Multiple sequence alignment - TraesCS4B01G034700

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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 TraesCS4B01G034700 chr4B 100.000 2663 0 0 1 2663 25443439 25446101 0.000000e+00 4918
1 TraesCS4B01G034700 chr4B 96.284 1453 51 1 1211 2663 390850619 390849170 0.000000e+00 2381
2 TraesCS4B01G034700 chr4B 97.063 749 22 0 1 749 1824624 1825372 0.000000e+00 1262
3 TraesCS4B01G034700 chr4B 96.929 749 23 0 1 749 484677701 484676953 0.000000e+00 1256
4 TraesCS4B01G034700 chr4B 96.662 749 25 0 1 749 512630745 512631493 0.000000e+00 1245
5 TraesCS4B01G034700 chr4B 92.077 467 25 1 749 1215 390860490 390860036 0.000000e+00 647
6 TraesCS4B01G034700 chr1B 96.974 1917 50 4 749 2663 669890512 669888602 0.000000e+00 3212
7 TraesCS4B01G034700 chr1B 96.929 749 23 0 1 749 23150562 23149814 0.000000e+00 1256
8 TraesCS4B01G034700 chr2B 96.548 1912 64 1 754 2663 49606250 49608161 0.000000e+00 3164
9 TraesCS4B01G034700 chr2B 94.356 691 29 3 749 1436 48807831 48808514 0.000000e+00 1051
10 TraesCS4B01G034700 chr7B 96.190 1916 59 3 749 2663 587964109 587962207 0.000000e+00 3121
11 TraesCS4B01G034700 chr7B 97.063 749 22 0 1 749 511507784 511508532 0.000000e+00 1262
12 TraesCS4B01G034700 chr7B 96.929 749 23 0 1 749 507811007 507810259 0.000000e+00 1256
13 TraesCS4B01G034700 chr5B 95.645 1722 51 2 942 2662 426618558 426616860 0.000000e+00 2743
14 TraesCS4B01G034700 chr5B 96.796 749 24 0 1 749 674602998 674602250 0.000000e+00 1251
15 TraesCS4B01G034700 chr5B 92.120 533 21 7 749 1274 426615559 426615041 0.000000e+00 732
16 TraesCS4B01G034700 chr5B 95.455 110 3 2 749 857 81559492 81559384 9.800000e-40 174
17 TraesCS4B01G034700 chr3A 95.161 1488 68 1 1148 2631 726094197 726092710 0.000000e+00 2346
18 TraesCS4B01G034700 chr3A 94.818 1486 72 2 1148 2628 732785192 732786677 0.000000e+00 2313
19 TraesCS4B01G034700 chr5A 94.740 1483 73 3 1148 2628 403870378 403871857 0.000000e+00 2302
20 TraesCS4B01G034700 chr7A 93.531 1484 95 1 1148 2631 297457133 297455651 0.000000e+00 2207
21 TraesCS4B01G034700 chr6B 97.063 749 22 0 1 749 207860158 207859410 0.000000e+00 1262
22 TraesCS4B01G034700 chr6B 90.960 708 51 5 749 1454 560809018 560808322 0.000000e+00 941
23 TraesCS4B01G034700 chrUn 96.796 749 24 0 1 749 2602135 2601387 0.000000e+00 1251
24 TraesCS4B01G034700 chr4A 95.612 547 21 3 754 1297 663309477 663308931 0.000000e+00 874
25 TraesCS4B01G034700 chr4A 95.255 548 22 3 754 1297 663307787 663307240 0.000000e+00 865


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 TraesCS4B01G034700 chr4B 25443439 25446101 2662 False 4918.0 4918 100.0000 1 2663 1 chr4B.!!$F2 2662
1 TraesCS4B01G034700 chr4B 390849170 390850619 1449 True 2381.0 2381 96.2840 1211 2663 1 chr4B.!!$R1 1452
2 TraesCS4B01G034700 chr4B 1824624 1825372 748 False 1262.0 1262 97.0630 1 749 1 chr4B.!!$F1 748
3 TraesCS4B01G034700 chr4B 484676953 484677701 748 True 1256.0 1256 96.9290 1 749 1 chr4B.!!$R3 748
4 TraesCS4B01G034700 chr4B 512630745 512631493 748 False 1245.0 1245 96.6620 1 749 1 chr4B.!!$F3 748
