 7.383572 GTCTAGACACCATGATATGAATGTGAC 59.616 40.741 18.20 0.00 32.06 3.67
2409 2536 6.541111 ACGTTTAGTTCATCTTCCTGTTTC 57.459 37.500 0.00 0.00 0.00 2.78
2630 2757 8.757982 ATAGAGCATTTCATCATTTGGTTAGT 57.242 30.769 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
415 494 8.336806 TGATGAATTTTGAAAAATGTTCAGTGC 58.663 29.630 9.96 4.64 38.53 4.40
610 706 9.542462 GACAGGCTTTTAACCTTTTTCTATTTT 57.458 29.630 0.00 0.00 34.42 1.82
644 740 0.179119 CGGCTAACCTACCAGTTCGG 60.179 60.000 0.00 0.00 42.50 4.30
686 782 0.898320 AACCAGGGATCTCACGACTG 59.102 55.000 0.00 0.00 0.00 3.51
755 851 1.289066 GCCGGCCCACTTCTTTTTC 59.711 57.895 18.11 0.00 0.00 2.29
865 961 7.696992 TTGTCCTTGTGTTAGAAAGAAAACT 57.303 32.000 0.00 0.00 0.00 2.66
867 963 9.364989 CATTTTGTCCTTGTGTTAGAAAGAAAA 57.635 29.630 0.00 0.00 0.00 2.29
870 966 7.556275 AGTCATTTTGTCCTTGTGTTAGAAAGA 59.444 33.333 0.00 0.00 0.00 2.52
871 967 7.707104 AGTCATTTTGTCCTTGTGTTAGAAAG 58.293 34.615 0.00 0.00 0.00 2.62
888 984 3.118592 CCTTCTCTCGGGCTAGTCATTTT 60.119 47.826 0.00 0.00 0.00 1.82
923 1019 2.044650 GAGCTGCATGGGCCAAGA 60.045 61.111 11.89 0.00 40.13 3.02
926 1022 2.044650 GAAGAGCTGCATGGGCCA 60.045 61.111 9.61 9.61 40.13 5.36
969 1069 1.144298 AGGGGTGGGCGATTTTATACC 59.856 52.381 0.00 0.00 0.00 2.73
1057 1166 4.704833 CGGTGGTGCCTGGTGAGG 62.705 72.222 0.00 0.00 43.19 3.86
1548 1657 4.651778 CAGAGAAAACCACCCAATAGACA 58.348 43.478 0.00 0.00 0.00 3.41
1645 1754 7.612677 ACCCAGTAGTAGTCTTAAAACATCTG 58.387 38.462 0.00 0.00 0.00 2.90
1700 1810 8.469309 ACCATATCAAAATTCCTCAACATAGG 57.531 34.615 0.00 0.00 38.06 2.57
1701 1811 9.740239 CAACCATATCAAAATTCCTCAACATAG 57.260 33.333 0.00 0.00 0.00 2.23
1702 1812 8.196771 GCAACCATATCAAAATTCCTCAACATA 58.803 33.333 0.00 0.00 0.00 2.29
1703 1813 7.043565 GCAACCATATCAAAATTCCTCAACAT 58.956 34.615 0.00 0.00 0.00 2.71
1708 1818 5.248870 ACGCAACCATATCAAAATTCCTC 57.751 39.130 0.00 0.00 0.00 3.71
1740 1850 9.607285 CATAAAACCGGACATAGCATAAAATAC 57.393 33.333 9.46 0.00 0.00 1.89
1756 1866 6.329496 ACAACATCATTTAGCATAAAACCGG 58.671 36.000 0.00 0.00 0.00 5.28
1757 1867 7.218773 CAGACAACATCATTTAGCATAAAACCG 59.781 37.037 0.00 0.00 0.00 4.44
1763 1875 8.146479 GTCATCAGACAACATCATTTAGCATA 57.854 34.615 0.00 0.00 44.34 3.14
1860 1972 5.243507 TGCAAAGAATAAAGAGCAACATGGA 59.756 36.000 0.00 0.00 0.00 3.41
1925 2037 9.717942 GTATCATCCTAAGCAAATCAGTCTTAT 57.282 33.333 0.00 0.00 0.00 1.73
2021 2133 5.291971 TCTCACGTCACATTCATATCATGG 58.708 41.667 0.00 0.00 0.00 3.66
2038 2150 3.983988 CCGATATCCTCAAACATCTCACG 59.016 47.826 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.