Multiple sequence alignment - TraesCS5D01G192900

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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 TraesCS5D01G192900 chr5D 100.000 3143 0 0 1 3143 297147950 297144808 0.000000e+00 5805.0
1 TraesCS5D01G192900 chr5D 93.609 1549 63 19 1603 3143 297121465 297119945 0.000000e+00 2279.0
2 TraesCS5D01G192900 chr5A 94.952 1664 63 13 1425 3071 401958955 401960614 0.000000e+00 2588.0
3 TraesCS5D01G192900 chr5A 92.760 1547 81 18 1603 3143 401965158 401966679 0.000000e+00 2207.0
4 TraesCS5D01G192900 chr5A 92.696 1547 82 18 1603 3143 402095948 402097469 0.000000e+00 2202.0
5 TraesCS5D01G192900 chr5A 94.184 1324 62 11 1825 3143 402089837 402091150 0.000000e+00 2004.0
6 TraesCS5D01G192900 chr5A 90.000 1010 68 14 802 1808 402031405 402032384 0.000000e+00 1275.0
7 TraesCS5D01G192900 chr5A 91.597 714 49 5 705 1415 401957727 401958432 0.000000e+00 976.0
8 TraesCS5D01G192900 chr5A 91.460 644 38 4 6 634 401957086 401957727 0.000000e+00 869.0
9 TraesCS5D01G192900 chr5A 90.179 448 33 6 373 812 402024660 402025104 9.780000e-160 573.0
10 TraesCS5D01G192900 chr5A 91.089 101 4 3 280 377 402024499 402024597 7.070000e-27 132.0
11 TraesCS5D01G192900 chr5B 99.038 728 3 1 1 724 337186155 337185428 0.000000e+00 1303.0
12 TraesCS5D01G192900 chr5B 98.246 684 12 0 708 1391 337184259 337183576 0.000000e+00 1197.0
13 TraesCS5D01G192900 chr5B 94.986 718 20 10 1603 2316 337180324 337179619 0.000000e+00 1112.0
14 TraesCS5D01G192900 chr5B 93.141 554 26 5 2344 2897 337176801 337176260 0.000000e+00 802.0
15 TraesCS5D01G192900 chr5B 94.758 248 9 3 2897 3143 337174732 337174488 1.770000e-102 383.0
16 TraesCS5D01G192900 chr5B 100.000 33 0 0 517 549 477885484 477885516 9.410000e-06 62.1
17 TraesCS5D01G192900 chrUn 100.000 361 0 0 1 361 480870133 480869773 0.000000e+00 667.0
18 TraesCS5D01G192900 chrUn 88.785 107 8 4 2415 2518 45529266 45529161 9.150000e-26 128.0
19 TraesCS5D01G192900 chrUn 81.560 141 21 3 2283 2419 45529446 45529307 9.210000e-21 111.0
20 TraesCS5D01G192900 chr6D 97.143 35 1 0 517 551 389874252 389874218 3.390000e-05 60.2
21 TraesCS5D01G192900 chr7D 90.476 42 4 0 519 560 106629390 106629349 4.380000e-04 56.5
22 TraesCS5D01G192900 chr7D 90.000 40 4 0 523 562 80454180 80454141 6.000000e-03 52.8
23 TraesCS5D01G192900 chr3B 96.970 33 1 0 519 551 532236625 532236657 4.380000e-04 56.5
24 TraesCS5D01G192900 chr1A 94.444 36 2 0 516 551 372547124 372547159 4.380000e-04 56.5


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 TraesCS5D01G192900 chr5D 297144808 297147950 3142 True 5805.000000 5805 100.000000 1 3143 1 chr5D.!!$R2 3142
1 TraesCS5D01G192900 chr5D 297119945 297121465 1520 True 2279.000000 2279 93.609000 1603 3143 1 chr5D.!!$R1 1540
