Multiple sequence alignment - TraesCS4A01G418300

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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 TraesCS4A01G418300 chr4A 100.000 3744 0 0 1 3744 688328706 688324963 0.000000e+00 6914.0
1 TraesCS4A01G418300 chr4A 96.164 3780 101 18 1 3744 688376318 688372547 0.000000e+00 6137.0
2 TraesCS4A01G418300 chr4A 91.111 1935 166 3 925 2859 687831029 687832957 0.000000e+00 2615.0
3 TraesCS4A01G418300 chr4A 90.557 1938 174 4 925 2859 687892532 687894463 0.000000e+00 2556.0
4 TraesCS4A01G418300 chr4A 90.036 1947 172 9 913 2859 687813479 687815403 0.000000e+00 2501.0
5 TraesCS4A01G418300 chr4A 91.748 1539 123 2 925 2463 687919347 687920881 0.000000e+00 2135.0
6 TraesCS4A01G418300 chr4A 84.902 510 68 7 2979 3487 528097636 528097135 1.200000e-139 507.0
7 TraesCS4A01G418300 chr4A 86.921 367 45 2 2493 2859 687920883 687921246 3.480000e-110 409.0
8 TraesCS4A01G418300 chr4A 84.236 203 31 1 3541 3743 641512913 641512712 2.950000e-46 196.0
9 TraesCS4A01G418300 chr4A 98.113 53 1 0 2890 2942 561442025 561441973 3.980000e-15 93.5
10 TraesCS4A01G418300 chr7A 91.572 1946 158 4 913 2857 35696589 35698529 0.000000e+00 2680.0
11 TraesCS4A01G418300 chr7A 92.829 767 47 5 878 1637 35746323 35747088 0.000000e+00 1105.0
12 TraesCS4A01G418300 chr7A 98.148 54 1 0 2889 2942 32956869 32956816 1.110000e-15 95.3
13 TraesCS4A01G418300 chr7D 90.154 1950 174 11 920 2857 36045154 36043211 0.000000e+00 2521.0
14 TraesCS4A01G418300 chr7D 90.401 1198 100 9 1669 2857 35552412 35553603 0.000000e+00 1561.0
15 TraesCS4A01G418300 chr7D 89.990 1019 102 0 1746 2764 35798298 35797280 0.000000e+00 1317.0
16 TraesCS4A01G418300 chr7D 89.583 864 72 13 1 857 35550543 35551395 0.000000e+00 1081.0
17 TraesCS4A01G418300 chr7D 95.266 676 31 1 893 1567 35551396 35552071 0.000000e+00 1070.0
18 TraesCS4A01G418300 chr7D 92.857 658 41 3 925 1580 35799097 35798444 0.000000e+00 950.0
19 TraesCS4A01G418300 chr7D 87.770 278 16 2 3484 3743 207595820 207596097 3.630000e-80 309.0
20 TraesCS4A01G418300 chr7D 84.109 258 28 8 592 841 35813678 35813426 1.740000e-58 237.0
21 TraesCS4A01G418300 chr3B 83.203 512 66 12 2979 3487 463076662 463076168 5.700000e-123 451.0
22 TraesCS4A01G418300 chr3B 84.937 239 30 6 2979 3215 463077450 463077216 1.740000e-58 237.0
23 TraesCS4A01G418300 chr3B 95.082 61 3 0 2882 2942 187492907 187492847 3.080000e-16 97.1
24 TraesCS4A01G418300 chr3B 98.113 53 1 0 2890 2942 6686011 6686063 3.980000e-15 93.5
25 TraesCS4A01G418300 chr5D 80.517 503 76 12 1071 1556 537088082 537088579 2.120000e-97 366.0
