Multiple sequence alignment - TraesCS6D01G147300

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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 TraesCS6D01G147300 chr6D 100.000 2771 0 0 1 2771 119295448 119298218 0.000000e+00 5118.0
1 TraesCS6D01G147300 chr6D 87.910 488 33 15 1965 2434 119964593 119965072 4.030000e-153 551.0
2 TraesCS6D01G147300 chr6D 93.496 123 6 1 2521 2643 119966199 119966319 6.100000e-42 182.0
3 TraesCS6D01G147300 chr6A 91.503 2189 93 37 471 2611 147473686 147475829 0.000000e+00 2926.0
4 TraesCS6D01G147300 chr6A 96.244 639 18 5 1994 2627 147476642 147477279 0.000000e+00 1042.0
5 TraesCS6D01G147300 chr6A 87.123 497 40 14 1963 2441 148241498 148241988 2.430000e-150 542.0
6 TraesCS6D01G147300 chr6A 86.910 466 28 10 1 462 147473166 147473602 2.480000e-135 492.0
7 TraesCS6D01G147300 chr6A 100.000 46 0 0 2726 2771 147477284 147477329 4.920000e-13 86.1
8 TraesCS6D01G147300 chr6B 92.074 2044 86 30 467 2470 211213640 211215647 0.000000e+00 2808.0
9 TraesCS6D01G147300 chr6B 97.494 399 9 1 1994 2391 211216622 211217020 0.000000e+00 680.0
10 TraesCS6D01G147300 chr6B 88.000 500 31 18 1982 2463 213006584 213006096 5.180000e-157 564.0
11 TraesCS6D01G147300 chr6B 95.115 348 11 3 2426 2771 211217020 211217363 6.750000e-151 544.0
12 TraesCS6D01G147300 chr6B 88.172 465 22 8 1 462 211213131 211213565 8.790000e-145 523.0
13 TraesCS6D01G147300 chr6B 100.000 30 0 0 2012 2041 211216595 211216624 3.860000e-04 56.5
14 TraesCS6D01G147300 chr7A 82.013 467 84 0 1105 1571 670536794 670537260 5.560000e-107 398.0
15 TraesCS6D01G147300 chr7B 80.728 467 90 0 1105 1571 642261312 642261778 5.640000e-97 364.0


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 TraesCS6D01G147300 chr6D 119295448 119298218 2770 False 5118.000 5118 100.00000 1 2771 1 chr6D.!!$F1 2770
1 TraesCS6D01G147300 chr6D 119964593 119966319 1726 False 366.500 551 90.70300 1965 2643 2 chr6D.!!$F2 678
2 TraesCS6D01G147300 chr6A 147473166 147477329 4163 False 1136.525 2926 93.66425 1 2771 4 chr6A.!!$F2 2770
3 TraesCS6D01G147300 chr6B 211213131 211217363 4232 False 922.300 2808 94.57100 1 2771 5 chr6B.!!$F1 2770

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
997 1097 2.030805 GGCTTTGCACGAACAAGATCTT 60.031 45.455 0.88 0.88 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 3702 0.040067 GAGGCAAACAAACAGAGGCG 60.04 55.0 0.0 0.0 0.0 5.52 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
41 45 2.032030 CACGCCACTCCACTTTTAACTG 60.032 50.000 0.00 0.00 0.00 3.16
