Multiple sequence alignment - TraesCS2B01G283400

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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 TraesCS2B01G283400 chr2B 100.000 2609 0 0 1 2609 391143792 391146400 0 4819
1 TraesCS2B01G283400 chr2B 97.359 2613 63 3 1 2609 391226256 391223646 0 4438
2 TraesCS2B01G283400 chr6B 98.200 2611 45 1 1 2609 596602871 596600261 0 4560
3 TraesCS2B01G283400 chr7A 98.047 2612 47 2 1 2609 638508678 638506068 0 4538
4 TraesCS2B01G283400 chr7A 97.894 2611 50 3 1 2609 708244614 708247221 0 4512
5 TraesCS2B01G283400 chrUn 98.047 2612 46 4 1 2609 171007273 171009882 0 4536
6 TraesCS2B01G283400 chr5B 97.742 2613 55 2 1 2609 567278982 567281594 0 4495
7 TraesCS2B01G283400 chr1B 97.664 2611 58 3 1 2609 672540211 672542820 0 4481
8 TraesCS2B01G283400 chr4B 97.317 2609 66 4 1 2609 495566953 495569557 0 4427
9 TraesCS2B01G283400 chr3B 96.180 2618 87 9 1 2609 39876066 39878679 0 4268


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 TraesCS2B01G283400 chr2B 391143792 391146400 2608 False 4819 4819 100.000 1 2609 1 chr2B.!!$F1 2608
1 TraesCS2B01G283400 chr2B 391223646 391226256 2610 True 4438 4438 97.359 1 2609 1 chr2B.!!$R1 2608
2 TraesCS2B01G283400 chr6B 596600261 596602871 2610 True 4560 4560 98.200 1 2609 1 chr6B.!!$R1 2608
3 TraesCS2B01G283400 chr7A 638506068 638508678 2610 True 4538 4538 98.047 1 2609 1 chr7A.!!$R1 2608
4 TraesCS2B01G283400 chr7A 708244614 708247221 2607 False 4512 4512 97.894 1 2609 1 chr7A.!!$F1 2608
5 TraesCS2B01G283400 chrUn 171007273 171009882 2609 False 4536 4536 98.047 1 2609 1 chrUn.!!$F1 2608
6 TraesCS2B01G283400 chr5B 567278982 567281594 2612 False 4495 4495 97.742 1 2609 1 chr5B.!!$F1 2608
7 TraesCS2B01G283400 chr1B 672540211 672542820 2609 False 4481 4481 97.664 1 2609 1 chr1B.!!$F1 2608
8 TraesCS2B01G283400 chr4B 495566953 495569557 2604 False 4427 4427 97.317 1 2609 1 chr4B.!!$F1 2608
9 TraesCS2B01G283400 chr3B 39876066 39878679 2613 False 4268 4268 96.180 1 2609 1 chr3B.!!$F1 2608


