Multiple sequence alignment - TraesCS7B01G109300

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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 TraesCS7B01G109300 chr7B 100.000 2757 0 0 1 2757 125245248 125242492 0.000000e+00 5092.0
1 TraesCS7B01G109300 chr7B 99.685 1588 4 1 1170 2757 125280443 125278857 0.000000e+00 2904.0
2 TraesCS7B01G109300 chr7B 99.370 1588 8 1 1170 2757 125313255 125311670 0.000000e+00 2876.0
3 TraesCS7B01G109300 chr7B 98.992 1488 12 3 1271 2757 125221189 125219704 0.000000e+00 2662.0
4 TraesCS7B01G109300 chr7B 100.000 850 0 0 1 850 125281303 125280454 0.000000e+00 1570.0
5 TraesCS7B01G109300 chr7B 100.000 850 0 0 1 850 125315184 125314335 0.000000e+00 1570.0
6 TraesCS7B01G109300 chr7B 93.656 993 58 4 948 1936 125356064 125355073 0.000000e+00 1480.0
7 TraesCS7B01G109300 chr7B 91.134 970 51 18 869 1815 125363369 125362412 0.000000e+00 1282.0
8 TraesCS7B01G109300 chr7B 92.422 739 36 11 1999 2732 125354943 125354220 0.000000e+00 1037.0
9 TraesCS7B01G109300 chr7B 84.534 944 123 18 876 1805 125192027 125191093 0.000000e+00 913.0
10 TraesCS7B01G109300 chr7B 98.305 472 8 0 287 758 125208373 125207902 0.000000e+00 828.0
11 TraesCS7B01G109300 chr7B 88.754 578 23 9 206 758 125337179 125336619 0.000000e+00 669.0
12 TraesCS7B01G109300 chr7B 88.581 578 24 9 206 758 125231242 125230682 0.000000e+00 664.0
13 TraesCS7B01G109300 chr7B 88.408 578 25 9 206 758 125303483 125302923 0.000000e+00 658.0
14 TraesCS7B01G109300 chr7B 88.062 578 27 9 206 758 125267418 125266858 0.000000e+00 647.0
15 TraesCS7B01G109300 chr7B 88.827 358 22 11 397 744 125419945 125419596 9.130000e-115 424.0
16 TraesCS7B01G109300 chr7B 94.606 241 9 4 1 239 125221412 125221174 1.210000e-98 370.0
17 TraesCS7B01G109300 chr7B 81.520 487 39 24 275 744 125356859 125356407 1.210000e-93 353.0
18 TraesCS7B01G109300 chr7B 93.846 195 12 0 1 195 453433701 453433895 7.470000e-76 294.0
19 TraesCS7B01G109300 chr7B 93.600 125 4 4 750 872 748183314 748183436 1.690000e-42 183.0
20 TraesCS7B01G109300 chr7B 94.068 118 7 0 870 987 125230693 125230576 2.180000e-41 180.0
21 TraesCS7B01G109300 chr7B 94.068 118 7 0 870 987 125266869 125266752 2.180000e-41 180.0
22 TraesCS7B01G109300 chr7B 94.068 118 7 0 870 987 125336630 125336513 2.180000e-41 180.0
23 TraesCS7B01G109300 chr7B 93.220 118 7 1 870 987 125302934 125302818 3.650000e-39 172.0
24 TraesCS7B01G109300 chr7B 96.296 81 3 0 1929 2009 125355040 125354960 1.720000e-27 134.0
25 TraesCS7B01G109300 chr7D 93.352 1083 56 5 870 1936 163251408 163250326 0.000000e+00 1587.0
26 TraesCS7B01G109300 chr7D 91.485 963 54 14 870 1815 163215746 163214795 0.000000e+00 1299.0
27 TraesCS7B01G109300 chr7D 88.889 846 73 13 1931 2757 163250291 163249448 0.000000e+00 1022.0
28 TraesCS7B01G109300 chr7D 93.443 305 16 1 454 758 163216035 163215735 1.510000e-122 449.0
29 TraesCS7B01G109300 chr7D 90.805 261 17 4 209 462 163219230 163218970 2.630000e-90 342.0
30 TraesCS7B01G109300 chr7D 82.212 416 27 19 367 758 163251789 163251397 5.730000e-82 315.0
31 TraesCS7B01G109300 chrUn 100.000 850 0 0 1 850 332928741 332927892 0.000000e+00 1570.0
32 TraesCS7B01G109300 chrUn 93.782 193 12 0 2 194 382411282 382411474 9.660000e-75 291.0
33 TraesCS7B01G109300 chr7A 90.010 971 65 15 870 1815 164182267 164181304 0.000000e+00 1227.0
34 TraesCS7B01G109300 chr7A 88.794 937 71 19 869 1781 164394176 164393250 0.000000e+00 1118.0
35 TraesCS7B01G109300 chr7A 86.076 395 26 14 212 593 164394672 164394294 5.530000e-107 398.0
36 TraesCS7B01G109300 chr7A 85.366 287 28 11 452 734 164182551 164182275 4.490000e-73 285.0
37 TraesCS7B01G109300 chr7A 82.011 189 23 6 876 1053 163991251 163991063 1.710000e-32 150.0
38 TraesCS7B01G109300 chr5B 95.897 195 8 0 1 195 262529565 262529759 1.590000e-82 316.0
39 TraesCS7B01G109300 chr5B 95.361 194 8 1 2 194 262709474 262709667 9.590000e-80 307.0
40 TraesCS7B01G109300 chr5B 93.814 194 12 0 1 194 638355521 638355328 2.690000e-75 292.0
41 TraesCS7B01G109300 chr6B 95.763 118 3 2 757 872 717855872 717855755 3.620000e-44 189.0
42 TraesCS7B01G109300 chr2B 95.763 118 3 2 757 872 199167238 199167121 3.620000e-44 189.0
43 TraesCS7B01G109300 chr2B 93.651 126 5 3 749 872 528830257 528830381 4.690000e-43 185.0
44 TraesCS7B01G109300 chr6D 92.424 132 7 3 744 872 292783836 292783967 4.690000e-43 185.0
45 TraesCS7B01G109300 chr3B 94.262 122 5 2 753 872 530993860 530993981 4.690000e-43 185.0
46 TraesCS7B01G109300 chr2D 94.737 38 1 1 2357 2394 617723967 617723931 1.070000e-04 58.4


