Multiple sequence alignment - TraesCS5B01G453300

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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 TraesCS5B01G453300 chr5B 100.000 2501 0 0 1 2501 626085854 626083354 0.000000e+00 4619
1 TraesCS5B01G453300 chr5B 95.269 2473 108 6 35 2501 631355096 631352627 0.000000e+00 3910
2 TraesCS5B01G453300 chr5B 92.133 2517 176 17 1 2501 626141554 626139044 0.000000e+00 3531
3 TraesCS5B01G453300 chr5B 89.431 2441 228 18 81 2501 626107817 626105387 0.000000e+00 3051
4 TraesCS5B01G453300 chr5B 92.281 1995 146 7 1 1990 631379601 631377610 0.000000e+00 2824
5 TraesCS5B01G453300 chr5B 88.247 519 51 7 1990 2501 631368714 631368199 1.640000e-171 612
6 TraesCS5B01G453300 chr5B 81.625 751 114 19 1043 1774 626090741 626089996 3.560000e-168 601
7 TraesCS5B01G453300 chr5B 83.422 187 25 5 2317 2501 631359088 631358906 4.280000e-38 169
8 TraesCS5B01G453300 chr5D 92.792 2511 158 17 8 2501 502538016 502535512 0.000000e+00 3613
9 TraesCS5B01G453300 chr5D 92.745 1971 118 20 547 2501 502365265 502363304 0.000000e+00 2824
10 TraesCS5B01G453300 chr5D 83.333 726 95 19 131 851 502377902 502377198 0.000000e+00 647
11 TraesCS5B01G453300 chr5D 77.721 781 158 8 1015 1782 502545226 502544449 4.870000e-127 464
12 TraesCS5B01G453300 chr5D 83.422 187 25 5 2317 2501 502544450 502544268 4.280000e-38 169
13 TraesCS5B01G453300 chr5D 83.069 189 24 6 2317 2501 502376246 502376062 5.530000e-37 165
14 TraesCS5B01G453300 chr5A 88.006 2518 240 32 2 2497 631085825 631083348 0.000000e+00 2920
15 TraesCS5B01G453300 chr5A 88.909 1100 83 17 1415 2501 631111366 631110293 0.000000e+00 1319
16 TraesCS5B01G453300 chr5A 88.095 756 82 7 8 756 631112117 631111363 0.000000e+00 891
17 TraesCS5B01G453300 chr5A 80.698 917 146 17 134 1039 631207446 631206550 0.000000e+00 684
18 TraesCS5B01G453300 chr5A 80.795 906 123 26 8 894 631254725 631253852 0.000000e+00 662


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 TraesCS5B01G453300 chr5B 626083354 626085854 2500 True 4619.0 4619 100.0000 1 2501 1 chr5B.!!$R1 2500
1 TraesCS5B01G453300 chr5B 626139044 626141554 2510 True 3531.0 3531 92.1330 1 2501 1 chr5B.!!$R4 2500
2 TraesCS5B01G453300 chr5B 626105387 626107817 2430 True 3051.0 3051 89.4310 81 2501 1 chr5B.!!$R3 2420
3 TraesCS5B01G453300 chr5B 631377610 631379601 1991 True 2824.0 2824 92.2810 1 1990 1 chr5B.!!$R6 1989
4 TraesCS5B01G453300 chr5B 631352627 631359088 6461 True 2039.5 3910 89.3455 35 2501 2 chr5B.!!$R7 2466
5 TraesCS5B01G453300 chr5B 631368199 631368714 515 True 612.0 612 88.2470 1990 2501 1 chr5B.!!$R5 511
6 TraesCS5B01G453300 chr5B 626089996 626090741 745 True 601.0 601 81.6250 1043 1774 1 chr5B.!!$R2 731
7 TraesCS5B01G453300 chr5D 502535512 502538016 2504 True 3613.0 3613 92.7920 8 2501 1 chr5D.!!$R2 2493
8 TraesCS5B01G453300 chr5D 502363304 502365265 1961 True 2824.0 2824 92.7450 547 2501 1 chr5D.!!$R1 1954
