Multiple sequence alignment - TraesCS4B01G124100

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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 TraesCS4B01G124100 chr4B 100.000 6744 0 0 1 6744 148999549 148992806 0.000000e+00 12454.0
1 TraesCS4B01G124100 chr4B 99.186 6754 44 3 1 6744 149035773 149029021 0.000000e+00 12157.0
2 TraesCS4B01G124100 chr4B 92.990 1555 79 14 350 1882 421859151 421857605 0.000000e+00 2241.0
3 TraesCS4B01G124100 chr4B 91.292 1355 84 17 5408 6743 414452698 414451359 0.000000e+00 1818.0
4 TraesCS4B01G124100 chr4B 94.374 551 29 2 2222 2770 414453229 414452679 0.000000e+00 845.0
5 TraesCS4B01G124100 chr4B 96.543 376 11 2 1 374 421859700 421859325 7.430000e-174 621.0
6 TraesCS4B01G124100 chr4B 98.148 54 1 0 2768 2821 595454407 595454354 2.000000e-15 95.3
7 TraesCS4B01G124100 chr7A 96.656 2602 80 4 2816 5412 109349368 109351967 0.000000e+00 4316.0
8 TraesCS4B01G124100 chr7A 94.899 1137 44 2 1 1123 629779786 629778650 0.000000e+00 1766.0
9 TraesCS4B01G124100 chr7A 93.425 943 48 8 1841 2770 629777747 629776806 0.000000e+00 1386.0
10 TraesCS4B01G124100 chr7A 89.393 1103 92 13 5408 6495 221746123 221745031 0.000000e+00 1365.0
11 TraesCS4B01G124100 chr7A 95.186 727 35 0 1120 1846 629778593 629777867 0.000000e+00 1149.0
12 TraesCS4B01G124100 chr7A 93.896 557 30 4 2217 2770 308454848 308455403 0.000000e+00 837.0
13 TraesCS4B01G124100 chr7A 92.043 553 29 6 6200 6743 629775758 629775212 0.000000e+00 763.0
14 TraesCS4B01G124100 chr2D 96.658 2603 76 5 2816 5412 106330110 106332707 0.000000e+00 4314.0
15 TraesCS4B01G124100 chr2D 96.614 2599 80 4 2816 5408 136424217 136426813 0.000000e+00 4305.0
16 TraesCS4B01G124100 chr6D 94.643 2800 115 11 1 2770 16117063 16119857 0.000000e+00 4307.0
17 TraesCS4B01G124100 chr6D 92.837 726 34 7 6030 6743 16120361 16121080 0.000000e+00 1037.0
18 TraesCS4B01G124100 chr3A 96.651 2598 75 6 2816 5405 217719924 217717331 0.000000e+00 4305.0
19 TraesCS4B01G124100 chr3A 94.239 2621 123 10 1 2597 296899495 296902111 0.000000e+00 3978.0
20 TraesCS4B01G124100 chr2A 96.682 2592 76 4 2816 5401 101857446 101854859 0.000000e+00 4301.0
21 TraesCS4B01G124100 chr2A 96.682 2592 76 4 2816 5401 421216692 421219279 0.000000e+00 4301.0
22 TraesCS4B01G124100 chr2A 96.364 55 2 0 2768 2822 388735607 388735553 2.590000e-14 91.6
23 TraesCS4B01G124100 chr6A 96.614 2599 74 6 2816 5408 58017844 58015254 0.000000e+00 4300.0
24 TraesCS4B01G124100 chr6A 94.614 557 24 5 2217 2770 388059022 388059575 0.000000e+00 857.0
25 TraesCS4B01G124100 chr4A 96.398 2610 86 4 2816 5419 438242031 438239424 0.000000e+00 4292.0
26 TraesCS4B01G124100 chr1A 94.394 2622 118 11 1 2597 176409720 176412337 0.000000e+00 4000.0
27 TraesCS4B01G124100 chr1B 93.296 2133 123 11 652 2770 538915712 538917838 0.000000e+00 3129.0
28 TraesCS4B01G124100 chr1B 92.280 2189 133 15 609 2770 117567862 117570041 0.000000e+00 3073.0
29 TraesCS4B01G124100 chr1B 91.654 1354 69 19 5408 6743 192689910 192688583 0.000000e+00 1834.0
30 TraesCS4B01G124100 chr1B 94.043 554 27 5 2222 2770 192690443 192689891 0.000000e+00 835.0
