Multiple sequence alignment - TraesCS1D01G203100

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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 TraesCS1D01G203100 chr1D 100.000 2874 0 0 1 2874 286749111 286751984 0.000000e+00 5308.0
1 TraesCS1D01G203100 chr1A 94.390 1925 84 8 1 1905 358150509 358152429 0.000000e+00 2935.0
2 TraesCS1D01G203100 chr1A 94.873 1814 59 13 115 1903 358174095 358175899 0.000000e+00 2804.0
3 TraesCS1D01G203100 chr1A 91.062 951 37 16 1958 2874 358176003 358176939 0.000000e+00 1242.0
4 TraesCS1D01G203100 chr1A 78.641 206 12 12 272 476 498685514 498685340 1.090000e-19 108.0
5 TraesCS1D01G203100 chr1B 97.048 1321 32 2 592 1905 389007215 389008535 0.000000e+00 2217.0
6 TraesCS1D01G203100 chr1B 96.972 1321 33 2 592 1905 389089427 389090747 0.000000e+00 2211.0
7 TraesCS1D01G203100 chr1B 96.201 974 26 10 1908 2874 389090792 389091761 0.000000e+00 1583.0
8 TraesCS1D01G203100 chr1B 92.115 520 32 5 1 514 388912379 388912895 0.000000e+00 725.0
9 TraesCS1D01G203100 chr1B 100.000 56 0 0 550 605 389001704 389001759 1.410000e-18 104.0
10 TraesCS1D01G203100 chr1B 95.000 60 3 0 546 605 389084321 389084380 8.480000e-16 95.3
11 TraesCS1D01G203100 chr1B 84.810 79 7 5 123 198 623460383 623460459 1.100000e-09 75.0
12 TraesCS1D01G203100 chr3D 73.944 284 70 4 1398 1679 157443216 157442935 8.420000e-21 111.0
13 TraesCS1D01G203100 chr3D 77.848 158 31 4 1398 1553 157540411 157540256 8.480000e-16 95.3
14 TraesCS1D01G203100 chr3D 90.909 55 4 1 145 198 15115171 15115225 3.970000e-09 73.1
15 TraesCS1D01G203100 chrUn 78.641 206 12 11 272 476 186202705 186202531 1.090000e-19 108.0
16 TraesCS1D01G203100 chr7B 78.641 206 12 12 272 476 716832850 716832676 1.090000e-19 108.0
17 TraesCS1D01G203100 chr7B 78.641 206 12 12 272 476 716873066 716872892 1.090000e-19 108.0
18 TraesCS1D01G203100 chr7B 78.155 206 13 11 272 476 742995161 742995335 5.070000e-18 102.0
19 TraesCS1D01G203100 chr4A 78.155 206 13 12 272 476 246680321 246680495 5.070000e-18 102.0
20 TraesCS1D01G203100 chr4A 84.946 93 14 0 1398 1490 26413652 26413560 8.480000e-16 95.3
21 TraesCS1D01G203100 chr4A 80.180 111 17 5 123 230 429565644 429565752 8.540000e-11 78.7
22 TraesCS1D01G203100 chr3A 73.611 288 67 8 1398 1679 170811851 170812135 5.070000e-18 102.0
23 TraesCS1D01G203100 chr5B 77.844 167 33 3 1397 1561 700997744 700997908 1.820000e-17 100.0
24 TraesCS1D01G203100 chr4B 86.022 93 13 0 1398 1490 547205193 547205285 1.820000e-17 100.0
25 TraesCS1D01G203100 chr3B 80.357 112 20 2 123 233 750411824 750411714 1.840000e-12 84.2


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 TraesCS1D01G203100 chr1D 286749111 286751984 2873 False 5308 5308 100.0000 1 2874 1 chr1D.!!$F1 2873
