Multiple sequence alignment - TraesCS1B01G042800

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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 TraesCS1B01G042800 chr1B 100.000 2602 0 0 1 2602 22275685 22273084 0.000000e+00 4806.0
1 TraesCS1B01G042800 chr1B 95.686 1808 50 5 1 1806 7553664 7551883 0.000000e+00 2881.0
2 TraesCS1B01G042800 chr1B 95.517 1807 54 5 1 1806 7545132 7543352 0.000000e+00 2863.0
3 TraesCS1B01G042800 chr1B 95.517 1807 54 4 1 1806 7549394 7547614 0.000000e+00 2863.0
4 TraesCS1B01G042800 chr1B 91.794 2023 131 22 598 2602 17254479 17256484 0.000000e+00 2784.0
5 TraesCS1B01G042800 chr1B 91.731 1294 79 14 500 1778 7364225 7365505 0.000000e+00 1772.0
6 TraesCS1B01G042800 chr1B 95.990 798 32 0 1805 2602 7547531 7546734 0.000000e+00 1297.0
7 TraesCS1B01G042800 chr1B 95.865 798 33 0 1805 2602 7551800 7551003 0.000000e+00 1291.0
8 TraesCS1B01G042800 chr1B 94.769 822 32 4 1780 2601 7543291 7542481 0.000000e+00 1269.0
9 TraesCS1B01G042800 chr1B 87.408 1088 102 20 1070 2140 6575039 6573970 0.000000e+00 1218.0
10 TraesCS1B01G042800 chr1B 93.532 603 7 3 1 596 17253862 17254439 0.000000e+00 869.0
11 TraesCS1B01G042800 chr1B 87.270 762 80 7 1844 2602 7366011 7366758 0.000000e+00 854.0
12 TraesCS1B01G042800 chr1B 77.218 1071 149 59 715 1740 7304614 7305634 2.950000e-149 538.0
13 TraesCS1B01G042800 chr1B 87.740 416 37 7 88 497 7363297 7363704 8.430000e-130 473.0
14 TraesCS1B01G042800 chr1B 85.354 396 29 12 1 374 7399983 7400371 1.460000e-102 383.0
15 TraesCS1B01G042800 chr1B 81.295 278 20 16 785 1061 6579157 6578911 2.040000e-46 196.0
16 TraesCS1B01G042800 chr1D 88.017 2153 197 30 496 2602 3451596 3453733 0.000000e+00 2490.0
17 TraesCS1B01G042800 chr1D 93.763 497 25 4 1 497 3998817 3998327 0.000000e+00 741.0
18 TraesCS1B01G042800 chr1D 86.100 518 40 13 1 497 3450559 3451065 1.770000e-146 529.0
19 TraesCS1B01G042800 chr1D 86.100 518 40 15 1 497 4980500 4979994 1.770000e-146 529.0
20 TraesCS1B01G042800 chr1D 81.053 95 12 3 747 841 3465710 3465798 1.290000e-08 71.3
21 TraesCS1B01G042800 chr1A 89.419 1257 109 14 501 1735 6023947 6022693 0.000000e+00 1563.0
22 TraesCS1B01G042800 chr1A 85.156 512 44 13 1 491 4542638 4543138 1.800000e-136 496.0
23 TraesCS1B01G042800 chr1A 88.998 409 34 8 91 497 6024869 6024470 1.800000e-136 496.0
24 TraesCS1B01G042800 chr1A 100.000 29 0 0 1 29 6025401 6025373 1.000000e-03 54.7


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 TraesCS1B01G042800 chr1B 22273084 22275685 2601 True 4806.000000 4806 100.000000 1 2602 1 chr1B.!!$R1 2601
1 TraesCS1B01G042800 chr1B 7542481 7553664 11183 True 2077.333333 2881 95.557333 1 2602 6 chr1B.!!$R3 2601
2 TraesCS1B01G042800 chr1B 17253862 17256484 2622 False 1826.500000 2784 92.663000 1 2602 2 chr1B.!!$F4 2601
3 TraesCS1B01G042800 chr1B 7363297 7366758 3461 False 1033.000000 1772 88.913667 88 2602 3 chr1B.!!$F3 2514
4 TraesCS1B01G042800 chr1B 6573970 6579157 5187 True 707.000000 1218 84.351500 785 2140 2 chr1B.!!$R2 1355
5 TraesCS1B01G042800 chr1B 7304614 7305634 1020 False 538.000000 538 77.218000 715 1740 1 chr1B.!!$F1 1025
6 TraesCS1B01G042800 chr1D 3450559 3453733 3174 False 1509.500000 2490 87.058500 1 2602 2 chr1D.!!$F2 2601
7 TraesCS1B01G042800 chr1D 4979994 4980500 506 True 529.000000 529 86.100000 1 497 1 chr1D.!!$R2 496
8 TraesCS1B01G042800 chr1A 6022693 6025401 2708 True 704.566667 1563 92.805667 1 1735 3 chr1A.!!$R1 1734
9 TraesCS1B01G042800 chr1A 4542638 4543138 500 False 496.000000 496 85.156000 1 491 1 chr1A.!!$F1 490

