Multiple sequence alignment - TraesCS4A01G228400

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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 TraesCS4A01G228400 chr4A 100.000 2430 0 0 1 2430 536821825 536819396 0.000000e+00 4488
1 TraesCS4A01G228400 chr4A 97.696 738 17 0 1 738 536867550 536866813 0.000000e+00 1269
2 TraesCS4A01G228400 chr5A 93.838 1071 33 14 1362 2430 582955925 582956964 0.000000e+00 1581
3 TraesCS4A01G228400 chr5A 96.825 630 17 1 739 1365 582955263 582955892 0.000000e+00 1050
4 TraesCS4A01G228400 chr5A 95.173 663 20 6 1778 2430 46505195 46505855 0.000000e+00 1037
5 TraesCS4A01G228400 chr5A 93.939 627 28 1 739 1365 46504101 46504717 0.000000e+00 939
6 TraesCS4A01G228400 chr5A 96.110 437 11 2 1362 1796 46504750 46505182 0.000000e+00 708
7 TraesCS4A01G228400 chrUn 93.623 737 40 7 7 738 100758333 100759067 0.000000e+00 1094
8 TraesCS4A01G228400 chrUn 92.318 742 43 10 8 738 60182611 60183349 0.000000e+00 1042
9 TraesCS4A01G228400 chr2D 93.522 741 37 6 7 738 494508527 494507789 0.000000e+00 1092
10 TraesCS4A01G228400 chr2D 95.816 478 16 3 1956 2430 532441292 532440816 0.000000e+00 769
11 TraesCS4A01G228400 chr2D 85.878 524 35 15 839 1334 532481305 532480793 2.770000e-144 521
12 TraesCS4A01G228400 chr2D 94.408 304 6 3 1614 1906 532441594 532441291 7.920000e-125 457
13 TraesCS4A01G228400 chr2D 96.732 153 3 2 1362 1514 532441753 532441603 1.120000e-63 254
14 TraesCS4A01G228400 chr5D 92.732 743 42 7 7 738 479231074 479231815 0.000000e+00 1062
15 TraesCS4A01G228400 chr5D 92.328 743 44 8 5 738 391349092 391349830 0.000000e+00 1044
16 TraesCS4A01G228400 chr1D 92.713 741 43 7 7 738 218767756 218768494 0.000000e+00 1059
17 TraesCS4A01G228400 chr1D 87.987 308 30 5 742 1045 185999361 185999057 8.260000e-95 357
18 TraesCS4A01G228400 chr1D 85.714 238 22 2 1128 1365 185999028 185998803 8.680000e-60 241
19 TraesCS4A01G228400 chr4B 92.493 746 43 6 5 738 55865115 55864371 0.000000e+00 1055
20 TraesCS4A01G228400 chr1A 92.318 742 45 7 7 738 117480354 117479615 0.000000e+00 1044
21 TraesCS4A01G228400 chr3A 96.044 632 24 1 734 1365 738748564 738747934 0.000000e+00 1027
22 TraesCS4A01G228400 chr3A 96.055 583 18 2 1362 1943 738747901 738747323 0.000000e+00 944
23 TraesCS4A01G228400 chr3A 96.162 495 17 2 1936 2430 738746692 738746200 0.000000e+00 808
24 TraesCS4A01G228400 chr2A 95.960 495 19 1 1936 2430 749961934 749961441 0.000000e+00 802
25 TraesCS4A01G228400 chr2A 98.165 109 2 0 1835 1943 749962227 749962119 8.870000e-45 191
26 TraesCS4A01G228400 chr2A 91.667 108 4 1 1506 1613 60760579 60760681 7.000000e-31 145
27 TraesCS4A01G228400 chr6D 85.648 648 50 10 739 1365 10347721 10347096 2.040000e-180 641
28 TraesCS4A01G228400 chr6A 84.067 659 48 27 739 1365 11856304 11855671 1.250000e-162 582
29 TraesCS4A01G228400 chr7B 80.891 539 66 27 734 1257 568492727 568493243 8.150000e-105 390
30 TraesCS4A01G228400 chr1B 92.195 205 11 3 739 939 483877949 483878152 3.950000e-73 285
31 TraesCS4A01G228400 chr7D 83.486 327 30 7 1039 1365 78993857 78994159 1.420000e-72 283
32 TraesCS4A01G228400 chr5B 92.593 108 4 1 1508 1615 510536120 510536017 4.180000e-33 152