45 49 4.386711 GCCACTCCACTTTTAACTGTAGT 58.613 43.478 0.00 0.00 0.00 2.73
60 64 9.452287 TTTAACTGTAGTTGAACTTTACAAGGT 57.548 29.630 1.97 0.00 38.90 3.50
61 65 7.933215 AACTGTAGTTGAACTTTACAAGGTT 57.067 32.000 1.97 2.03 36.80 3.50
62 66 7.933215 ACTGTAGTTGAACTTTACAAGGTTT 57.067 32.000 1.97 0.00 0.00 3.27
63 67 7.758495 ACTGTAGTTGAACTTTACAAGGTTTG 58.242 34.615 1.97 0.00 0.00 2.93
64 68 7.090953 TGTAGTTGAACTTTACAAGGTTTGG 57.909 36.000 1.97 0.00 34.12 3.28
65 69 5.006153 AGTTGAACTTTACAAGGTTTGGC 57.994 39.130 0.00 0.00 34.12 4.52
66 70 4.464597 AGTTGAACTTTACAAGGTTTGGCA 59.535 37.500 0.00 0.00 34.12 4.92
67 71 5.128663 AGTTGAACTTTACAAGGTTTGGCAT 59.871 36.000 0.00 0.00 34.12 4.40
68 72 5.195001 TGAACTTTACAAGGTTTGGCATC 57.805 39.130 0.00 0.00 34.12 3.91
69 73 4.892934 TGAACTTTACAAGGTTTGGCATCT 59.107 37.500 0.00 0.00 34.12 2.90
99 103 8.623903 TGTGATATTGACTTAATTCAATGCTCC 58.376 33.333 23.92 15.78 44.33 4.70
105 109 6.480763 TGACTTAATTCAATGCTCCTGGTTA 58.519 36.000 0.00 0.00 0.00 2.85
226 230 4.202111 GGTTTATGTGCCTTTTCTGTGTGT 60.202 41.667 0.00 0.00 0.00 3.72
257 261 2.298163 CCTGCTTGCACTGAAAATCCTT 59.702 45.455 0.00 0.00 0.00 3.36
260 264 4.397420 TGCTTGCACTGAAAATCCTTAGA 58.603 39.130 0.00 0.00 0.00 2.10
261 265 4.216257 TGCTTGCACTGAAAATCCTTAGAC 59.784 41.667 0.00 0.00 0.00 2.59
262 266 4.216257 GCTTGCACTGAAAATCCTTAGACA 59.784 41.667 0.00 0.00 0.00 3.41
263 267 5.105997 GCTTGCACTGAAAATCCTTAGACAT 60.106 40.000 0.00 0.00 0.00 3.06
264 268 5.885230 TGCACTGAAAATCCTTAGACATG 57.115 39.130 0.00 0.00 0.00 3.21
265 269 5.316167 TGCACTGAAAATCCTTAGACATGT 58.684 37.500 0.00 0.00 0.00 3.21
266 270 5.181811 TGCACTGAAAATCCTTAGACATGTG 59.818 40.000 1.15 0.00 0.00 3.21
267 271 5.392380 GCACTGAAAATCCTTAGACATGTGG 60.392 44.000 1.15 0.00 0.00 4.17
268 272 5.707298 CACTGAAAATCCTTAGACATGTGGT 59.293 40.000 1.15 0.00 0.00 4.16
269 273 5.707298 ACTGAAAATCCTTAGACATGTGGTG 59.293 40.000 1.15 0.00 0.00 4.17
270 274 5.630121 TGAAAATCCTTAGACATGTGGTGT 58.370 37.500 1.15 0.00 45.83 4.16
301 305 6.309712 TGATTTGAAGCTCTGAACTTTCTG 57.690 37.500 0.00 0.00 0.00 3.02
309 313 7.663081 TGAAGCTCTGAACTTTCTGTATGATTT 59.337 33.333 0.00 0.00 0.00 2.17
312 316 8.097038 AGCTCTGAACTTTCTGTATGATTTGTA 58.903 33.333 0.00 0.00 0.00 2.41
372 376 7.440523 AATATTGGACTCTTCTGTGTTTGTC 57.559 36.000 0.00 0.00 0.00 3.18
373 377 3.194005 TGGACTCTTCTGTGTTTGTCC 57.806 47.619 0.00 0.00 42.87 4.02
374 378 3.194005 GGACTCTTCTGTGTTTGTCCA 57.806 47.619 0.00 0.00 42.32 4.02
