Multiple sequence alignment - TraesCS4B01G284300

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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 TraesCS4B01G284300 chr4B 100.000 3623 0 0 1 3623 567677983 567681605 0.000000e+00 6691
1 TraesCS4B01G284300 chr4B 94.032 3435 180 15 207 3623 338723259 338719832 0.000000e+00 5184
2 TraesCS4B01G284300 chr4B 92.277 3535 249 18 102 3623 447262775 447259252 0.000000e+00 4994
3 TraesCS4B01G284300 chr1B 92.983 3634 237 8 2 3623 593273430 593269803 0.000000e+00 5282
4 TraesCS4B01G284300 chr7B 91.462 3631 278 21 7 3623 242307482 242303870 0.000000e+00 4959
5 TraesCS4B01G284300 chr7B 91.606 3562 274 19 77 3623 387406984 387410535 0.000000e+00 4898
6 TraesCS4B01G284300 chr7B 91.560 3531 271 20 110 3623 246678694 246675174 0.000000e+00 4844
7 TraesCS4B01G284300 chr7B 87.879 231 26 2 1 229 182942617 182942387 1.660000e-68 270
8 TraesCS4B01G284300 chr3B 91.503 3519 271 21 121 3623 528819598 528816092 0.000000e+00 4817
9 TraesCS4B01G284300 chr3B 91.152 3515 271 27 122 3623 51346890 51350377 0.000000e+00 4732
10 TraesCS4B01G284300 chr2B 91.147 3558 292 17 80 3623 566810057 566806509 0.000000e+00 4804
11 TraesCS4B01G284300 chr2B 85.737 1283 118 34 2355 3623 405162906 405164137 0.000000e+00 1295
12 TraesCS4B01G284300 chr2B 86.409 1192 98 39 2442 3623 749455139 749456276 0.000000e+00 1245
13 TraesCS4B01G284300 chr2B 86.314 1191 99 40 2442 3623 637508454 637507319 0.000000e+00 1238
14 TraesCS4B01G284300 chr2B 90.430 930 65 12 2707 3623 279187925 279187007 0.000000e+00 1203
15 TraesCS4B01G284300 chr2B 95.652 230 10 0 1 230 337504246 337504475 1.590000e-98 370


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 TraesCS4B01G284300 chr4B 567677983 567681605 3622 False 6691 6691 100.000 1 3623 1 chr4B.!!$F1 3622
1 TraesCS4B01G284300 chr4B 338719832 338723259 3427 True 5184 5184 94.032 207 3623 1 chr4B.!!$R1 3416
2 TraesCS4B01G284300 chr4B 447259252 447262775 3523 True 4994 4994 92.277 102 3623 1 chr4B.!!$R2 3521
3 TraesCS4B01G284300 chr1B 593269803 593273430 3627 True 5282 5282 92.983 2 3623 1 chr1B.!!$R1 3621
4 TraesCS4B01G284300 chr7B 242303870 242307482 3612 True 4959 4959 91.462 7 3623 1 chr7B.!!$R2 3616
5 TraesCS4B01G284300 chr7B 387406984 387410535 3551 False 4898 4898 91.606 77 3623 1 chr7B.!!$F1 3546
6 TraesCS4B01G284300 chr7B 246675174 246678694 3520 True 4844 4844 91.560 110 3623 1 chr7B.!!$R3 3513
7 TraesCS4B01G284300 chr3B 528816092 528819598 3506 True 4817 4817 91.503 121 3623 1 chr3B.!!$R1 3502
