Multiple sequence alignment - TraesCS5A01G379600

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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 TraesCS5A01G379600 chr5A 100.000 2943 0 0 96 3038 577267720 577270662 0.000000e+00 5435.0
1 TraesCS5A01G379600 chr5A 99.798 2478 5 0 561 3038 577079785 577077308 0.000000e+00 4549.0
2 TraesCS5A01G379600 chr5A 99.657 1456 5 0 96 1551 576948615 576950070 0.000000e+00 2662.0
3 TraesCS5A01G379600 chr5A 99.694 1308 4 0 1731 3038 576950267 576951574 0.000000e+00 2394.0
4 TraesCS5A01G379600 chr5A 98.821 1103 13 0 985 2087 577432377 577433479 0.000000e+00 1965.0
5 TraesCS5A01G379600 chr5A 92.857 1176 45 16 713 1880 576596157 576597301 0.000000e+00 1670.0
6 TraesCS5A01G379600 chr5A 98.844 865 10 0 96 960 577422719 577423583 0.000000e+00 1543.0
7 TraesCS5A01G379600 chr5A 93.084 535 37 0 2504 3038 576612469 576613003 0.000000e+00 784.0
8 TraesCS5A01G379600 chr5A 89.194 546 45 9 2084 2624 577433591 577434127 0.000000e+00 669.0
9 TraesCS5A01G379600 chr5A 94.839 310 16 0 2623 2932 577434050 577434359 4.550000e-133 484.0
10 TraesCS5A01G379600 chr5A 90.361 332 26 4 2192 2519 576611266 576611595 6.020000e-117 431.0
11 TraesCS5A01G379600 chr5A 78.615 650 117 17 1042 1683 687655407 687656042 7.840000e-111 411.0
12 TraesCS5A01G379600 chr5A 95.312 256 7 1 1959 2209 576610966 576611221 4.720000e-108 401.0
13 TraesCS5A01G379600 chr5A 96.330 109 4 0 1878 1986 576601431 576601539 2.410000e-41 180.0
14 TraesCS5A01G379600 chr5A 94.495 109 6 0 1878 1986 576601917 576602025 5.210000e-38 169.0
15 TraesCS5A01G379600 chr5A 95.556 90 3 1 1878 1967 576602283 576602371 3.160000e-30 143.0
16 TraesCS5A01G379600 chr5A 95.062 81 4 0 2619 2699 576612508 576612588 8.840000e-26 128.0
17 TraesCS5A01G379600 chr5A 100.000 59 0 0 1 59 577267625 577267683 3.200000e-20 110.0
18 TraesCS5A01G379600 chr5A 92.105 76 6 0 2549 2624 576612590 576612665 1.150000e-19 108.0
19 TraesCS5A01G379600 chr5A 98.305 59 1 0 1 59 576948492 576948550 1.490000e-18 104.0
20 TraesCS5A01G379600 chr5A 98.305 59 1 0 1 59 577080428 577080370 1.490000e-18 104.0
21 TraesCS5A01G379600 chr5D 94.514 1112 55 5 1044 2151 458643562 458644671 0.000000e+00 1711.0
22 TraesCS5A01G379600 chr5D 85.176 425 54 1 2623 3038 458645298 458645722 7.780000e-116 427.0
23 TraesCS5A01G379600 chr5D 93.846 130 8 0 787 916 458643317 458643446 2.390000e-46 196.0
24 TraesCS5A01G379600 chr5D 83.616 177 27 2 2448 2622 458645197 458645373 6.740000e-37 165.0
25 TraesCS5A01G379600 chr5B 94.660 1030 55 0 1035 2064 562118774 562119803 0.000000e+00 1598.0
26 TraesCS5A01G379600 chr5B 88.129 278 24 6 643 916 562118422 562118694 3.780000e-84 322.0
27 TraesCS5A01G379600 chr5B 86.473 207 23 2 685 888 562073743 562073947 3.940000e-54 222.0
28 TraesCS5A01G379600 chr5B 83.696 184 17 5 2063 2239 562119867 562120044 8.720000e-36 161.0
29 TraesCS5A01G379600 chr5B 84.516 155 24 0 750 904 658559336 658559490 1.460000e-33 154.0
30 TraesCS5A01G379600 chr1D 82.974 975 145 17 1058 2017 442910545 442909577 0.000000e+00 861.0
31 TraesCS5A01G379600 chr2B 77.586 986 178 34 1042 2007 18839579 18840541 9.510000e-155 556.0
32 TraesCS5A01G379600 chr2B 79.128 436 82 9 105 535 385156532 385156101 2.960000e-75 292.0
33 TraesCS5A01G379600 chr7D 74.118 765 166 25 1175 1915 24326750 24327506 1.380000e-73 287.0
34 TraesCS5A01G379600 chr7D 73.800 771 155 35 1175 1915 24118490 24117737 8.350000e-66 261.0
35 TraesCS5A01G379600 chr7D 83.660 153 25 0 741 893 24021206 24021054 8.780000e-31 145.0
36 TraesCS5A01G379600 chr6A 77.055 523 100 16 97 608 579812894 579813407 1.780000e-72 283.0
37 TraesCS5A01G379600 chr6B 77.966 472 89 12 142 609 654776259 654776719 6.410000e-72 281.0
38 TraesCS5A01G379600 chr6D 77.119 472 83 18 151 608 311902242 311902702 1.810000e-62 250.0
39 TraesCS5A01G379600 chrUn 79.143 350 65 7 264 609 56506639 56506984 5.060000e-58 235.0
40 TraesCS5A01G379600 chrUn 79.143 350 65 7 264 609 322674779 322675124 5.060000e-58 235.0
41 TraesCS5A01G379600 chr4B 77.202 386 79 9 155 535 489640602 489640983 1.830000e-52 217.0
42 TraesCS5A01G379600 chr4A 75.260 481 94 20 1175 1642 707487893 707488361 3.970000e-49 206.0
43 TraesCS5A01G379600 chr4A 74.298 463 96 18 1175 1625 707305190 707304739 1.120000e-39 174.0
44 TraesCS5A01G379600 chr4A 81.818 154 26 2 741 893 707674839 707674991 8.840000e-26 128.0
45 TraesCS5A01G379600 chr2D 94.444 36 2 0 2286 2321 167011876 167011841 4.230000e-04 56.5