1 TraesCS1D01G203100 chr1A 358150509 358152429 1920 False 2935 2935 94.3900 1 1905 1 chr1A.!!$F1 1904
2 TraesCS1D01G203100 chr1A 358174095 358176939 2844 False 2023 2804 92.9675 115 2874 2 chr1A.!!$F2 2759
3 TraesCS1D01G203100 chr1B 389007215 389008535 1320 False 2217 2217 97.0480 592 1905 1 chr1B.!!$F3 1313
4 TraesCS1D01G203100 chr1B 389089427 389091761 2334 False 1897 2211 96.5865 592 2874 2 chr1B.!!$F6 2282
5 TraesCS1D01G203100 chr1B 388912379 388912895 516 False 725 725 92.1150 1 514 1 chr1B.!!$F1 513

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
548 570 0.8364 ACTGCTTCTCCGGAAAGGGA 60.836 55.0 20.68 4.93 41.52 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 1956 0.109723 AAAACGGTAGAGGGCAGCAA 59.89 50.0 0.0 0.0 0.0 3.91 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
19 20 1.742761 AGATTGCATTGGACCTCACG 58.257 50.000 0.00 0.00 0.00 4.35
36 37 2.568062 TCACGGAGTAGGGTAAAATGCA 59.432 45.455 0.00 0.00 41.61 3.96
58 59 5.347342 CACAACACACAATTGTAACCACAT 58.653 37.500 11.53 0.00 38.22 3.21
85 86 4.819105 ATGGTCTAGAACATTTGTCGGA 57.181 40.909 17.86 0.00 34.53 4.55
125 126 4.105057 ACTTTGTAATGGTACCCCTCACAA 59.895 41.667 10.07 11.32 0.00 3.33
131 132 1.003812 TGGTACCCCTCACAAAATCGG 59.996 52.381 10.07 0.00 0.00 4.18
253 254 5.221682 TGGACAGGTATCAACGACCTTAAAA 60.222 40.000 0.00 0.00 45.40 1.52
255 256 6.128363 GGACAGGTATCAACGACCTTAAAAAG 60.128 42.308 0.00 0.00 45.40 2.27
339 341 9.777575 GCTAGTTTTGAGTTTGTTTTAAGTACA 57.222 29.630 0.00 0.00 0.00 2.90
433 441 7.224557 GGAATTGCTTTGCTCTTTTCTTTACAA 59.775 33.333 0.00 0.00 0.00 2.41
482 491 4.985538 TGCTTTTATTTGAGTGAGGTCCT 58.014 39.130 0.00 0.00 0.00 3.85
484 493 4.762251 GCTTTTATTTGAGTGAGGTCCTGT 59.238 41.667 0.00 0.00 0.00 4.00
517 529 3.748048 CGTGGCTAAATCATTGATCCGAT 59.252 43.478 0.00 0.00 0.00 4.18
529 541 1.490069 TGATCCGATGGCCAAGATCAA 59.510 47.619 29.87 19.46 41.51 2.57
538 550 1.742268 GGCCAAGATCAACTGCTTCTC 59.258 52.381 0.00 0.00 0.00 2.87
548 570 0.836400 ACTGCTTCTCCGGAAAGGGA 60.836 55.000 20.68 4.93 41.52 4.20
646 672 8.746052 TCCCAGAAAAATAACATATCGTGATT 57.254 30.769 0.00 0.00 28.80 2.57
702 728 4.806342 TCCTTTTCGAAGGAGAAAAACG 57.194 40.909 1.50 0.00 45.78 3.60
804 830 1.560923 AATCTCCACGATTTCGCGAG 58.439 50.000 9.59 0.00 39.28 5.03
982 1013 4.020543 AGAAGAGAGCACTACTACAAGGG 58.979 47.826 0.00 0.00 0.00 3.95
1187 1224 3.313690 CACTGCACACGTACTACATTGA 58.686 45.455 0.00 0.00 0.00 2.57
1555 1597 2.409055 CGTCCCCGTCATGTACCGA 61.409 63.158 0.00 0.00 0.00 4.69
1679 1721 1.450312 GAGATGTGGGTGAAGGGCG 60.450 63.158 0.00 0.00 0.00 6.13
1893 1935 0.456995 GAGTCGAAGCGAAGGTCTGG 60.457 60.000 0.00 0.00 37.72 3.86
1907 1949 2.203394 CTGGGGCACAGCACACTT 60.203 61.111 2.59 0.00 40.97 3.16
1908 1950 2.519063 TGGGGCACAGCACACTTG 60.519 61.111 0.00 0.00 30.93 3.16
