Multiple sequence alignment - TraesCS3D01G231300

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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 TraesCS3D01G231300 chr3D 100.000 5310 0 0 1 5310 316171893 316166584 0.000000e+00 9806
1 TraesCS3D01G231300 chr3B 96.571 5337 145 18 1 5310 403904293 403909618 0.000000e+00 8807
2 TraesCS3D01G231300 chr3A 97.361 3032 61 5 2284 5310 413680050 413683067 0.000000e+00 5138
3 TraesCS3D01G231300 chr3A 96.063 2235 68 9 1 2230 413677834 413680053 0.000000e+00 3622
4 TraesCS3D01G231300 chr1D 80.507 631 93 22 1256 1877 484419147 484418538 1.740000e-124 457
5 TraesCS3D01G231300 chr1A 80.507 631 90 23 1256 1877 581832371 581831765 2.250000e-123 453
6 TraesCS3D01G231300 chr1B 80.159 630 85 28 1256 1877 674671206 674670609 8.170000e-118 435


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 TraesCS3D01G231300 chr3D 316166584 316171893 5309 True 9806 9806 100.000 1 5310 1 chr3D.!!$R1 5309
1 TraesCS3D01G231300 chr3B 403904293 403909618 5325 False 8807 8807 96.571 1 5310 1 chr3B.!!$F1 5309
2 TraesCS3D01G231300 chr3A 413677834 413683067 5233 False 4380 5138 96.712 1 5310 2 chr3A.!!$F1 5309
3 TraesCS3D01G231300 chr1D 484418538 484419147 609 True 457 457 80.507 1256 1877 1 chr1D.!!$R1 621
4 TraesCS3D01G231300 chr1A 581831765 581832371 606 True 453 453 80.507 1256 1877 1 chr1A.!!$R1 621
5 TraesCS3D01G231300 chr1B 674670609 674671206 597 True 435 435 80.159 1256 1877 1 chr1B.!!$R1 621

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
640 661 0.317436 CTGAGATACTCGCAGCGTCC 60.317 60.000 15.93 0.82 37.48 4.79 F
936 958 0.823356 GCCTGCTTGTTTGGTCAGGA 60.823 55.000 10.95 0.00 46.80 3.86 F
1208 1230 1.152830 AGTCAAATGTTGGGGCGGT 59.847 52.632 0.00 0.00 0.00 5.68 F
2763 2803 1.153086 ATCATCCCTCGCTTGTGCC 60.153 57.895 0.00 0.00 35.36 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 2315 0.179062 AAACGCCCAATTTGCTTGCA 60.179 45.000 0.00 0.0 33.20 4.08 R
2745 2785 1.153086 GGCACAAGCGAGGGATGAT 60.153 57.895 0.00 0.0 43.41 2.45 R
2962 3002 1.134670 ACTAGCATGCCCGAGAGTTTC 60.135 52.381 15.66 0.0 0.00 2.78 R
4677 4722 2.991540 GCAACCAGCAACCCCCTC 60.992 66.667 0.00 0.0 44.79 4.30 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
117 118 7.665559 ACCGCATCATCAATATTTACCTTATGT 59.334 33.333 0.00 0.00 0.00 2.29
149 150 9.959721 ATAGTGGCGTTCCATCTAAAATTATAT 57.040 29.630 0.00 0.00 45.62 0.86
