Multiple sequence alignment - TraesCS5A01G013300

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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 TraesCS5A01G013300 chr5A 100.000 2858 0 0 1 2858 9320083 9322940 0.000000e+00 5278
1 TraesCS5A01G013300 chr5A 99.090 2636 22 2 1 2635 605341458 605344092 0.000000e+00 4734
2 TraesCS5A01G013300 chr5A 98.619 1376 18 1 1243 2618 643872000 643870626 0.000000e+00 2435
3 TraesCS5A01G013300 chr5A 94.980 1474 70 4 1165 2637 464479990 464481460 0.000000e+00 2309
4 TraesCS5A01G013300 chr5A 100.000 426 0 0 3177 3602 9323259 9323684 0.000000e+00 787
5 TraesCS5A01G013300 chr5A 73.400 703 163 21 3 693 275254031 275253341 1.290000e-59 241
6 TraesCS5A01G013300 chr6A 99.014 2636 25 1 1 2635 38479508 38482143 0.000000e+00 4723
7 TraesCS5A01G013300 chr6A 98.621 1885 23 3 751 2634 100350242 100352124 0.000000e+00 3334
8 TraesCS5A01G013300 chr1A 98.596 2636 28 2 1 2635 496093940 496091313 0.000000e+00 4654
9 TraesCS5A01G013300 chr1A 98.374 2091 32 2 547 2635 541889198 541887108 0.000000e+00 3672
10 TraesCS5A01G013300 chrUn 98.481 2634 36 4 3 2635 252265787 252263157 0.000000e+00 4639
11 TraesCS5A01G013300 chr2A 98.105 2638 34 5 1 2634 705849879 705852504 0.000000e+00 4580
12 TraesCS5A01G013300 chr3B 95.172 1657 77 3 982 2636 734423038 734424693 0.000000e+00 2614
13 TraesCS5A01G013300 chr3B 96.061 990 34 2 1 986 734409888 734410876 0.000000e+00 1607
14 TraesCS5A01G013300 chr4B 94.418 1057 43 4 608 1663 54797554 54798595 0.000000e+00 1611
15 TraesCS5A01G013300 chr4B 95.034 584 28 1 1 584 54788492 54787910 0.000000e+00 917
16 TraesCS5A01G013300 chr5D 93.204 412 18 5 3177 3588 10897215 10897616 6.660000e-167 597
17 TraesCS5A01G013300 chr5D 93.363 226 8 4 2634 2858 10896916 10897135 9.640000e-86 327
18 TraesCS5A01G013300 chr5B 93.201 353 15 5 3250 3602 11454818 11455161 8.920000e-141 510
19 TraesCS5A01G013300 chr7B 79.157 451 89 5 17 465 203653516 203653963 1.260000e-79 307


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 TraesCS5A01G013300 chr5A 9320083 9323684 3601 False 3032.5 5278 100.0000 1 3602 2 chr5A.!!$F3 3601
1 TraesCS5A01G013300 chr5A 605341458 605344092 2634 False 4734.0 4734 99.0900 1 2635 1 chr5A.!!$F2 2634
2 TraesCS5A01G013300 chr5A 643870626 643872000 1374 True 2435.0 2435 98.6190 1243 2618 1 chr5A.!!$R2 1375
3 TraesCS5A01G013300 chr5A 464479990 464481460 1470 False 2309.0 2309 94.9800 1165 2637 1 chr5A.!!$F1 1472