26 TraesCS4A01G418300 chr5D 80.279 502 78 12 1071 1556 537162869 537162373 3.560000e-95 359.0
27 TraesCS4A01G418300 chr5D 78.488 516 97 7 1054 1556 512534348 512534862 3.610000e-85 326.0
28 TraesCS4A01G418300 chr5D 88.448 277 14 2 3485 3743 130528605 130528329 6.030000e-83 318.0
29 TraesCS4A01G418300 chr5D 87.726 277 16 2 3485 3743 546141574 546141850 1.310000e-79 307.0
30 TraesCS4A01G418300 chr5D 87.773 229 27 1 3260 3488 417674075 417674302 2.220000e-67 267.0
31 TraesCS4A01G418300 chr5D 97.059 34 1 0 2943 2976 513899636 513899603 1.450000e-04 58.4
32 TraesCS4A01G418300 chr6D 91.154 260 20 3 3485 3743 83360499 83360242 2.140000e-92 350.0
33 TraesCS4A01G418300 chr6D 88.809 277 13 2 3485 3743 89882875 89882599 1.300000e-84 324.0
34 TraesCS4A01G418300 chr6D 88.087 277 14 3 3485 3743 266120378 266120103 1.010000e-80 311.0
35 TraesCS4A01G418300 chr2D 89.531 277 11 2 3485 3743 378796921 378797197 5.990000e-88 335.0
36 TraesCS4A01G418300 chr2D 100.000 32 0 0 2945 2976 465570309 465570278 4.040000e-05 60.2
37 TraesCS4A01G418300 chrUn 89.209 278 12 2 3484 3743 20067469 20067192 7.750000e-87 331.0
38 TraesCS4A01G418300 chrUn 98.113 53 1 0 2890 2942 288184219 288184271 3.980000e-15 93.5
39 TraesCS4A01G418300 chrUn 100.000 32 0 0 2945 2976 433066353 433066322 4.040000e-05 60.2
40 TraesCS4A01G418300 chrUn 97.059 34 1 0 2943 2976 71517798 71517765 1.450000e-04 58.4
41 TraesCS4A01G418300 chr3D 88.889 279 13 2 3483 3743 472075290 472075012 1.000000e-85 327.0
42 TraesCS4A01G418300 chr3D 96.552 58 2 0 2885 2942 372921073 372921130 3.080000e-16 97.1
43 TraesCS4A01G418300 chr3D 86.667 75 6 2 2872 2942 597211032 597211106 3.100000e-11 80.5
44 TraesCS4A01G418300 chr4D 88.686 274 13 2 3488 3743 113551844 113551571 6.030000e-83 318.0
45 TraesCS4A01G418300 chr4D 88.406 276 14 2 3486 3743 501946540 501946815 2.170000e-82 316.0
46 TraesCS4A01G418300 chr4D 78.614 505 82 18 1071 1556 479540673 479541170 1.010000e-80 311.0
47 TraesCS4A01G418300 chr4D 87.726 277 16 2 3485 3743 470350829 470350553 1.310000e-79 307.0
48 TraesCS4A01G418300 chr4D 76.375 491 96 13 1085 1559 479637265 479636779 2.890000e-61 246.0
49 TraesCS4A01G418300 chr4D 76.375 491 96 13 1085 1559 479638722 479638236 2.890000e-61 246.0
50 TraesCS4A01G418300 chr4D 76.375 491 96 13 1085 1559 479676413 479675927 2.890000e-61 246.0
51 TraesCS4A01G418300 chr4D 75.098 510 95 23 1072 1556 5290348 5289846 3.790000e-50 209.0
52 TraesCS4A01G418300 chr3A 87.681 276 16 2 3486 3743 385344949 385345224 4.700000e-79 305.0
