Multiple sequence alignment - TraesCS3D01G300400

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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 TraesCS3D01G300400 chr3D 100.000 2219 0 0 1 2219 415165304 415163086 0.000000e+00 4098.0
1 TraesCS3D01G300400 chr3D 86.786 280 27 6 1 273 375211031 375210755 9.960000e-79 303.0
2 TraesCS3D01G300400 chr3B 93.208 2120 76 24 119 2219 541207743 541205673 0.000000e+00 3055.0
3 TraesCS3D01G300400 chr3A 89.908 1417 50 25 1 1393 535190138 535191485 0.000000e+00 1738.0
4 TraesCS3D01G300400 chr3A 96.247 826 25 3 1394 2216 535191526 535192348 0.000000e+00 1349.0
5 TraesCS3D01G300400 chr1A 84.934 531 47 18 1 505 508198067 508197544 7.070000e-140 507.0
6 TraesCS3D01G300400 chr1A 86.689 293 30 5 21 305 398448447 398448156 1.280000e-82 316.0
7 TraesCS3D01G300400 chr4D 85.658 509 37 13 32 505 416450964 416451471 9.150000e-139 503.0
8 TraesCS3D01G300400 chr4D 90.217 92 6 2 516 605 416451552 416451642 1.390000e-22 117.0
9 TraesCS3D01G300400 chr4A 84.124 548 41 19 1 505 47627424 47626880 2.560000e-134 488.0
10 TraesCS3D01G300400 chr4A 82.000 200 27 7 300 493 593353592 593353788 6.340000e-36 161.0
11 TraesCS3D01G300400 chr4B 83.852 514 41 13 32 505 513100681 513101192 3.360000e-123 451.0
12 TraesCS3D01G300400 chr4B 94.444 72 3 1 516 587 513101273 513101343 2.330000e-20 110.0
13 TraesCS3D01G300400 chr5D 86.538 312 33 6 1 305 458926165 458926474 3.530000e-88 335.0
14 TraesCS3D01G300400 chr1B 87.713 293 27 5 21 305 429584001 429583710 1.270000e-87 333.0
15 TraesCS3D01G300400 chr7D 86.601 306 31 6 1 299 175919217 175918915 1.640000e-86 329.0
16 TraesCS3D01G300400 chr7B 86.364 308 29 8 1 299 141798805 141798502 7.640000e-85 324.0
17 TraesCS3D01G300400 chr1D 85.616 292 33 5 21 304 317427333 317427043 4.630000e-77 298.0
18 TraesCS3D01G300400 chr5A 83.828 303 32 8 1 296 577963785 577964077 2.810000e-69 272.0
19 TraesCS3D01G300400 chr2D 86.585 82 9 1 300 379 566987084 566987003 3.030000e-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 TraesCS3D01G300400 chr3D 415163086 415165304 2218 True 4098.0 4098 100.0000 1 2219 1 chr3D.!!$R2 2218
1 TraesCS3D01G300400 chr3B 541205673 541207743 2070 True 3055.0 3055 93.2080 119 2219 1 chr3B.!!$R1 2100
2 TraesCS3D01G300400 chr3A 535190138 535192348 2210 False 1543.5 1738 93.0775 1 2216 2 chr3A.!!$F1 2215
3 TraesCS3D01G300400 chr1A 508197544 508198067 523 True 507.0 507 84.9340 1 505 1 chr1A.!!$R2 504
4 TraesCS3D01G300400 chr4D 416450964 416451642 678 False 310.0 503 87.9375 32 605 2 chr4D.!!$F1 573