5 TraesCS4B01G034700 chr1B 669888602 669890512 1910 True 3212.0 3212 96.9740 749 2663 1 chr1B.!!$R2 1914
6 TraesCS4B01G034700 chr1B 23149814 23150562 748 True 1256.0 1256 96.9290 1 749 1 chr1B.!!$R1 748
7 TraesCS4B01G034700 chr2B 49606250 49608161 1911 False 3164.0 3164 96.5480 754 2663 1 chr2B.!!$F2 1909
8 TraesCS4B01G034700 chr2B 48807831 48808514 683 False 1051.0 1051 94.3560 749 1436 1 chr2B.!!$F1 687
9 TraesCS4B01G034700 chr7B 587962207 587964109 1902 True 3121.0 3121 96.1900 749 2663 1 chr7B.!!$R2 1914
10 TraesCS4B01G034700 chr7B 511507784 511508532 748 False 1262.0 1262 97.0630 1 749 1 chr7B.!!$F1 748
11 TraesCS4B01G034700 chr7B 507810259 507811007 748 True 1256.0 1256 96.9290 1 749 1 chr7B.!!$R1 748
12 TraesCS4B01G034700 chr5B 426615041 426618558 3517 True 1737.5 2743 93.8825 749 2662 2 chr5B.!!$R3 1913
13 TraesCS4B01G034700 chr5B 674602250 674602998 748 True 1251.0 1251 96.7960 1 749 1 chr5B.!!$R2 748
14 TraesCS4B01G034700 chr3A 726092710 726094197 1487 True 2346.0 2346 95.1610 1148 2631 1 chr3A.!!$R1 1483
15 TraesCS4B01G034700 chr3A 732785192 732786677 1485 False 2313.0 2313 94.8180 1148 2628 1 chr3A.!!$F1 1480
16 TraesCS4B01G034700 chr5A 403870378 403871857 1479 False 2302.0 2302 94.7400 1148 2628 1 chr5A.!!$F1 1480
17 TraesCS4B01G034700 chr7A 297455651 297457133 1482 True 2207.0 2207 93.5310 1148 2631 1 chr7A.!!$R1 1483
18 TraesCS4B01G034700 chr6B 207859410 207860158 748 True 1262.0 1262 97.0630 1 749 1 chr6B.!!$R1 748
19 TraesCS4B01G034700 chr6B 560808322 560809018 696 True 941.0 941 90.9600 749 1454 1 chr6B.!!$R2 705
20 TraesCS4B01G034700 chrUn 2601387 2602135 748 True 1251.0 1251 96.7960 1 749 1 chrUn.!!$R1 748
21 TraesCS4B01G034700 chr4A 663307240 663309477 2237 True 869.5 874 95.4335 754 1297 2 chr4A.!!$R1 543

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
885 887 1.042229 TTTTCTCCTGGACCGTCGAA 58.958 50.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2118 0.379669 GACTCGGCTTGCCATTGATG 59.62 55.0 12.45 0.0 0.0 3.07 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
71 72 7.353414 TCTATCACTTTTAGCTAGCACAGAT 57.647 36.000 18.83 11.76 0.00 2.90
137 138 1.130613 GTGTTGCTGCTTAGACGCG 59.869 57.895 3.53 3.53 0.00 6.01
153 154 1.665599 GCGGAGAAAAACGGACCGA 60.666 57.895 23.38 0.00 45.31 4.69
334 335 9.394477 GTAAAATGTATTCTTGTGGTTCTTGTC 57.606 33.333 0.00 0.00 0.00 3.18
505 506 4.988540 CGTGATGGTTGAGTTAGAGAAACA 59.011 41.667 0.00 0.00 40.83 2.83
727 728 2.678836 CAGTAAAAACACCCACACGACA 59.321 45.455 0.00 0.00 0.00 4.35
780 781 1.991121 TGTCTCAGTTGGTAGGTCGT 58.009 50.000 0.00 0.00 0.00 4.34
885 887 1.042229 TTTTCTCCTGGACCGTCGAA 58.958 50.000 0.00 0.00 0.00 3.71
932 934 3.522731 CAGGTAGCGAGCGAGGCT 61.523 66.667 4.67 4.67 43.88 4.58
940 942 2.320587 CGAGCGAGGCTTGCAAGTT 61.321 57.895 27.72 15.83 39.88 2.66
1030 1034 4.954118 ACGCACACCCTCCCTCCA 62.954 66.667 0.00 0.00 0.00 3.86
1049 1053 4.109675 AAACCCTAGCCGCCGCAT 62.110 61.111 0.00 0.00 37.52 4.73
1068 1072 0.719015 TGAGGGAAGAGATGAGGGGT 59.281 55.000 0.00 0.00 0.00 4.95