33 TraesCS4A01G228400 chr5B 90.741 108 6 2 1506 1613 678998040 678998143 9.060000e-30 141
34 TraesCS4A01G228400 chr7A 90.909 110 5 1 1506 1615 723363193 723363089 2.520000e-30 143
35 TraesCS4A01G228400 chr7A 90.741 108 5 3 1508 1615 6966566 6966464 3.260000e-29 139
36 TraesCS4A01G228400 chr3D 90.000 110 6 1 1506 1615 26467366 26467470 1.170000e-28 137


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 TraesCS4A01G228400 chr4A 536819396 536821825 2429 True 4488.000000 4488 100.0000 1 2430 1 chr4A.!!$R1 2429
1 TraesCS4A01G228400 chr4A 536866813 536867550 737 True 1269.000000 1269 97.6960 1 738 1 chr4A.!!$R2 737
2 TraesCS4A01G228400 chr5A 582955263 582956964 1701 False 1315.500000 1581 95.3315 739 2430 2 chr5A.!!$F2 1691
3 TraesCS4A01G228400 chr5A 46504101 46505855 1754 False 894.666667 1037 95.0740 739 2430 3 chr5A.!!$F1 1691
4 TraesCS4A01G228400 chrUn 100758333 100759067 734 False 1094.000000 1094 93.6230 7 738 1 chrUn.!!$F2 731
5 TraesCS4A01G228400 chrUn 60182611 60183349 738 False 1042.000000 1042 92.3180 8 738 1 chrUn.!!$F1 730
6 TraesCS4A01G228400 chr2D 494507789 494508527 738 True 1092.000000 1092 93.5220 7 738 1 chr2D.!!$R1 731
7 TraesCS4A01G228400 chr2D 532480793 532481305 512 True 521.000000 521 85.8780 839 1334 1 chr2D.!!$R2 495
8 TraesCS4A01G228400 chr2D 532440816 532441753 937 True 493.333333 769 95.6520 1362 2430 3 chr2D.!!$R3 1068
9 TraesCS4A01G228400 chr5D 479231074 479231815 741 False 1062.000000 1062 92.7320 7 738 1 chr5D.!!$F2 731
10 TraesCS4A01G228400 chr5D 391349092 391349830 738 False 1044.000000 1044 92.3280 5 738 1 chr5D.!!$F1 733
11 TraesCS4A01G228400 chr1D 218767756 218768494 738 False 1059.000000 1059 92.7130 7 738 1 chr1D.!!$F1 731
12 TraesCS4A01G228400 chr1D 185998803 185999361 558 True 299.000000 357 86.8505 742 1365 2 chr1D.!!$R1 623
13 TraesCS4A01G228400 chr4B 55864371 55865115 744 True 1055.000000 1055 92.4930 5 738 1 chr4B.!!$R1 733
14 TraesCS4A01G228400 chr1A 117479615 117480354 739 True 1044.000000 1044 92.3180 7 738 1 chr1A.!!$R1 731
15 TraesCS4A01G228400 chr3A 738746200 738748564 2364 True 926.333333 1027 96.0870 734 2430 3 chr3A.!!$R1 1696
16 TraesCS4A01G228400 chr2A 749961441 749962227 786 True 496.500000 802 97.0625 1835 2430 2 chr2A.!!$R1 595
17 TraesCS4A01G228400 chr6D 10347096 10347721 625 True 641.000000 641 85.6480 739 1365 1 chr6D.!!$R1 626
18 TraesCS4A01G228400 chr6A 11855671 11856304 633 True 582.000000 582 84.0670 739 1365 1 chr6A.!!$R1 626
19 TraesCS4A01G228400 chr7B 568492727 568493243 516 False 390.000000 390 80.8910 734 1257 1 chr7B.!!$F1 523

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
47 48 0.455815 TGTCCGATCATCACGTGAGG 59.544 55.0 23.54 23.54 40.92 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1769 0.667993 ACCACACAGAATTGCAACGG 59.332 50.0 0.0 0.0 0.0 4.44 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
47 48 0.455815 TGTCCGATCATCACGTGAGG 59.544 55.000 23.54 23.54 40.92 3.86
527 539 3.375299 GTCATCTCGCCAACTATTGCTTT 59.625 43.478 0.00 0.00 0.00 3.51
717 735 3.755378 ACAACATGCCTTGCAAAAACAAA 59.245 34.783 0.00 0.00 43.62 2.83