5 TraesCS3D01G300400 chr4A 47626880 47627424 544 True 488.0 488 84.1240 1 505 1 chr4A.!!$R1 504
6 TraesCS3D01G300400 chr4B 513100681 513101343 662 False 280.5 451 89.1480 32 587 2 chr4B.!!$F1 555

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
680 822 0.460987 GTGGTGCTCAGATTCCCGAG 60.461 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2161 8.321353 AGTTGATTAGTTCACCATAATGACAGA 58.679 33.333 0.0 0.0 32.84 3.41 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
54 55 5.843673 TGTTAAGAGTGGCAAACAATCAA 57.156 34.783 0.00 0.00 46.19 2.57
68 75 7.254863 GGCAAACAATCAAACAAATCTTGTCAT 60.255 33.333 0.00 0.00 44.59 3.06
74 82 8.370321 CAATCAAACAAATCTTGTCATTGATCG 58.630 33.333 14.95 5.66 44.28 3.69
112 120 8.623903 ACTGGATAGCAAAATTATGTGTATGTG 58.376 33.333 0.00 0.00 0.00 3.21
113 121 7.424803 TGGATAGCAAAATTATGTGTATGTGC 58.575 34.615 0.00 0.00 0.00 4.57
184 195 5.357314 AGCTAACGCAATAGACTTGACTCTA 59.643 40.000 0.00 0.00 39.10 2.43
286 299 2.257207 ACCTCAAGTCCTCAAATCGGA 58.743 47.619 0.00 0.00 0.00 4.55
536 663 3.842925 TTGTTGGGCTGAGACGGGC 62.843 63.158 0.00 0.00 34.35 6.13
679 821 0.904865 AGTGGTGCTCAGATTCCCGA 60.905 55.000 0.00 0.00 0.00 5.14
680 822 0.460987 GTGGTGCTCAGATTCCCGAG 60.461 60.000 0.00 0.00 0.00 4.63
684 826 3.962557 CTCAGATTCCCGAGCCCT 58.037 61.111 0.00 0.00 0.00 5.19
685 827 1.745264 CTCAGATTCCCGAGCCCTC 59.255 63.158 0.00 0.00 0.00 4.30
686 828 1.753368 CTCAGATTCCCGAGCCCTCC 61.753 65.000 0.00 0.00 0.00 4.30
687 829 2.840102 AGATTCCCGAGCCCTCCG 60.840 66.667 0.00 0.00 0.00 4.63
688 830 4.610714 GATTCCCGAGCCCTCCGC 62.611 72.222 0.00 0.00 37.98 5.54
837 999 2.052690 GGTGCTCTCTCCAGCCGTA 61.053 63.158 0.00 0.00 38.80 4.02
940 1103 1.002624 GCCATCACGAACAAGGGGA 60.003 57.895 0.00 0.00 0.00 4.81
1009 1172 4.101448 GGCAGGCCATGTCCGAGT 62.101 66.667 5.01 0.00 35.81 4.18
1260 1426 5.102953 TCTGATTTGGGTGTAGAATCCAG 57.897 43.478 0.00 0.00 31.59 3.86
1262 1428 4.843728 TGATTTGGGTGTAGAATCCAGAC 58.156 43.478 0.00 0.00 31.59 3.51
1360 1526 0.460987 AGTGAGCGAGCCATGCTTAC 60.461 55.000 8.67 8.67 46.05 2.34
1401 1607 5.533903 ACCTGCTTGGAAGATATTTAGCATG 59.466 40.000 0.00 0.00 37.91 4.06
1403 1609 4.888823 TGCTTGGAAGATATTTAGCATGCA 59.111 37.500 21.98 2.77 34.05 3.96
1453 1659 2.432146 TGCCTGTAGGATAGTGCTGAAG 59.568 50.000 1.17 0.00 37.39 3.02
1464 1670 1.707427 AGTGCTGAAGAACCAGGGAAT 59.293 47.619 0.00 0.00 34.82 3.01
1486 1692 7.973944 GGAATTTGGTCAGTTCCAATGTTATAC 59.026 37.037 10.38 0.00 45.30 1.47
1753 1959 7.234782 TGGATATCGTAACTTCCAGTTCCATAT 59.765 37.037 0.00 0.00 39.51 1.78