390 394 7.007723 TGTTTGTCCATACTCCTTAACCAATT 58.992 34.615 0.00 0.00 0.00 2.32
418 422 5.111293 CAGGGATTGATTGGTTATGCAAAC 58.889 41.667 0.00 0.00 0.00 2.93
419 423 4.776837 AGGGATTGATTGGTTATGCAAACA 59.223 37.500 11.93 0.00 0.00 2.83
427 431 7.089538 TGATTGGTTATGCAAACATACACTTG 58.910 34.615 11.93 0.00 38.50 3.16
443 448 8.313292 ACATACACTTGCAAATTATGGATTGTT 58.687 29.630 18.71 2.56 31.29 2.83
447 452 8.313292 ACACTTGCAAATTATGGATTGTTGTAT 58.687 29.630 0.00 0.00 0.00 2.29
506 586 8.855110 TGTTCTGATGATACTTTTGCCTTTAAA 58.145 29.630 0.00 0.00 0.00 1.52
514 594 9.705290 TGATACTTTTGCCTTTAAATCCTTTTC 57.295 29.630 0.00 0.00 0.00 2.29
539 619 3.000041 TCAGTTGCTTTATGTGTAGCGG 59.000 45.455 0.00 0.00 40.26 5.52
540 620 2.742053 CAGTTGCTTTATGTGTAGCGGT 59.258 45.455 0.00 0.00 40.26 5.68
624 704 9.590451 CAATTGATAGTTGCATTATGAAGGTTT 57.410 29.630 0.00 0.00 0.00 3.27
666 746 2.863809 AGGTTGATGGGAACTTGTGAC 58.136 47.619 0.00 0.00 0.00 3.67
678 758 8.472007 TGGGAACTTGTGACTTTTATTTACAT 57.528 30.769 0.00 0.00 0.00 2.29
679 759 8.356657 TGGGAACTTGTGACTTTTATTTACATG 58.643 33.333 0.00 0.00 0.00 3.21
775 872 7.936584 ACGAGAATCTTTTTGTGTTTGGAATA 58.063 30.769 0.00 0.00 0.00 1.75
791 888 4.016444 TGGAATACTGCAATGGACCTTTC 58.984 43.478 0.00 0.00 0.00 2.62
809 906 8.360390 GGACCTTTCAGATTAAATGTTGAGTTT 58.640 33.333 0.00 0.00 0.00 2.66
964 1064 2.791383 TATTGTTTTGCGCAGTGCTT 57.209 40.000 11.31 0.00 46.63 3.91
997 1097 2.030805 GGCTTTGCACGAACAAGATCTT 60.031 45.455 0.88 0.88 0.00 2.40
1113 1213 4.883354 CCTGCCGCCATTCCTCCC 62.883 72.222 0.00 0.00 0.00 4.30
1140 1240 2.757099 CCAGCAGTGCCATTCCCC 60.757 66.667 12.58 0.00 0.00 4.81
1203 1303 2.289819 CCAACAAGCCCAGCAATTTCAT 60.290 45.455 0.00 0.00 0.00 2.57
1479 1579 3.508762 CTTGCAGAAGAATGACATTGCC 58.491 45.455 5.14 0.00 0.00 4.52
1506 1606 4.040952 GCCATTACCAGGACTGACATCTAT 59.959 45.833 0.00 0.00 0.00 1.98
1572 1672 2.757077 CTTGGGCTTCCGAGGGTT 59.243 61.111 0.00 0.00 38.21 4.11
1686 1786 1.210204 ATGGTGGTCAGCAGGGTCAT 61.210 55.000 8.79 0.00 42.52 3.06
1917 2017 3.071167 GGGTTCCTAATGGTAGCTTCGAT 59.929 47.826 0.00 0.00 32.69 3.59
2087 3702 0.036732 TTGGTGGAGGCTGATGTCAC 59.963 55.000 0.00 0.00 0.00 3.67
2321 3952 5.075858 ACATGAATTATTGTGGCTGTTGG 57.924 39.130 0.00 0.00 0.00 3.77
2406 4038 0.249657 GCATGGTCGCCCTTCTCTAG 60.250 60.000 0.00 0.00 0.00 2.43
2519 4273 2.910319 TGGTTGTCAGTAGGCCTGTAAT 59.090 45.455 17.99 0.00 42.19 1.89
2554 5263 4.528596 TCTCAACAAGTAGAAAGAGAGGGG 59.471 45.833 0.00 0.00 0.00 4.79