4 TraesCS5A01G013300 chr5A 275253341 275254031 690 True 241.0 241 73.4000 3 693 1 chr5A.!!$R1 690
5 TraesCS5A01G013300 chr6A 38479508 38482143 2635 False 4723.0 4723 99.0140 1 2635 1 chr6A.!!$F1 2634
6 TraesCS5A01G013300 chr6A 100350242 100352124 1882 False 3334.0 3334 98.6210 751 2634 1 chr6A.!!$F2 1883
7 TraesCS5A01G013300 chr1A 496091313 496093940 2627 True 4654.0 4654 98.5960 1 2635 1 chr1A.!!$R1 2634
8 TraesCS5A01G013300 chr1A 541887108 541889198 2090 True 3672.0 3672 98.3740 547 2635 1 chr1A.!!$R2 2088
9 TraesCS5A01G013300 chrUn 252263157 252265787 2630 True 4639.0 4639 98.4810 3 2635 1 chrUn.!!$R1 2632
10 TraesCS5A01G013300 chr2A 705849879 705852504 2625 False 4580.0 4580 98.1050 1 2634 1 chr2A.!!$F1 2633
11 TraesCS5A01G013300 chr3B 734423038 734424693 1655 False 2614.0 2614 95.1720 982 2636 1 chr3B.!!$F2 1654
12 TraesCS5A01G013300 chr3B 734409888 734410876 988 False 1607.0 1607 96.0610 1 986 1 chr3B.!!$F1 985
13 TraesCS5A01G013300 chr4B 54797554 54798595 1041 False 1611.0 1611 94.4180 608 1663 1 chr4B.!!$F1 1055
14 TraesCS5A01G013300 chr4B 54787910 54788492 582 True 917.0 917 95.0340 1 584 1 chr4B.!!$R1 583
15 TraesCS5A01G013300 chr5D 10896916 10897616 700 False 462.0 597 93.2835 2634 3588 2 chr5D.!!$F1 954

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
215 216 2.785713 TCATGCATGCATTTCATCCG 57.214 45.0 30.32 16.98 33.90 4.18 F
1621 1630 2.634639 TCCTACAGGTAAGAGGGCAA 57.365 50.0 0.00 0.00 36.34 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 2037 2.741759 ACAGTCATGTGTATGCGTGA 57.258 45.0 0.0 0.0 38.57 4.35 R
3538 3550 0.249238 ATCAGCCTCTAAAGCGAGCG 60.249 55.0 0.0 0.0 34.64 5.03 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
215 216 2.785713 TCATGCATGCATTTCATCCG 57.214 45.000 30.32 16.98 33.90 4.18
299 300 2.915604 AGACAGGGATGTCCTTTGTCAT 59.084 45.455 24.94 14.87 45.47 3.06
507 511 8.611757 GCTTTTAGACCATTTTTGTTGTGATTT 58.388 29.630 0.00 0.00 0.00 2.17
1621 1630 2.634639 TCCTACAGGTAAGAGGGCAA 57.365 50.000 0.00 0.00 36.34 4.52
1822 1832 9.350357 CTTTGATTACATCTCAACATCCAAAAG 57.650 33.333 0.00 0.00 32.57 2.27
2027 2037 2.961062 AGTTGCAGGCTTCTTCAACAAT 59.039 40.909 16.05 0.68 43.68 2.71
2671 2682 2.093890 TGGGTTGACATCATCATGTGC 58.906 47.619 0.00 0.00 43.79 4.57
2703 2714 5.258841 TGGATCAATTCTTGTTCTCAGCAT 58.741 37.500 0.00 0.00 31.61 3.79
2729 2740 7.664082 TTTTTGTGTGCTTGAATTGAAAGAA 57.336 28.000 2.35 0.00 0.00 2.52
