Multiple sequence alignment - TraesCS1D01G136100

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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 TraesCS1D01G136100 chr1D 100.000 2312 0 0 1 2312 180355349 180357660 0.000000e+00 4233
1 TraesCS1D01G136100 chr1D 97.131 1638 46 1 676 2312 254477369 254475732 0.000000e+00 2763
2 TraesCS1D01G136100 chr1D 95.113 1637 77 2 676 2312 244201661 244200028 0.000000e+00 2577
3 TraesCS1D01G136100 chr1D 94.685 1637 76 7 676 2311 244768849 244767223 0.000000e+00 2531
4 TraesCS1D01G136100 chr1D 96.279 1290 47 1 1023 2312 290507190 290505902 0.000000e+00 2115
5 TraesCS1D01G136100 chr1D 99.249 666 4 1 1 665 254477542 254476877 0.000000e+00 1201
6 TraesCS1D01G136100 chr1A 97.740 1637 37 0 676 2312 554447575 554449211 0.000000e+00 2819
7 TraesCS1D01G136100 chr1A 99.699 664 2 0 2 665 554447403 554448066 0.000000e+00 1216
8 TraesCS1D01G136100 chr1A 99.549 665 3 0 1 665 554445594 554446258 0.000000e+00 1212
9 TraesCS1D01G136100 chr3B 97.253 1638 44 1 676 2312 201493374 201491737 0.000000e+00 2774
10 TraesCS1D01G136100 chr3B 99.098 665 6 0 1 665 201493547 201492883 0.000000e+00 1195
11 TraesCS1D01G136100 chr5D 97.068 1637 47 1 676 2312 6235530 6237165 0.000000e+00 2756
12 TraesCS1D01G136100 chr5D 97.212 1614 44 1 700 2312 503331258 503329645 0.000000e+00 2730
13 TraesCS1D01G136100 chr5D 98.797 665 8 0 1 665 6235357 6236021 0.000000e+00 1184
14 TraesCS1D01G136100 chr2D 97.126 1392 39 1 676 2066 648662932 648664323 0.000000e+00 2348
15 TraesCS1D01G136100 chr2D 99.549 665 3 0 1 665 648660420 648661084 0.000000e+00 1212
16 TraesCS1D01G136100 chr2D 99.249 666 4 1 1 665 648662759 648663424 0.000000e+00 1201
17 TraesCS1D01G136100 chrUn 99.549 665 3 0 1 665 457255594 457254930 0.000000e+00 1212
18 TraesCS1D01G136100 chrUn 99.549 665 3 0 1 665 465172006 465171342 0.000000e+00 1212
19 TraesCS1D01G136100 chrUn 99.249 666 4 1 1 665 426379841 426380506 0.000000e+00 1201
20 TraesCS1D01G136100 chrUn 97.611 628 15 0 676 1303 465171833 465171206 0.000000e+00 1077
21 TraesCS1D01G136100 chr7A 94.881 293 15 0 1950 2242 647115792 647116084 2.090000e-125 459


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 TraesCS1D01G136100 chr1D 180355349 180357660 2311 False 4233.0 4233 100.000000 1 2312 1 chr1D.!!$F1 2311
1 TraesCS1D01G136100 chr1D 244200028 244201661 1633 True 2577.0 2577 95.113000 676 2312 1 chr1D.!!$R1 1636
2 TraesCS1D01G136100 chr1D 244767223 244768849 1626 True 2531.0 2531 94.685000 676 2311 1 chr1D.!!$R2 1635
3 TraesCS1D01G136100 chr1D 290505902 290507190 1288 True 2115.0 2115 96.279000 1023 2312 1 chr1D.!!$R3 1289
4 TraesCS1D01G136100 chr1D 254475732 254477542 1810 True 1982.0 2763 98.190000 1 2312 2 chr1D.!!$R4 2311
5 TraesCS1D01G136100 chr1A 554445594 554449211 3617 False 1749.0 2819 98.996000 1 2312 3 chr1A.!!$F1 2311
6 TraesCS1D01G136100 chr3B 201491737 201493547 1810 True 1984.5 2774 98.175500 1 2312 2 chr3B.!!$R1 2311
7 TraesCS1D01G136100 chr5D 503329645 503331258 1613 True 2730.0 2730 97.212000 700 2312 1 chr5D.!!$R1 1612
8 TraesCS1D01G136100 chr5D 6235357 6237165 1808 False 1970.0 2756 97.932500 1 2312 2 chr5D.!!$F1 2311