53 TraesCS4A01G418300 chr3A 100.000 32 0 0 2945 2976 76319692 76319661 4.040000e-05 60.2
54 TraesCS4A01G418300 chr1A 98.113 53 1 0 2890 2942 172002094 172002146 3.980000e-15 93.5
55 TraesCS4A01G418300 chr6B 100.000 32 0 0 2945 2976 132740113 132740082 4.040000e-05 60.2
56 TraesCS4A01G418300 chr6A 100.000 32 0 0 2945 2976 11114488 11114457 4.040000e-05 60.2
57 TraesCS4A01G418300 chr1D 100.000 32 0 0 2945 2976 322476654 322476685 4.040000e-05 60.2


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 TraesCS4A01G418300 chr4A 688324963 688328706 3743 True 6914.000000 6914 100.0000 1 3744 1 chr4A.!!$R4 3743
1 TraesCS4A01G418300 chr4A 688372547 688376318 3771 True 6137.000000 6137 96.1640 1 3744 1 chr4A.!!$R5 3743
2 TraesCS4A01G418300 chr4A 687831029 687832957 1928 False 2615.000000 2615 91.1110 925 2859 1 chr4A.!!$F2 1934
3 TraesCS4A01G418300 chr4A 687892532 687894463 1931 False 2556.000000 2556 90.5570 925 2859 1 chr4A.!!$F3 1934
4 TraesCS4A01G418300 chr4A 687813479 687815403 1924 False 2501.000000 2501 90.0360 913 2859 1 chr4A.!!$F1 1946
5 TraesCS4A01G418300 chr4A 687919347 687921246 1899 False 1272.000000 2135 89.3345 925 2859 2 chr4A.!!$F4 1934
6 TraesCS4A01G418300 chr4A 528097135 528097636 501 True 507.000000 507 84.9020 2979 3487 1 chr4A.!!$R1 508
7 TraesCS4A01G418300 chr7A 35696589 35698529 1940 False 2680.000000 2680 91.5720 913 2857 1 chr7A.!!$F1 1944
8 TraesCS4A01G418300 chr7A 35746323 35747088 765 False 1105.000000 1105 92.8290 878 1637 1 chr7A.!!$F2 759
9 TraesCS4A01G418300 chr7D 36043211 36045154 1943 True 2521.000000 2521 90.1540 920 2857 1 chr7D.!!$R2 1937
10 TraesCS4A01G418300 chr7D 35550543 35553603 3060 False 1237.333333 1561 91.7500 1 2857 3 chr7D.!!$F2 2856
11 TraesCS4A01G418300 chr7D 35797280 35799097 1817 True 1133.500000 1317 91.4235 925 2764 2 chr7D.!!$R3 1839
12 TraesCS4A01G418300 chr3B 463076168 463077450 1282 True 344.000000 451 84.0700 2979 3487 2 chr3B.!!$R2 508
13 TraesCS4A01G418300 chr5D 512534348 512534862 514 False 326.000000 326 78.4880 1054 1556 1 chr5D.!!$F2 502
14 TraesCS4A01G418300 chr4D 479636779 479638722 1943 True 246.000000 246 76.3750 1085 1559 2 chr4D.!!$R5 474
15 TraesCS4A01G418300 chr4D 5289846 5290348 502 True 209.000000 209 75.0980 1072 1556 1 chr4D.!!$R1 484

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
202 203 0.035534 TACATTGGCCGCTGTCACAT 60.036 50.0 12.84 0.00 0.00 3.21 F
760 773 0.752743 TGGATGTTATGCAGCTGGGC 60.753 55.0 17.12 1.74 33.29 5.36 F
