Multiple sequence alignment - TraesCS5B01G323500

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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 TraesCS5B01G323500 chr5B 100.000 4714 0 0 1 4714 508025289 508020576 0.000000e+00 8706.0
1 TraesCS5B01G323500 chr5B 98.236 3459 38 3 442 3878 21709922 21713379 0.000000e+00 6028.0
2 TraesCS5B01G323500 chr5B 98.420 443 6 1 3879 4320 21713412 21713854 0.000000e+00 778.0
3 TraesCS5B01G323500 chr5B 97.487 398 9 1 4317 4714 21722641 21723037 0.000000e+00 678.0
4 TraesCS5B01G323500 chr5B 91.286 241 10 4 4485 4714 596389898 596390138 7.610000e-83 318.0
5 TraesCS5B01G323500 chr5B 93.659 205 11 1 1 205 21708233 21708435 5.930000e-79 305.0
6 TraesCS5B01G323500 chr5A 98.638 4184 52 4 535 4714 633009048 633004866 0.000000e+00 7406.0
7 TraesCS5B01G323500 chr5A 96.589 2140 66 4 1740 3878 437179550 437177417 0.000000e+00 3541.0
8 TraesCS5B01G323500 chr5A 92.391 1577 45 17 181 1707 437181099 437179548 0.000000e+00 2178.0
9 TraesCS5B01G323500 chr5A 94.567 681 32 5 4033 4711 437177099 437176422 0.000000e+00 1048.0
10 TraesCS5B01G323500 chr5A 95.335 493 18 5 1 492 633010383 633009895 0.000000e+00 778.0
11 TraesCS5B01G323500 chr5A 93.488 215 12 2 1 215 633012365 633012153 7.610000e-83 318.0
12 TraesCS5B01G323500 chr5A 94.472 199 10 1 3879 4076 437177316 437177118 5.930000e-79 305.0
13 TraesCS5B01G323500 chr1A 96.931 2965 84 5 915 3878 539297442 539294484 0.000000e+00 4964.0
14 TraesCS5B01G323500 chr1A 94.745 685 31 5 4033 4714 539294166 539293484 0.000000e+00 1061.0
15 TraesCS5B01G323500 chr1A 89.159 452 19 9 181 610 539311749 539311306 1.930000e-148 536.0
16 TraesCS5B01G323500 chr1A 95.608 296 6 1 591 879 539297737 539297442 7.140000e-128 468.0
17 TraesCS5B01G323500 chr1A 94.472 199 10 1 3879 4076 539294383 539294185 5.930000e-79 305.0
18 TraesCS5B01G323500 chr1A 94.175 103 4 2 3777 3878 539294517 539294416 6.320000e-34 156.0
19 TraesCS5B01G323500 chr4A 95.155 2766 76 18 181 2894 173641297 173644056 0.000000e+00 4313.0
20 TraesCS5B01G323500 chr4A 88.889 1917 194 12 1973 3878 222156107 222154199 0.000000e+00 2342.0
21 TraesCS5B01G323500 chr4A 96.226 954 33 3 2932 3884 173644055 173645006 0.000000e+00 1559.0
22 TraesCS5B01G323500 chr4A 89.591 855 86 3 683 1536 222384367 222383515 0.000000e+00 1083.0
23 TraesCS5B01G323500 chr4A 86.215 856 85 17 3879 4713 222154166 222153323 0.000000e+00 896.0
24 TraesCS5B01G323500 chr4A 96.019 427 16 1 4033 4459 173645319 173645744 0.000000e+00 693.0
25 TraesCS5B01G323500 chr4A 90.591 457 32 3 1532 1977 222218842 222218386 3.140000e-166 595.0
26 TraesCS5B01G323500 chr4A 94.975 199 9 1 3879 4076 173645102 173645300 1.270000e-80 311.0
27 TraesCS5B01G323500 chr4A 93.431 137 7 2 4577 4711 173646136 173646272 8.000000e-48 202.0
28 TraesCS5B01G323500 chr2A 94.440 2500 113 12 1401 3878 775743251 775740756 0.000000e+00 3823.0
29 TraesCS5B01G323500 chr2A 94.922 1477 71 3 2400 3875 775674065 775675538 0.000000e+00 2309.0
30 TraesCS5B01G323500 chr2A 95.224 1026 48 1 1400 2425 775673024 775674048 0.000000e+00 1622.0
31 TraesCS5B01G323500 chr2A 95.153 619 28 2 3258 3875 775675803 775676420 0.000000e+00 976.0
32 TraesCS5B01G323500 chr2A 87.805 205 22 2 4 205 775745714 775745510 2.190000e-58 237.0
33 TraesCS5B01G323500 chr2A 86.036 222 25 5 1 218 775670624 775670843 2.840000e-57 233.0
34 TraesCS5B01G323500 chr2A 84.426 244 24 12 373 608 775743523 775743286 1.320000e-55 228.0
35 TraesCS5B01G323500 chr2A 100.000 83 0 0 3959 4041 775675544 775675626 2.270000e-33 154.0
36 TraesCS5B01G323500 chr2A 100.000 83 0 0 3959 4041 775676426 775676508 2.270000e-33 154.0
37 TraesCS5B01G323500 chr2D 85.771 506 45 11 3879 4366 11190408 11190904 1.170000e-140 510.0
38 TraesCS5B01G323500 chr2D 85.098 255 27 8 4468 4713 11190918 11191170 2.820000e-62 250.0
39 TraesCS5B01G323500 chr2D 95.146 103 3 2 3879 3980 565925737 565925838 1.360000e-35 161.0
40 TraesCS5B01G323500 chr2D 97.727 44 1 0 4306 4349 565925883 565925840 5.060000e-10 76.8
41 TraesCS5B01G323500 chr1B 90.934 364 32 1 1927 2290 592968926 592968564 5.480000e-134 488.0
42 TraesCS5B01G323500 chr6D 73.680 1193 265 34 2584 3756 434795163 434796326 7.300000e-113 418.0
43 TraesCS5B01G323500 chr6A 90.226 266 20 3 4227 4490 85048606 85048867 4.520000e-90 342.0
44 TraesCS5B01G323500 chr6A 91.216 148 11 2 4564 4710 85049235 85049381 2.880000e-47 200.0
45 TraesCS5B01G323500 chr7A 87.805 205 20 4 4 204 709851607 709851404 7.890000e-58 235.0
46 TraesCS5B01G323500 chr6B 82.209 163 28 1 1 163 161243137 161243298 6.360000e-29 139.0