9 TraesCS1D01G136100 chr2D 648660420 648664323 3903 False 1587.0 2348 98.641333 1 2066 3 chr2D.!!$F1 2065
10 TraesCS1D01G136100 chrUn 457254930 457255594 664 True 1212.0 1212 99.549000 1 665 1 chrUn.!!$R1 664
11 TraesCS1D01G136100 chrUn 426379841 426380506 665 False 1201.0 1201 99.249000 1 665 1 chrUn.!!$F1 664
12 TraesCS1D01G136100 chrUn 465171206 465172006 800 True 1144.5 1212 98.580000 1 1303 2 chrUn.!!$R2 1302

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
635 3832 7.168972 CCAGAGAAGCTTTCTAGTTATGAATCG 59.831 40.741 0.0 0.0 40.87 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 5264 1.831736 GGTCTGCTTGCCTAGGACTTA 59.168 52.381 14.75 0.0 0.0 2.24 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
633 3830 7.856415 ACCAGAGAAGCTTTCTAGTTATGAAT 58.144 34.615 0.00 0.00 40.87 2.57
634 3831 7.984617 ACCAGAGAAGCTTTCTAGTTATGAATC 59.015 37.037 0.00 0.00 40.87 2.52
635 3832 7.168972 CCAGAGAAGCTTTCTAGTTATGAATCG 59.831 40.741 0.00 0.00 40.87 3.34
636 3833 7.168972 CAGAGAAGCTTTCTAGTTATGAATCGG 59.831 40.741 0.00 0.00 40.87 4.18
637 3834 6.284459 AGAAGCTTTCTAGTTATGAATCGGG 58.716 40.000 0.00 0.00 38.49 5.14
638 3835 5.615925 AGCTTTCTAGTTATGAATCGGGT 57.384 39.130 0.00 0.00 0.00 5.28
640 3837 7.304497 AGCTTTCTAGTTATGAATCGGGTAT 57.696 36.000 0.00 0.00 0.00 2.73
641 3838 8.418597 AGCTTTCTAGTTATGAATCGGGTATA 57.581 34.615 0.00 0.00 0.00 1.47
642 3839 8.524487 AGCTTTCTAGTTATGAATCGGGTATAG 58.476 37.037 0.00 0.00 0.00 1.31
643 3840 8.521176 GCTTTCTAGTTATGAATCGGGTATAGA 58.479 37.037 0.00 0.00 0.00 1.98
662 3859 4.147587 CCCATGGGAGGGGCTTGG 62.148 72.222 28.27 0.00 45.60 3.61
663 3860 4.147587 CCATGGGAGGGGCTTGGG 62.148 72.222 2.85 0.00 0.00 4.12
664 3861 3.350163 CATGGGAGGGGCTTGGGT 61.350 66.667 0.00 0.00 0.00 4.51
936 4582 8.888716 GGAAAAGAGAGAAGTTCTGGATAAATC 58.111 37.037 10.90 0.84 35.87 2.17
946 4592 6.582636 AGTTCTGGATAAATCGACAATGCTA 58.417 36.000 0.00 0.00 0.00 3.49
1077 4724 7.047271 GCCTTATTCCTATTTTGGCATTTTCA 58.953 34.615 0.00 0.00 38.79 2.69
1084 4731 8.915057 TCCTATTTTGGCATTTTCAATTTCAA 57.085 26.923 0.00 0.00 0.00 2.69
1097 4744 5.371115 TCAATTTCAAGACTTTTAGCCCG 57.629 39.130 0.00 0.00 0.00 6.13
1175 4823 0.040499 GGGGCTTGGGTACAATTCCA 59.960 55.000 0.00 0.00 35.73 3.53
1247 4895 2.770232 CCGTCTTTCTATACCCTTGGGT 59.230 50.000 16.31 16.31 0.00 4.51
1257 4905 7.519347 TCTATACCCTTGGGTAATGAGTTTT 57.481 36.000 20.95 6.18 0.00 2.43
1275 4923 5.801380 AGTTTTGACGTATTGGGTGTATCT 58.199 37.500 0.00 0.00 0.00 1.98
1293 4941 8.021396 GGTGTATCTGTTTTTATCGAAGCTTTT 58.979 33.333 0.00 0.00 0.00 2.27
1310 4959 7.045354 CGAAGCTTTTATTTTCGTGCTTATCTG 60.045 37.037 0.00 0.00 40.26 2.90
1331 4980 7.504924 TCTGAGTTGTTGGTTTAGTTTATGG 57.495 36.000 0.00 0.00 0.00 2.74
1343 4992 6.349860 GGTTTAGTTTATGGATGGCGAAAAGT 60.350 38.462 0.00 0.00 0.00 2.66
1528 5181 7.310634 TCTCTAGTTTATGGCCCCTTCTATAA 58.689 38.462 0.00 0.00 0.00 0.98
1611 5264 5.996644 TCGTTATGGATTGGTACCAAGATT 58.003 37.500 30.00 15.71 40.93 2.40
1641 5294 6.547510 CCTAGGCAAGCAGACCTAATTTTAAT 59.452 38.462 0.00 0.00 38.07 1.40
1668 5321 5.883503 GGTACGGTAACAATGAAAATGGA 57.116 39.130 0.00 0.00 0.00 3.41
