Multiple sequence alignment - TraesCS1B01G190100

Loading Multiple Alignment...

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 TraesCS1B01G190100 chr1B 100.000 2602 0 0 1 2602 340984772 340987373 0 4806
1 TraesCS1B01G190100 chr1B 94.337 2013 92 10 608 2602 82746253 82748261 0 3066
2 TraesCS1B01G190100 chr6B 95.260 2616 83 11 1 2602 209598017 209600605 0 4106
3 TraesCS1B01G190100 chr6B 93.280 2619 152 14 1 2602 174542783 174540172 0 3840
4 TraesCS1B01G190100 chr6B 92.698 2643 146 15 1 2602 392466972 392464336 0 3768
5 TraesCS1B01G190100 chr6B 92.923 1724 96 12 902 2602 673867980 673866260 0 2484
6 TraesCS1B01G190100 chr4B 95.036 2619 109 9 3 2602 523190634 523193250 0 4096
7 TraesCS1B01G190100 chr3B 95.456 2487 96 9 1 2472 193598218 193595734 0 3951
8 TraesCS1B01G190100 chr3B 92.849 2643 141 16 1 2602 706230007 706227372 0 3790
9 TraesCS1B01G190100 chr3B 93.386 2026 109 16 1 2004 751329071 751327049 0 2976
10 TraesCS1B01G190100 chr3B 92.749 1724 100 12 902 2602 12925567 12923846 0 2468
11 TraesCS1B01G190100 chr2A 92.490 2623 163 18 1 2602 733317072 733319681 0 3722
12 TraesCS1B01G190100 chr5B 91.447 2619 172 31 1 2602 130903536 130900953 0 3548
13 TraesCS1B01G190100 chr5B 89.093 2338 223 27 1 2331 194199767 194197455 0 2876
14 TraesCS1B01G190100 chr5B 93.039 1724 93 14 902 2602 426079265 426080984 0 2494
15 TraesCS1B01G190100 chr7A 92.743 2439 149 17 1 2423 24841732 24839306 0 3498


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 TraesCS1B01G190100 chr1B 340984772 340987373 2601 False 4806 4806 100.000 1 2602 1 chr1B.!!$F2 2601
1 TraesCS1B01G190100 chr1B 82746253 82748261 2008 False 3066 3066 94.337 608 2602 1 chr1B.!!$F1 1994
2 TraesCS1B01G190100 chr6B 209598017 209600605 2588 False 4106 4106 95.260 1 2602 1 chr6B.!!$F1 2601
3 TraesCS1B01G190100 chr6B 174540172 174542783 2611 True 3840 3840 93.280 1 2602 1 chr6B.!!$R1 2601
4 TraesCS1B01G190100 chr6B 392464336 392466972 2636 True 3768 3768 92.698 1 2602 1 chr6B.!!$R2 2601
5 TraesCS1B01G190100 chr6B 673866260 673867980 1720 True 2484 2484 92.923 902 2602 1 chr6B.!!$R3 1700
6 TraesCS1B01G190100 chr4B 523190634 523193250 2616 False 4096 4096 95.036 3 2602 1 chr4B.!!$F1 2599
7 TraesCS1B01G190100 chr3B 193595734 193598218 2484 True 3951 3951 95.456 1 2472 1 chr3B.!!$R2 2471
8 TraesCS1B01G190100 chr3B 706227372 706230007 2635 True 3790 3790 92.849 1 2602 1 chr3B.!!$R3 2601
9 TraesCS1B01G190100 chr3B 751327049 751329071 2022 True 2976 2976 93.386 1 2004 1 chr3B.!!$R4 2003
10 TraesCS1B01G190100 chr3B 12923846 12925567 1721 True 2468 2468 92.749 902 2602 1 chr3B.!!$R1 1700
11 TraesCS1B01G190100 chr2A 733317072 733319681 2609 False 3722 3722 92.490 1 2602 1 chr2A.!!$F1 2601
12 TraesCS1B01G190100 chr5B 130900953 130903536 2583 True 3548 3548 91.447 1 2602 1 chr5B.!!$R1 2601
13 TraesCS1B01G190100 chr5B 194197455 194199767 2312 True 2876 2876 89.093 1 2331 1 chr5B.!!$R2 2330
14 TraesCS1B01G190100 chr5B 426079265 426080984 1719 False 2494 2494 93.039 902 2602 1 chr5B.!!$F1 1700
15 TraesCS1B01G190100 chr7A 24839306 24841732 2426 True 3498 3498 92.743 1 2423 1 chr7A.!!$R1 2422