8 TraesCS4B01G284300 chr3B 51346890 51350377 3487 False 4732 4732 91.152 122 3623 1 chr3B.!!$F1 3501
9 TraesCS4B01G284300 chr2B 566806509 566810057 3548 True 4804 4804 91.147 80 3623 1 chr2B.!!$R2 3543
10 TraesCS4B01G284300 chr2B 405162906 405164137 1231 False 1295 1295 85.737 2355 3623 1 chr2B.!!$F2 1268
11 TraesCS4B01G284300 chr2B 749455139 749456276 1137 False 1245 1245 86.409 2442 3623 1 chr2B.!!$F3 1181
12 TraesCS4B01G284300 chr2B 637507319 637508454 1135 True 1238 1238 86.314 2442 3623 1 chr2B.!!$R3 1181
13 TraesCS4B01G284300 chr2B 279187007 279187925 918 True 1203 1203 90.430 2707 3623 1 chr2B.!!$R1 916

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
841 846 0.322816 AAGCTGCAATCCGTGACCAT 60.323 50.000 1.02 0.0 0.00 3.55 F
1142 1148 0.322975 AGCCTCGTGCAATCAGAAGT 59.677 50.000 0.00 0.0 44.83 3.01 F
1965 1971 1.754226 GAAGATCCAGAGGAAGAGCGT 59.246 52.381 0.00 0.0 34.34 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2018 1.891150 CACTTGGGAATTGCAGCTCTT 59.109 47.619 0.0 0.0 0.00 2.85 R
2493 2499 2.906389 AGAGACAATGCAAGTGGTAGGA 59.094 45.455 0.0 0.0 35.33 2.94 R
3445 3490 2.099263 CGAAGTGACATACCACCGATCT 59.901 50.000 0.0 0.0 37.76 2.75 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
46 47 6.857777 AAGCAAAGATAATCTTCATCTCCG 57.142 37.500 0.00 0.00 35.27 4.63
55 56 2.337583 TCTTCATCTCCGTTTGCTTCG 58.662 47.619 0.00 0.00 0.00 3.79
80 81 6.071728 GGTGTCATTTCCTTTGTTGATGATCT 60.072 38.462 0.00 0.00 0.00 2.75
82 83 8.514594 GTGTCATTTCCTTTGTTGATGATCTTA 58.485 33.333 0.00 0.00 0.00 2.10
89 90 9.436957 TTCCTTTGTTGATGATCTTAGTTAGTC 57.563 33.333 0.00 0.00 0.00 2.59
93 94 9.996554 TTTGTTGATGATCTTAGTTAGTCTTGA 57.003 29.630 0.00 0.00 0.00 3.02
94 95 8.988064 TGTTGATGATCTTAGTTAGTCTTGAC 57.012 34.615 0.00 0.00 0.00 3.18
112 113 8.940952 AGTCTTGACTTAATATTCTGCTTTCAC 58.059 33.333 0.00 0.00 0.00 3.18
174 175 2.363795 TCGCCTAGTCCCTGTGGG 60.364 66.667 0.00 0.00 46.11 4.61
194 195 0.503117 GAACACGACACTCGCAGTTC 59.497 55.000 12.04 12.04 45.12 3.01
229 233 4.109766 CCGCTGTACTTACAATCGATCAA 58.890 43.478 0.00 0.00 35.59 2.57
238 242 1.745087 ACAATCGATCAATTTGGCGCT 59.255 42.857 7.64 0.00 0.00 5.92
243 247 1.401409 CGATCAATTTGGCGCTGTTGT 60.401 47.619 7.64 0.00 0.00 3.32
428 433 5.535030 TGTGAGCGTGTGTAGGATATCTTAT 59.465 40.000 2.05 0.00 0.00 1.73
491 496 5.407387 GCTTTAGTACGTGATCTTTGGTTGA 59.593 40.000 0.00 0.00 0.00 3.18
500 505 5.333339 CGTGATCTTTGGTTGACAAGTAGTG 60.333 44.000 0.00 0.00 40.82 2.74
667 672 5.012148 GGAGTATGCCAATACAGTCCAGTAT 59.988 44.000 0.00 0.00 41.09 2.12
