Multiple sequence alignment - TraesCS4A01G035000

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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 TraesCS4A01G035000 chr4A 100.000 2015 0 0 604 2618 26644471 26646485 0.000000e+00 3722.0
1 TraesCS4A01G035000 chr4A 97.674 2021 29 6 604 2618 26629178 26631186 0.000000e+00 3456.0
2 TraesCS4A01G035000 chr4A 100.000 503 0 0 1 503 26643868 26644370 0.000000e+00 929.0
3 TraesCS4A01G035000 chr4A 94.737 95 5 0 2079 2173 26645852 26645946 5.840000e-32 148.0
4 TraesCS4A01G035000 chr4A 94.737 95 5 0 1985 2079 26645946 26646040 5.840000e-32 148.0
5 TraesCS4A01G035000 chr4A 93.684 95 6 0 1985 2079 26630647 26630741 2.720000e-30 143.0
6 TraesCS4A01G035000 chr4A 96.667 60 2 0 2114 2173 26630588 26630647 1.660000e-17 100.0
7 TraesCS4A01G035000 chr4D 92.730 1183 59 10 615 1793 441061570 441060411 0.000000e+00 1683.0
8 TraesCS4A01G035000 chr4B 92.886 731 44 4 1000 1729 546649498 546648775 0.000000e+00 1055.0
9 TraesCS4A01G035000 chr4B 99.205 503 4 0 1 503 583079202 583078700 0.000000e+00 907.0
10 TraesCS4A01G035000 chr4B 91.884 345 25 3 615 958 546656671 546656329 1.820000e-131 479.0
11 TraesCS4A01G035000 chr4B 87.079 178 17 6 2073 2247 546584537 546584363 2.060000e-46 196.0
12 TraesCS4A01G035000 chr4B 87.079 178 17 6 2073 2247 546607191 546607017 2.060000e-46 196.0
13 TraesCS4A01G035000 chr4B 89.691 97 9 1 1983 2079 546584533 546584438 3.540000e-24 122.0
14 TraesCS4A01G035000 chr4B 89.691 97 9 1 1983 2079 546607187 546607092 3.540000e-24 122.0
15 TraesCS4A01G035000 chr4B 84.146 82 5 7 1720 1793 546648544 546648463 3.610000e-09 73.1
16 TraesCS4A01G035000 chrUn 100.000 519 0 0 604 1122 314737252 314737770 0.000000e+00 959.0
17 TraesCS4A01G035000 chrUn 99.404 503 3 0 1 503 8130949 8130447 0.000000e+00 913.0
18 TraesCS4A01G035000 chrUn 99.205 503 4 0 1 503 83334951 83335453 0.000000e+00 907.0
19 TraesCS4A01G035000 chrUn 94.350 354 17 2 2267 2618 88753384 88753736 8.240000e-150 540.0
20 TraesCS4A01G035000 chrUn 83.778 487 78 1 1142 1628 338978903 338979388 6.600000e-126 460.0
21 TraesCS4A01G035000 chrUn 87.079 178 17 6 2073 2247 350651024 350650850 2.060000e-46 196.0
22 TraesCS4A01G035000 chrUn 89.691 97 9 1 1983 2079 350651020 350650925 3.540000e-24 122.0
23 TraesCS4A01G035000 chr5B 99.404 503 3 0 1 503 281441967 281441465 0.000000e+00 913.0
24 TraesCS4A01G035000 chr5B 94.017 351 19 1 2270 2618 26946487 26946837 4.960000e-147 531.0
25 TraesCS4A01G035000 chr7B 99.205 503 4 0 1 503 510516488 510515986 0.000000e+00 907.0
26 TraesCS4A01G035000 chr7B 83.962 636 85 12 1000 1631 584186030 584185408 6.240000e-166 593.0
27 TraesCS4A01G035000 chr7B 94.302 351 18 1 2270 2618 695710105 695709755 1.070000e-148 536.0
28 TraesCS4A01G035000 chr6A 99.205 503 4 0 1 503 315476968 315477470 0.000000e+00 907.0
29 TraesCS4A01G035000 chr6A 99.205 503 4 0 1 503 383535214 383535716 0.000000e+00 907.0
30 TraesCS4A01G035000 chr1A 99.205 503 4 0 1 503 21177750 21178252 0.000000e+00 907.0
31 TraesCS4A01G035000 chr1A 99.205 503 4 0 1 503 590338442 590337940 0.000000e+00 907.0
32 TraesCS4A01G035000 chr7A 83.333 636 91 13 999 1631 622742207 622741584 8.130000e-160 573.0
33 TraesCS4A01G035000 chr6B 95.029 342 17 0 2277 2618 77802617 77802276 2.960000e-149 538.0
34 TraesCS4A01G035000 chr3D 94.302 351 18 1 2270 2618 508062438 508062788 1.070000e-148 536.0
35 TraesCS4A01G035000 chr3D 94.302 351 18 1 2270 2618 602107467 602107117 1.070000e-148 536.0
36 TraesCS4A01G035000 chr1B 94.017 351 19 1 2270 2618 301254140 301254490 4.960000e-147 531.0
37 TraesCS4A01G035000 chr1D 93.983 349 21 0 2270 2618 20657822 20657474 1.780000e-146 529.0
38 TraesCS4A01G035000 chr5D 83.778 487 78 1 1142 1628 493710593 493711078 6.600000e-126 460.0
39 TraesCS4A01G035000 chr5D 83.778 487 78 1 1142 1628 493714165 493714650 6.600000e-126 460.0
40 TraesCS4A01G035000 chr5D 83.778 487 78 1 1142 1628 493716646 493717131 6.600000e-126 460.0