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
76 77 0.034059 CGGCACCTGAGGATACCATC 59.966 60.000 4.99 0.0 37.17 3.51 F
457 462 1.426621 GGAGCGACGTACATCGACA 59.573 57.895 16.54 0.0 45.13 4.35 F
560 565 1.741401 ACATCGATGTGTGTGCCGG 60.741 57.895 29.49 0.0 40.03 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 1377 0.307760 GAACACGCAAACAGGACAGG 59.692 55.000 0.00 0.00 0.0 4.00 R
1481 1503 4.691216 GTGTAGATTTTTCGGAGCTCAACT 59.309 41.667 17.19 0.16 0.0 3.16 R
2537 2619 1.819632 GGCGATGTGACATGGTCCC 60.820 63.158 1.23 0.00 0.0 4.46 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
76 77 0.034059 CGGCACCTGAGGATACCATC 59.966 60.000 4.99 0.0 37.17 3.51
79 80 2.042464 GCACCTGAGGATACCATCAGA 58.958 52.381 4.99 0.0 44.68 3.27
422 427 3.144506 ACAGCTCATGTTTGGACAGAAG 58.855 45.455 0.00 0.0 39.96 2.85
457 462 1.426621 GGAGCGACGTACATCGACA 59.573 57.895 16.54 0.0 45.13 4.35
560 565 1.741401 ACATCGATGTGTGTGCCGG 60.741 57.895 29.49 0.0 40.03 6.13
756 763 6.457934 CCATCTTCTGCACTTGTGATTATGTC 60.458 42.308 4.79 0.0 0.00 3.06
758 765 4.186856 TCTGCACTTGTGATTATGTCGA 57.813 40.909 4.79 0.0 0.00 4.20
975 992 4.745125 TCTTTTTGTGTAGTCTGCTTCTCG 59.255 41.667 0.00 0.0 0.00 4.04
1035 1055 2.158652 CCAGGATCTTGCACCTCATGAT 60.159 50.000 0.00 0.0 40.86 2.45
1101 1121 5.534654 CCTGAAGAACCAACATTTTGAGGTA 59.465 40.000 0.00 0.0 34.24 3.08
1187 1207 2.711009 ACCTCAAAGAGACATGGAACCA 59.289 45.455 0.00 0.0 0.00 3.67
1291 1311 2.053747 TAACCCCCTCCTTCATGTGT 57.946 50.000 0.00 0.0 0.00 3.72
1309 1329 4.532276 TGTGTCGTTTACATCAATGCAAC 58.468 39.130 0.00 0.0 41.10 4.17
1357 1377 5.975410 ATTGAAGTCTATCTTTGCTACGC 57.025 39.130 0.00 0.0 36.40 4.42
1385 1407 4.154015 CCTGTTTGCGTGTTCATCTGAATA 59.846 41.667 0.00 0.0 36.33 1.75
1511 1533 5.066505 GCTCCGAAAAATCTACACATGGAAT 59.933 40.000 0.00 0.0 0.00 3.01
1710 1736 4.983215 TGTTTGTGTGCTATGTTACGAG 57.017 40.909 0.00 0.0 0.00 4.18
2029 2074 3.008923 TGATCATGTAGCCACAACCTTGA 59.991 43.478 0.00 0.0 38.42 3.02
2120 2168 3.316283 TCTAAACCGCGTCGTATTTGTT 58.684 40.909 4.92 0.0 0.00 2.83
2537 2619 5.047188 GGGTACAAAACAAAATGTCCACAG 58.953 41.667 0.00 0.0 0.00 3.66
2591 2673 1.229177 ATTGCCCGCCCCTTTCTTT 60.229 52.632 0.00 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 3.494048 GCACTTCTGATGGTATCCTCAGG 60.494 52.174 8.25 0.00 39.48 3.86
76 77 2.034687 CCAGGGGTGGCACTTCTG 59.965 66.667 23.67 23.67 0.00 3.02
79 80 2.084930 AGAACCAGGGGTGGCACTT 61.085 57.895 18.45 2.02 35.34 3.16
236 237 4.336993 TGTGGTCATTTACGCTTTCAACTT 59.663 37.500 0.00 0.00 0.00 2.66
422 427 2.523015 CTCCGCATTGAATGACTTTGC 58.477 47.619 9.76 0.00 0.00 3.68
451 456 1.475751 GGCAAGATCACCCATGTCGAT 60.476 52.381 0.00 0.00 0.00 3.59
457 462 0.179000 GACTCGGCAAGATCACCCAT 59.821 55.000 0.00 0.00 0.00 4.00
486 491 4.143263 ACATTCGTCGACATTTTACCGTTC 60.143 41.667 17.16 0.00 0.00 3.95
560 565 6.635641 CACACTGTAATGCATGATTATCTTGC 59.364 38.462 21.36 21.36 44.74 4.01
756 763 3.557577 TGCCACATGAAAACATCTTCG 57.442 42.857 0.00 0.00 0.00 3.79
758 765 4.624015 CTGTTGCCACATGAAAACATCTT 58.376 39.130 0.00 0.00 32.47 2.40
975 992 8.309163 TGACCTGCATTTGAAATTGAATAAAC 57.691 30.769 0.00 0.00 0.00 2.01
1101 1121 3.328382 TCCGAACGGATTGAATCAAGT 57.672 42.857 12.04 3.77 39.76 3.16
1187 1207 4.935808 GGACCTTTGAATGTTCGTAGTGAT 59.064 41.667 0.00 0.00 0.00 3.06
1291 1311 2.490115 GGGGTTGCATTGATGTAAACGA 59.510 45.455 4.21 0.00 40.39 3.85
1309 1329 2.383855 TGTGACAACAAAAAGAGGGGG 58.616 47.619 0.00 0.00 31.82 5.40
1357 1377 0.307760 GAACACGCAAACAGGACAGG 59.692 55.000 0.00 0.00 0.00 4.00
1481 1503 4.691216 GTGTAGATTTTTCGGAGCTCAACT 59.309 41.667 17.19 0.16 0.00 3.16
1511 1533 6.183360 TGTTGAAATCTTCATTCGTCAACCAA 60.183 34.615 10.79 0.00 38.19 3.67
2120 2168 8.596293 TGACTCTGCATGACATATATTTCCATA 58.404 33.333 0.00 0.00 0.00 2.74
2218 2267 6.530120 ACCGTATCTGCCATGTTAATTATGA 58.470 36.000 4.71 0.00 0.00 2.15
2289 2338 6.710295 TGTACTAAATATGCCATGCTAGTTGG 59.290 38.462 8.94 8.94 37.31 3.77
2537 2619 1.819632 GGCGATGTGACATGGTCCC 60.820 63.158 1.23 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.