2564 5276 1.821088 AAGAGAGGGGTGACAGGTTT 58.179 50.000 0.00 0.00 0.00 3.27
2710 5422 1.908619 TGTGAATGGCCTCTTCTGCTA 59.091 47.619 16.40 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 45 5.975344 GCCAAACCTTGTAAAGTTCAACTAC 59.025 40.000 0.00 0.00 44.25 2.73
45 49 5.362430 AGATGCCAAACCTTGTAAAGTTCAA 59.638 36.000 0.00 0.00 44.25 2.69
57 61 1.985159 TCACACCTAGATGCCAAACCT 59.015 47.619 0.00 0.00 0.00 3.50
58 62 2.489938 TCACACCTAGATGCCAAACC 57.510 50.000 0.00 0.00 0.00 3.27
59 63 5.822519 TCAATATCACACCTAGATGCCAAAC 59.177 40.000 0.00 0.00 0.00 2.93
60 64 5.822519 GTCAATATCACACCTAGATGCCAAA 59.177 40.000 0.00 0.00 0.00 3.28
61 65 5.130975 AGTCAATATCACACCTAGATGCCAA 59.869 40.000 0.00 0.00 0.00 4.52
62 66 4.655649 AGTCAATATCACACCTAGATGCCA 59.344 41.667 0.00 0.00 0.00 4.92
63 67 5.220710 AGTCAATATCACACCTAGATGCC 57.779 43.478 0.00 0.00 0.00 4.40
64 68 8.839310 ATTAAGTCAATATCACACCTAGATGC 57.161 34.615 0.00 0.00 0.00 3.91
94 98 2.584835 ACTTGCATTAACCAGGAGCA 57.415 45.000 0.00 0.00 0.00 4.26
99 103 7.633621 CAGTATCATGTACTTGCATTAACCAG 58.366 38.462 3.90 0.00 0.00 4.00
105 109 4.785301 AGGCAGTATCATGTACTTGCATT 58.215 39.130 18.88 11.28 0.00 3.56
164 168 1.645710 TGGGAGTCTCCAGAAAGGAC 58.354 55.000 20.72 1.08 43.07 3.85
226 230 0.394938 TGCAAGCAGGTTCCGTAGAA 59.605 50.000 0.00 0.00 0.00 2.10
263 267 4.916183 TCAAATCATCCATGTACACCACA 58.084 39.130 0.00 0.00 42.69 4.17
264 268 5.677091 GCTTCAAATCATCCATGTACACCAC 60.677 44.000 0.00 0.00 0.00 4.16
265 269 4.398988 GCTTCAAATCATCCATGTACACCA 59.601 41.667 0.00 0.00 0.00 4.17
266 270 4.641989 AGCTTCAAATCATCCATGTACACC 59.358 41.667 0.00 0.00 0.00 4.16
267 271 5.587844 AGAGCTTCAAATCATCCATGTACAC 59.412 40.000 0.00 0.00 0.00 2.90
268 272 5.587443 CAGAGCTTCAAATCATCCATGTACA 59.413 40.000 0.00 0.00 0.00 2.90
269 273 5.819379 TCAGAGCTTCAAATCATCCATGTAC 59.181 40.000 0.00 0.00 0.00 2.90
270 274 5.993055 TCAGAGCTTCAAATCATCCATGTA 58.007 37.500 0.00 0.00 0.00 2.29
282 286 6.524734 TCATACAGAAAGTTCAGAGCTTCAA 58.475 36.000 0.00 0.00 0.00 2.69
301 305 8.088981 AGTTAGATGGATCGGTACAAATCATAC 58.911 37.037 8.46 0.00 0.00 2.39
309 313 3.704566 AGCAAGTTAGATGGATCGGTACA 59.295 43.478 0.00 0.00 0.00 2.90
312 316 3.914426 AAGCAAGTTAGATGGATCGGT 57.086 42.857 0.00 0.00 0.00 4.69
372 376 7.201821 CCTGCTAAAATTGGTTAAGGAGTATGG 60.202 40.741 0.00 0.00 0.00 2.74
373 377 7.201821 CCCTGCTAAAATTGGTTAAGGAGTATG 60.202 40.741 0.00 0.00 0.00 2.39
374 378 6.833933 CCCTGCTAAAATTGGTTAAGGAGTAT 59.166 38.462 0.00 0.00 0.00 2.12
