Multiple sequence alignment - TraesCS2B01G523000

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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 TraesCS2B01G523000 chr2B 100.000 2264 0 0 1 2264 717652052 717654315 0 4181
1 TraesCS2B01G523000 chr2B 95.532 1701 59 4 571 2264 45596552 45598242 0 2704
2 TraesCS2B01G523000 chr2B 96.278 806 23 4 1 800 42193433 42194237 0 1315
3 TraesCS2B01G523000 chr2B 93.308 523 33 2 1742 2264 138733566 138734086 0 771
4 TraesCS2B01G523000 chr1B 97.968 2264 46 0 1 2264 550440098 550437835 0 3927
5 TraesCS2B01G523000 chr1B 96.015 803 26 3 1 797 38183421 38184223 0 1301
6 TraesCS2B01G523000 chr7B 95.916 1763 62 5 512 2264 235457593 235455831 0 2848
7 TraesCS2B01G523000 chr7B 97.378 1602 41 1 663 2264 130334623 130336223 0 2724
8 TraesCS2B01G523000 chr7B 92.836 1703 74 12 591 2264 577211915 577213598 0 2425
9 TraesCS2B01G523000 chr7B 96.650 806 21 3 1 800 235458064 235457259 0 1334
10 TraesCS2B01G523000 chr7B 96.650 806 21 3 1 800 687040652 687041457 0 1334
11 TraesCS2B01G523000 chr5B 95.379 1753 71 5 521 2264 530940320 530938569 0 2780
12 TraesCS2B01G523000 chr5B 97.022 806 18 3 1 800 464634136 464634941 0 1351
13 TraesCS2B01G523000 chr6B 96.548 1680 46 4 591 2264 114144244 114142571 0 2771
14 TraesCS2B01G523000 chr6B 94.239 1649 61 15 591 2233 661052199 661053819 0 2488
15 TraesCS2B01G523000 chr6B 94.778 517 25 2 1748 2264 650644914 650644400 0 804
16 TraesCS2B01G523000 chr4B 95.028 1770 67 7 496 2264 49106178 49107927 0 2761
17 TraesCS2B01G523000 chr4B 96.278 806 24 3 1 800 402787173 402786368 0 1317
18 TraesCS2B01G523000 chr3B 96.402 806 22 4 1 800 16124406 16123602 0 1321
19 TraesCS2B01G523000 chr3B 94.197 517 28 2 1748 2264 393330850 393331364 0 787
20 TraesCS2B01G523000 chr4A 96.278 806 24 3 1 800 712877508 712878313 0 1317
21 TraesCS2B01G523000 chr4A 95.358 517 24 0 1748 2264 712879259 712879775 0 822


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 TraesCS2B01G523000 chr2B 717652052 717654315 2263 False 4181.0 4181 100.000 1 2264 1 chr2B.!!$F4 2263
1 TraesCS2B01G523000 chr2B 45596552 45598242 1690 False 2704.0 2704 95.532 571 2264 1 chr2B.!!$F2 1693
2 TraesCS2B01G523000 chr2B 42193433 42194237 804 False 1315.0 1315 96.278 1 800 1 chr2B.!!$F1 799
3 TraesCS2B01G523000 chr2B 138733566 138734086 520 False 771.0 771 93.308 1742 2264 1 chr2B.!!$F3 522
4 TraesCS2B01G523000 chr1B 550437835 550440098 2263 True 3927.0 3927 97.968 1 2264 1 chr1B.!!$R1 2263
5 TraesCS2B01G523000 chr1B 38183421 38184223 802 False 1301.0 1301 96.015 1 797 1 chr1B.!!$F1 796
6 TraesCS2B01G523000 chr7B 130334623 130336223 1600 False 2724.0 2724 97.378 663 2264 1 chr7B.!!$F1 1601
7 TraesCS2B01G523000 chr7B 577211915 577213598 1683 False 2425.0 2425 92.836 591 2264 1 chr7B.!!$F2 1673
8 TraesCS2B01G523000 chr7B 235455831 235458064 2233 True 2091.0 2848 96.283 1 2264 2 chr7B.!!$R1 2263
9 TraesCS2B01G523000 chr7B 687040652 687041457 805 False 1334.0 1334 96.650 1 800 1 chr7B.!!$F3 799
10 TraesCS2B01G523000 chr5B 530938569 530940320 1751 True 2780.0 2780 95.379 521 2264 1 chr5B.!!$R1 1743
11 TraesCS2B01G523000 chr5B 464634136 464634941 805 False 1351.0 1351 97.022 1 800 1 chr5B.!!$F1 799
12 TraesCS2B01G523000 chr6B 114142571 114144244 1673 True 2771.0 2771 96.548 591 2264 1 chr6B.!!$R1 1673
13 TraesCS2B01G523000 chr6B 661052199 661053819 1620 False 2488.0 2488 94.239 591 2233 1 chr6B.!!$F1 1642
14 TraesCS2B01G523000 chr6B 650644400 650644914 514 True 804.0 804 94.778 1748 2264 1 chr6B.!!$R2 516
15 TraesCS2B01G523000 chr4B 49106178 49107927 1749 False 2761.0 2761 95.028 496 2264 1 chr4B.!!$F1 1768
16 TraesCS2B01G523000 chr4B 402786368 402787173 805 True 1317.0 1317 96.278 1 800 1 chr4B.!!$R1 799
17 TraesCS2B01G523000 chr3B 16123602 16124406 804 True 1321.0 1321 96.402 1 800 1 chr3B.!!$R1 799
18 TraesCS2B01G523000 chr3B 393330850 393331364 514 False 787.0 787 94.197 1748 2264 1 chr3B.!!$F1 516
19 TraesCS2B01G523000 chr4A 712877508 712879775 2267 False 1069.5 1317 95.818 1 2264 2 chr4A.!!$F1 2263