9 TraesCS5B01G453300 chr5D 502376062 502377902 1840 True 406.0 647 83.2010 131 2501 2 chr5D.!!$R3 2370
10 TraesCS5B01G453300 chr5D 502544268 502545226 958 True 316.5 464 80.5715 1015 2501 2 chr5D.!!$R4 1486
11 TraesCS5B01G453300 chr5A 631083348 631085825 2477 True 2920.0 2920 88.0060 2 2497 1 chr5A.!!$R1 2495
12 TraesCS5B01G453300 chr5A 631110293 631112117 1824 True 1105.0 1319 88.5020 8 2501 2 chr5A.!!$R4 2493
13 TraesCS5B01G453300 chr5A 631206550 631207446 896 True 684.0 684 80.6980 134 1039 1 chr5A.!!$R2 905
14 TraesCS5B01G453300 chr5A 631253852 631254725 873 True 662.0 662 80.7950 8 894 1 chr5A.!!$R3 886

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
26 27 0.248289 GCCAAAAGCATGTGCAGGAT 59.752 50.0 7.83 0.0 45.16 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 6094 1.073284 GGGCCAACTACAGAAGGTTCA 59.927 52.381 4.39 0.0 0.0 3.18 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
26 27 0.248289 GCCAAAAGCATGTGCAGGAT 59.752 50.000 7.83 0.00 45.16 3.24
176 4140 0.331616 ATGGTGGTGGAAAGCCTACC 59.668 55.000 0.00 0.00 36.48 3.18
322 4287 2.992689 TAGGGCTCAACGCGGTGA 60.993 61.111 27.49 27.49 40.44 4.02
356 4322 1.272147 ACTGGGAAAATGTCTGGAGGC 60.272 52.381 0.00 0.00 0.00 4.70
372 4338 3.576550 TGGAGGCATGGGTTTTTAACTTC 59.423 43.478 0.00 0.00 0.00 3.01
533 4512 3.546543 CCCATTCGGCGGCTAGGA 61.547 66.667 7.21 0.00 0.00 2.94
586 4565 3.782443 GGCGGGTGGTAGACAGGG 61.782 72.222 0.00 0.00 0.00 4.45
590 4569 1.002533 GGGTGGTAGACAGGGCCTA 59.997 63.158 5.28 0.00 0.00 3.93
772 4752 8.882415 TTCTAGTTTTAGTGGAGTACAACTTG 57.118 34.615 0.00 0.00 29.20 3.16
970 4962 3.053544 TGTCTACGATCCCCTTCTTCTCT 60.054 47.826 0.00 0.00 0.00 3.10
971 4963 3.955551 GTCTACGATCCCCTTCTTCTCTT 59.044 47.826 0.00 0.00 0.00 2.85
1152 5189 1.492993 GGGTGGTTGAAGAGGCCTCT 61.493 60.000 30.40 30.40 42.75 3.69
1227 5265 1.971481 CAATGATGGAGGCGGAATCA 58.029 50.000 2.33 2.33 34.96 2.57
1537 5582 2.431954 AGTCAATTATGGCTGCTGCT 57.568 45.000 15.64 0.00 40.84 4.24
1584 5639 4.305989 TCGTTTTGCTGCTTCATTTTCT 57.694 36.364 0.00 0.00 0.00 2.52
1652 5715 4.233729 ACTAACAGTTGGGGGTGTAGTTA 58.766 43.478 1.24 0.00 0.00 2.24
1685 5748 6.143915 AGGGTTAGGAGATCTTAGTTGCATA 58.856 40.000 0.00 0.00 0.00 3.14
1688 5751 7.149307 GGTTAGGAGATCTTAGTTGCATACTC 58.851 42.308 0.00 0.00 38.33 2.59
1782 5849 5.939447 AGGATGATTTCTCCTTGGATCTTC 58.061 41.667 0.00 0.00 40.29 2.87
1992 6067 5.796502 AAATATTGAGAAAGGAGGGGTGA 57.203 39.130 0.00 0.00 0.00 4.02
1993 6068 5.379706 AATATTGAGAAAGGAGGGGTGAG 57.620 43.478 0.00 0.00 0.00 3.51
2019 6094 2.984672 AGGTTTTGGCCTTTACCCATT 58.015 42.857 3.32 0.00 34.71 3.16
2096 6172 2.042433 CCAGGTTGGTGGGATAGGAAAA 59.958 50.000 0.00 0.00 33.46 2.29
2114 6190 6.365520 AGGAAAACACTTAAGGAGAATGTGT 58.634 36.000 7.53 0.00 42.68 3.72
2153 6229 2.192664 TTTAGATGCTTTGGTCCGCA 57.807 45.000 0.00 0.00 40.87 5.69
2161 6237 0.676782 CTTTGGTCCGCACCCTAAGG 60.677 60.000 0.00 0.00 42.99 2.69
