Multiple sequence alignment - TraesCS5A01G223900

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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 TraesCS5A01G223900 chr5A 100.000 2201 0 0 1 2201 439552039 439549839 0.000000e+00 4065.0
1 TraesCS5A01G223900 chr5D 94.370 1634 66 12 575 2201 338656320 338654706 0.000000e+00 2484.0
2 TraesCS5A01G223900 chr5D 88.869 566 23 17 4 558 338656991 338656455 0.000000e+00 660.0
3 TraesCS5A01G223900 chr5B 93.648 1653 93 8 553 2201 397834050 397832406 0.000000e+00 2460.0
4 TraesCS5A01G223900 chr5B 91.650 515 26 7 1 500 397834852 397834340 0.000000e+00 697.0
5 TraesCS5A01G223900 chr1D 80.952 105 20 0 103 207 291842116 291842220 1.400000e-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 TraesCS5A01G223900 chr5A 439549839 439552039 2200 True 4065.0 4065 100.0000 1 2201 1 chr5A.!!$R1 2200
1 TraesCS5A01G223900 chr5D 338654706 338656991 2285 True 1572.0 2484 91.6195 4 2201 2 chr5D.!!$R1 2197
2 TraesCS5A01G223900 chr5B 397832406 397834852 2446 True 1578.5 2460 92.6490 1 2201 2 chr5B.!!$R1 2200

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
737 1027 0.324943 GCTGCTTACAGTCCTCCCAA 59.675 55.0 0.0 0.0 46.3 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2452 0.382158 TGCCGTCAGATAAGAGCTCG 59.618 55.0 8.37 0.0 0.0 5.03 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
31 33 7.548097 TCTCTGTTCCTCATATCTGTAACAAC 58.452 38.462 0.00 0.00 0.00 3.32
41 43 2.743538 GTAACAACGGCGGGGGAC 60.744 66.667 13.24 1.86 0.00 4.46
52 55 0.609662 GCGGGGGACACTTTGTAGTA 59.390 55.000 0.00 0.00 31.96 1.82
58 61 4.961099 GGGGGACACTTTGTAGTATCTAGT 59.039 45.833 0.00 0.00 31.96 2.57
81 84 1.146263 GGATGGCCCAGACTAACGG 59.854 63.158 0.00 0.00 34.14 4.44
113 116 2.086869 TCTGCTTGCAGGCTGATTTAC 58.913 47.619 23.46 0.00 35.75 2.01
367 374 9.330063 TCTGCCTATATGATTTGACAAAACTAG 57.670 33.333 4.41 1.15 0.00 2.57
374 381 5.507077 TGATTTGACAAAACTAGTCGCAAC 58.493 37.500 4.41 0.00 38.83 4.17
425 432 6.693545 GCTGCGTAGTAAGATCCATATATCAC 59.306 42.308 1.53 0.00 0.00 3.06
447 456 4.744631 ACCTGAATTTTGATTGTGTTTCGC 59.255 37.500 0.00 0.00 0.00 4.70
468 477 3.823304 GCCACTCTTTCCTGAATTCAAGT 59.177 43.478 9.88 6.02 0.00 3.16
474 491 7.594015 CACTCTTTCCTGAATTCAAGTTTGATG 59.406 37.037 9.88 0.00 37.00 3.07
500 518 5.301298 AGGGCTAAATGCAGAAAGATTGATC 59.699 40.000 0.00 0.00 45.15 2.92
509 527 7.572523 TGCAGAAAGATTGATCGGAAAATAT 57.427 32.000 0.00 0.00 0.00 1.28
510 528 8.675705 TGCAGAAAGATTGATCGGAAAATATA 57.324 30.769 0.00 0.00 0.00 0.86
512 530 9.950680 GCAGAAAGATTGATCGGAAAATATAAA 57.049 29.630 0.00 0.00 0.00 1.40
558 576 3.762779 CCGAATCCTGAAAACATTCTGC 58.237 45.455 0.00 0.00 0.00 4.26
568 854 2.936919 AACATTCTGCTCTGGACACA 57.063 45.000 0.00 0.00 0.00 3.72
574 860 1.143305 CTGCTCTGGACACAAGAACG 58.857 55.000 0.00 0.00 0.00 3.95
597 883 4.752661 GTGTTCGCACATACCCTTTTAA 57.247 40.909 0.00 0.00 46.85 1.52
601 887 5.299782 TGTTCGCACATACCCTTTTAACTTT 59.700 36.000 0.00 0.00 0.00 2.66
