Multiple sequence alignment - TraesCS5D01G176000

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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 TraesCS5D01G176000 chr5D 100.000 1752 0 0 879 2630 276264480 276262729 0.000000e+00 3236
1 TraesCS5D01G176000 chr5D 100.000 591 0 0 1 591 276265358 276264768 0.000000e+00 1092
2 TraesCS5D01G176000 chr5A 92.052 1774 116 14 879 2630 364671361 364669591 0.000000e+00 2471
3 TraesCS5D01G176000 chr5A 88.985 581 41 7 9 579 364672258 364671691 0.000000e+00 697
4 TraesCS5D01G176000 chr5A 81.156 467 78 9 2170 2629 575258954 575258491 1.490000e-97 366
5 TraesCS5D01G176000 chr5A 77.211 588 120 11 2050 2630 575263241 575262661 5.430000e-87 331
6 TraesCS5D01G176000 chr5B 93.996 1449 67 13 879 2309 313115565 313114119 0.000000e+00 2176
7 TraesCS5D01G176000 chr5B 90.741 594 32 8 1 591 313116165 313115592 0.000000e+00 771
8 TraesCS5D01G176000 chr5B 78.743 541 107 6 2050 2584 386026334 386026872 3.220000e-94 355
9 TraesCS5D01G176000 chr6B 82.684 462 75 3 2173 2630 477688711 477688251 3.150000e-109 405
10 TraesCS5D01G176000 chr6B 80.403 546 96 6 2088 2628 702670705 702671244 3.150000e-109 405
11 TraesCS5D01G176000 chr7A 81.151 504 85 6 2047 2542 106741064 106741565 1.900000e-106 396
12 TraesCS5D01G176000 chr3D 78.268 589 110 11 2050 2630 61840706 61840128 1.920000e-96 363
13 TraesCS5D01G176000 chr4D 78.030 528 107 8 2073 2596 113415344 113414822 9.080000e-85 324


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 TraesCS5D01G176000 chr5D 276262729 276265358 2629 True 2164.0 3236 100.0000 1 2630 2 chr5D.!!$R1 2629
1 TraesCS5D01G176000 chr5A 364669591 364672258 2667 True 1584.0 2471 90.5185 9 2630 2 chr5A.!!$R1 2621
2 TraesCS5D01G176000 chr5A 575258491 575263241 4750 True 348.5 366 79.1835 2050 2630 2 chr5A.!!$R2 580
3 TraesCS5D01G176000 chr5B 313114119 313116165 2046 True 1473.5 2176 92.3685 1 2309 2 chr5B.!!$R1 2308
4 TraesCS5D01G176000 chr5B 386026334 386026872 538 False 355.0 355 78.7430 2050 2584 1 chr5B.!!$F1 534
5 TraesCS5D01G176000 chr6B 702670705 702671244 539 False 405.0 405 80.4030 2088 2628 1 chr6B.!!$F1 540
6 TraesCS5D01G176000 chr7A 106741064 106741565 501 False 396.0 396 81.1510 2047 2542 1 chr7A.!!$F1 495
7 TraesCS5D01G176000 chr3D 61840128 61840706 578 True 363.0 363 78.2680 2050 2630 1 chr3D.!!$R1 580
8 TraesCS5D01G176000 chr4D 113414822 113415344 522 True 324.0 324 78.0300 2073 2596 1 chr4D.!!$R1 523

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
580 591 2.047655 CTTCCACGCACGGCCTAA 60.048 61.111 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 2543 0.037882 CTCACAGAGGCTTTCGCTGA 60.038 55.0 7.83 0.0 44.55 4.26 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 2.361104 GGTCGCATTGAAGCCCCA 60.361 61.111 0.00 0.00 0.00 4.96