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 TraesCS4A01G035000 chr4A 26643868 26646485 2617 False 1236.75 3722 97.368500 1 2618 4 chr4A.!!$F2 2617
1 TraesCS4A01G035000 chr4A 26629178 26631186 2008 False 1233.00 3456 96.008333 604 2618 3 chr4A.!!$F1 2014
2 TraesCS4A01G035000 chr4D 441060411 441061570 1159 True 1683.00 1683 92.730000 615 1793 1 chr4D.!!$R1 1178
3 TraesCS4A01G035000 chr4B 583078700 583079202 502 True 907.00 907 99.205000 1 503 1 chr4B.!!$R2 502
4 TraesCS4A01G035000 chr4B 546648463 546649498 1035 True 564.05 1055 88.516000 1000 1793 2 chr4B.!!$R5 793
5 TraesCS4A01G035000 chrUn 314737252 314737770 518 False 959.00 959 100.000000 604 1122 1 chrUn.!!$F3 518
6 TraesCS4A01G035000 chrUn 8130447 8130949 502 True 913.00 913 99.404000 1 503 1 chrUn.!!$R1 502
7 TraesCS4A01G035000 chrUn 83334951 83335453 502 False 907.00 907 99.205000 1 503 1 chrUn.!!$F1 502
8 TraesCS4A01G035000 chr5B 281441465 281441967 502 True 913.00 913 99.404000 1 503 1 chr5B.!!$R1 502
9 TraesCS4A01G035000 chr7B 510515986 510516488 502 True 907.00 907 99.205000 1 503 1 chr7B.!!$R1 502
10 TraesCS4A01G035000 chr7B 584185408 584186030 622 True 593.00 593 83.962000 1000 1631 1 chr7B.!!$R2 631
11 TraesCS4A01G035000 chr6A 315476968 315477470 502 False 907.00 907 99.205000 1 503 1 chr6A.!!$F1 502
12 TraesCS4A01G035000 chr6A 383535214 383535716 502 False 907.00 907 99.205000 1 503 1 chr6A.!!$F2 502
13 TraesCS4A01G035000 chr1A 21177750 21178252 502 False 907.00 907 99.205000 1 503 1 chr1A.!!$F1 502
14 TraesCS4A01G035000 chr1A 590337940 590338442 502 True 907.00 907 99.205000 1 503 1 chr1A.!!$R1 502
15 TraesCS4A01G035000 chr7A 622741584 622742207 623 True 573.00 573 83.333000 999 1631 1 chr7A.!!$R1 632
16 TraesCS4A01G035000 chr5D 493710593 493717131 6538 False 460.00 460 83.778000 1142 1628 3 chr5D.!!$F1 486