1339 1501 2.505982 GGGCCGAGAAGCATAGCA 59.494 61.111 0.00 0.00 0.00 3.49
1384 1546 0.405585 ATCACCCAAGGTTGTCAGGG 59.594 55.000 0.00 0.00 46.96 4.45
1542 1704 0.916358 CAACCCACCTCCTCCTCCAT 60.916 60.000 0.00 0.00 0.00 3.41
1607 1769 3.563808 GCACACCTGAACTGAACATGTTA 59.436 43.478 11.95 0.00 0.00 2.41
1848 2010 2.032528 TCTCGGCAAGGCAAGTGG 59.967 61.111 0.00 0.00 0.00 4.00
1951 2113 1.216990 CAGGAAGCCAGGGAATAGGT 58.783 55.000 0.00 0.00 0.00 3.08
1956 2118 1.825622 GCCAGGGAATAGGTGCAGC 60.826 63.158 8.11 8.11 0.00 5.25
1980 2142 2.125512 GGCAAGCCGAGTCGACAT 60.126 61.111 19.50 2.45 0.00 3.06
2009 2171 8.267620 ACTTCACACATCAAATCGAATCAATA 57.732 30.769 0.00 0.00 0.00 1.90
2024 2187 8.827177 TCGAATCAATAGTGTTTTTCTACTGT 57.173 30.769 0.00 0.00 0.00 3.55
2105 2270 6.420008 GTGTTGTGTCACTAAGTTACGATCTT 59.580 38.462 4.27 0.00 35.68 2.40
2115 2280 1.852895 GTTACGATCTTAGCTGCGGTG 59.147 52.381 0.00 0.00 0.00 4.94
2386 2556 8.574251 AAACTACAAGTATTTGGTGCATGATA 57.426 30.769 0.00 0.00 38.66 2.15
2420 2590 3.008485 CAGGCTAATCCTCCCCTAATGTC 59.992 52.174 0.00 0.00 45.52 3.06
2432 2602 6.272324 CCTCCCCTAATGTCCATAATGTTCTA 59.728 42.308 0.00 0.00 0.00 2.10
2591 2761 9.522804 GGATCTTATAGAATTATAGAGTTGGCG 57.477 37.037 0.00 0.00 0.00 5.69
2620 2790 5.738909 TGAAAATCATGGTGTTGGTGTTTT 58.261 33.333 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 6.907853 AGTGCACTAATCTCATCTATAGCA 57.092 37.500 20.16 0.00 0.00 3.49
137 138 1.154197 CCTTCGGTCCGTTTTTCTCC 58.846 55.000 11.88 0.00 0.00 3.71
153 154 5.673130 AGCCTCTATTCTAGTACTCCCTT 57.327 43.478 0.00 0.00 0.00 3.95
334 335 6.260936 TGACTAGAAAAGCAAGACCAAAGAAG 59.739 38.462 0.00 0.00 0.00 2.85
490 491 7.279615 TCAACCTCATTGTTTCTCTAACTCAA 58.720 34.615 0.00 0.00 39.54 3.02
532 533 8.539117 TCTGACATCATATTTCTTGGAGTCTA 57.461 34.615 0.00 0.00 0.00 2.59
597 598 0.899717 TGGGCCAGAACAAGCATTCC 60.900 55.000 0.00 0.00 0.00 3.01
727 728 1.466167 CTAGCTTCACATGCTTTGCGT 59.534 47.619 0.00 0.00 41.46 5.24
780 781 3.252944 GGACGAAAATAAAACCCGGAACA 59.747 43.478 0.73 0.00 0.00 3.18
953 957 7.604549 TGGTTTTCTTTCGTAGGTTTTCTTTT 58.395 30.769 0.00 0.00 0.00 2.27
994 998 1.543944 TTGCCTCGCTCCATCACTCA 61.544 55.000 0.00 0.00 0.00 3.41
998 1002 2.125552 CGTTGCCTCGCTCCATCA 60.126 61.111 0.00 0.00 0.00 3.07
1049 1053 0.719015 ACCCCTCATCTCTTCCCTCA 59.281 55.000 0.00 0.00 0.00 3.86
1319 1481 1.757306 CTATGCTTCTCGGCCCCAT 59.243 57.895 0.00 0.00 0.00 4.00
1384 1546 2.401195 GAAGTTGAGCGCGATGGC 59.599 61.111 12.10 0.00 0.00 4.40
1848 2010 2.706339 AGAGCCCATCTGAATGTGAC 57.294 50.000 0.00 0.00 36.69 3.67
1951 2113 1.216977 GCTTGCCATTGATGCTGCA 59.783 52.632 4.13 4.13 0.00 4.41
1956 2118 0.379669 GACTCGGCTTGCCATTGATG 59.620 55.000 12.45 0.00 0.00 3.07
2009 2171 6.851222 CTGATGTGACAGTAGAAAAACACT 57.149 37.500 0.00 0.00 33.73 3.55
2105 2270 4.760878 TGAAAATATGTACACCGCAGCTA 58.239 39.130 0.00 0.00 0.00 3.32
2432 2602 6.388689 TCTCCTTTACCCATATTGTGTACCAT 59.611 38.462 0.00 0.00 0.00 3.55
2591 2761 2.807676 ACACCATGATTTTCAGACCCC 58.192 47.619 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.