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 TraesCS7B01G109300 chr7B 125242492 125245248 2756 True 5092.000000 5092 100.0000 1 2757 1 chr7B.!!$R3 2756
1 TraesCS7B01G109300 chr7B 125278857 125281303 2446 True 2237.000000 2904 99.8425 1 2757 2 chr7B.!!$R9 2756
2 TraesCS7B01G109300 chr7B 125311670 125315184 3514 True 2223.000000 2876 99.6850 1 2757 2 chr7B.!!$R11 2756
3 TraesCS7B01G109300 chr7B 125219704 125221412 1708 True 1516.000000 2662 96.7990 1 2757 2 chr7B.!!$R6 2756
4 TraesCS7B01G109300 chr7B 125362412 125363369 957 True 1282.000000 1282 91.1340 869 1815 1 chr7B.!!$R4 946
5 TraesCS7B01G109300 chr7B 125191093 125192027 934 True 913.000000 913 84.5340 876 1805 1 chr7B.!!$R1 929
6 TraesCS7B01G109300 chr7B 125354220 125356859 2639 True 751.000000 1480 90.9735 275 2732 4 chr7B.!!$R13 2457
7 TraesCS7B01G109300 chr7B 125336513 125337179 666 True 424.500000 669 91.4110 206 987 2 chr7B.!!$R12 781
8 TraesCS7B01G109300 chr7B 125230576 125231242 666 True 422.000000 664 91.3245 206 987 2 chr7B.!!$R7 781
9 TraesCS7B01G109300 chr7B 125302818 125303483 665 True 415.000000 658 90.8140 206 987 2 chr7B.!!$R10 781
10 TraesCS7B01G109300 chr7B 125266752 125267418 666 True 413.500000 647 91.0650 206 987 2 chr7B.!!$R8 781
11 TraesCS7B01G109300 chr7D 163249448 163251789 2341 True 974.666667 1587 88.1510 367 2757 3 chr7D.!!$R2 2390
12 TraesCS7B01G109300 chr7D 163214795 163219230 4435 True 696.666667 1299 91.9110 209 1815 3 chr7D.!!$R1 1606
13 TraesCS7B01G109300 chrUn 332927892 332928741 849 True 1570.000000 1570 100.0000 1 850 1 chrUn.!!$R1 849
14 TraesCS7B01G109300 chr7A 164393250 164394672 1422 True 758.000000 1118 87.4350 212 1781 2 chr7A.!!$R3 1569
15 TraesCS7B01G109300 chr7A 164181304 164182551 1247 True 756.000000 1227 87.6880 452 1815 2 chr7A.!!$R2 1363