31 32 2.247358 GAAGCCCCAATTCAAGGAACA 58.753 47.619 0.00 0.00 0.00 3.18
65 66 3.002791 GAGTTCCAAGATTCGTGCATGA 58.997 45.455 3.97 3.97 0.00 3.07
72 73 4.275196 CCAAGATTCGTGCATGAATGATCT 59.725 41.667 33.32 23.55 38.65 2.75
151 152 8.416485 AGTACCGCAAAAGTTATATTGAGTAC 57.584 34.615 9.40 9.40 37.69 2.73
158 159 8.717821 GCAAAAGTTATATTGAGTACTGTGTGA 58.282 33.333 0.00 0.00 0.00 3.58
181 183 8.268738 GTGAACAAGTCAACAATTTTTAGATGC 58.731 33.333 0.00 0.00 38.23 3.91
187 189 5.511729 GTCAACAATTTTTAGATGCCTACGC 59.488 40.000 0.00 0.00 0.00 4.42
213 215 4.026640 TCGACGGTAAAGTTTTCTTTCACG 60.027 41.667 0.00 12.00 45.77 4.35
214 216 4.521010 GACGGTAAAGTTTTCTTTCACGG 58.479 43.478 15.47 0.00 45.77 4.94
233 235 4.154015 CACGGAAAGAACATTGCATCACTA 59.846 41.667 0.00 0.00 0.00 2.74
248 250 5.893255 TGCATCACTAAAAGGCCTGAAATAT 59.107 36.000 5.69 0.00 0.00 1.28
251 253 7.522236 GCATCACTAAAAGGCCTGAAATATACC 60.522 40.741 5.69 0.00 0.00 2.73
252 254 7.208064 TCACTAAAAGGCCTGAAATATACCT 57.792 36.000 5.69 0.00 0.00 3.08
268 270 6.861065 ATATACCTCGAAAAATGCGACAAT 57.139 33.333 0.00 0.00 33.71 2.71
286 288 5.122239 CGACAATCAGTGCCAAATCTAAGAA 59.878 40.000 0.00 0.00 0.00 2.52
379 382 6.349300 ACATGTGACGAATAGCTAATTTCCT 58.651 36.000 0.00 0.00 0.00 3.36
401 404 7.732996 TCCTAGACCTAATAATTACTTGTGCC 58.267 38.462 0.00 0.00 0.00 5.01
402 405 7.567622 TCCTAGACCTAATAATTACTTGTGCCT 59.432 37.037 0.00 0.00 0.00 4.75
403 406 8.211629 CCTAGACCTAATAATTACTTGTGCCTT 58.788 37.037 0.00 0.00 0.00 4.35
404 407 7.865706 AGACCTAATAATTACTTGTGCCTTG 57.134 36.000 0.00 0.00 0.00 3.61
405 408 7.402862 AGACCTAATAATTACTTGTGCCTTGT 58.597 34.615 0.00 0.00 0.00 3.16
406 409 7.336931 AGACCTAATAATTACTTGTGCCTTGTG 59.663 37.037 0.00 0.00 0.00 3.33
407 410 6.127730 ACCTAATAATTACTTGTGCCTTGTGC 60.128 38.462 0.00 0.00 41.77 4.57
580 591 2.047655 CTTCCACGCACGGCCTAA 60.048 61.111 0.00 0.00 0.00 2.69
944 985 3.817084 ACGTCGTCGATATCAATCCCTAA 59.183 43.478 9.47 0.00 40.62 2.69
1099 1140 1.202359 GCTGCTTCCTCTTAGTCCTCG 60.202 57.143 0.00 0.00 0.00 4.63
1110 1151 5.817816 CCTCTTAGTCCTCGTTGCATTATTT 59.182 40.000 0.00 0.00 0.00 1.40
1691 1732 8.161425 ACTACTCAAGCAGGAATTAACCTTTTA 58.839 33.333 0.00 0.00 38.32 1.52
1742 1783 1.229951 TGGAGCTGGGGAGGAATGT 60.230 57.895 0.00 0.00 0.00 2.71
1975 2016 1.001378 CTGAAACTTTTCCTGGTGCCG 60.001 52.381 0.00 0.00 36.36 5.69
2010 2051 3.925379 TGCATTTTCTCGAGCACTAAGA 58.075 40.909 7.81 0.00 31.05 2.10
2012 2053 4.754618 TGCATTTTCTCGAGCACTAAGAAA 59.245 37.500 7.81 0.00 37.27 2.52
2016 2057 5.862924 TTTCTCGAGCACTAAGAAATTGG 57.137 39.130 7.81 0.00 34.87 3.16
2017 2058 3.861840 TCTCGAGCACTAAGAAATTGGG 58.138 45.455 7.81 0.00 0.00 4.12
2019 2060 3.596214 TCGAGCACTAAGAAATTGGGTC 58.404 45.455 0.00 0.00 0.00 4.46