1756 5409 7.475798 GCCTATACTATTACAGGGGGAATGTTT 60.476 40.741 0.00 0.00 32.02 2.83
1863 5516 5.011738 CGGAGGCAGTTATAGATTCCCTAAA 59.988 44.000 0.00 0.00 0.00 1.85
1975 5628 2.295253 ATGTTAGGCGCAGTACTCAC 57.705 50.000 10.83 0.00 0.00 3.51
2250 5904 6.070021 ACATGAGGTGGTTCATAGATCTTTGA 60.070 38.462 11.36 11.36 36.08 2.69
2251 5905 6.566079 TGAGGTGGTTCATAGATCTTTGAT 57.434 37.500 15.44 1.17 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
636 3833 1.985895 CCCTCCCATGGGTTCTATACC 59.014 57.143 30.28 0.00 46.99 2.73
637 3834 1.985895 CCCCTCCCATGGGTTCTATAC 59.014 57.143 30.28 0.00 45.70 1.47
638 3835 1.768725 GCCCCTCCCATGGGTTCTATA 60.769 57.143 30.28 9.15 45.70 1.31
640 3837 1.696314 GCCCCTCCCATGGGTTCTA 60.696 63.158 30.28 10.36 45.70 2.10
641 3838 3.023735 GCCCCTCCCATGGGTTCT 61.024 66.667 30.28 0.00 45.70 3.01
642 3839 2.626467 AAGCCCCTCCCATGGGTTC 61.626 63.158 30.28 15.00 45.70 3.62
643 3840 2.537959 AAGCCCCTCCCATGGGTT 60.538 61.111 30.28 13.43 45.70 4.11
644 3841 3.350163 CAAGCCCCTCCCATGGGT 61.350 66.667 30.28 7.14 45.70 4.51
645 3842 4.147587 CCAAGCCCCTCCCATGGG 62.148 72.222 26.30 26.30 46.56 4.00
646 3843 4.147587 CCCAAGCCCCTCCCATGG 62.148 72.222 4.14 4.14 0.00 3.66
647 3844 3.350163 ACCCAAGCCCCTCCCATG 61.350 66.667 0.00 0.00 0.00 3.66
714 4360 5.175859 ACTTTCTCGTTTCACTTTGTCTCA 58.824 37.500 0.00 0.00 0.00 3.27
936 4582 8.894409 TTAGTCAATTCAATTTAGCATTGTCG 57.106 30.769 0.00 0.00 0.00 4.35
1049 4696 6.813293 ATGCCAAAATAGGAATAAGGCTTT 57.187 33.333 4.45 0.00 41.12 3.51
1077 4724 3.509967 CCCGGGCTAAAAGTCTTGAAATT 59.490 43.478 8.08 0.00 0.00 1.82
1084 4731 2.027469 CACTAACCCGGGCTAAAAGTCT 60.027 50.000 24.08 0.00 0.00 3.24
1097 4744 2.537143 TCTCTGGTCCTTCACTAACCC 58.463 52.381 0.00 0.00 31.78 4.11
1175 4823 7.904977 CGAGCGCAAACATATAATAGCATATTT 59.095 33.333 11.47 0.00 0.00 1.40
1247 4895 5.998981 ACACCCAATACGTCAAAACTCATTA 59.001 36.000 0.00 0.00 0.00 1.90
1257 4905 4.811969 AACAGATACACCCAATACGTCA 57.188 40.909 0.00 0.00 0.00 4.35
1275 4923 9.453325 ACGAAAATAAAAGCTTCGATAAAAACA 57.547 25.926 8.59 0.00 43.53 2.83
1293 4941 7.360861 CCAACAACTCAGATAAGCACGAAAATA 60.361 37.037 0.00 0.00 0.00 1.40
1310 4959 7.312899 CCATCCATAAACTAAACCAACAACTC 58.687 38.462 0.00 0.00 0.00 3.01
1343 4992 4.534500 TCAGTTAAGACCATTCCAAGGCTA 59.466 41.667 0.00 0.00 0.00 3.93
1407 5060 9.753674 AGGGAAACTCAATCAAATTCATAACTA 57.246 29.630 0.00 0.00 0.00 2.24
1528 5181 7.581213 TTCAATGAAACAACAACTGGTATCT 57.419 32.000 0.00 0.00 0.00 1.98
1611 5264 1.831736 GGTCTGCTTGCCTAGGACTTA 59.168 52.381 14.75 0.00 0.00 2.24
1668 5321 7.094118 GCTCGTATAATCTCACTAAAGAGGGAT 60.094 40.741 0.00 0.00 33.50 3.85
1756 5409 7.600375 CGAACAGTACTATAGGAATCCGTACTA 59.400 40.741 14.44 0.00 38.84 1.82
1863 5516 6.529125 TCGCGATATCTTCTTACGAAGTTTTT 59.471 34.615 3.71 0.00 45.47 1.94
1975 5628 6.320171 CAATTCTTGCTCATAAGTTCCTGTG 58.680 40.000 0.00 0.00 0.00 3.66
2172 5826 3.204526 GCATTGTCTTCATCTCTCCCTG 58.795 50.000 0.00 0.00 0.00 4.45
2250 5904 5.835819 TCTCTATTCCTCGGTGATCAAAGAT 59.164 40.000 0.00 0.00 0.00 2.40
2251 5905 5.067936 GTCTCTATTCCTCGGTGATCAAAGA 59.932 44.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.