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
75 76 0.596600 GGCCATGCTCGCATTTGATG 60.597 55.0 0.0 0.0 33.9 3.07 F
697 797 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1056 1186 1.299976 GGCCTCCATCCACGTCTTT 59.700 57.895 0.0 0.0 0.00 2.52 R
1574 1704 2.491621 CTCCTCTCGTGCATCGCA 59.508 61.111 0.0 0.0 39.67 5.10 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
75 76 0.596600 GGCCATGCTCGCATTTGATG 60.597 55.000 0.00 0.00 33.90 3.07
78 79 1.402613 CCATGCTCGCATTTGATGACA 59.597 47.619 0.85 0.00 33.90 3.58
82 83 1.733912 GCTCGCATTTGATGACAGTGA 59.266 47.619 0.00 0.00 0.00 3.41
278 279 4.271661 ACGAAGGGTAGAAGGAGAACTAG 58.728 47.826 0.00 0.00 0.00 2.57
375 376 2.275318 GCTCCTGACACTATCAACTGC 58.725 52.381 0.00 0.00 36.69 4.40
572 573 2.223803 AGTGCTAGAGGTGCTAGTGT 57.776 50.000 0.00 0.00 46.81 3.55
574 575 2.494073 AGTGCTAGAGGTGCTAGTGTTC 59.506 50.000 0.00 0.00 46.81 3.18
577 578 2.681848 GCTAGAGGTGCTAGTGTTCGTA 59.318 50.000 0.00 0.00 46.81 3.43
579 580 3.069079 AGAGGTGCTAGTGTTCGTAGA 57.931 47.619 0.00 0.00 0.00 2.59
580 581 3.011119 AGAGGTGCTAGTGTTCGTAGAG 58.989 50.000 0.00 0.00 38.43 2.43
582 583 1.134560 GGTGCTAGTGTTCGTAGAGGG 59.865 57.143 0.00 0.00 38.43 4.30
583 584 2.089980 GTGCTAGTGTTCGTAGAGGGA 58.910 52.381 0.00 0.00 38.43 4.20
585 586 2.290768 TGCTAGTGTTCGTAGAGGGAGT 60.291 50.000 0.00 0.00 38.43 3.85
587 588 3.312146 GCTAGTGTTCGTAGAGGGAGTAC 59.688 52.174 0.00 0.00 38.43 2.73
588 589 3.430042 AGTGTTCGTAGAGGGAGTACA 57.570 47.619 0.00 0.00 38.43 2.90
590 591 3.757493 AGTGTTCGTAGAGGGAGTACAAG 59.243 47.826 0.00 0.00 38.43 3.16
591 592 3.505293 GTGTTCGTAGAGGGAGTACAAGT 59.495 47.826 0.00 0.00 38.43 3.16
592 593 3.504906 TGTTCGTAGAGGGAGTACAAGTG 59.495 47.826 0.00 0.00 38.43 3.16
593 594 2.089980 TCGTAGAGGGAGTACAAGTGC 58.910 52.381 0.00 0.00 0.00 4.40
677 777 1.292223 GTGGTGGTCGAGCTAGCAA 59.708 57.895 18.83 0.00 37.80 3.91
695 795 2.154462 CAAAAGTGCTAGAGGTGGTGG 58.846 52.381 0.00 0.00 0.00 4.61
696 796 1.435256 AAAGTGCTAGAGGTGGTGGT 58.565 50.000 0.00 0.00 0.00 4.16
697 797 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
698 798 1.215647 GTGCTAGAGGTGGTGGTCG 59.784 63.158 0.00 0.00 0.00 4.79
1056 1186 1.685224 GGACCAAGAGGACATGCCA 59.315 57.895 8.58 0.00 40.02 4.92
1574 1704 3.183793 CAAGAAAACTTGCAAGGGCTT 57.816 42.857 29.18 21.07 41.91 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.221742 GCCAATGATACTTACTAGGCCTCTT 60.222 44.000 9.68 0.00 34.94 2.85
75 76 0.039437 TTCTCGCCTTCGTCACTGTC 60.039 55.000 0.00 0.00 36.96 3.51