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 TraesCS5B01G323500 chr5B 508020576 508025289 4713 True 8706.000000 8706 100.000000 1 4714 1 chr5B.!!$R1 4713
1 TraesCS5B01G323500 chr5B 21708233 21713854 5621 False 2370.333333 6028 96.771667 1 4320 3 chr5B.!!$F3 4319
2 TraesCS5B01G323500 chr5A 633004866 633012365 7499 True 2834.000000 7406 95.820333 1 4714 3 chr5A.!!$R2 4713
3 TraesCS5B01G323500 chr5A 437176422 437181099 4677 True 1768.000000 3541 94.504750 181 4711 4 chr5A.!!$R1 4530
4 TraesCS5B01G323500 chr1A 539293484 539297737 4253 True 1390.800000 4964 95.186200 591 4714 5 chr1A.!!$R2 4123
5 TraesCS5B01G323500 chr4A 222153323 222156107 2784 True 1619.000000 2342 87.552000 1973 4713 2 chr4A.!!$R3 2740
6 TraesCS5B01G323500 chr4A 173641297 173646272 4975 False 1415.600000 4313 95.161200 181 4711 5 chr4A.!!$F1 4530
7 TraesCS5B01G323500 chr4A 222383515 222384367 852 True 1083.000000 1083 89.591000 683 1536 1 chr4A.!!$R2 853
8 TraesCS5B01G323500 chr2A 775740756 775745714 4958 True 1429.333333 3823 88.890333 4 3878 3 chr2A.!!$R1 3874
9 TraesCS5B01G323500 chr2A 775670624 775676508 5884 False 908.000000 2309 95.222500 1 4041 6 chr2A.!!$F1 4040
10 TraesCS5B01G323500 chr2D 11190408 11191170 762 False 380.000000 510 85.434500 3879 4713 2 chr2D.!!$F2 834
11 TraesCS5B01G323500 chr6D 434795163 434796326 1163 False 418.000000 418 73.680000 2584 3756 1 chr6D.!!$F1 1172
12 TraesCS5B01G323500 chr6A 85048606 85049381 775 False 271.000000 342 90.721000 4227 4710 2 chr6A.!!$F1 483