2020 2061 3.260884 TCGAGCACTAAGAAATTGGGTCT 59.739 43.478 0.00 0.00 0.00 3.85
2021 2062 4.464951 TCGAGCACTAAGAAATTGGGTCTA 59.535 41.667 0.00 0.00 0.00 2.59
2024 2065 6.067217 AGCACTAAGAAATTGGGTCTATGT 57.933 37.500 0.00 0.00 0.00 2.29
2025 2066 6.485171 AGCACTAAGAAATTGGGTCTATGTT 58.515 36.000 0.00 0.00 0.00 2.71
2026 2067 6.948309 AGCACTAAGAAATTGGGTCTATGTTT 59.052 34.615 0.00 0.00 0.00 2.83
2028 2069 7.094377 GCACTAAGAAATTGGGTCTATGTTTGA 60.094 37.037 0.00 0.00 0.00 2.69
2029 2070 8.237267 CACTAAGAAATTGGGTCTATGTTTGAC 58.763 37.037 0.00 0.00 0.00 3.18
2030 2071 7.942341 ACTAAGAAATTGGGTCTATGTTTGACA 59.058 33.333 0.00 0.00 36.26 3.58
2031 2072 7.595819 AAGAAATTGGGTCTATGTTTGACAA 57.404 32.000 0.00 0.00 36.26 3.18
2033 2074 8.017418 AGAAATTGGGTCTATGTTTGACAAAA 57.983 30.769 1.27 0.00 36.26 2.44
2034 2075 8.650490 AGAAATTGGGTCTATGTTTGACAAAAT 58.350 29.630 1.27 2.11 36.26 1.82
2036 2077 7.781324 ATTGGGTCTATGTTTGACAAAATCT 57.219 32.000 1.27 0.00 36.26 2.40
2037 2078 8.877864 ATTGGGTCTATGTTTGACAAAATCTA 57.122 30.769 1.27 0.00 36.26 1.98
2038 2079 8.877864 TTGGGTCTATGTTTGACAAAATCTAT 57.122 30.769 1.27 0.00 36.26 1.98
2039 2080 8.279970 TGGGTCTATGTTTGACAAAATCTATG 57.720 34.615 1.27 0.00 36.26 2.23
2041 2082 8.956426 GGGTCTATGTTTGACAAAATCTATGAA 58.044 33.333 1.27 0.00 36.26 2.57
2042 2083 9.994432 GGTCTATGTTTGACAAAATCTATGAAG 57.006 33.333 1.27 0.00 36.26 3.02
2043 2084 9.495754 GTCTATGTTTGACAAAATCTATGAAGC 57.504 33.333 1.27 0.00 34.80 3.86
2069 2128 3.740495 TTTGGTTGCCCGGGCTCAA 62.740 57.895 43.34 36.07 42.51 3.02
2127 2186 0.409092 AACCATGCCCATCAGGAACA 59.591 50.000 0.00 0.00 38.24 3.18
2149 2208 1.640428 CGAATCGGCAGTTTCTAGCA 58.360 50.000 0.00 0.00 0.00 3.49
2160 2219 1.197036 GTTTCTAGCAACAACGGCTCC 59.803 52.381 0.00 0.00 42.62 4.70
2239 2298 0.778815 CTCACGCGTGTCTCTGAAAC 59.221 55.000 35.74 0.00 0.00 2.78
2317 2380 1.948104 TCACCTCACCGTTGAAACTG 58.052 50.000 0.00 0.00 0.00 3.16
2380 2445 2.887568 CGACACCGATGAGCAGGC 60.888 66.667 0.00 0.00 38.22 4.85
2441 2514 1.535896 TGACTCGTGTCCTCTTCTTCG 59.464 52.381 14.57 0.00 42.28 3.79
2464 2541 2.038975 TTCCTGTCTCCCTCGGGG 59.961 66.667 0.00 0.00 46.11 5.73
2466 2543 2.284699 CCTGTCTCCCTCGGGGTT 60.285 66.667 0.00 0.00 44.74 4.11
2473 2550 3.702048 CCCTCGGGGTTCAGCGAA 61.702 66.667 0.00 0.00 38.25 4.70
2490 2567 2.064762 CGAAAGCCTCTGTGAGTTCAG 58.935 52.381 0.00 0.00 36.85 3.02
2526 6776 9.095700 TCTCTGTACTCATTCTAGCTAGATCTA 57.904 37.037 23.81 10.12 31.40 1.98
2535 6785 8.801299 TCATTCTAGCTAGATCTAAGAACATGG 58.199 37.037 23.81 6.78 31.40 3.66
2604 6854 6.070767 ACCATCTTGTAGCATTGTACACTACT 60.071 38.462 17.96 7.27 37.70 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.532115 AATTGGGGCTTCAATGCGAC 59.468 50.000 7.22 0.00 37.42 5.19