2 TraesCS5D01G192900 chr5A 401965158 401966679 1521 False 2207.000000 2207 92.760000 1603 3143 1 chr5A.!!$F1 1540
3 TraesCS5D01G192900 chr5A 402095948 402097469 1521 False 2202.000000 2202 92.696000 1603 3143 1 chr5A.!!$F4 1540
4 TraesCS5D01G192900 chr5A 402089837 402091150 1313 False 2004.000000 2004 94.184000 1825 3143 1 chr5A.!!$F3 1318
5 TraesCS5D01G192900 chr5A 401957086 401960614 3528 False 1477.666667 2588 92.669667 6 3071 3 chr5A.!!$F5 3065
6 TraesCS5D01G192900 chr5A 402031405 402032384 979 False 1275.000000 1275 90.000000 802 1808 1 chr5A.!!$F2 1006
7 TraesCS5D01G192900 chr5A 402024499 402025104 605 False 352.500000 573 90.634000 280 812 2 chr5A.!!$F6 532
8 TraesCS5D01G192900 chr5B 337174488 337186155 11667 True 959.400000 1303 96.033800 1 3143 5 chr5B.!!$R1 3142

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
536 615 1.227645 GGCCGCATGCATCACTCTA 60.228 57.895 19.57 0.0 43.89 2.43 F
1148 2427 0.195096 AGAGGTTGGGGGTGGAACTA 59.805 55.000 0.00 0.0 36.74 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 6157 0.890683 GTGCCCTTTGAGGAATGTGG 59.109 55.000 0.0 0.0 37.67 4.17 R
2992 11659 2.152016 GAGGTTAGCTTTGGGTGTGAC 58.848 52.381 0.0 0.0 0.00 3.67 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
399 471 6.262207 ACTCCAAACTAGAACCTAGTACCAT 58.738 40.000 7.03 0.00 0.00 3.55
536 615 1.227645 GGCCGCATGCATCACTCTA 60.228 57.895 19.57 0.00 43.89 2.43
911 2190 5.300286 CCCCCATTCAAGATATTCACACTTC 59.700 44.000 0.00 0.00 0.00 3.01
915 2194 8.206867 CCCATTCAAGATATTCACACTTCTCTA 58.793 37.037 0.00 0.00 0.00 2.43
1031 2310 3.985925 GGAGCAGCACTGAAAATTTCAAG 59.014 43.478 9.85 6.66 39.58 3.02
1148 2427 0.195096 AGAGGTTGGGGGTGGAACTA 59.805 55.000 0.00 0.00 36.74 2.24
1528 4168 1.577328 ATCAGACTTGGCGCAAACCG 61.577 55.000 10.83 0.00 40.75 4.44
1559 4199 2.158986 CGAGAGTCTGATGCTCCCAATT 60.159 50.000 0.00 0.00 33.69 2.32
1567 4207 4.773674 TCTGATGCTCCCAATTTTGTGAAT 59.226 37.500 0.00 0.00 0.00 2.57
1568 4208 5.246656 TCTGATGCTCCCAATTTTGTGAATT 59.753 36.000 0.00 0.00 0.00 2.17
1630 5951 1.072965 CTGGTGAAGGAAGCTTGGAGT 59.927 52.381 2.10 0.00 0.00 3.85
1761 6083 0.413037 TTTTGGGTGGATGATGCCCT 59.587 50.000 0.00 0.00 42.77 5.19
1762 6084 0.324552 TTTGGGTGGATGATGCCCTG 60.325 55.000 0.00 0.00 42.77 4.45
2178 6512 7.684062 TTTCGAAAAAGAAAGATTTGCTCTG 57.316 32.000 8.44 0.00 35.44 3.35
2249 6583 6.030228 GCACATATGGCAGAGAAAAACTTAC 58.970 40.000 7.80 0.00 0.00 2.34
2525 9659 1.609208 ACCAAACACACTGATCAGCC 58.391 50.000 22.83 0.00 0.00 4.85
2766 9901 4.392940 AGCAACCCATCTATGATAGCAAC 58.607 43.478 0.00 0.00 0.00 4.17
2857 9995 6.227298 TCTTGATCTCTGTACCTCCAATTC 57.773 41.667 0.00 0.00 0.00 2.17