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
850 3852 1.040646 CCGGCCTCTGCATAACTAGA 58.959 55.0 0.0 0.0 40.13 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2665 6532 6.64377 TGAGACAGTCGTAAACAAAATAGGTC 59.356 38.462 0.0 0.0 0.0 3.85 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
850 3852 1.040646 CCGGCCTCTGCATAACTAGA 58.959 55.000 0.00 0.0 40.13 2.43
851 3853 1.620819 CCGGCCTCTGCATAACTAGAT 59.379 52.381 0.00 0.0 40.13 1.98
852 3854 2.826128 CCGGCCTCTGCATAACTAGATA 59.174 50.000 0.00 0.0 40.13 1.98
853 3855 3.367498 CCGGCCTCTGCATAACTAGATAC 60.367 52.174 0.00 0.0 40.13 2.24
854 3856 3.255888 CGGCCTCTGCATAACTAGATACA 59.744 47.826 0.00 0.0 40.13 2.29
855 3857 4.561105 GGCCTCTGCATAACTAGATACAC 58.439 47.826 0.00 0.0 40.13 2.90
856 3858 4.039245 GGCCTCTGCATAACTAGATACACA 59.961 45.833 0.00 0.0 40.13 3.72
857 3859 4.985409 GCCTCTGCATAACTAGATACACAC 59.015 45.833 0.00 0.0 37.47 3.82
858 3860 5.451937 GCCTCTGCATAACTAGATACACACA 60.452 44.000 0.00 0.0 37.47 3.72
859 3861 6.212235 CCTCTGCATAACTAGATACACACAG 58.788 44.000 0.00 0.0 0.00 3.66
860 3862 5.592054 TCTGCATAACTAGATACACACAGC 58.408 41.667 0.00 0.0 0.00 4.40
861 3863 4.693283 TGCATAACTAGATACACACAGCC 58.307 43.478 0.00 0.0 0.00 4.85
862 3864 4.161377 TGCATAACTAGATACACACAGCCA 59.839 41.667 0.00 0.0 0.00 4.75
863 3865 5.116180 GCATAACTAGATACACACAGCCAA 58.884 41.667 0.00 0.0 0.00 4.52
864 3866 5.584649 GCATAACTAGATACACACAGCCAAA 59.415 40.000 0.00 0.0 0.00 3.28
865 3867 6.093495 GCATAACTAGATACACACAGCCAAAA 59.907 38.462 0.00 0.0 0.00 2.44
866 3868 7.201732 GCATAACTAGATACACACAGCCAAAAT 60.202 37.037 0.00 0.0 0.00 1.82
867 3869 6.743575 AACTAGATACACACAGCCAAAATC 57.256 37.500 0.00 0.0 0.00 2.17
943 3962 1.541889 CCCACCCATCTCATCATCACG 60.542 57.143 0.00 0.0 0.00 4.35
987 4281 1.702886 CAGAAGCCACACACGTAGAG 58.297 55.000 0.00 0.0 0.00 2.43
999 4294 6.965500 CCACACACGTAGAGTATAAAGTACAG 59.035 42.308 0.00 0.0 0.00 2.74
1168 4465 2.930019 TGCTGCAGTGCCCCTACT 60.930 61.111 16.64 0.0 0.00 2.57
2665 6532 2.256174 CCAAGATCATTTGCACGCTTG 58.744 47.619 0.00 0.0 34.18 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
850 3852 9.273016 GTATATACTGATTTTGGCTGTGTGTAT 57.727 33.333 5.58 0.0 0.00 2.29
851 3853 8.482943 AGTATATACTGATTTTGGCTGTGTGTA 58.517 33.333 14.71 0.0 34.72 2.90
852 3854 7.338710 AGTATATACTGATTTTGGCTGTGTGT 58.661 34.615 14.71 0.0 34.72 3.72
853 3855 7.792374 AGTATATACTGATTTTGGCTGTGTG 57.208 36.000 14.71 0.0 34.72 3.82
881 3883 5.250774 TGGTTTATATAGGCTCTGGGGATTC 59.749 44.000 0.00 0.0 0.00 2.52
943 3962 2.478831 GCCTTGGATTGTCTCTCGATC 58.521 52.381 0.00 0.0 36.48 3.69
987 4281 5.462405 CGAGGAGCCATCTGTACTTTATAC 58.538 45.833 0.00 0.0 0.00 1.47
999 4294 3.839642 GAGAGCGCGAGGAGCCATC 62.840 68.421 12.10 0.0 44.76 3.51
1159 4456 2.831742 CGCCTCGTAGTAGGGGCA 60.832 66.667 17.13 0.0 44.27 5.36
2665 6532 6.643770 TGAGACAGTCGTAAACAAAATAGGTC 59.356 38.462 0.00 0.0 0.00 3.85


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

AutoCloner maintained by Alex Coulton.