674 679 4.444733 CCAATACAGTCCAGTATCATGGCA 60.445 45.833 0.00 0.00 40.41 4.92
748 753 4.501743 GCTGCTAAGGACTGGTACTATTCC 60.502 50.000 7.46 7.46 0.00 3.01
801 806 4.503741 TTTCACAAGCTTTCCTGCATAC 57.496 40.909 0.00 0.00 34.99 2.39
841 846 0.322816 AAGCTGCAATCCGTGACCAT 60.323 50.000 1.02 0.00 0.00 3.55
865 870 1.267806 CTCAGTTTTGCGCAAGATGGT 59.732 47.619 23.68 5.17 43.02 3.55
1032 1038 4.520492 GGTGGAACAATCATGAACAAGACT 59.480 41.667 0.00 0.00 44.16 3.24
1035 1041 5.239306 TGGAACAATCATGAACAAGACTGTC 59.761 40.000 0.00 0.00 30.42 3.51
1142 1148 0.322975 AGCCTCGTGCAATCAGAAGT 59.677 50.000 0.00 0.00 44.83 3.01
1342 1348 5.013079 ACTGTAGATCAGATGGAAACCACAA 59.987 40.000 0.00 0.00 46.27 3.33
1355 1361 4.142381 GGAAACCACAATAGCAGATCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1535 1541 2.660572 TGCCCACACTTGTGTTACAAT 58.339 42.857 8.52 0.00 44.21 2.71
1536 1542 2.360483 TGCCCACACTTGTGTTACAATG 59.640 45.455 8.52 0.00 44.21 2.82
1794 1800 3.258372 GGTGGAAGTCATCAGTGTCACTA 59.742 47.826 4.85 0.00 0.00 2.74
1894 1900 8.899427 ACCAGATCATGTTAGTGAATATTCAG 57.101 34.615 18.47 5.43 37.98 3.02
1904 1910 7.293299 TGTTAGTGAATATTCAGAGATGGGGAT 59.707 37.037 18.47 0.00 37.98 3.85
1963 1969 4.021192 CCATAGAAGATCCAGAGGAAGAGC 60.021 50.000 0.00 0.00 34.34 4.09
1965 1971 1.754226 GAAGATCCAGAGGAAGAGCGT 59.246 52.381 0.00 0.00 34.34 5.07
1983 1989 3.007398 AGCGTCCTCAACTTGAAGAAGAT 59.993 43.478 0.00 0.00 32.98 2.40
1984 1990 3.748568 GCGTCCTCAACTTGAAGAAGATT 59.251 43.478 0.00 0.00 32.98 2.40
1988 1994 6.423905 CGTCCTCAACTTGAAGAAGATTTACA 59.576 38.462 0.00 0.00 32.98 2.41
1989 1995 7.042051 CGTCCTCAACTTGAAGAAGATTTACAA 60.042 37.037 0.00 0.00 32.98 2.41
2012 2018 6.119240 AGAAGACAAGGAACAAGATGATCA 57.881 37.500 0.00 0.00 0.00 2.92
2019 2025 4.515361 AGGAACAAGATGATCAAGAGCTG 58.485 43.478 0.00 0.00 0.00 4.24
2020 2026 3.065095 GGAACAAGATGATCAAGAGCTGC 59.935 47.826 0.00 0.00 0.00 5.25
2023 2029 4.270834 ACAAGATGATCAAGAGCTGCAAT 58.729 39.130 0.00 0.00 0.00 3.56
2024 2030 4.705507 ACAAGATGATCAAGAGCTGCAATT 59.294 37.500 0.00 0.00 0.00 2.32
2025 2031 5.163642 ACAAGATGATCAAGAGCTGCAATTC 60.164 40.000 0.00 0.00 0.00 2.17
2063 2069 7.284489 AGTTGAAGACTCATCATCTACTACTCC 59.716 40.741 0.00 0.00 37.03 3.85
2085 2091 3.403038 TGAAGAAGTACAAGAAGCTGCC 58.597 45.455 0.00 0.00 0.00 4.85
2105 2111 4.081697 TGCCGTAGATGAAGATGAAGAACA 60.082 41.667 0.00 0.00 0.00 3.18
2177 2183 3.284617 CCAATCCTCTTGATGACATGCA 58.715 45.455 0.00 0.00 32.68 3.96
2321 2327 5.410924 TGATGATCACAGTTACTTTCCTCG 58.589 41.667 0.00 0.00 0.00 4.63