815 833 2.103263 GGACCTTGGATCAATAGCGAGT 59.897 50.000 0.00 0.00 0.00 4.18
851 869 1.741770 GGAGCACTAACCAGCCACG 60.742 63.158 0.00 0.00 0.00 4.94
1065 1128 1.000955 CTACTTCAGGCAACGACCACT 59.999 52.381 0.00 0.00 46.39 4.00
1236 1304 2.877097 TTCTAGTGCAGCCAATTGGA 57.123 45.000 29.02 3.79 37.39 3.53
1528 1637 4.410400 CTCACCCTCGCCCCCAAC 62.410 72.222 0.00 0.00 0.00 3.77
1529 1638 4.974438 TCACCCTCGCCCCCAACT 62.974 66.667 0.00 0.00 0.00 3.16
1530 1639 4.410400 CACCCTCGCCCCCAACTC 62.410 72.222 0.00 0.00 0.00 3.01
1531 1640 4.658786 ACCCTCGCCCCCAACTCT 62.659 66.667 0.00 0.00 0.00 3.24
1600 1709 1.885871 GGTGTAAGTCCGCCGTAGT 59.114 57.895 0.00 0.00 0.00 2.73
1657 1769 3.369451 TCTTCGTTTTTGTTTGCTTTGGC 59.631 39.130 0.00 0.00 39.26 4.52
1858 2012 2.756760 GGCCACACATCACATTGATCTT 59.243 45.455 0.00 0.00 34.28 2.40
1906 2749 6.148480 TGCAGAGAGAAGCTTCAAGTATTTTC 59.852 38.462 27.57 13.66 0.00 2.29
1949 2792 7.845622 GCAAACAATCACATTCAAAAACTACAC 59.154 33.333 0.00 0.00 0.00 2.90
2145 3000 5.468072 AGAGAACTGCAAAATCAGTGTACAG 59.532 40.000 0.00 0.00 45.77 2.74
2315 3171 2.779951 TAGCGATGCGTGGCTGTGTT 62.780 55.000 23.94 1.33 39.89 3.32
2332 3188 2.037251 GTGTTGCTCTACTTCACCTCCA 59.963 50.000 0.00 0.00 0.00 3.86
2363 3219 2.336341 CGAGCTCTTCGCCTCCTAT 58.664 57.895 12.85 0.00 43.22 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 4.471904 TCACCATTGATGACTACTCCAC 57.528 45.455 0.00 0.00 0.00 4.02
527 539 6.319405 TCACTATGTGGTAGCGATAGTTGTAA 59.681 38.462 11.72 0.36 31.82 2.41
717 735 4.381718 GCCACAAAGTAGAGGACGTCTAAT 60.382 45.833 16.46 2.98 39.61 1.73
815 833 0.329261 CCCACCTTTGATCTCTGCCA 59.671 55.000 0.00 0.00 0.00 4.92
851 869 6.350696 GGGGGTTATGTGAAAAATGGAGTTAC 60.351 42.308 0.00 0.00 0.00 2.50
964 987 2.202703 GTCGCCGTCGCATAGGTT 60.203 61.111 0.00 0.00 35.26 3.50
1236 1304 4.047627 ACTAACCAAAAGCTAGCCCAAT 57.952 40.909 12.13 0.00 0.00 3.16
1499 1608 2.100989 GAGGGTGAGATTACACTCGGT 58.899 52.381 0.00 0.00 44.88 4.69
1528 1637 8.091449 AGTACATTTACAAAGGTTGAGAGAGAG 58.909 37.037 0.00 0.00 34.45 3.20
1529 1638 7.963532 AGTACATTTACAAAGGTTGAGAGAGA 58.036 34.615 0.00 0.00 34.45 3.10
1530 1639 8.091449 AGAGTACATTTACAAAGGTTGAGAGAG 58.909 37.037 0.00 0.00 34.45 3.20
1531 1640 7.963532 AGAGTACATTTACAAAGGTTGAGAGA 58.036 34.615 0.00 0.00 34.45 3.10
1630 1742 7.042791 CCAAAGCAAACAAAAACGAAGATACAT 60.043 33.333 0.00 0.00 0.00 2.29
1657 1769 0.667993 ACCACACAGAATTGCAACGG 59.332 50.000 0.00 0.00 0.00 4.44
1858 2012 1.620739 GGTGCCATGAGAGCTCAGGA 61.621 60.000 17.77 0.00 43.36 3.86
1906 2749 1.511850 TGCTGGTCATCGACAAACTG 58.488 50.000 0.00 0.00 33.68 3.16
2009 2860 0.944386 GGAGCACACTCGCAAAAAGA 59.056 50.000 0.00 0.00 44.48 2.52
2145 3000 6.873944 ACGCTACGTCGTTCTCTGAAGAAC 62.874 50.000 1.78 8.00 44.64 3.01
2184 3039 1.593196 CTCGAAGGGCAACTTGACAA 58.407 50.000 0.00 0.00 40.21 3.18
2189 3044 1.172812 GCAACCTCGAAGGGCAACTT 61.173 55.000 5.98 0.00 40.58 2.66
2315 3171 1.561643 CCTGGAGGTGAAGTAGAGCA 58.438 55.000 0.00 0.00 0.00 4.26
2363 3219 1.304381 GCAAGGGATTGGGACTGCA 60.304 57.895 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.