1910 1952 3.297620 GGGCACAGCACACTTGGG 61.298 66.667 0.00 0.00 0.00 4.12
1911 1953 2.519302 GGCACAGCACACTTGGGT 60.519 61.111 0.00 0.00 0.00 4.51
1913 1955 1.823470 GCACAGCACACTTGGGTGA 60.823 57.895 7.25 0.00 45.61 4.02
1914 1956 1.174712 GCACAGCACACTTGGGTGAT 61.175 55.000 7.25 0.00 45.61 3.06
1915 1957 1.321474 CACAGCACACTTGGGTGATT 58.679 50.000 7.25 0.00 45.61 2.57
1916 1958 1.001048 CACAGCACACTTGGGTGATTG 60.001 52.381 7.25 6.77 45.61 2.67
1917 1959 0.038892 CAGCACACTTGGGTGATTGC 60.039 55.000 7.25 2.84 45.61 3.56
1939 2025 2.036992 TGCCCTCTACCGTTTTTCGTTA 59.963 45.455 0.00 0.00 37.94 3.18
2056 2150 2.288334 TGCAGCACGATCAAAGCAAAAT 60.288 40.909 0.00 0.00 0.00 1.82
2057 2151 2.091588 GCAGCACGATCAAAGCAAAATG 59.908 45.455 0.00 0.00 0.00 2.32
2232 2326 3.685139 TTCTCCTGACAAGAAATCGCT 57.315 42.857 0.00 0.00 30.00 4.93
2239 2333 4.092091 CCTGACAAGAAATCGCTTACAGAC 59.908 45.833 0.00 0.00 35.48 3.51
2243 2337 6.871492 TGACAAGAAATCGCTTACAGACAATA 59.129 34.615 0.00 0.00 0.00 1.90
2260 2356 9.520204 ACAGACAATAAAACTTTGTTGAAGATG 57.480 29.630 15.81 11.05 40.38 2.90
2325 2422 4.146564 GTTGCCTTACCCCTTCTTTTACA 58.853 43.478 0.00 0.00 0.00 2.41
2421 2524 4.039245 TCGAGAAGACACAATCAAGGAGTT 59.961 41.667 0.00 0.00 0.00 3.01
2469 2572 2.847327 TTCAAGCAGAAGGACCTGAG 57.153 50.000 0.00 0.00 36.29 3.35
2708 2836 5.734035 GCAAAGCAAAAGAAACAATGTGAAC 59.266 36.000 0.00 0.00 0.00 3.18
2746 2874 5.220681 GGACTAACGGATGAAAGAATCTTGC 60.221 44.000 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.076394 TGTTGTGCATTTTACCCTACTCC 58.924 43.478 0.00 0.00 0.00 3.85
36 37 5.126222 TCATGTGGTTACAATTGTGTGTTGT 59.874 36.000 21.42 0.00 40.84 3.32
58 59 7.359595 CGACAAATGTTCTAGACCATTTTTCA 58.640 34.615 27.43 7.28 0.00 2.69
78 79 3.495377 CGGTAAATGTGACTTTCCGACAA 59.505 43.478 5.71 0.00 38.96 3.18
125 126 8.349983 GGCTAAACATAACAATATCACCGATTT 58.650 33.333 0.00 0.00 0.00 2.17
131 132 8.673711 TGACTTGGCTAAACATAACAATATCAC 58.326 33.333 0.00 0.00 0.00 3.06
166 167 8.739039 CATGAGAGGTATGTTTTGGAATAACAA 58.261 33.333 0.00 0.00 38.82 2.83
383 391 9.233649 TCCAACATAAATTGTCTACCGTAAAAT 57.766 29.630 0.00 0.00 37.68 1.82
458 467 6.012745 AGGACCTCACTCAAATAAAAGCATT 58.987 36.000 0.00 0.00 0.00 3.56
459 468 5.416952 CAGGACCTCACTCAAATAAAAGCAT 59.583 40.000 0.00 0.00 0.00 3.79
482 491 4.308458 CCACGGGCACGGAAGACA 62.308 66.667 15.46 0.00 46.48 3.41
517 529 1.074405 AGAAGCAGTTGATCTTGGCCA 59.926 47.619 0.00 0.00 0.00 5.36
529 541 0.836400 TCCCTTTCCGGAGAAGCAGT 60.836 55.000 3.34 0.00 32.35 4.40
538 550 1.002502 GGGTGTCTTCCCTTTCCGG 60.003 63.158 0.00 0.00 43.85 5.14
548 570 1.779061 ATGAACAGGCCGGGTGTCTT 61.779 55.000 8.08 0.00 0.00 3.01
646 672 7.338196 TGTTGGAACTGTGTCTTTCAATTTCTA 59.662 33.333 0.00 0.00 0.00 2.10
654 680 3.632189 GCATGTTGGAACTGTGTCTTTC 58.368 45.455 0.00 0.00 0.00 2.62