2204 6280 4.000988 CGATGTGTGGTAAGGCTTTACTT 58.999 43.478 17.16 0.00 39.30 2.24
2210 6286 2.235402 TGGTAAGGCTTTACTTCTCCGG 59.765 50.000 17.16 0.00 39.30 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.099113 TGTTTCAGTCATGGCATGTTTTGA 59.901 37.500 25.62 21.99 0.00 2.69
322 4287 2.047274 CAGTTCGTCCACCGGCAT 60.047 61.111 0.00 0.00 37.11 4.40
335 4300 2.819348 GCCTCCAGACATTTTCCCAGTT 60.819 50.000 0.00 0.00 0.00 3.16
356 4322 7.217447 CGCGTAATAAGAAGTTAAAAACCCATG 59.783 37.037 0.00 0.00 0.00 3.66
533 4512 0.112995 ATCCAGCACCCAACATGTGT 59.887 50.000 0.00 0.00 36.11 3.72
586 4565 4.337555 TGGTAAACGATGTCTAGTCTAGGC 59.662 45.833 4.41 4.41 0.00 3.93
772 4752 2.376518 TCCTATCAAGATCCCAATGCCC 59.623 50.000 0.00 0.00 0.00 5.36
853 4843 3.428999 CGAGATTAGTGTGGGATCAACGT 60.429 47.826 0.00 0.00 0.00 3.99
952 4943 3.052793 AGGAAGAGAAGAAGGGGATCGTA 60.053 47.826 0.00 0.00 0.00 3.43
970 4962 0.178944 TGAGACGGAGGTTGGAGGAA 60.179 55.000 0.00 0.00 0.00 3.36
971 4963 0.612174 CTGAGACGGAGGTTGGAGGA 60.612 60.000 0.00 0.00 0.00 3.71
1026 5018 4.488136 ATTGCCGCCGCCATGAGA 62.488 61.111 0.00 0.00 0.00 3.27
1152 5189 3.652869 AGATCCAACTTTGTTCCTCCTCA 59.347 43.478 0.00 0.00 0.00 3.86
1227 5265 2.680913 GCGCTGCACTGGATCGTTT 61.681 57.895 0.00 0.00 0.00 3.60
1537 5582 2.239439 AGTCCTCGACTCCTCCCCA 61.239 63.158 0.00 0.00 38.71 4.96
1652 5715 5.707495 AGATCTCCTAACCCTATTTCTCGT 58.293 41.667 0.00 0.00 0.00 4.18
1769 5836 4.080695 TCAACATCAGGAAGATCCAAGGAG 60.081 45.833 0.00 0.00 39.61 3.69
1782 5849 6.298361 TGATATTGTGGGTATCAACATCAGG 58.702 40.000 0.00 0.00 34.97 3.86
1827 5897 9.184523 CCACCAGTAACATCTAATTCCAATTAA 57.815 33.333 0.00 0.00 31.03 1.40
1828 5898 8.553153 TCCACCAGTAACATCTAATTCCAATTA 58.447 33.333 0.00 0.00 0.00 1.40
1830 5900 6.969043 TCCACCAGTAACATCTAATTCCAAT 58.031 36.000 0.00 0.00 0.00 3.16
1831 5901 6.381498 TCCACCAGTAACATCTAATTCCAA 57.619 37.500 0.00 0.00 0.00 3.53
1832 5902 6.381498 TTCCACCAGTAACATCTAATTCCA 57.619 37.500 0.00 0.00 0.00 3.53
1833 5903 7.775561 AGATTTCCACCAGTAACATCTAATTCC 59.224 37.037 0.00 0.00 0.00 3.01
1834 5904 8.738645 AGATTTCCACCAGTAACATCTAATTC 57.261 34.615 0.00 0.00 0.00 2.17
1980 6052 3.465966 ACCTTAAAACTCACCCCTCCTTT 59.534 43.478 0.00 0.00 0.00 3.11
2019 6094 1.073284 GGGCCAACTACAGAAGGTTCA 59.927 52.381 4.39 0.00 0.00 3.18
2096 6172 6.226787 CAGAAGACACATTCTCCTTAAGTGT 58.773 40.000 0.97 0.00 45.21 3.55
2114 6190 1.064003 TACCCAAAGGCAGCAGAAGA 58.936 50.000 0.00 0.00 36.11 2.87
2153 6229 1.361197 CCCACCAAATTCCCTTAGGGT 59.639 52.381 18.01 0.00 44.74 4.34
2161 6237 2.093537 TTGCACGCCCACCAAATTCC 62.094 55.000 0.00 0.00 0.00 3.01
2204 6280 4.790962 AGGTAGCGTCGCCGGAGA 62.791 66.667 14.86 3.81 33.68 3.71
2210 6286 2.202623 CTCACCAGGTAGCGTCGC 60.203 66.667 9.80 9.80 0.00 5.19
2217 6293 0.984230 CCCTTCTTGCTCACCAGGTA 59.016 55.000 0.00 0.00 0.00 3.08
2267 6343 5.141910 CCCCCTTTTGTTGAAACTACCTTA 58.858 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.