632 918 8.786898 TCATAAACATTTCAGAGAAGAACCAAG 58.213 33.333 0.00 0.00 0.00 3.61
634 920 4.464008 ACATTTCAGAGAAGAACCAAGCA 58.536 39.130 0.00 0.00 0.00 3.91
651 938 5.902431 ACCAAGCATACTAGATCTTTCCTCT 59.098 40.000 0.00 0.00 0.00 3.69
682 969 1.328430 ACTGGTAAGCTACGGGCCTC 61.328 60.000 0.84 0.00 43.05 4.70
736 1026 0.545309 AGCTGCTTACAGTCCTCCCA 60.545 55.000 0.00 0.00 46.30 4.37
737 1027 0.324943 GCTGCTTACAGTCCTCCCAA 59.675 55.000 0.00 0.00 46.30 4.12
940 1230 1.578206 GCTTCACTTCCGTGGGCTTC 61.578 60.000 0.00 0.00 41.53 3.86
1018 1308 3.951769 ATGCCCCTTGCTGCTCCAC 62.952 63.158 0.00 0.00 42.00 4.02
1087 1377 2.550180 GAGTTGGTCCTTGAAGCTGTTC 59.450 50.000 0.00 0.00 0.00 3.18
1099 1389 0.106519 AGCTGTTCCTGCCAACAACT 60.107 50.000 0.00 0.00 35.83 3.16
1102 1392 2.023673 CTGTTCCTGCCAACAACTTGA 58.976 47.619 0.00 0.00 35.83 3.02
1105 1395 2.887152 GTTCCTGCCAACAACTTGATCT 59.113 45.455 0.00 0.00 0.00 2.75
1145 1435 2.555757 ACAACTTGATCCTTGAAGCTGC 59.444 45.455 0.00 0.00 0.00 5.25
1237 1527 1.662044 CAGCTTGTTTGGGTGCCTC 59.338 57.895 0.00 0.00 0.00 4.70
1312 1602 3.649277 CTCTCCGCCGTCAGTTGGG 62.649 68.421 0.00 0.00 0.00 4.12
1402 1692 3.102985 CGGTCGTTTTGTGTGGCA 58.897 55.556 0.00 0.00 0.00 4.92
1446 1736 3.710677 AGCTTCTTGACATCTATCAGGCT 59.289 43.478 0.00 0.00 0.00 4.58
1450 1740 2.904697 TGACATCTATCAGGCTGCAG 57.095 50.000 10.11 10.11 0.00 4.41
1517 1808 4.660168 AGAAGAAGCAAATGATCAGGTGT 58.340 39.130 0.09 0.00 0.00 4.16
1530 1821 4.780554 TGATCAGGTGTGGTTATGGTCTTA 59.219 41.667 0.00 0.00 0.00 2.10
1535 1826 7.691213 TCAGGTGTGGTTATGGTCTTATAAAA 58.309 34.615 0.00 0.00 0.00 1.52
1548 1839 7.857456 TGGTCTTATAAAAGGTGAGATAGCAA 58.143 34.615 0.00 0.00 33.22 3.91
1554 1845 2.409948 AGGTGAGATAGCAAACAGGC 57.590 50.000 0.00 0.00 0.00 4.85
1581 1872 3.701205 TCAAGTCTGCTTCCATGCTTA 57.299 42.857 0.00 0.00 31.49 3.09
1985 2278 6.778821 TCTCTGAACAAGATTATGGACCAAA 58.221 36.000 0.00 0.00 33.29 3.28
1986 2279 7.405292 TCTCTGAACAAGATTATGGACCAAAT 58.595 34.615 0.00 0.00 33.29 2.32
2129 2422 8.281212 ACCCAACTAATATAGCAACTTTCAAG 57.719 34.615 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 20 1.202604 CCCCGCCGTTGTTACAGATAT 60.203 52.381 0.00 0.00 0.00 1.63
31 33 3.242897 TACAAAGTGTCCCCCGCCG 62.243 63.158 0.00 0.00 0.00 6.46
52 55 4.042187 GTCTGGGCCATCCAAATACTAGAT 59.958 45.833 6.72 0.00 46.51 1.98
58 61 3.433031 CGTTAGTCTGGGCCATCCAAATA 60.433 47.826 6.72 0.00 46.51 1.40
81 84 5.289434 GCCTGCAAGCAGAAAATAATTACAC 59.711 40.000 22.76 0.00 46.30 2.90
231 238 1.622811 CACTTCTCTCAGGAGGCAAGT 59.377 52.381 7.55 7.55 37.21 3.16
367 374 0.651031 GAGGCGGATAAAGTTGCGAC 59.349 55.000 0.00 0.00 38.98 5.19
374 381 5.542779 AGCTAATAACAGAGGCGGATAAAG 58.457 41.667 0.00 0.00 0.00 1.85
425 432 4.150451 GGCGAAACACAATCAAAATTCAGG 59.850 41.667 0.00 0.00 0.00 3.86
436 443 2.293399 GGAAAGAGTGGCGAAACACAAT 59.707 45.455 7.83 0.00 43.72 2.71
447 456 6.039717 TCAAACTTGAATTCAGGAAAGAGTGG 59.960 38.462 23.00 11.41 33.55 4.00
468 477 4.854173 TCTGCATTTAGCCCTACATCAAA 58.146 39.130 0.00 0.00 44.83 2.69