256 257 6.759356 TCATTTACATCACTTACATGGTACCG 59.241 38.462 7.57 0.00 0.00 4.02
529 547 4.457257 GTCCAAGAAGACAGAATCCCAAAG 59.543 45.833 0.00 0.00 36.73 2.77
640 661 0.317436 CTGAGATACTCGCAGCGTCC 60.317 60.000 15.93 0.82 37.48 4.79
714 735 2.909662 CAGTCCTCTCCCCTTTCTTCTT 59.090 50.000 0.00 0.00 0.00 2.52
715 736 3.055458 CAGTCCTCTCCCCTTTCTTCTTC 60.055 52.174 0.00 0.00 0.00 2.87
716 737 2.237643 GTCCTCTCCCCTTTCTTCTTCC 59.762 54.545 0.00 0.00 0.00 3.46
717 738 2.114506 TCCTCTCCCCTTTCTTCTTCCT 59.885 50.000 0.00 0.00 0.00 3.36
936 958 0.823356 GCCTGCTTGTTTGGTCAGGA 60.823 55.000 10.95 0.00 46.80 3.86
1208 1230 1.152830 AGTCAAATGTTGGGGCGGT 59.847 52.632 0.00 0.00 0.00 5.68
1648 1685 1.227205 CTGCAGGAGATGACTCGCC 60.227 63.158 5.57 0.00 43.44 5.54
1682 1719 2.180159 TACAAGAAGGGGAGGCACGC 62.180 60.000 0.00 0.00 0.00 5.34
2127 2164 3.186119 TCTTTCTTTTTGTTTGCGCTGG 58.814 40.909 9.73 0.00 0.00 4.85
2156 2193 3.266772 TGATTGGGGATTGTTACTGCTCT 59.733 43.478 0.00 0.00 0.00 4.09
2177 2214 2.102420 TGTGTGGTCTGTTTGATCGTCT 59.898 45.455 0.00 0.00 0.00 4.18
2190 2227 5.405935 TTGATCGTCTCTCTCCAATTTGA 57.594 39.130 0.00 0.00 0.00 2.69
2194 2231 5.924475 TCGTCTCTCTCCAATTTGAAAAC 57.076 39.130 0.00 0.00 0.00 2.43
2259 2299 2.551459 GTTGAGCTGTGAGTGAGCAAAT 59.449 45.455 0.00 0.00 39.05 2.32
2275 2315 2.494870 GCAAATGCCAGGATCTTGTCTT 59.505 45.455 3.93 0.00 34.31 3.01
2458 2498 1.375268 GCACTGTCCTGACCTGAGC 60.375 63.158 0.00 0.00 0.00 4.26
2513 2553 3.551082 TGCTTGTTTTGTTGCTGAAATCG 59.449 39.130 0.00 0.00 0.00 3.34
2523 2563 5.837437 TGTTGCTGAAATCGGTGTTATTTT 58.163 33.333 0.00 0.00 0.00 1.82
2528 2568 7.821652 TGCTGAAATCGGTGTTATTTTCATTA 58.178 30.769 0.00 0.00 37.43 1.90
2553 2593 4.158786 TCAGGCTGGGAATGATTGAAAAA 58.841 39.130 15.73 0.00 0.00 1.94
2652 2692 2.299993 TGCATCTAGGAAGAAGCACG 57.700 50.000 1.49 0.00 46.48 5.34
2745 2785 3.071892 ACTCGTCCCAGTTGGTAAATTCA 59.928 43.478 0.00 0.00 34.77 2.57
2763 2803 1.153086 ATCATCCCTCGCTTGTGCC 60.153 57.895 0.00 0.00 35.36 5.01
2794 2834 7.563906 TCTTTCAAGTGTTGGAAAATGGAAAT 58.436 30.769 0.00 0.00 33.05 2.17
2795 2835 7.495279 TCTTTCAAGTGTTGGAAAATGGAAATG 59.505 33.333 0.00 0.00 33.05 2.32
2817 2857 8.986477 AATGGTTTTACATTGTAGATTCTTGC 57.014 30.769 0.00 0.00 39.47 4.01
2962 3002 2.067091 TACTATCTTGGACGGCGGCG 62.067 60.000 31.06 31.06 0.00 6.46