1967 2175 7.991084 ATCATGGTAATCTGTCATTATGGTG 57.009 36.000 0.00 0.00 0.00 4.17
1970 2178 7.498900 TCATGGTAATCTGTCATTATGGTGAAC 59.501 37.037 0.00 0.00 0.00 3.18
2020 2228 7.545965 AGTGTCGTCTTGAATAGGTATTGAAAG 59.454 37.037 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.254166 ACTCTAACGACGCCACTCTTAAA 59.746 43.478 0.00 0.00 0.00 1.52
54 55 4.766891 ACCCGATCAATGACAAGATTTGTT 59.233 37.500 0.00 0.00 45.52 2.83
68 75 3.556213 CCAGTACTTGAACACCCGATCAA 60.556 47.826 0.00 0.00 33.39 2.57
74 82 3.055385 TGCTATCCAGTACTTGAACACCC 60.055 47.826 0.07 0.00 0.00 4.61
130 138 3.181475 CGGACTTGCTATCCAGTACATGT 60.181 47.826 2.69 2.69 35.83 3.21
184 195 4.202441 GTCTATTGCATCAATCAGGTGGT 58.798 43.478 0.00 0.00 35.54 4.16
351 378 2.281761 CCACTGCGCTTCCTTGGT 60.282 61.111 9.73 0.00 0.00 3.67
536 663 1.964373 CCCAACAAAGTCGTCCCGG 60.964 63.158 0.00 0.00 0.00 5.73
545 685 3.384467 TGAGAAAGAAAGGCCCAACAAAG 59.616 43.478 0.00 0.00 0.00 2.77
603 745 3.498397 CAGTGTGGACGCTACAGATTTTT 59.502 43.478 0.00 0.00 34.49 1.94
687 829 3.610791 GACCGCTGGCCGAAAAAGC 62.611 63.158 0.00 0.00 40.02 3.51
688 830 1.586154 ATGACCGCTGGCCGAAAAAG 61.586 55.000 0.00 0.00 40.02 2.27
689 831 1.582610 GATGACCGCTGGCCGAAAAA 61.583 55.000 0.00 0.00 40.02 1.94
690 832 2.033448 ATGACCGCTGGCCGAAAA 59.967 55.556 0.00 0.00 40.02 2.29
691 833 2.435938 GATGACCGCTGGCCGAAA 60.436 61.111 0.00 0.00 40.02 3.46
692 834 4.812476 CGATGACCGCTGGCCGAA 62.812 66.667 0.00 0.00 40.02 4.30
695 837 4.899239 CTCCGATGACCGCTGGCC 62.899 72.222 0.00 0.00 36.84 5.36
696 838 3.781770 CTCTCCGATGACCGCTGGC 62.782 68.421 0.00 0.00 36.84 4.85
697 839 2.121538 TCTCTCCGATGACCGCTGG 61.122 63.158 0.00 0.00 36.84 4.85
698 840 1.064946 GTCTCTCCGATGACCGCTG 59.935 63.158 0.00 0.00 36.84 5.18
837 999 2.233271 CAGAGGCACACAAGGAAACAT 58.767 47.619 0.00 0.00 0.00 2.71
883 1046 1.272781 CAGAGTTCGTCGAATCAGCC 58.727 55.000 11.45 0.00 0.00 4.85
1122 1285 3.938112 ACGAAGTTGCTGTCGAGC 58.062 55.556 0.00 0.00 37.78 5.03
1260 1426 6.093495 TCCCAAATTATGTTCATCAGTTCGTC 59.907 38.462 0.00 0.00 0.00 4.20
1262 1428 6.435430 TCCCAAATTATGTTCATCAGTTCG 57.565 37.500 0.00 0.00 0.00 3.95
1360 1526 7.436080 CCAAGCAGGTTATTTGCACTAATAATG 59.564 37.037 6.81 4.30 43.92 1.90
1401 1607 4.712476 AGACTATCAATCAGACCCATTGC 58.288 43.478 0.00 0.00 32.17 3.56
1403 1609 6.496565 CCTAGAGACTATCAATCAGACCCATT 59.503 42.308 0.00 0.00 0.00 3.16
1953 2161 8.321353 AGTTGATTAGTTCACCATAATGACAGA 58.679 33.333 0.00 0.00 32.84 3.41


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

AutoCloner maintained by Alex Coulton.