2493 2499 6.936900 CGATTGATGACTTGGAGGGTATTATT 59.063 38.462 0.00 0.00 0.00 1.40
2846 2862 7.718753 TGCTGAAATCAAATGTTATTTGGGTTT 59.281 29.630 12.72 13.04 0.00 3.27
3050 3069 9.077885 ACTTAATCATTTTCTGCTTTTACCTCA 57.922 29.630 0.00 0.00 0.00 3.86
3199 3219 5.248640 TGGAGAAGTGATGATTCCTGTTTC 58.751 41.667 0.00 0.00 0.00 2.78
3399 3421 2.041216 GTGGTATGTTCCTTTGGGGAGT 59.959 50.000 0.00 0.00 46.01 3.85
3460 3505 2.219458 TCTCGAGATCGGTGGTATGTC 58.781 52.381 12.08 0.00 40.29 3.06
3461 3506 1.947456 CTCGAGATCGGTGGTATGTCA 59.053 52.381 6.58 0.00 40.29 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.909357 GCAAACGGAGATGAAGATTATCTTTG 59.091 38.462 8.99 0.91 36.73 2.77
46 47 2.293399 AGGAAATGACACCGAAGCAAAC 59.707 45.455 0.00 0.00 0.00 2.93
55 56 5.452078 TCATCAACAAAGGAAATGACACC 57.548 39.130 0.00 0.00 0.00 4.16
89 90 8.044060 TGGTGAAAGCAGAATATTAAGTCAAG 57.956 34.615 0.00 0.00 40.88 3.02
112 113 5.996644 TCTAGGTAACACAATATTGGGTGG 58.003 41.667 23.69 10.06 45.74 4.61
174 175 0.874607 AACTGCGAGTGTCGTGTTCC 60.875 55.000 0.00 0.00 42.81 3.62
198 199 5.601583 TGTAAGTACAGCGGGATATTTCA 57.398 39.130 0.00 0.00 0.00 2.69
199 200 6.128902 CGATTGTAAGTACAGCGGGATATTTC 60.129 42.308 0.00 0.00 37.52 2.17
229 233 2.625823 CCCGACAACAGCGCCAAAT 61.626 57.895 2.29 0.00 0.00 2.32
238 242 1.870055 GACGCTAGTCCCCGACAACA 61.870 60.000 0.00 0.00 41.41 3.33
243 247 2.513204 CTCGACGCTAGTCCCCGA 60.513 66.667 0.00 0.00 44.28 5.14
269 273 7.852971 ATACTAAGCCTAGTCTATAGCTTCG 57.147 40.000 16.56 13.94 44.13 3.79
392 397 3.066621 ACACGCTCACAAACATCAAACAT 59.933 39.130 0.00 0.00 0.00 2.71
491 496 2.626266 TCATCGTGTCCACACTACTTGT 59.374 45.455 8.19 0.00 44.34 3.16
500 505 1.741770 GCCCTGTCATCGTGTCCAC 60.742 63.158 0.00 0.00 0.00 4.02
667 672 1.758280 GCATCTTGGGAAATGCCATGA 59.242 47.619 11.08 11.08 41.92 3.07
674 679 5.513233 ACACTTGATAGCATCTTGGGAAAT 58.487 37.500 0.00 0.00 0.00 2.17
832 837 3.543680 AAACTGAGGATATGGTCACGG 57.456 47.619 0.00 0.00 0.00 4.94
841 846 3.052455 TCTTGCGCAAAACTGAGGATA 57.948 42.857 25.01 0.00 0.00 2.59
865 870 2.762887 AGCTGCATACAAGCTCTCACTA 59.237 45.455 1.02 0.00 32.98 2.74
1032 1038 3.055458 TGAGAATAATTGCACCCTCGACA 60.055 43.478 0.00 0.00 0.00 4.35
1035 1041 4.576053 TCAATGAGAATAATTGCACCCTCG 59.424 41.667 0.00 0.00 0.00 4.63
1127 1133 2.287644 CACACAACTTCTGATTGCACGA 59.712 45.455 0.00 0.00 0.00 4.35
1128 1134 2.032054 ACACACAACTTCTGATTGCACG 59.968 45.455 0.00 0.00 0.00 5.34
1142 1148 5.432645 TCTGTTCACTTATGGAACACACAA 58.567 37.500 4.02 0.00 46.95 3.33
1313 1319 7.038302 TGGTTTCCATCTGATCTACAGTAGTTT 60.038 37.037 7.50 0.00 45.86 2.66