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 TraesCS5A01G379600 chr5A 577267625 577270662 3037 False 2772.500000 5435 100.000000 1 3038 2 chr5A.!!$F7 3037
1 TraesCS5A01G379600 chr5A 577077308 577080428 3120 True 2326.500000 4549 99.051500 1 3038 2 chr5A.!!$R1 3037
2 TraesCS5A01G379600 chr5A 576948492 576951574 3082 False 1720.000000 2662 99.218667 1 3038 3 chr5A.!!$F6 3037
3 TraesCS5A01G379600 chr5A 576596157 576597301 1144 False 1670.000000 1670 92.857000 713 1880 1 chr5A.!!$F1 1167
4 TraesCS5A01G379600 chr5A 577422719 577423583 864 False 1543.000000 1543 98.844000 96 960 1 chr5A.!!$F2 864
5 TraesCS5A01G379600 chr5A 577432377 577434359 1982 False 1039.333333 1965 94.284667 985 2932 3 chr5A.!!$F8 1947
6 TraesCS5A01G379600 chr5A 687655407 687656042 635 False 411.000000 411 78.615000 1042 1683 1 chr5A.!!$F3 641
7 TraesCS5A01G379600 chr5A 576610966 576613003 2037 False 370.400000 784 93.184800 1959 3038 5 chr5A.!!$F5 1079
8 TraesCS5A01G379600 chr5D 458643317 458645722 2405 False 624.750000 1711 89.288000 787 3038 4 chr5D.!!$F1 2251
9 TraesCS5A01G379600 chr5B 562118422 562120044 1622 False 693.666667 1598 88.828333 643 2239 3 chr5B.!!$F3 1596
10 TraesCS5A01G379600 chr1D 442909577 442910545 968 True 861.000000 861 82.974000 1058 2017 1 chr1D.!!$R1 959
11 TraesCS5A01G379600 chr2B 18839579 18840541 962 False 556.000000 556 77.586000 1042 2007 1 chr2B.!!$F1 965
12 TraesCS5A01G379600 chr7D 24326750 24327506 756 False 287.000000 287 74.118000 1175 1915 1 chr7D.!!$F1 740
13 TraesCS5A01G379600 chr7D 24117737 24118490 753 True 261.000000 261 73.800000 1175 1915 1 chr7D.!!$R2 740
14 TraesCS5A01G379600 chr6A 579812894 579813407 513 False 283.000000 283 77.055000 97 608 1 chr6A.!!$F1 511

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
169 198 1.364171 GACGCCGTCCATAGCAGAT 59.636 57.895 5.81 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 2968 8.097662 ACTTGTAAAACTCTATTCTCTCCTTGG 58.902 37.037 0.0 0.0 0.0 3.61 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
27 28 1.598701 GCCCTGCTTTCGCATCCTTT 61.599 55.000 0.00 0.0 46.74 3.11
169 198 1.364171 GACGCCGTCCATAGCAGAT 59.636 57.895 5.81 0.0 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.795698 TAATGACGACGTCGGACGAA 59.204 50.000 37.89 19.66 46.05 3.85
107 136 0.662085 CTACGGACGAAGCCTAGGTC 59.338 60.000 11.31 2.66 0.00 3.85
559 591 9.775854 ATTAATCAAATTGACCAACATGTGAAA 57.224 25.926 0.00 0.00 0.00 2.69
2291 2968 8.097662 ACTTGTAAAACTCTATTCTCTCCTTGG 58.902 37.037 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.