2170 2823 0.467384 CGACCATGATGAGCCCTCTT 59.533 55.0 0.00 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 2402 2.549282 CGGCCGTGTTCTTGAACG 59.451 61.111 19.50 0.00 39.48 3.95 R
2600 3253 2.095364 GCAAGGCAAGAGTGAACATGAG 60.095 50.000 0.00 0.00 0.00 2.90 R
3280 4738 6.032985 GCGACTATTCAATAGATCAGCTTACG 59.967 42.308 11.62 4.21 36.68 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
129 130 8.234136 TCGGGGTAAGCTGAGTATATATTATG 57.766 38.462 0.00 0.00 0.00 1.90
187 188 4.647853 TGTTAATAGACACTCGGCCTACAT 59.352 41.667 0.00 0.00 0.00 2.29
202 203 0.035534 TACATTGGCCGCTGTCACAT 60.036 50.000 12.84 0.00 0.00 3.21
209 210 1.021390 GCCGCTGTCACATAGCTGTT 61.021 55.000 0.00 0.00 39.00 3.16
224 225 1.596496 CTGTTAAGGGGTGGGAGGAT 58.404 55.000 0.00 0.00 0.00 3.24
282 283 1.493311 GCCGAGTGCTTTTCTCACG 59.507 57.895 0.00 0.00 39.31 4.35
292 293 2.414161 GCTTTTCTCACGGTATGCCAAC 60.414 50.000 0.00 0.00 34.09 3.77
307 308 4.991153 TGCCAACATTTGTGTAGAAACA 57.009 36.364 0.00 0.00 0.00 2.83
348 349 2.501723 ACTCGGCCTGTGTGAAGATAAT 59.498 45.455 0.00 0.00 0.00 1.28
373 374 4.284550 ACAGCCGGTTGCCATGGT 62.285 61.111 19.28 0.00 42.71 3.55
403 404 2.854522 GCACTCGGCTTATGGTGTT 58.145 52.632 0.00 0.00 40.25 3.32
438 439 7.489113 GGTGGCAGATAATTTACACTTGATTTG 59.511 37.037 0.00 0.00 0.00 2.32
456 459 6.890558 TGATTTGCGTTTAAACACTAGGTAC 58.109 36.000 18.07 3.53 0.00 3.34
459 462 4.897140 TGCGTTTAAACACTAGGTACCAT 58.103 39.130 15.94 1.66 0.00 3.55
470 473 6.123651 ACACTAGGTACCATTGTGTTTTTCA 58.876 36.000 23.08 0.00 38.51 2.69
498 501 5.071250 AGTGGTACAAGTTTATGAGTGTCCA 59.929 40.000 0.00 0.00 44.16 4.02
583 588 9.793252 AAAATCCTTTATTCGATCAACAATGAG 57.207 29.630 0.00 0.00 39.39 2.90
587 592 9.443323 TCCTTTATTCGATCAACAATGAGTAAA 57.557 29.630 0.00 0.00 39.39 2.01
663 668 4.677378 CGTCTTCATTCTATAGCCGTCTTG 59.323 45.833 0.00 0.00 0.00 3.02
665 670 3.386768 TCATTCTATAGCCGTCTTGCC 57.613 47.619 0.00 0.00 0.00 4.52
683 691 3.078837 TGCCTTTTTAGAAAGCGTAGGG 58.921 45.455 0.18 0.00 40.75 3.53
684 692 2.159421 GCCTTTTTAGAAAGCGTAGGGC 60.159 50.000 0.18 0.00 40.75 5.19
760 773 0.752743 TGGATGTTATGCAGCTGGGC 60.753 55.000 17.12 1.74 33.29 5.36
866 883 6.833416 ACTTTATATATCCAGTTGGCTTGCAA 59.167 34.615 0.00 0.00 34.44 4.08
874 891 3.460103 CAGTTGGCTTGCAAAAATCAGT 58.540 40.909 0.00 0.00 0.00 3.41
1020 1046 2.184322 CTGTACCGCGTGCTGGAT 59.816 61.111 4.92 0.00 0.00 3.41
1752 2402 1.011451 GTTCTGGTGCTCTCTGCGAC 61.011 60.000 0.00 0.00 46.63 5.19
1831 2481 1.813859 CATTGTGCTCATGCTGGGG 59.186 57.895 0.00 0.00 40.48 4.96