31 TraesCS4B01G124100 chrUn 92.511 2190 134 13 609 2770 286669929 286672116 0.000000e+00 3109.0
32 TraesCS4B01G124100 chrUn 92.466 2190 135 13 609 2770 286677286 286675099 0.000000e+00 3103.0
33 TraesCS4B01G124100 chrUn 91.159 984 73 3 609 1579 316389957 316390939 0.000000e+00 1323.0
34 TraesCS4B01G124100 chrUn 96.296 54 2 0 2768 2821 27369187 27369134 9.320000e-14 89.8
35 TraesCS4B01G124100 chrUn 96.296 54 2 0 2768 2821 401416105 401416052 9.320000e-14 89.8
36 TraesCS4B01G124100 chrUn 96.296 54 2 0 2768 2821 402129564 402129617 9.320000e-14 89.8
37 TraesCS4B01G124100 chr5D 92.984 1354 66 17 5408 6741 249151062 249149718 0.000000e+00 1947.0
38 TraesCS4B01G124100 chr5D 86.283 226 14 9 386 595 65039254 65039030 5.260000e-56 230.0
39 TraesCS4B01G124100 chr5D 87.368 190 8 9 386 559 65007507 65007696 3.190000e-48 204.0
40 TraesCS4B01G124100 chr5D 96.364 55 2 0 2768 2822 147804880 147804826 2.590000e-14 91.6
41 TraesCS4B01G124100 chr2B 92.910 1354 64 17 5408 6744 220361805 220363143 0.000000e+00 1940.0
42 TraesCS4B01G124100 chr2B 91.061 1018 70 12 5741 6744 421412783 421411773 0.000000e+00 1356.0
43 TraesCS4B01G124100 chr2B 93.739 559 30 5 2217 2770 220361266 220361824 0.000000e+00 833.0
44 TraesCS4B01G124100 chr6B 92.183 1356 90 4 1 1342 328339253 328340606 0.000000e+00 1903.0
45 TraesCS4B01G124100 chr6B 92.030 1355 82 13 5408 6743 393761614 393762961 0.000000e+00 1881.0
46 TraesCS4B01G124100 chr3D 92.256 1330 68 20 5408 6717 256145129 256143815 0.000000e+00 1853.0
47 TraesCS4B01G124100 chr3D 95.281 551 23 3 2222 2770 256145659 256145110 0.000000e+00 870.0
48 TraesCS4B01G124100 chr3B 91.530 1216 77 12 5544 6741 277659002 277660209 0.000000e+00 1652.0
49 TraesCS4B01G124100 chr3B 94.973 915 29 7 1 901 286888041 286887130 0.000000e+00 1419.0
50 TraesCS4B01G124100 chr4D 96.296 54 2 0 2768 2821 12278726 12278673 9.320000e-14 89.8
51 TraesCS4B01G124100 chr4D 96.296 54 2 0 2768 2821 35299570 35299623 9.320000e-14 89.8


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 TraesCS4B01G124100 chr4B 148992806 148999549 6743 True 12454.0 12454 100.00000 1 6744 1 chr4B.!!$R1 6743
1 TraesCS4B01G124100 chr4B 149029021 149035773 6752 True 12157.0 12157 99.18600 1 6744 1 chr4B.!!$R2 6743
2 TraesCS4B01G124100 chr4B 421857605 421859700 2095 True 1431.0 2241 94.76650 1 1882 2 chr4B.!!$R5 1881
3 TraesCS4B01G124100 chr4B 414451359 414453229 1870 True 1331.5 1818 92.83300 2222 6743 2 chr4B.!!$R4 4521
4 TraesCS4B01G124100 chr7A 109349368 109351967 2599 False 4316.0 4316 96.65600 2816 5412 1 chr7A.!!$F1 2596
5 TraesCS4B01G124100 chr7A 221745031 221746123 1092 True 1365.0 1365 89.39300 5408 6495 1 chr7A.!!$R1 1087
6 TraesCS4B01G124100 chr7A 629775212 629779786 4574 True 1266.0 1766 93.88825 1 6743 4 chr7A.!!$R2 6742
7 TraesCS4B01G124100 chr7A 308454848 308455403 555 False 837.0 837 93.89600 2217 2770 1 chr7A.!!$F2 553
8 TraesCS4B01G124100 chr2D 106330110 106332707 2597 False 4314.0 4314 96.65800 2816 5412 1 chr2D.!!$F1 2596