2986 3026 0.461548 TCTCGGGCATGCTAGTTGAG 59.538 55.000 18.92 16.18 0.00 3.02
3038 3078 1.357420 ACATGGCATTGGGAAGGTACA 59.643 47.619 0.00 0.00 0.00 2.90
3393 3433 3.746492 AGAAAGCCGTTGATGACTGTAAC 59.254 43.478 0.00 0.00 0.00 2.50
3502 3542 3.226777 TGTTTTTGACATCCCATTCCGT 58.773 40.909 0.00 0.00 32.00 4.69
3771 3811 9.476202 AGTTTTGCTCAAATAATACTTGTTTCC 57.524 29.630 0.00 0.00 0.00 3.13
3950 3990 0.874390 TGCTTGCCTGTCGTTTCATC 59.126 50.000 0.00 0.00 0.00 2.92
4294 4334 2.929531 ACTCAGTGAGACACTATGCG 57.070 50.000 26.86 0.00 43.43 4.73
4360 4400 1.548357 TTCCTCTGCCAGCCAGTCTC 61.548 60.000 0.00 0.00 42.38 3.36
4677 4722 4.015730 AGAATATCATAGAGGGAGAGGGGG 60.016 50.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 2.772077 TGGAACGCCACTATGCTTTA 57.228 45.000 0.00 0.00 39.92 1.85
149 150 5.241285 ACGGCGGAGTTATTTTCCTTTTAAA 59.759 36.000 13.24 0.00 32.34 1.52
160 161 3.598019 TTGTTCTACGGCGGAGTTATT 57.402 42.857 20.25 0.00 0.00 1.40
161 162 3.598019 TTTGTTCTACGGCGGAGTTAT 57.402 42.857 20.25 0.00 0.00 1.89
196 197 8.793592 GTTAGTGGATTTAGAAATGAACTTGGT 58.206 33.333 0.00 0.00 0.00 3.67
247 248 2.222886 TGTGTTTTGACCGGTACCATG 58.777 47.619 7.34 4.69 0.00 3.66
256 257 8.723942 ATCTAGACATAAGATGTGTTTTGACC 57.276 34.615 0.00 0.00 45.03 4.02
529 547 1.369625 CGGTTTGGTGCCATAGAGTC 58.630 55.000 0.00 0.00 0.00 3.36
714 735 3.841255 GAGAAGAAGGAAGGAAGGAAGGA 59.159 47.826 0.00 0.00 0.00 3.36
715 736 3.054728 GGAGAAGAAGGAAGGAAGGAAGG 60.055 52.174 0.00 0.00 0.00 3.46
716 737 3.054728 GGGAGAAGAAGGAAGGAAGGAAG 60.055 52.174 0.00 0.00 0.00 3.46
717 738 2.913617 GGGAGAAGAAGGAAGGAAGGAA 59.086 50.000 0.00 0.00 0.00 3.36
936 958 1.684049 CCGCAACTCCTCCTCCTCT 60.684 63.158 0.00 0.00 0.00 3.69
1648 1685 2.230508 TCTTGTACCACTCGTTGCCTAG 59.769 50.000 0.00 0.00 0.00 3.02
2127 2164 1.756538 ACAATCCCCAATCAAATCGGC 59.243 47.619 0.00 0.00 0.00 5.54
2156 2193 2.102420 AGACGATCAAACAGACCACACA 59.898 45.455 0.00 0.00 0.00 3.72
2177 2214 7.416964 TTCCTTTGTTTTCAAATTGGAGAGA 57.583 32.000 0.00 0.00 46.72 3.10
2190 2227 6.706295 TCTGTCACCAAAATTCCTTTGTTTT 58.294 32.000 0.00 0.00 42.57 2.43
2194 2231 9.143631 GATAATTCTGTCACCAAAATTCCTTTG 57.856 33.333 0.00 0.00 43.56 2.77
2234 2272 2.141517 CTCACTCACAGCTCAACCAAG 58.858 52.381 0.00 0.00 0.00 3.61
2237 2275 0.250038 TGCTCACTCACAGCTCAACC 60.250 55.000 0.00 0.00 37.79 3.77