474 491 5.590259 TCAATCTTTCTGCATTTAGCCCTAC 59.410 40.000 0.00 0.00 44.83 3.18
509 527 8.995027 AACCAGCCTCACATGAATATAATTTA 57.005 30.769 0.00 0.00 0.00 1.40
510 528 7.255242 CGAACCAGCCTCACATGAATATAATTT 60.255 37.037 0.00 0.00 0.00 1.82
512 530 5.702670 CGAACCAGCCTCACATGAATATAAT 59.297 40.000 0.00 0.00 0.00 1.28
513 531 5.056480 CGAACCAGCCTCACATGAATATAA 58.944 41.667 0.00 0.00 0.00 0.98
514 532 4.631131 CGAACCAGCCTCACATGAATATA 58.369 43.478 0.00 0.00 0.00 0.86
558 576 2.223829 ACACTCGTTCTTGTGTCCAGAG 60.224 50.000 0.00 0.00 42.95 3.35
581 867 6.443792 AGAAAAAGTTAAAAGGGTATGTGCG 58.556 36.000 0.00 0.00 0.00 5.34
582 868 7.923878 TGAAGAAAAAGTTAAAAGGGTATGTGC 59.076 33.333 0.00 0.00 0.00 4.57
651 938 7.012704 CCGTAGCTTACCAGTGTATCTTAACTA 59.987 40.741 0.00 0.00 0.00 2.24
682 969 7.013750 TGCTCTCTGTATGGTTATCTAAGTCAG 59.986 40.741 0.00 0.00 0.00 3.51
736 1026 9.300681 TCTGGTCAATGAAGAGAAAATATGTTT 57.699 29.630 0.00 0.00 0.00 2.83
737 1027 8.868522 TCTGGTCAATGAAGAGAAAATATGTT 57.131 30.769 0.00 0.00 0.00 2.71
854 1144 1.909986 GGGGCTCTTCTTACTCCTTGT 59.090 52.381 0.00 0.00 0.00 3.16
855 1145 2.192263 AGGGGCTCTTCTTACTCCTTG 58.808 52.381 0.00 0.00 0.00 3.61
856 1146 2.651642 AGGGGCTCTTCTTACTCCTT 57.348 50.000 0.00 0.00 0.00 3.36
1018 1308 3.648009 GAGGAGGATATTCGACAAGCTG 58.352 50.000 0.00 0.00 0.00 4.24
1066 1356 2.262423 ACAGCTTCAAGGACCAACTC 57.738 50.000 0.00 0.00 0.00 3.01
1087 1377 3.318839 TCAAAGATCAAGTTGTTGGCAGG 59.681 43.478 2.11 0.00 34.09 4.85
1099 1389 4.261741 GGCAGAAACAGCTTCAAAGATCAA 60.262 41.667 0.00 0.00 36.40 2.57
1102 1392 3.225104 TGGCAGAAACAGCTTCAAAGAT 58.775 40.909 0.00 0.00 36.40 2.40
1105 1395 2.495270 TGTTGGCAGAAACAGCTTCAAA 59.505 40.909 0.00 0.00 35.16 2.69
1145 1435 1.970352 GAGCTCAGGGGAGGCAGAAG 61.970 65.000 9.40 0.00 41.67 2.85
1312 1602 0.875059 GTTCAAGCAGTGTACCAGCC 59.125 55.000 0.00 0.00 0.00 4.85
1420 1710 5.233902 CCTGATAGATGTCAAGAAGCTTTCG 59.766 44.000 0.00 0.00 34.02 3.46
1450 1740 7.761651 AAACAAAGCAGACAAAAAGAAGATC 57.238 32.000 0.00 0.00 0.00 2.75
1517 1808 8.153221 TCTCACCTTTTATAAGACCATAACCA 57.847 34.615 0.00 0.00 32.92 3.67
1530 1821 5.358160 GCCTGTTTGCTATCTCACCTTTTAT 59.642 40.000 0.00 0.00 0.00 1.40
1535 1826 1.406069 CGCCTGTTTGCTATCTCACCT 60.406 52.381 0.00 0.00 0.00 4.00
1548 1839 3.375299 GCAGACTTGATAAATCGCCTGTT 59.625 43.478 0.00 0.00 0.00 3.16
1554 1845 5.745514 CATGGAAGCAGACTTGATAAATCG 58.254 41.667 0.00 0.00 35.82 3.34
1621 1912 9.927081 ACTGAATGGAAACTTGATCCTAATAAT 57.073 29.630 0.00 0.00 37.85 1.28
1629 1920 7.712639 TCTGCTATACTGAATGGAAACTTGATC 59.287 37.037 0.00 0.00 0.00 2.92
1637 1928 7.981789 CAGTACTTTCTGCTATACTGAATGGAA 59.018 37.037 4.59 0.00 44.81 3.53
1985 2278 1.961394 GAGGGCATGCATGATGTTCAT 59.039 47.619 30.64 10.58 37.65 2.57
1986 2279 1.341187 TGAGGGCATGCATGATGTTCA 60.341 47.619 30.64 21.43 34.14 3.18
2159 2452 0.382158 TGCCGTCAGATAAGAGCTCG 59.618 55.000 8.37 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.