2730 2741 6.890663 TTTGTGTGCTTGAATTGAAAGAAG 57.109 33.333 2.35 0.00 0.00 2.85
2731 2742 5.833406 TGTGTGCTTGAATTGAAAGAAGA 57.167 34.783 2.35 0.00 0.00 2.87
2732 2743 6.206395 TGTGTGCTTGAATTGAAAGAAGAA 57.794 33.333 2.35 0.00 0.00 2.52
2733 2744 6.267817 TGTGTGCTTGAATTGAAAGAAGAAG 58.732 36.000 2.35 0.00 0.00 2.85
2737 2748 8.034215 TGTGCTTGAATTGAAAGAAGAAGAAAA 58.966 29.630 2.35 0.00 0.00 2.29
2766 2777 4.174704 TGCAATGGAAGATGATTAGCCT 57.825 40.909 0.00 0.00 0.00 4.58
2819 2831 2.563179 TCTTCTCCTTTCCCGTTCTCTG 59.437 50.000 0.00 0.00 0.00 3.35
3198 3210 1.595382 CCCGCACCAGATTCGATCC 60.595 63.158 0.00 0.00 0.00 3.36
3199 3211 1.443407 CCGCACCAGATTCGATCCT 59.557 57.895 0.00 0.00 0.00 3.24
3219 3231 2.282887 CCCTCCCAAAACCCACGG 60.283 66.667 0.00 0.00 0.00 4.94
3254 3266 2.435234 CCGAATCCGCCGTTTCCA 60.435 61.111 0.00 0.00 0.00 3.53
3255 3267 2.746803 CCGAATCCGCCGTTTCCAC 61.747 63.158 0.00 0.00 0.00 4.02
3292 3304 3.303928 GAGATCGGGCCCGGTAGG 61.304 72.222 42.36 16.42 40.25 3.18
3328 3340 2.413765 GATCTGTCCGTCCGAGCC 59.586 66.667 0.00 0.00 0.00 4.70
3329 3341 3.140225 GATCTGTCCGTCCGAGCCC 62.140 68.421 0.00 0.00 0.00 5.19
3355 3367 4.277593 CGCGAGGAGGCTAGCTGG 62.278 72.222 15.72 0.00 0.00 4.85
3357 3369 2.123683 CGAGGAGGCTAGCTGGGA 60.124 66.667 15.72 0.00 0.00 4.37
3359 3371 1.381872 GAGGAGGCTAGCTGGGACA 60.382 63.158 15.72 0.00 0.00 4.02
3361 3373 2.736826 GGAGGCTAGCTGGGACACC 61.737 68.421 15.72 1.52 37.24 4.16
3502 3514 1.202065 GCACGCTTACATGTGATGTGG 60.202 52.381 18.55 4.37 44.60 4.17
3503 3515 2.076100 CACGCTTACATGTGATGTGGT 58.924 47.619 9.11 0.00 44.60 4.16
3504 3516 2.076100 ACGCTTACATGTGATGTGGTG 58.924 47.619 9.11 0.00 44.60 4.17
3505 3517 1.202065 CGCTTACATGTGATGTGGTGC 60.202 52.381 9.11 0.00 44.60 5.01
3584 3596 3.713936 GGTACCTGCCGAAATTTGC 57.286 52.632 4.06 0.00 0.00 3.68
3588 3600 0.827507 ACCTGCCGAAATTTGCCAGT 60.828 50.000 0.00 0.00 0.00 4.00
3589 3601 1.173043 CCTGCCGAAATTTGCCAGTA 58.827 50.000 0.00 0.00 0.00 2.74
3590 3602 1.135402 CCTGCCGAAATTTGCCAGTAC 60.135 52.381 0.00 0.00 0.00 2.73
3591 3603 0.885196 TGCCGAAATTTGCCAGTACC 59.115 50.000 0.00 0.00 0.00 3.34
3592 3604 1.173913 GCCGAAATTTGCCAGTACCT 58.826 50.000 0.00 0.00 0.00 3.08
3593 3605 1.135402 GCCGAAATTTGCCAGTACCTG 60.135 52.381 0.00 0.00 0.00 4.00
3594 3606 2.432444 CCGAAATTTGCCAGTACCTGA 58.568 47.619 0.00 0.00 32.44 3.86
3595 3607 2.817258 CCGAAATTTGCCAGTACCTGAA 59.183 45.455 0.00 0.00 32.44 3.02