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
136 137 0.934496 CGCGTTTTCAGTGGAGTTCA 59.066 50.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 8325 0.603975 GCAGCGGGAGAAACTGAAGT 60.604 55.0 0.0 0.0 33.1 3.01 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
136 137 0.934496 CGCGTTTTCAGTGGAGTTCA 59.066 50.000 0.00 0.0 0.00 3.18
142 143 5.475719 CGTTTTCAGTGGAGTTCAGGTATA 58.524 41.667 0.00 0.0 0.00 1.47
1164 1177 1.523258 CATCAGCGGCTTCCTCCAG 60.523 63.158 0.00 0.0 0.00 3.86
1761 8069 2.063266 GCCGTTCACGTACTTTGATGA 58.937 47.619 0.00 0.0 37.74 2.92
2008 8320 8.639761 GGGCTATCTAACAATAAGAAGAGTACA 58.360 37.037 0.00 0.0 0.00 2.90
2009 8321 9.685828 GGCTATCTAACAATAAGAAGAGTACAG 57.314 37.037 0.00 0.0 0.00 2.74
2018 8330 9.298250 ACAATAAGAAGAGTACAGTCTACTTCA 57.702 33.333 0.00 0.0 39.22 3.02
2161 8473 2.999507 TGCAAAAGTCGTGTGTTTGT 57.000 40.000 0.00 0.0 35.22 2.83
2309 8622 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.0 40.13 4.45
2391 8704 4.510038 AAGACTAAAGCCGTCGTCTAAA 57.490 40.909 0.00 0.0 35.82 1.85
2400 8713 2.600556 GCCGTCGTCTAAACAACAAACC 60.601 50.000 0.00 0.0 0.00 3.27
2410 8723 1.873698 ACAACAAACCGTCGCTACAT 58.126 45.000 0.00 0.0 0.00 2.29
2419 8732 1.880675 CCGTCGCTACATCTATCCAGT 59.119 52.381 0.00 0.0 0.00 4.00
2454 8767 2.906389 CAGATAGCCTGGGCCTAATACA 59.094 50.000 4.53 0.0 43.17 2.29
2589 8902 1.363744 CACCGCTCCATCTTCAGAAC 58.636 55.000 0.00 0.0 0.00 3.01
2599 8912 5.970592 TCCATCTTCAGAACTGTACTGATG 58.029 41.667 6.77 0.0 42.68 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 5.163447 CGGATATACCTGAACTCCACTGAAA 60.163 44.000 0.00 0.00 36.31 2.69
136 137 1.687123 GCCACTGTGACGGATATACCT 59.313 52.381 9.86 0.00 36.31 3.08
142 143 1.746615 GCATGCCACTGTGACGGAT 60.747 57.895 6.36 0.00 0.00 4.18
1164 1177 2.750237 CACTTGCCGGCCTTACCC 60.750 66.667 26.77 0.00 33.26 3.69
1446 7512 3.501911 ACCACCTTGGCCAGCACT 61.502 61.111 5.11 0.00 42.67 4.40
1888 8200 2.675317 CGAGAGCAAGAACAAGGTAGGG 60.675 54.545 0.00 0.00 0.00 3.53
2008 8320 2.231721 GCGGGAGAAACTGAAGTAGACT 59.768 50.000 0.00 0.00 0.00 3.24
2009 8321 2.231721 AGCGGGAGAAACTGAAGTAGAC 59.768 50.000 0.00 0.00 0.00 2.59
2010 8322 2.231478 CAGCGGGAGAAACTGAAGTAGA 59.769 50.000 0.00 0.00 33.10 2.59
2011 8323 2.611518 CAGCGGGAGAAACTGAAGTAG 58.388 52.381 0.00 0.00 33.10 2.57
2012 8324 1.337823 GCAGCGGGAGAAACTGAAGTA 60.338 52.381 0.00 0.00 33.10 2.24
2013 8325 0.603975 GCAGCGGGAGAAACTGAAGT 60.604 55.000 0.00 0.00 33.10 3.01
2014 8326 1.301677 GGCAGCGGGAGAAACTGAAG 61.302 60.000 0.00 0.00 33.10 3.02
2015 8327 1.302511 GGCAGCGGGAGAAACTGAA 60.303 57.895 0.00 0.00 33.10 3.02
2016 8328 2.050836 TTGGCAGCGGGAGAAACTGA 62.051 55.000 0.00 0.00 33.10 3.41
2017 8329 0.962356 ATTGGCAGCGGGAGAAACTG 60.962 55.000 0.00 0.00 34.48 3.16
2018 8330 0.618458 TATTGGCAGCGGGAGAAACT 59.382 50.000 0.00 0.00 0.00 2.66
2161 8473 6.263392 TGGTGTTTGAAATTCTCGGAACAATA 59.737 34.615 0.00 0.00 35.63 1.90
2309 8622 1.006832 AAAGTGACCGTATGCATCGC 58.993 50.000 0.19 0.00 0.00 4.58
2381 8694 2.282290 ACGGTTTGTTGTTTAGACGACG 59.718 45.455 0.00 0.00 42.16 5.12
2391 8704 1.796459 GATGTAGCGACGGTTTGTTGT 59.204 47.619 4.26 0.00 34.15 3.32
2400 8713 3.003378 TCAACTGGATAGATGTAGCGACG 59.997 47.826 0.00 0.00 0.00 5.12
2410 8723 2.439507 GCCCCTTCATCAACTGGATAGA 59.560 50.000 0.00 0.00 33.95 1.98
2419 8732 0.836606 TATCTGCGCCCCTTCATCAA 59.163 50.000 4.18 0.00 0.00 2.57
2454 8767 0.035317 TTGGCTGCGATGTCTGTTCT 59.965 50.000 0.00 0.00 0.00 3.01
2589 8902 6.237675 CGAGTAAAGTTGATGCATCAGTACAG 60.238 42.308 27.25 19.22 38.19 2.74


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

AutoCloner maintained by Alex Coulton.