2054 2707 2.685017 ATGGTCGCCAGCTCCTCA 60.685 61.111 4.90 0.00 36.75 3.86
2170 2823 0.467384 CGACCATGATGAGCCCTCTT 59.533 55.000 0.00 0.00 0.00 2.85
2924 3591 5.010012 CCAATAAAGCAAGGTGTGTTTCTCT 59.990 40.000 0.00 0.00 29.15 3.10
3280 4738 3.877508 ACCTATGGCGTTAAGAAATCTGC 59.122 43.478 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 4.163458 TCATATATGTAAGCCGGGAATCCC 59.837 45.833 8.64 8.64 41.09 3.85
187 188 1.745115 GCTATGTGACAGCGGCCAA 60.745 57.895 2.24 0.00 0.00 4.52
202 203 1.580059 CTCCCACCCCTTAACAGCTA 58.420 55.000 0.00 0.00 0.00 3.32
209 210 1.696314 GCCATCCTCCCACCCCTTA 60.696 63.158 0.00 0.00 0.00 2.69
236 237 2.203126 GGCTCGGCATAAGCAGCT 60.203 61.111 6.55 0.00 44.61 4.24
282 283 5.637006 TTCTACACAAATGTTGGCATACC 57.363 39.130 0.00 0.00 40.48 2.73
307 308 6.027749 CGAGTACAGCACAAAAAGAACTTTT 58.972 36.000 6.70 6.70 43.88 2.27
323 324 0.317160 TTCACACAGGCCGAGTACAG 59.683 55.000 0.00 0.00 0.00 2.74
348 349 3.884774 AACCGGCTGTGGCTTGGA 61.885 61.111 0.00 0.00 37.38 3.53
438 439 5.179929 ACAATGGTACCTAGTGTTTAAACGC 59.820 40.000 21.58 21.58 39.63 4.84
470 473 7.676947 ACACTCATAAACTTGTACCACTATGT 58.323 34.615 0.00 0.00 0.00 2.29
483 486 5.401531 ACATACGTGGACACTCATAAACT 57.598 39.130 0.00 0.00 0.00 2.66
583 588 7.041576 AGGACGGAAACAACAAGATAAGTTTAC 60.042 37.037 0.00 0.00 34.62 2.01
587 592 4.969484 AGGACGGAAACAACAAGATAAGT 58.031 39.130 0.00 0.00 0.00 2.24
663 668 2.159421 GCCCTACGCTTTCTAAAAAGGC 60.159 50.000 0.58 0.00 41.87 4.35
683 691 1.282248 TGCTGACGAACGTGCTTAGC 61.282 55.000 4.19 0.00 0.00 3.09
684 692 1.136690 TTGCTGACGAACGTGCTTAG 58.863 50.000 4.19 0.00 0.00 2.18
685 693 1.525197 CTTTGCTGACGAACGTGCTTA 59.475 47.619 4.19 0.00 0.00 3.09
687 695 1.934463 CTTTGCTGACGAACGTGCT 59.066 52.632 4.19 0.00 0.00 4.40
709 717 6.627395 TGTCCGAAGAACACATAAAATTGT 57.373 33.333 0.00 0.00 0.00 2.71
966 992 0.907486 CATGGAGGTGGCAGAAGAGA 59.093 55.000 0.00 0.00 0.00 3.10
1020 1046 2.702751 ATTTCACCGACGTCACCGCA 62.703 55.000 17.16 0.00 37.70 5.69
1680 2330 8.451908 ACCCTTTATGCAGACAAAGTATAATC 57.548 34.615 13.90 0.00 31.20 1.75
1752 2402 2.549282 CGGCCGTGTTCTTGAACG 59.451 61.111 19.50 0.00 39.48 3.95
2170 2823 4.697828 CGAGCTATCTTATAGGTCTGCTCA 59.302 45.833 18.71 0.00 43.84 4.26
2600 3253 2.095364 GCAAGGCAAGAGTGAACATGAG 60.095 50.000 0.00 0.00 0.00 2.90
3062 4517 6.313164 TCATTATTATTTTGGACGTGCGTGTA 59.687 34.615 0.67 0.00 0.00 2.90
3280 4738 6.032985 GCGACTATTCAATAGATCAGCTTACG 59.967 42.308 11.62 4.21 36.68 3.18


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

AutoCloner maintained by Alex Coulton.