3596 3608 3.443681 CCGAAATTTGCCAGTACCTGAAT 59.556 43.478 0.00 0.00 32.44 2.57
3597 3609 4.414852 CGAAATTTGCCAGTACCTGAATG 58.585 43.478 0.00 0.00 32.44 2.67
3598 3610 4.155826 CGAAATTTGCCAGTACCTGAATGA 59.844 41.667 0.00 0.00 32.44 2.57
3599 3611 5.644644 GAAATTTGCCAGTACCTGAATGAG 58.355 41.667 0.00 0.00 32.44 2.90
3600 3612 2.113860 TTGCCAGTACCTGAATGAGC 57.886 50.000 0.00 0.00 32.44 4.26
3601 3613 1.279496 TGCCAGTACCTGAATGAGCT 58.721 50.000 0.00 0.00 32.44 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 216 6.033831 CCATTAATGATCACTGAAAACGTTGC 59.966 38.462 17.23 0.00 0.00 4.17
246 247 9.211485 CTCTGGAACTATTGAATTTTGCAAAAT 57.789 29.630 27.73 27.73 40.15 1.82
299 300 4.385825 ACTGCAAGGACAAAAAGATACGA 58.614 39.130 0.00 0.00 39.30 3.43
507 511 1.777878 TCCAGTTTGGAGTTTGCCCTA 59.222 47.619 0.00 0.00 42.67 3.53
912 920 6.737720 TCTTCTCAATACATACATCAGCCT 57.262 37.500 0.00 0.00 0.00 4.58
1621 1630 8.319057 TCATTGATATGTTTGGAGTACCTACT 57.681 34.615 0.00 0.00 34.70 2.57
1960 1970 3.433274 TGTTGCTGAGCGAAGTTCTTATG 59.567 43.478 0.00 0.00 39.00 1.90
2027 2037 2.741759 ACAGTCATGTGTATGCGTGA 57.258 45.000 0.00 0.00 38.57 4.35
2663 2674 2.481441 TCCAGGAGTTAGGCACATGAT 58.519 47.619 0.00 0.00 0.00 2.45
2711 2722 6.698008 TCTTCTTCTTTCAATTCAAGCACA 57.302 33.333 0.00 0.00 0.00 4.57
2737 2748 9.542462 CTAATCATCTTCCATTGCAATGATTTT 57.458 29.630 35.47 19.18 41.77 1.82
2819 2831 0.892063 GAGTGAGTGAGTGAGGGGAC 59.108 60.000 0.00 0.00 0.00 4.46
3198 3210 2.167037 TGGGTTTTGGGAGGGGGAG 61.167 63.158 0.00 0.00 0.00 4.30
3199 3211 2.037128 TGGGTTTTGGGAGGGGGA 60.037 61.111 0.00 0.00 0.00 4.81
3219 3231 3.082055 GGAAGGAGACGGGTCCCC 61.082 72.222 1.00 0.00 37.31 4.81
3233 3245 3.256824 AAACGGCGGATTCGGGGAA 62.257 57.895 13.24 0.00 36.79 3.97
3504 3516 3.588337 CGCGCGCAAGAAAATCGC 61.588 61.111 32.61 0.00 44.76 4.58
3505 3517 3.588337 GCGCGCGCAAGAAAATCG 61.588 61.111 46.11 12.36 41.49 3.34
3538 3550 0.249238 ATCAGCCTCTAAAGCGAGCG 60.249 55.000 0.00 0.00 34.64 5.03
3539 3551 1.216122 CATCAGCCTCTAAAGCGAGC 58.784 55.000 0.00 0.00 34.64 5.03
3540 3552 2.200067 CACATCAGCCTCTAAAGCGAG 58.800 52.381 0.00 0.00 34.64 5.03
3541 3553 1.550524 ACACATCAGCCTCTAAAGCGA 59.449 47.619 0.00 0.00 34.64 4.93
3542 3554 2.015736 ACACATCAGCCTCTAAAGCG 57.984 50.000 0.00 0.00 34.64 4.68


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

AutoCloner maintained by Alex Coulton.