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
62 63 0.670239 GCCATTGTTTCGGGGCTTTG 60.670 55.000 0.00 0.0 43.09 2.77 F
1042 6380 1.068055 ACGAGTACGCGAAGGAAATGT 60.068 47.619 25.90 0.0 43.96 2.71 F
1262 6600 9.365906 TGCCATAAAATCATATAACTGGAATGT 57.634 29.630 0.00 0.0 0.00 2.71 F
2132 7472 2.490217 CGCGGACGAGAAGATGGT 59.510 61.111 0.00 0.0 43.93 3.55 F
2807 8190 1.939934 GAATGGCGCTGTAAGTATGCA 59.060 47.619 7.64 0.0 35.30 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 6396 3.175240 CTCCACTTCGCGCGTCTG 61.175 66.667 30.98 21.21 0.00 3.51 R
2132 7472 1.002624 GGACCCGTGAAGGATGCAA 60.003 57.895 0.00 0.00 45.00 4.08 R
2327 7668 2.502142 TTCAGCACTAGACCCGACTA 57.498 50.000 0.00 0.00 0.00 2.59 R
3481 8872 1.128692 CCGTCTTTTTGTCTCGGCATC 59.871 52.381 0.00 0.00 35.01 3.91 R
4554 11023 3.220110 TGTAACAGAGGAGTTCGACTGT 58.780 45.455 0.00 0.00 43.92 3.55 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
62 63 0.670239 GCCATTGTTTCGGGGCTTTG 60.670 55.000 0.00 0.0 43.09 2.77
79 80 3.372822 GCTTTGTCATCGGGAAAATCGTA 59.627 43.478 0.00 0.0 0.00 3.43
751 6053 3.695830 ACGGAGAAGTTTATTGCTCCA 57.304 42.857 0.00 0.0 45.65 3.86
1042 6380 1.068055 ACGAGTACGCGAAGGAAATGT 60.068 47.619 25.90 0.0 43.96 2.71
1262 6600 9.365906 TGCCATAAAATCATATAACTGGAATGT 57.634 29.630 0.00 0.0 0.00 2.71
2132 7472 2.490217 CGCGGACGAGAAGATGGT 59.510 61.111 0.00 0.0 43.93 3.55
2327 7668 5.539955 ACCCACAGAAAGAAAATGCAGTATT 59.460 36.000 0.00 0.0 0.00 1.89
2396 7737 3.314553 CGACAACAATCTGTAAGGACGT 58.685 45.455 0.00 0.0 0.00 4.34
2681 8064 3.887716 AGGGTTTATATCGACACGCTAGT 59.112 43.478 0.00 0.0 31.15 2.57
2807 8190 1.939934 GAATGGCGCTGTAAGTATGCA 59.060 47.619 7.64 0.0 35.30 3.96
3297 8687 4.183539 GAAGATTGCTTCGATGGTAACG 57.816 45.455 0.00 0.0 40.96 3.18
3481 8872 3.536956 TGGCCAATAAAGGAGTACGAG 57.463 47.619 0.61 0.0 0.00 4.18
3765 9159 2.912956 TGGAGAAGGAATAAGTGCCAGT 59.087 45.455 0.00 0.0 0.00 4.00
3931 10298 8.725606 ATTATTATGGCTATTTGGTGATTGGT 57.274 30.769 0.00 0.0 0.00 3.67
4315 10775 2.480845 GACTAAACCTCACAAGTGCGT 58.519 47.619 0.00 0.0 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.353030 GCGACGTTGGTTTGGTGC 60.353 61.111 4.64 0.00 0.00 5.01
62 63 5.789710 TTTTCTACGATTTTCCCGATGAC 57.210 39.130 0.00 0.00 0.00 3.06
95 96 6.290294 AGCCAGTTTGCATATTTTTCTGAT 57.710 33.333 0.00 0.00 0.00 2.90
249 3119 2.360165 CCATTCAGTAATTCTGCTGGCC 59.640 50.000 0.00 0.00 43.32 5.36
254 3127 2.360165 CTGGCCCATTCAGTAATTCTGC 59.640 50.000 0.00 0.00 43.32 4.26
635 5930 5.067283 GGCAAGAAACTTCACTTTACCTTCA 59.933 40.000 0.00 0.00 0.00 3.02
751 6053 1.672356 GCGTGCACCACTTCTCCAT 60.672 57.895 12.15 0.00 31.34 3.41
1042 6380 3.250040 GCGTCTGCAAACTTAGAAGGAAA 59.750 43.478 0.00 0.00 42.15 3.13
1058 6396 3.175240 CTCCACTTCGCGCGTCTG 61.175 66.667 30.98 21.21 0.00 3.51
2132 7472 1.002624 GGACCCGTGAAGGATGCAA 60.003 57.895 0.00 0.00 45.00 4.08
2327 7668 2.502142 TTCAGCACTAGACCCGACTA 57.498 50.000 0.00 0.00 0.00 2.59
2396 7737 5.369404 TGCTCCTCAGTCCCATTATTATTCA 59.631 40.000 0.00 0.00 0.00 2.57
2681 8064 3.513680 TTAAATGCTTCGGCGAGTCTA 57.486 42.857 10.46 0.00 45.37 2.59
3114 8497 8.679100 TGTACAAAAAGTTTGCTATGTACTGTT 58.321 29.630 21.80 0.00 38.63 3.16
3297 8687 9.619316 TGTATTCATGTTATGCAAAGTTGTTAC 57.381 29.630 0.00 0.00 0.00 2.50
3481 8872 1.128692 CCGTCTTTTTGTCTCGGCATC 59.871 52.381 0.00 0.00 35.01 3.91
4554 11023 3.220110 TGTAACAGAGGAGTTCGACTGT 58.780 45.455 0.00 0.00 43.92 3.55


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

AutoCloner maintained by Alex Coulton.