31 32 5.694995 TCTTGGAACTCATCTTCAAAGGTT 58.305 37.500 0.00 0.00 33.49 3.50
41 42 3.002791 TGCACGAATCTTGGAACTCATC 58.997 45.455 0.00 0.00 0.00 2.92
128 129 8.036575 ACAGTACTCAATATAACTTTTGCGGTA 58.963 33.333 0.00 0.00 0.00 4.02
151 152 6.949578 AAAATTGTTGACTTGTTCACACAG 57.050 33.333 0.00 0.00 33.22 3.66
158 159 7.500141 AGGCATCTAAAAATTGTTGACTTGTT 58.500 30.769 0.00 0.00 0.00 2.83
181 183 0.168788 TTTACCGTCGACTGCGTAGG 59.831 55.000 14.70 8.66 39.60 3.18
187 189 5.005971 TGAAAGAAAACTTTACCGTCGACTG 59.994 40.000 14.70 9.99 0.00 3.51
213 215 6.587608 CCTTTTAGTGATGCAATGTTCTTTCC 59.412 38.462 0.00 0.00 0.00 3.13
214 216 6.089954 GCCTTTTAGTGATGCAATGTTCTTTC 59.910 38.462 0.00 0.00 0.00 2.62
233 235 5.367945 TCGAGGTATATTTCAGGCCTTTT 57.632 39.130 0.00 0.00 0.00 2.27
248 250 3.997681 TGATTGTCGCATTTTTCGAGGTA 59.002 39.130 0.00 0.00 36.56 3.08
251 253 3.842428 CACTGATTGTCGCATTTTTCGAG 59.158 43.478 0.00 0.00 36.56 4.04
252 254 3.809234 CACTGATTGTCGCATTTTTCGA 58.191 40.909 0.00 0.00 0.00 3.71
268 270 6.716628 AGTTCAATTCTTAGATTTGGCACTGA 59.283 34.615 14.39 0.00 0.00 3.41
286 288 7.405292 TCTTATGGTGGAATCAAGAGTTCAAT 58.595 34.615 0.00 0.00 0.00 2.57
379 382 8.545472 ACAAGGCACAAGTAATTATTAGGTCTA 58.455 33.333 0.00 0.00 0.00 2.59
401 404 2.158449 GTCAAGATTGGTCTCGCACAAG 59.842 50.000 0.00 0.00 32.15 3.16
402 405 2.143122 GTCAAGATTGGTCTCGCACAA 58.857 47.619 0.00 0.00 32.15 3.33
403 406 1.344438 AGTCAAGATTGGTCTCGCACA 59.656 47.619 0.00 0.00 32.15 4.57
404 407 2.086054 AGTCAAGATTGGTCTCGCAC 57.914 50.000 0.00 0.00 32.15 5.34
405 408 2.612972 GGAAGTCAAGATTGGTCTCGCA 60.613 50.000 0.00 0.00 32.15 5.10
406 409 2.003301 GGAAGTCAAGATTGGTCTCGC 58.997 52.381 0.00 0.00 32.15 5.03
407 410 2.094700 TCGGAAGTCAAGATTGGTCTCG 60.095 50.000 0.00 0.00 32.15 4.04
1099 1140 2.159572 ACGAGCCGACAAATAATGCAAC 60.160 45.455 0.00 0.00 0.00 4.17
1110 1151 2.046988 TAGACCGACGAGCCGACA 60.047 61.111 0.00 0.00 0.00 4.35
1298 1339 2.488820 GGTAGGAGACGACGGTGC 59.511 66.667 0.00 0.00 36.74 5.01
1437 1478 2.791868 GGCCTTCTCGCTCTCCTCC 61.792 68.421 0.00 0.00 0.00 4.30
1742 1783 9.930693 TTACATCACAGTACAAACATGTGTATA 57.069 29.630 0.00 0.00 43.73 1.47
1816 1857 4.561735 AATCCACGTTGACGAAACAAAT 57.438 36.364 10.87 0.00 43.02 2.32
1920 1961 5.008118 TGCGTGTGTTTCATAGATTTTGTCA 59.992 36.000 0.00 0.00 0.00 3.58
1936 1977 5.324784 TCAGATTCTAGTAATGCGTGTGT 57.675 39.130 0.00 0.00 0.00 3.72
1939 1980 6.893958 AGTTTCAGATTCTAGTAATGCGTG 57.106 37.500 0.00 0.00 0.00 5.34
1975 2016 4.580580 AGAAAATGCACTCGGGAAATATCC 59.419 41.667 0.00 0.00 45.77 2.59
2010 2051 8.650490 AGATTTTGTCAAACATAGACCCAATTT 58.350 29.630 0.00 0.00 35.15 1.82
2012 2053 7.781324 AGATTTTGTCAAACATAGACCCAAT 57.219 32.000 0.00 0.00 35.15 3.16