390 394 5.068987 GCATAACCAATCAATCCCTGCTAAA 59.931 40.000 0.00 0.00 0.00 1.85
418 422 8.597227 CAACAATCCATAATTTGCAAGTGTATG 58.403 33.333 14.53 14.53 0.00 2.39
419 423 8.313292 ACAACAATCCATAATTTGCAAGTGTAT 58.687 29.630 0.00 0.00 0.00 2.29
427 431 6.475076 TCGCAATACAACAATCCATAATTTGC 59.525 34.615 0.00 0.00 0.00 3.68
462 467 5.860182 CAGAACACAAACAGCAATGGATAAG 59.140 40.000 0.00 0.00 0.00 1.73
464 469 5.069318 TCAGAACACAAACAGCAATGGATA 58.931 37.500 0.00 0.00 0.00 2.59
465 470 3.890756 TCAGAACACAAACAGCAATGGAT 59.109 39.130 0.00 0.00 0.00 3.41
469 549 5.717078 ATCATCAGAACACAAACAGCAAT 57.283 34.783 0.00 0.00 0.00 3.56
506 586 8.370182 ACATAAAGCAACTGAAATGAAAAGGAT 58.630 29.630 0.00 0.00 0.00 3.24
514 594 5.509272 CGCTACACATAAAGCAACTGAAATG 59.491 40.000 0.00 0.00 38.70 2.32
539 619 9.968870 AGTATTCCGAACAGAGAAAGATTATAC 57.031 33.333 0.00 0.00 0.00 1.47
540 620 9.967346 CAGTATTCCGAACAGAGAAAGATTATA 57.033 33.333 0.00 0.00 0.00 0.98
629 709 7.607991 CCATCAACCTTATCCCTAATATGTGTC 59.392 40.741 0.00 0.00 0.00 3.67
678 758 6.128553 GCAGAAATGAAATCGAACAGACTACA 60.129 38.462 0.00 0.00 0.00 2.74
679 759 6.091441 AGCAGAAATGAAATCGAACAGACTAC 59.909 38.462 0.00 0.00 0.00 2.73
689 769 2.159421 AGCAGCAGCAGAAATGAAATCG 60.159 45.455 3.17 0.00 45.49 3.34
775 872 2.957402 TCTGAAAGGTCCATTGCAGT 57.043 45.000 0.03 0.00 0.00 4.40
791 888 8.752766 AGCAATCAAACTCAACATTTAATCTG 57.247 30.769 0.00 0.00 0.00 2.90
809 906 4.518590 TGAACGAAGGAATCAAAGCAATCA 59.481 37.500 0.00 0.00 0.00 2.57
883 980 9.396022 AGAAAGATCAGAACAAGTTTACAAGAA 57.604 29.630 0.00 0.00 0.00 2.52
964 1064 3.587923 GTGCAAAGCCAAATATCTTGCA 58.412 40.909 3.80 3.80 0.00 4.08
966 1066 4.095410 TCGTGCAAAGCCAAATATCTTG 57.905 40.909 0.00 0.00 0.00 3.02
997 1097 1.048160 TGCGAGGATGGCTCCATGTA 61.048 55.000 6.07 0.00 44.79 2.29
1203 1303 0.101040 GCTGTTGCTGCAGTTGTTGA 59.899 50.000 16.64 0.00 38.65 3.18
1479 1579 1.091771 CAGTCCTGGTAATGGCAGCG 61.092 60.000 0.00 0.00 0.00 5.18
1506 1606 4.326826 GAATGATGTCCACCAAGAAGTCA 58.673 43.478 0.00 0.00 0.00 3.41
1581 1681 4.560743 GCCCCTAGAGCAGCTGGC 62.561 72.222 17.12 1.33 45.30 4.85
1686 1786 1.153188 CCACGCATATGCCACTGGA 60.153 57.895 21.77 0.00 37.91 3.86
2087 3702 0.040067 GAGGCAAACAAACAGAGGCG 60.040 55.000 0.00 0.00 0.00 5.52
2406 4038 9.688592 ATGAACAAGAATCTGAATTTGTCTTTC 57.311 29.630 5.62 2.46 32.97 2.62
2494 4248 2.795329 AGGCCTACTGACAACCAAATG 58.205 47.619 1.29 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.