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
934 1988 0.671781 GCTGACAGATGAAGGTGCGT 60.672 55.0 6.65 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 12107 0.475906 CCATTGGATGTCCTCCCCTC 59.524 60.0 0.0 0.0 44.23 4.3 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
32 33 6.710597 TGTTGAGATAAATAGAGTAGCGGT 57.289 37.500 0.00 0.0 0.00 5.68
491 942 6.727824 ATGTAACTGAGAGTTGTACATTGC 57.272 37.500 0.00 0.0 35.15 3.56
677 1713 1.366111 CTTTGGGCGGTATGGTCACG 61.366 60.000 0.00 0.0 0.00 4.35
757 1794 1.455849 CTCCTTGCCCTTGTCCACA 59.544 57.895 0.00 0.0 0.00 4.17
934 1988 0.671781 GCTGACAGATGAAGGTGCGT 60.672 55.000 6.65 0.0 0.00 5.24
1176 10367 4.315803 GCCAAGAAGAACTAGTAACAGCA 58.684 43.478 0.00 0.0 0.00 4.41
1287 10500 2.362369 CGTCCCCAGCTGTGAGGAT 61.362 63.158 17.48 0.0 0.00 3.24
1331 10544 2.115910 CAGGGCCAGGTGCAAAGA 59.884 61.111 6.18 0.0 43.89 2.52
1709 10939 9.124807 CGCGTCTGTAATGAGATATATTTGTAA 57.875 33.333 0.00 0.0 0.00 2.41
1880 11679 1.843368 ACTAGCGCTACCACTACCAA 58.157 50.000 14.45 0.0 0.00 3.67
1901 11706 5.461526 CAATACGACTACGGTCATCATCAT 58.538 41.667 0.00 0.0 42.21 2.45
1909 11714 1.586422 GGTCATCATCATCACCACCG 58.414 55.000 0.00 0.0 0.00 4.94
2161 11989 9.936329 ATTTTATTAGTTCCCATGATACCACTT 57.064 29.630 0.00 0.0 0.00 3.16
2220 12049 2.354821 ACGCTCCTGTGAAACTTTGAAC 59.645 45.455 0.00 0.0 38.04 3.18
2278 12107 3.977244 AAAACCCTTGCTGCCGCG 61.977 61.111 0.00 0.0 39.65 6.46
2432 12262 4.020039 TCCCTTTTCATCGTAACCTTAGCA 60.020 41.667 0.00 0.0 0.00 3.49
2514 16598 0.770499 TGTGCTGGAGATTGTTCCCA 59.230 50.000 0.00 0.0 36.35 4.37
2533 16617 1.671054 CTCGCATTTGGTGGTCGGT 60.671 57.895 0.00 0.0 0.00 4.69
2539 16623 2.157305 ATTTGGTGGTCGGTCGCGTA 62.157 55.000 5.77 0.0 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 494 0.036010 CATGAAAGGACCGCCTCAGT 60.036 55.000 0.00 0.00 46.28 3.41
431 882 3.914364 GCACAAACATGATTCGGACTTTC 59.086 43.478 0.00 0.00 0.00 2.62
491 942 1.156736 GTTTGATGGCCCGGATATCG 58.843 55.000 0.73 0.00 38.88 2.92
570 1563 4.821260 TGTACTCGTGTTACAACCACTAGA 59.179 41.667 0.00 0.00 0.00 2.43
677 1713 1.066257 CAACACAAGCCCAGCACAC 59.934 57.895 0.00 0.00 0.00 3.82
757 1794 3.181487 GCTGGTTGTGTCTTGTGTTTCAT 60.181 43.478 0.00 0.00 0.00 2.57
1541 10756 5.963214 TCATAGCAGCATCCATACCATAT 57.037 39.130 0.00 0.00 0.00 1.78
1711 10941 9.677567 TGAAACAGAAAACTGAATATGCTAAAC 57.322 29.630 0.00 0.00 0.00 2.01
1880 11679 4.760204 TGATGATGATGACCGTAGTCGTAT 59.240 41.667 0.00 0.00 46.74 3.06
1901 11706 5.064558 TGAAAATTTAAGTAGCGGTGGTGA 58.935 37.500 0.00 0.00 0.00 4.02
2161 11989 4.126520 AGTTTCCTTCCCCAAATTGCTA 57.873 40.909 0.00 0.00 0.00 3.49
2188 12017 3.069318 GGAGCGTCTCGGGAGGTT 61.069 66.667 6.88 0.00 0.00 3.50
2262 12091 4.947147 TCGCGGCAGCAAGGGTTT 62.947 61.111 10.08 0.00 45.49 3.27
2278 12107 0.475906 CCATTGGATGTCCTCCCCTC 59.524 60.000 0.00 0.00 44.23 4.30
2432 12262 4.166725 TCAAGTTGGCCTCTCATGGATAAT 59.833 41.667 3.32 0.00 0.00 1.28
2514 16598 1.671054 CCGACCACCAAATGCGAGT 60.671 57.895 0.00 0.00 0.00 4.18
2533 16617 1.712018 CCAGATCTGGTCGTACGCGA 61.712 60.000 30.55 4.68 45.53 5.87


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

AutoCloner maintained by Alex Coulton.