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
861 867 1.303806 TCTGATCGACCCGGACACA 60.304 57.895 0.73 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2412 0.594028 GCGTATCACGGATCGAGCAA 60.594 55.0 1.84 0.0 42.82 3.91 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
433 434 4.405680 TGAAGAGTACCCGATGACATTCAT 59.594 41.667 0.00 0.0 40.34 2.57
838 844 2.858476 TGGGGGAGAAGCAAGCCA 60.858 61.111 0.00 0.0 0.00 4.75
861 867 1.303806 TCTGATCGACCCGGACACA 60.304 57.895 0.73 0.0 0.00 3.72
1040 1046 6.462768 CCAACATTCAAGTTCCATTTCAAGGA 60.463 38.462 0.00 0.0 0.00 3.36
1043 1049 6.550854 ACATTCAAGTTCCATTTCAAGGAAGA 59.449 34.615 0.00 0.0 45.27 2.87
1108 1114 4.003648 GGTCTCTGGTTTGATGGTTGTAG 58.996 47.826 0.00 0.0 0.00 2.74
1121 1127 6.245408 TGATGGTTGTAGGTGCTAAAAATCT 58.755 36.000 0.00 0.0 0.00 2.40
1168 1174 4.521639 TCCTAGTCTTTTGCGACACTTCTA 59.478 41.667 0.00 0.0 36.38 2.10
1293 1300 8.675705 TCAATATTCAAATAGCGGAGATTCAA 57.324 30.769 0.00 0.0 0.00 2.69
1593 1600 5.751586 AGGACTACAAAGGTGAAAAGACAA 58.248 37.500 0.00 0.0 0.00 3.18
1606 1613 6.316390 GGTGAAAAGACAAGATGTATTCCGAT 59.684 38.462 0.00 0.0 29.51 4.18
1863 1870 1.679898 CCGGGACTTTCCTCTGCTT 59.320 57.895 0.00 0.0 36.57 3.91
1881 1888 3.587061 TGCTTGAGATCTTAGAACCCCAA 59.413 43.478 0.00 0.0 0.00 4.12
1988 1998 6.703319 TGTATTGTTTCTCGAATTGGTAGGA 58.297 36.000 0.00 0.0 0.00 2.94
2016 2026 9.507329 TCTCGAAGTAGTTTTAGTAGGTTTCTA 57.493 33.333 0.00 0.0 0.00 2.10
2049 2059 1.382146 CCGAGGCCCCTACTTACCA 60.382 63.158 0.00 0.0 0.00 3.25
2092 2102 0.907230 GAGTGGGTCAGAGGGCTTCT 60.907 60.000 0.00 0.0 36.25 2.85
2134 2152 6.564328 TCTTTCTCTTTTGAGTTTTTCTGGC 58.436 36.000 0.00 0.0 46.30 4.85
2161 2180 0.909623 GATCTTTGGTCTTCCCCCGA 59.090 55.000 0.00 0.0 0.00 5.14
2246 2265 2.840974 GGGGATGACATTATCGCCG 58.159 57.895 4.31 0.0 46.11 6.46
2262 2281 3.191669 TCGCCGTTGATTGAATTCGTAT 58.808 40.909 0.04 0.0 0.00 3.06
2362 2382 2.344872 CTTGCCCTGCCTTTTGCC 59.655 61.111 0.00 0.0 40.16 4.52
2363 2383 2.122901 TTGCCCTGCCTTTTGCCT 60.123 55.556 0.00 0.0 40.16 4.75
2392 2412 6.398918 AGTGTAGTTCGAGCATTCTATTGTT 58.601 36.000 1.01 0.0 0.00 2.83
2517 2537 1.371558 GCACTCGGGTTCTCCTGTT 59.628 57.895 0.00 0.0 40.77 3.16
2592 2613 1.913778 TGAGGGTACGAGCAACACTA 58.086 50.000 0.00 0.0 28.36 2.74
2599 2620 2.335316 ACGAGCAACACTACCCAAAA 57.665 45.000 0.00 0.0 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
433 434 2.368548 CCGATGGGTCTACATTCATCCA 59.631 50.000 0.00 0.00 34.24 3.41
585 586 8.528044 TTTGGATATTAAGGAAGCCGTATTTT 57.472 30.769 0.00 0.00 0.00 1.82
792 798 5.140454 GCCTATGAAATGGATAACCCTTGT 58.860 41.667 0.00 0.00 35.38 3.16
838 844 0.613853 TCCGGGTCGATCAGAGGTTT 60.614 55.000 0.00 0.00 0.00 3.27
861 867 0.098728 CGGCGCCGAGAATTTTTGAT 59.901 50.000 44.86 0.00 42.83 2.57
1040 1046 4.978083 AGTATCATGGTACGTCGTTCTT 57.022 40.909 10.46 0.00 0.00 2.52
1043 1049 5.100259 CAGAAAGTATCATGGTACGTCGTT 58.900 41.667 10.46 4.16 0.00 3.85
1108 1114 5.448632 CGGAATGTACCAGATTTTTAGCACC 60.449 44.000 0.00 0.00 0.00 5.01
1121 1127 3.318557 GGGAAACAAAACGGAATGTACCA 59.681 43.478 0.00 0.00 31.89 3.25
1168 1174 9.201127 GTCGAGACCTAACAAAATAAGTAAACT 57.799 33.333 0.00 0.00 0.00 2.66
1293 1300 6.346096 TGGTAAATAGCGCAATACTTCTTCT 58.654 36.000 11.47 0.00 0.00 2.85
1593 1600 4.978099 AGGCATTTCATCGGAATACATCT 58.022 39.130 0.00 0.00 31.93 2.90
1606 1613 4.785301 CTCCTAGAATCCAAGGCATTTCA 58.215 43.478 0.00 0.00 32.55 2.69
1863 1870 6.498651 GGATATCTTGGGGTTCTAAGATCTCA 59.501 42.308 14.62 0.00 44.48 3.27
1900 1907 0.598419 CACTGCTTGTGCGAGTGAGA 60.598 55.000 11.98 0.00 43.88 3.27
1988 1998 9.636879 GAAACCTACTAAAACTACTTCGAGAAT 57.363 33.333 0.00 0.00 0.00 2.40
2016 2026 2.224402 GCCTCGGCATCTCTATTTCCTT 60.224 50.000 2.41 0.00 41.49 3.36
2049 2059 2.115605 CCTTCCCCCTACCTACCCATAT 59.884 54.545 0.00 0.00 0.00 1.78
2092 2102 4.623932 AAGAGAGGTATGCACTGTGAAA 57.376 40.909 12.86 0.00 0.00 2.69
2134 2152 1.021390 AGACCAAAGATCTTGCGCGG 61.021 55.000 9.17 9.96 0.00 6.46
2161 2180 1.268625 GACCCGCTTTTTCATCGGTTT 59.731 47.619 0.00 0.00 41.46 3.27
2246 2265 7.004225 GCGATAGACATACGAATTCAATCAAC 58.996 38.462 6.22 0.00 39.76 3.18
2262 2281 1.248785 GCCCGGGATAGCGATAGACA 61.249 60.000 29.31 0.00 39.76 3.41
2362 2382 1.813178 TGCTCGAACTACACTCTCCAG 59.187 52.381 0.00 0.00 0.00 3.86
2363 2383 1.905637 TGCTCGAACTACACTCTCCA 58.094 50.000 0.00 0.00 0.00 3.86
2392 2412 0.594028 GCGTATCACGGATCGAGCAA 60.594 55.000 1.84 0.00 42.82 3.91



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

AutoCloner maintained by Alex Coulton.