9 TraesCS4B01G124100 chr2D 136424217 136426813 2596 False 4305.0 4305 96.61400 2816 5408 1 chr2D.!!$F2 2592
10 TraesCS4B01G124100 chr6D 16117063 16121080 4017 False 2672.0 4307 93.74000 1 6743 2 chr6D.!!$F1 6742
11 TraesCS4B01G124100 chr3A 217717331 217719924 2593 True 4305.0 4305 96.65100 2816 5405 1 chr3A.!!$R1 2589
12 TraesCS4B01G124100 chr3A 296899495 296902111 2616 False 3978.0 3978 94.23900 1 2597 1 chr3A.!!$F1 2596
13 TraesCS4B01G124100 chr2A 101854859 101857446 2587 True 4301.0 4301 96.68200 2816 5401 1 chr2A.!!$R1 2585
14 TraesCS4B01G124100 chr2A 421216692 421219279 2587 False 4301.0 4301 96.68200 2816 5401 1 chr2A.!!$F1 2585
15 TraesCS4B01G124100 chr6A 58015254 58017844 2590 True 4300.0 4300 96.61400 2816 5408 1 chr6A.!!$R1 2592
16 TraesCS4B01G124100 chr6A 388059022 388059575 553 False 857.0 857 94.61400 2217 2770 1 chr6A.!!$F1 553
17 TraesCS4B01G124100 chr4A 438239424 438242031 2607 True 4292.0 4292 96.39800 2816 5419 1 chr4A.!!$R1 2603
18 TraesCS4B01G124100 chr1A 176409720 176412337 2617 False 4000.0 4000 94.39400 1 2597 1 chr1A.!!$F1 2596
19 TraesCS4B01G124100 chr1B 538915712 538917838 2126 False 3129.0 3129 93.29600 652 2770 1 chr1B.!!$F2 2118
20 TraesCS4B01G124100 chr1B 117567862 117570041 2179 False 3073.0 3073 92.28000 609 2770 1 chr1B.!!$F1 2161
21 TraesCS4B01G124100 chr1B 192688583 192690443 1860 True 1334.5 1834 92.84850 2222 6743 2 chr1B.!!$R1 4521
22 TraesCS4B01G124100 chrUn 286669929 286672116 2187 False 3109.0 3109 92.51100 609 2770 1 chrUn.!!$F1 2161
23 TraesCS4B01G124100 chrUn 286675099 286677286 2187 True 3103.0 3103 92.46600 609 2770 1 chrUn.!!$R2 2161
24 TraesCS4B01G124100 chrUn 316389957 316390939 982 False 1323.0 1323 91.15900 609 1579 1 chrUn.!!$F2 970
25 TraesCS4B01G124100 chr5D 249149718 249151062 1344 True 1947.0 1947 92.98400 5408 6741 1 chr5D.!!$R3 1333
26 TraesCS4B01G124100 chr2B 220361266 220363143 1877 False 1386.5 1940 93.32450 2217 6744 2 chr2B.!!$F1 4527
27 TraesCS4B01G124100 chr2B 421411773 421412783 1010 True 1356.0 1356 91.06100 5741 6744 1 chr2B.!!$R1 1003
28 TraesCS4B01G124100 chr6B 328339253 328340606 1353 False 1903.0 1903 92.18300 1 1342 1 chr6B.!!$F1 1341
29 TraesCS4B01G124100 chr6B 393761614 393762961 1347 False 1881.0 1881 92.03000 5408 6743 1 chr6B.!!$F2 1335
30 TraesCS4B01G124100 chr3D 256143815 256145659 1844 True 1361.5 1853 93.76850 2222 6717 2 chr3D.!!$R1 4495
31 TraesCS4B01G124100 chr3B 277659002 277660209 1207 False 1652.0 1652 91.53000 5544 6741 1 chr3B.!!$F1 1197
32 TraesCS4B01G124100 chr3B 286887130 286888041 911 True 1419.0 1419 94.97300 1 901 1 chr3B.!!$R1 900

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
949 1171 0.736053 TTTCGTCCTTGTGCGCTTTT 59.264 45.000 9.73 0.0 0.00 2.27 F
1355 1645 0.107654 CCATCCAGACTTTCCCGTCC 60.108 60.000 0.00 0.0 34.46 4.79 F
2849 3286 1.492993 GGAGTTCTGGGAAGGCCTGT 61.493 60.000 5.69 0.0 0.00 4.00 F
3617 4058 0.035439 CTCCACCAACGGTTAGGCAT 60.035 55.000 8.61 0.0 31.02 4.40 F
4246 4689 6.262496 TGGTACGACAACTTATGGAGAGATAG 59.738 42.308 0.00 0.0 0.00 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2933 3370 1.535204 CCATGCGCCCCTTCAAAACT 61.535 55.000 4.18 0.0 0.00 2.66 R