702 728 2.285977 CTGGTAGGCCGGATTTTGTAC 58.714 52.381 5.05 0.00 43.97 2.90
982 1013 0.169009 ATTGCCTTCGCTTCGCTTTC 59.831 50.000 0.00 0.00 35.36 2.62
1187 1224 5.279306 GGAATAAGCATGCATGGTCATTGAT 60.279 40.000 27.72 16.08 37.57 2.57
1375 1417 4.096003 GGCGAGCCCCTGTAGCAA 62.096 66.667 1.97 0.00 0.00 3.91
1711 1753 2.362760 TACGAGGCGCCCCAGTTA 60.363 61.111 26.15 4.65 0.00 2.24
1893 1935 3.297620 CCCAAGTGTGCTGTGCCC 61.298 66.667 0.00 0.00 0.00 5.36
1905 1947 1.304713 AGGGCAGCAATCACCCAAG 60.305 57.895 0.00 0.00 46.88 3.61
1906 1948 1.304381 GAGGGCAGCAATCACCCAA 60.304 57.895 0.00 0.00 46.88 4.12
1907 1949 0.913934 TAGAGGGCAGCAATCACCCA 60.914 55.000 0.00 0.00 46.88 4.51
1908 1950 0.464554 GTAGAGGGCAGCAATCACCC 60.465 60.000 0.00 0.00 44.62 4.61
1910 1952 0.811616 CGGTAGAGGGCAGCAATCAC 60.812 60.000 0.00 0.00 0.00 3.06
1911 1953 1.264749 ACGGTAGAGGGCAGCAATCA 61.265 55.000 0.00 0.00 0.00 2.57
1913 1955 0.328258 AAACGGTAGAGGGCAGCAAT 59.672 50.000 0.00 0.00 0.00 3.56
1914 1956 0.109723 AAAACGGTAGAGGGCAGCAA 59.890 50.000 0.00 0.00 0.00 3.91
1915 1957 0.109723 AAAAACGGTAGAGGGCAGCA 59.890 50.000 0.00 0.00 0.00 4.41
1916 1958 0.803117 GAAAAACGGTAGAGGGCAGC 59.197 55.000 0.00 0.00 0.00 5.25
1917 1959 1.076332 CGAAAAACGGTAGAGGGCAG 58.924 55.000 0.00 0.00 38.46 4.85
2027 2121 2.221169 TGATCGTGCTGCAGAGTTTTT 58.779 42.857 20.43 0.00 0.00 1.94
2056 2150 2.223923 GGCACAATACAACCTGCAAACA 60.224 45.455 0.00 0.00 0.00 2.83
2057 2151 2.035832 AGGCACAATACAACCTGCAAAC 59.964 45.455 0.00 0.00 0.00 2.93
2197 2291 6.547141 TGTCAGGAGAATTGATCTTTGTTTGT 59.453 34.615 0.00 0.00 38.96 2.83
2198 2292 6.973843 TGTCAGGAGAATTGATCTTTGTTTG 58.026 36.000 0.00 0.00 38.96 2.93
2200 2294 7.000472 TCTTGTCAGGAGAATTGATCTTTGTT 59.000 34.615 0.00 0.00 38.96 2.83
2201 2295 6.537355 TCTTGTCAGGAGAATTGATCTTTGT 58.463 36.000 0.00 0.00 38.96 2.83
2202 2296 7.444629 TTCTTGTCAGGAGAATTGATCTTTG 57.555 36.000 0.00 0.00 38.96 2.77
2203 2297 8.647256 ATTTCTTGTCAGGAGAATTGATCTTT 57.353 30.769 0.00 0.00 38.96 2.52
2204 2298 7.065563 CGATTTCTTGTCAGGAGAATTGATCTT 59.934 37.037 0.00 0.00 38.96 2.40
2239 2333 7.358352 GGACGCATCTTCAACAAAGTTTTATTG 60.358 37.037 3.80 3.80 36.31 1.90
2243 2337 4.359706 GGACGCATCTTCAACAAAGTTTT 58.640 39.130 0.00 0.00 36.31 2.43
2257 2353 3.119602 GGACTTTAAAAAGGGGACGCATC 60.120 47.826 7.34 0.00 40.31 3.91
2259 2355 2.158579 AGGACTTTAAAAAGGGGACGCA 60.159 45.455 7.34 0.00 40.31 5.24
2260 2356 2.511659 AGGACTTTAAAAAGGGGACGC 58.488 47.619 7.34 0.00 40.31 5.19
2400 2502 6.931840 ACTTAACTCCTTGATTGTGTCTTCTC 59.068 38.462 0.00 0.00 0.00 2.87
2421 2524 7.227873 TGGATGTGTGGATACTTTTGAACTTA 58.772 34.615 0.00 0.00 37.61 2.24
2708 2836 4.537965 CGTTAGTCCTTCAGTATCATCCG 58.462 47.826 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.