2888 10026 9.801873 CCTTTATCTGTAAACCAAACCATAATG 57.198 33.333 0.00 0.00 0.00 1.90
2934 11600 5.141182 CACCACCATAGTAGGATCACTAGT 58.859 45.833 0.00 0.00 38.80 2.57
2936 11602 4.021894 CCACCATAGTAGGATCACTAGTGC 60.022 50.000 18.45 4.96 36.06 4.40
2944 11610 6.071320 AGTAGGATCACTAGTGCATATGTGA 58.929 40.000 18.45 16.78 42.50 3.58
3003 11670 0.034574 ACACAGCTGTCACACCCAAA 60.035 50.000 18.64 0.00 0.00 3.28
3098 11773 3.580895 TCAGTCAAACCTATAGCCACACA 59.419 43.478 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
915 2194 9.160496 TCTTCAATATTTTGCTTGTGTTTTGTT 57.840 25.926 0.00 0.00 32.61 2.83
937 2216 4.817318 ACTTCCCAGTCTTGATCTCTTC 57.183 45.455 0.00 0.00 0.00 2.87
1031 2310 4.270808 CACAACTTCCAAATTTGCTTCCAC 59.729 41.667 12.92 0.00 0.00 4.02
1436 4076 1.002888 CTCAGGTGCACAGATGTTCCT 59.997 52.381 20.43 0.00 33.44 3.36
1528 4168 7.307101 GGAGCATCAGACTCTCGAAAATAATTC 60.307 40.741 0.00 0.00 36.25 2.17
1559 4199 2.357323 TGCTGTTCAGCGAATTCACAAA 59.643 40.909 17.95 0.00 37.69 2.83
1567 4207 1.600636 CCCCTTGCTGTTCAGCGAA 60.601 57.895 17.95 12.61 37.69 4.70
1568 4208 2.032528 CCCCTTGCTGTTCAGCGA 59.967 61.111 17.95 15.59 37.69 4.93
1761 6083 5.182380 GGCTAACAAGTTTACAATACTGCCA 59.818 40.000 0.00 0.00 32.74 4.92
1762 6084 5.182380 TGGCTAACAAGTTTACAATACTGCC 59.818 40.000 0.00 0.00 32.97 4.85
1834 6157 0.890683 GTGCCCTTTGAGGAATGTGG 59.109 55.000 0.00 0.00 37.67 4.17
2021 6354 6.418819 CCAGTTTTGAGAGTTTAACAAGCATG 59.581 38.462 0.00 0.00 0.00 4.06
2178 6512 5.869753 TTCAGAGTTTAAGAAGCATCAGC 57.130 39.130 0.00 0.00 42.56 4.26
2249 6583 8.748412 AGCTATCCATCAGTTTAGCTATAAGAG 58.252 37.037 0.00 0.00 44.11 2.85
2362 9492 5.843969 ACCTTTGGTATTTCATTTGGTCCTT 59.156 36.000 0.00 0.00 32.11 3.36
2500 9634 5.048782 GCTGATCAGTGTGTTTGGTATTTCA 60.049 40.000 23.38 0.00 0.00 2.69
2525 9659 5.716094 TCATTCATGCCTTCACTTGATTTG 58.284 37.500 0.00 0.00 0.00 2.32
2766 9901 2.557056 CCATGCTGCTCATTAAGATGGG 59.443 50.000 0.00 0.00 36.79 4.00
2857 9995 8.417884 TGGTTTGGTTTACAGATAAAGGAAAAG 58.582 33.333 0.00 0.00 30.79 2.27
2879 10017 8.686334 GTTGTCTCATTGGATTACATTATGGTT 58.314 33.333 0.00 0.00 0.00 3.67
2888 10026 8.827677 GGTGTATAAGTTGTCTCATTGGATTAC 58.172 37.037 0.00 0.00 0.00 1.89
2934 11600 5.882000 ACTGCTACTTTTGATCACATATGCA 59.118 36.000 1.58 1.71 0.00 3.96
2936 11602 7.312657 ACACTGCTACTTTTGATCACATATG 57.687 36.000 0.00 0.00 0.00 1.78
2944 11610 5.746990 ACTAGGACACTGCTACTTTTGAT 57.253 39.130 0.00 0.00 0.00 2.57
2992 11659 2.152016 GAGGTTAGCTTTGGGTGTGAC 58.848 52.381 0.00 0.00 0.00 3.67
3035 11710 7.615365 AGATCAATTTAGTGCTTGGATTGGTAA 59.385 33.333 0.00 0.00 0.00 2.85
3098 11773 6.120220 GCTAAATATGTGTGGGGAGTAGTTT 58.880 40.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.