2016 2057 9.994432 CTTCATAGATTTTGTCAAACATAGACC 57.006 33.333 0.00 0.00 35.15 3.85
2017 2058 9.495754 GCTTCATAGATTTTGTCAAACATAGAC 57.504 33.333 0.00 0.00 36.55 2.59
2019 2060 9.282247 GTGCTTCATAGATTTTGTCAAACATAG 57.718 33.333 0.00 0.00 0.00 2.23
2020 2061 8.791675 TGTGCTTCATAGATTTTGTCAAACATA 58.208 29.630 0.00 0.00 0.00 2.29
2021 2062 7.596248 GTGTGCTTCATAGATTTTGTCAAACAT 59.404 33.333 0.00 0.00 0.00 2.71
2024 2065 6.142139 CGTGTGCTTCATAGATTTTGTCAAA 58.858 36.000 0.00 0.00 0.00 2.69
2025 2066 5.238432 ACGTGTGCTTCATAGATTTTGTCAA 59.762 36.000 0.00 0.00 0.00 3.18
2026 2067 4.754618 ACGTGTGCTTCATAGATTTTGTCA 59.245 37.500 0.00 0.00 0.00 3.58
2028 2069 4.515191 ACACGTGTGCTTCATAGATTTTGT 59.485 37.500 22.71 0.00 0.00 2.83
2029 2070 5.034554 ACACGTGTGCTTCATAGATTTTG 57.965 39.130 22.71 0.00 0.00 2.44
2030 2071 5.689383 AACACGTGTGCTTCATAGATTTT 57.311 34.783 24.16 0.00 0.00 1.82
2031 2072 5.451908 CAAACACGTGTGCTTCATAGATTT 58.548 37.500 24.16 4.91 0.00 2.17
2033 2074 3.436704 CCAAACACGTGTGCTTCATAGAT 59.563 43.478 24.16 0.00 0.00 1.98
2034 2075 2.805671 CCAAACACGTGTGCTTCATAGA 59.194 45.455 24.16 0.00 0.00 1.98
2036 2077 2.566913 ACCAAACACGTGTGCTTCATA 58.433 42.857 24.16 0.00 0.00 2.15
2037 2078 1.388547 ACCAAACACGTGTGCTTCAT 58.611 45.000 24.16 1.40 0.00 2.57
2038 2079 1.135546 CAACCAAACACGTGTGCTTCA 60.136 47.619 24.16 0.00 0.00 3.02
2039 2080 1.544686 CAACCAAACACGTGTGCTTC 58.455 50.000 24.16 0.00 0.00 3.86
2041 2082 1.138671 GCAACCAAACACGTGTGCT 59.861 52.632 24.16 10.04 0.00 4.40
2042 2083 1.876263 GGCAACCAAACACGTGTGC 60.876 57.895 24.16 19.30 0.00 4.57
2043 2084 4.393308 GGCAACCAAACACGTGTG 57.607 55.556 24.16 12.66 0.00 3.82
2069 2128 3.737172 GCGACGCAGGCCAAACAT 61.737 61.111 16.42 0.00 0.00 2.71
2160 2219 2.746375 CCCCTCCCCTCAATCGGTG 61.746 68.421 0.00 0.00 0.00 4.94
2239 2298 0.381801 CCGAAATTCTCCCGCCAATG 59.618 55.000 0.00 0.00 0.00 2.82
2317 2380 1.532238 GGGGGAGAATGGTGGTAGC 59.468 63.158 0.00 0.00 0.00 3.58
2419 2492 2.279935 AGAAGAGGACACGAGTCACT 57.720 50.000 14.98 10.11 46.80 3.41
2421 2494 1.535896 CGAAGAAGAGGACACGAGTCA 59.464 52.381 14.98 0.00 46.80 3.41
2441 2514 2.297597 CCGAGGGAGACAGGAACATATC 59.702 54.545 0.00 0.00 0.00 1.63
2464 2541 0.514691 CACAGAGGCTTTCGCTGAAC 59.485 55.000 7.83 0.00 44.55 3.18
2466 2543 0.037882 CTCACAGAGGCTTTCGCTGA 60.038 55.000 7.83 0.00 44.55 4.26
2473 2550 2.042464 TGACTGAACTCACAGAGGCTT 58.958 47.619 0.00 0.00 40.63 4.35
2490 2567 4.537135 TGAGTACAGAGAAATGGGTGAC 57.463 45.455 0.00 0.00 0.00 3.67
2526 6776 2.719705 TCAAACCCTACCCCATGTTCTT 59.280 45.455 0.00 0.00 0.00 2.52
2535 6785 2.158885 GCTCTCAGATCAAACCCTACCC 60.159 54.545 0.00 0.00 0.00 3.69
2604 6854 5.410439 CACAACATCACATTCTCACAGATCA 59.590 40.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.