1317 1323 5.719563 TGTGGTTTCCATCTGATCTACAGTA 59.280 40.000 0.00 0.00 45.86 2.74
1342 1348 3.181447 CCATGAGGTGTTGGATCTGCTAT 60.181 47.826 0.00 0.00 34.81 2.97
1355 1361 2.559668 ACAGTTTCATTGCCATGAGGTG 59.440 45.455 0.24 3.23 40.66 4.00
1535 1541 4.473196 TCTTGACAAATAGCCCAGATACCA 59.527 41.667 0.00 0.00 0.00 3.25
1536 1542 5.036117 TCTTGACAAATAGCCCAGATACC 57.964 43.478 0.00 0.00 0.00 2.73
1794 1800 5.316167 TCACCATCACTGCTAAGTTTCAAT 58.684 37.500 0.00 0.00 32.98 2.57
1894 1900 4.219115 TGAGTCTGAAGTATCCCCATCTC 58.781 47.826 0.00 0.00 0.00 2.75
1904 1910 7.171508 CAGCAACACTTAATTGAGTCTGAAGTA 59.828 37.037 9.82 0.00 0.00 2.24
1963 1969 5.931441 AAATCTTCTTCAAGTTGAGGACG 57.069 39.130 16.57 14.86 31.94 4.79
1965 1971 8.210946 TCTTGTAAATCTTCTTCAAGTTGAGGA 58.789 33.333 13.28 13.28 37.39 3.71
1983 1989 7.773224 TCATCTTGTTCCTTGTCTTCTTGTAAA 59.227 33.333 0.00 0.00 0.00 2.01
1984 1990 7.279615 TCATCTTGTTCCTTGTCTTCTTGTAA 58.720 34.615 0.00 0.00 0.00 2.41
1988 1994 6.537355 TGATCATCTTGTTCCTTGTCTTCTT 58.463 36.000 0.00 0.00 0.00 2.52
1989 1995 6.119240 TGATCATCTTGTTCCTTGTCTTCT 57.881 37.500 0.00 0.00 0.00 2.85
2012 2018 1.891150 CACTTGGGAATTGCAGCTCTT 59.109 47.619 0.00 0.00 0.00 2.85
2019 2025 4.022068 TCAACTTGATCACTTGGGAATTGC 60.022 41.667 10.92 0.00 0.00 3.56
2020 2026 5.710513 TCAACTTGATCACTTGGGAATTG 57.289 39.130 10.92 0.00 0.00 2.32
2023 2029 4.821805 GTCTTCAACTTGATCACTTGGGAA 59.178 41.667 10.92 4.79 0.00 3.97
2024 2030 4.103153 AGTCTTCAACTTGATCACTTGGGA 59.897 41.667 10.92 7.93 33.03 4.37
2025 2031 4.392940 AGTCTTCAACTTGATCACTTGGG 58.607 43.478 10.92 6.31 33.03 4.12
2063 2069 3.434984 GGCAGCTTCTTGTACTTCTTCAG 59.565 47.826 0.00 0.00 0.00 3.02
2085 2091 7.199078 TCTCATGTTCTTCATCTTCATCTACG 58.801 38.462 0.00 0.00 34.09 3.51
2105 2111 7.834881 ATGACAATAGGCAAATGAATCTCAT 57.165 32.000 0.00 0.00 39.09 2.90
2177 2183 7.001073 GGTAGAAGCAAAGGAATCATAAGGAT 58.999 38.462 0.00 0.00 38.05 3.24
2321 2327 6.538742 TGTTTCATTAAGCATAGGTCTAGCAC 59.461 38.462 0.00 0.00 0.00 4.40
2493 2499 2.906389 AGAGACAATGCAAGTGGTAGGA 59.094 45.455 0.00 0.00 35.33 2.94
2846 2862 6.350110 GGCAACATTTAAGACATGGCTTAAGA 60.350 38.462 28.14 20.64 40.35 2.10
3050 3069 5.416271 AAACGTGGTGATCTAGGTGTATT 57.584 39.130 0.00 0.00 0.00 1.89
3199 3219 8.015087 TCTTAAATGAACAACGCATAAGAACAG 58.985 33.333 0.00 0.00 0.00 3.16
3445 3490 2.099263 CGAAGTGACATACCACCGATCT 59.901 50.000 0.00 0.00 37.76 2.75


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

AutoCloner maintained by Alex Coulton.