78 79 0.387929 TGTTTCTCGCCTTCGTCACT 59.612 50.000 0.00 0.00 36.96 3.41
82 83 2.736144 TGTATGTTTCTCGCCTTCGT 57.264 45.000 0.00 0.00 36.96 3.85
278 279 1.421646 CCATATCACCCCTGAACCTCC 59.578 57.143 0.00 0.00 0.00 4.30
566 567 4.511527 TGTACTCCCTCTACGAACACTAG 58.488 47.826 0.00 0.00 0.00 2.57
572 573 2.490903 GCACTTGTACTCCCTCTACGAA 59.509 50.000 0.00 0.00 0.00 3.85
574 575 2.093106 AGCACTTGTACTCCCTCTACG 58.907 52.381 0.00 0.00 0.00 3.51
577 578 3.626222 CCTCTAGCACTTGTACTCCCTCT 60.626 52.174 0.00 0.00 0.00 3.69
579 580 2.043252 ACCTCTAGCACTTGTACTCCCT 59.957 50.000 0.00 0.00 0.00 4.20
580 581 2.166664 CACCTCTAGCACTTGTACTCCC 59.833 54.545 0.00 0.00 0.00 4.30
582 583 2.826725 ACCACCTCTAGCACTTGTACTC 59.173 50.000 0.00 0.00 0.00 2.59
583 584 2.563179 CACCACCTCTAGCACTTGTACT 59.437 50.000 0.00 0.00 0.00 2.73
585 586 1.899814 CCACCACCTCTAGCACTTGTA 59.100 52.381 0.00 0.00 0.00 2.41
587 588 0.687354 ACCACCACCTCTAGCACTTG 59.313 55.000 0.00 0.00 0.00 3.16
588 589 0.977395 GACCACCACCTCTAGCACTT 59.023 55.000 0.00 0.00 0.00 3.16
590 591 1.215647 CGACCACCACCTCTAGCAC 59.784 63.158 0.00 0.00 0.00 4.40
591 592 0.965866 CTCGACCACCACCTCTAGCA 60.966 60.000 0.00 0.00 0.00 3.49
592 593 1.810532 CTCGACCACCACCTCTAGC 59.189 63.158 0.00 0.00 0.00 3.42
593 594 0.681564 AGCTCGACCACCACCTCTAG 60.682 60.000 0.00 0.00 0.00 2.43
677 777 1.348036 GACCACCACCTCTAGCACTTT 59.652 52.381 0.00 0.00 0.00 2.66
687 787 2.352032 GCTAGCTCGACCACCACCT 61.352 63.158 7.70 0.00 0.00 4.00
688 788 2.184579 GCTAGCTCGACCACCACC 59.815 66.667 7.70 0.00 0.00 4.61
689 789 1.446272 GTGCTAGCTCGACCACCAC 60.446 63.158 17.23 0.00 0.00 4.16
690 790 1.468506 TTGTGCTAGCTCGACCACCA 61.469 55.000 17.23 0.00 0.00 4.17
691 791 0.737715 CTTGTGCTAGCTCGACCACC 60.738 60.000 17.23 0.00 0.00 4.61
692 792 0.038159 ACTTGTGCTAGCTCGACCAC 60.038 55.000 17.23 4.92 0.00 4.16
693 793 0.038251 CACTTGTGCTAGCTCGACCA 60.038 55.000 17.23 2.09 0.00 4.02
694 794 1.355066 GCACTTGTGCTAGCTCGACC 61.355 60.000 17.23 0.00 0.00 4.79
695 795 0.389166 AGCACTTGTGCTAGCTCGAC 60.389 55.000 24.50 6.50 44.28 4.20
696 796 1.173913 TAGCACTTGTGCTAGCTCGA 58.826 50.000 25.81 11.44 44.28 4.04
697 797 3.721625 TAGCACTTGTGCTAGCTCG 57.278 52.632 25.81 3.24 44.28 5.03
1056 1186 1.299976 GGCCTCCATCCACGTCTTT 59.700 57.895 0.00 0.00 0.00 2.52
1163 1293 2.191128 ACCTTCTGTCCATGACTTGC 57.809 50.000 0.00 0.00 33.15 4.01
1574 1704 2.491621 CTCCTCTCGTGCATCGCA 59.508 61.111 0.00 0.00 39.67 5.10


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

AutoCloner maintained by Alex Coulton.