2259 2299 0.401356 TGCAAGACAAGATCCTGGCA 59.599 50.000 0.00 0.00 0.00 4.92
2275 2315 0.179062 AAACGCCCAATTTGCTTGCA 60.179 45.000 0.00 0.00 33.20 4.08
2458 2498 8.124823 ACATCTGAATAATAACACTGAATTGCG 58.875 33.333 0.00 0.00 0.00 4.85
2513 2553 7.492344 CCAGCCTGAAATAATGAAAATAACACC 59.508 37.037 0.00 0.00 0.00 4.16
2523 2563 5.128033 TCATTCCCAGCCTGAAATAATGA 57.872 39.130 0.00 0.48 31.41 2.57
2528 2568 3.985127 TCAATCATTCCCAGCCTGAAAT 58.015 40.909 0.00 0.00 0.00 2.17
2553 2593 2.659610 GTGAAGTGCCTCCTCGCT 59.340 61.111 0.00 0.00 0.00 4.93
2571 2611 1.509923 GTGAAGATGCCTGGCTTGC 59.490 57.895 21.03 8.96 0.00 4.01
2652 2692 2.738743 TCTCCAATTTTCCTGGCATCC 58.261 47.619 0.00 0.00 33.63 3.51
2730 2770 5.203528 AGGGATGATGAATTTACCAACTGG 58.796 41.667 0.00 0.00 42.17 4.00
2745 2785 1.153086 GGCACAAGCGAGGGATGAT 60.153 57.895 0.00 0.00 43.41 2.45
2763 2803 8.598075 CATTTTCCAACACTTGAAAGAAAGAAG 58.402 33.333 0.00 0.00 0.00 2.85
2794 2834 7.759489 AGCAAGAATCTACAATGTAAAACCA 57.241 32.000 0.00 0.00 0.00 3.67
2795 2835 9.162764 TCTAGCAAGAATCTACAATGTAAAACC 57.837 33.333 0.00 0.00 0.00 3.27
2962 3002 1.134670 ACTAGCATGCCCGAGAGTTTC 60.135 52.381 15.66 0.00 0.00 2.78
2986 3026 5.107453 GGCTCGCACAATATGTACATAAGAC 60.107 44.000 19.11 8.86 0.00 3.01
3038 3078 2.176247 ACAGGGTTGGAGGATCGTAT 57.824 50.000 0.00 0.00 34.37 3.06
3393 3433 0.924090 GCTGTATTCTCAACGCCTCG 59.076 55.000 0.00 0.00 0.00 4.63
3470 3510 5.733620 ATGTCAAAAACATGAGAATGCCT 57.266 34.783 0.00 0.00 47.00 4.75
3502 3542 4.381505 GGAAGAGGTCAACAAAACAGCAAA 60.382 41.667 0.00 0.00 0.00 3.68
3771 3811 3.344904 ACGGATATCGGAACTGTAACG 57.655 47.619 16.44 3.57 44.45 3.18
3882 3922 5.784177 ACACTATAAACCTATCCAGATGCG 58.216 41.667 0.00 0.00 0.00 4.73
3950 3990 4.712337 AGTAGACAACAGATACCCCTGAAG 59.288 45.833 0.00 0.00 37.59 3.02
4090 4130 6.751888 AGTGACTTGCAAAAATGTTGTAACTC 59.248 34.615 0.00 0.00 0.00 3.01
4100 4140 6.449635 TGTCTGTTAGTGACTTGCAAAAAT 57.550 33.333 0.00 0.00 35.63 1.82
4294 4334 4.479786 AGCTTCTCAAGAACTGGATACC 57.520 45.455 0.00 0.00 0.00 2.73
4360 4400 3.996363 GCAAATTTGGGACCTAAAGCAAG 59.004 43.478 19.47 0.81 0.00 4.01
4677 4722 2.991540 GCAACCAGCAACCCCCTC 60.992 66.667 0.00 0.00 44.79 4.30
4975 5025 2.716217 AGGAATAACCAACAGCAGAGC 58.284 47.619 0.00 0.00 42.04 4.09


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

AutoCloner maintained by Alex Coulton.