3504 3945 5.265191 TCTAGGTTGTCTGCACTCTTATCT 58.735 41.667 0.00 0.0 0.00 1.98 R
4246 4689 2.816672 CAAGTCCTTCTTTTGCTCCCTC 59.183 50.000 0.00 0.0 33.63 4.30 R
5245 5693 3.944087 AGCTCTTTGGTGATACTCCAAC 58.056 45.455 5.04 0.0 43.45 3.77 R
6191 6682 2.549926 TGCATAGATGTAGTTGCACCG 58.450 47.619 0.00 0.0 39.98 4.94 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
949 1171 0.736053 TTTCGTCCTTGTGCGCTTTT 59.264 45.000 9.73 0.00 0.00 2.27
1347 1637 5.965033 ACACTTCATATCCATCCAGACTT 57.035 39.130 0.00 0.00 0.00 3.01
1355 1645 0.107654 CCATCCAGACTTTCCCGTCC 60.108 60.000 0.00 0.00 34.46 4.79
1408 1698 4.289672 ACACCTTGGTCCAGATTCAGTTAT 59.710 41.667 0.00 0.00 0.00 1.89
2390 2820 5.395682 TTTGCTTATGCTTCATGCTTTCT 57.604 34.783 1.96 0.00 43.37 2.52
2717 3148 7.316544 ACAAATTGAAAGTTACTCTCGTTGT 57.683 32.000 0.00 0.00 0.00 3.32
2849 3286 1.492993 GGAGTTCTGGGAAGGCCTGT 61.493 60.000 5.69 0.00 0.00 4.00
2933 3370 3.555377 CCACGTGGGTACATCTAACACAA 60.555 47.826 27.57 0.00 30.61 3.33
3504 3945 2.940158 TGCTTCAGACGCCTATACCTA 58.060 47.619 0.00 0.00 0.00 3.08
3590 4031 1.648467 GAAGCAAGGTGTCGGGCATC 61.648 60.000 0.00 0.00 0.00 3.91
3617 4058 0.035439 CTCCACCAACGGTTAGGCAT 60.035 55.000 8.61 0.00 31.02 4.40
4246 4689 6.262496 TGGTACGACAACTTATGGAGAGATAG 59.738 42.308 0.00 0.00 0.00 2.08
5245 5693 3.447586 TCCGTTAAGAGAGACATGAAGGG 59.552 47.826 0.00 0.00 0.00 3.95
5938 6404 9.748708 GCAAAATGTTATTTATTATGCTCCTGA 57.251 29.630 0.00 0.00 0.00 3.86
6191 6682 6.095377 GGATTTGAATTGGACACTGTCATTC 58.905 40.000 11.34 11.93 33.68 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
949 1171 2.502947 ACAGAGCCAGAGCACATCAATA 59.497 45.455 0.00 0.00 43.56 1.90
1347 1637 0.824182 AAACAATTGGCGGACGGGAA 60.824 50.000 10.83 0.00 0.00 3.97
1355 1645 4.732784 AGTGTAGCATTAAACAATTGGCG 58.267 39.130 10.83 0.00 0.00 5.69
1408 1698 1.186200 CATGTCCAACTCGAGAGGGA 58.814 55.000 21.68 21.07 33.92 4.20
1893 2311 5.262804 AGGTCCGAGTTATTGAGAACTACT 58.737 41.667 0.00 0.00 39.79 2.57
2433 2863 4.019411 TCAGCTCCCACAATCAGTAATCAA 60.019 41.667 0.00 0.00 0.00 2.57
2774 3211 1.915078 ATGTCTTCCAGGCCTTCCCG 61.915 60.000 0.00 0.00 39.21 5.14
2849 3286 5.245751 TCGGTACACTCCTAACCATGTTTTA 59.754 40.000 0.00 0.00 32.55 1.52
2933 3370 1.535204 CCATGCGCCCCTTCAAAACT 61.535 55.000 4.18 0.00 0.00 2.66
3504 3945 5.265191 TCTAGGTTGTCTGCACTCTTATCT 58.735 41.667 0.00 0.00 0.00 1.98
3563 4004 1.956477 GACACCTTGCTTCACCAACAT 59.044 47.619 0.00 0.00 0.00 2.71
3590 4031 1.293498 CGTTGGTGGAGGTCCTCAG 59.707 63.158 20.72 0.00 36.82 3.35
3617 4058 0.036306 GTCCCTTTCGCCTTCCTTCA 59.964 55.000 0.00 0.00 0.00 3.02
4246 4689 2.816672 CAAGTCCTTCTTTTGCTCCCTC 59.183 50.000 0.00 0.00 33.63 4.30
5245 5693 3.944087 AGCTCTTTGGTGATACTCCAAC 58.056 45.455 5.04 0.00 43.45 3.77
5938 6404 6.825721 GTGGAAGAAAATGTCTGAGGATACAT 59.174 38.462 0.00 0.00 36.40 2.29
6191 6682 2.549926 TGCATAGATGTAGTTGCACCG 58.450 47.619 0.00 0.00 39.98 4.94


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

AutoCloner maintained by Alex Coulton.