Multiple sequence alignment - TraesCS3D01G348700

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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 TraesCS3D01G348700 chr3D 100.000 3092 0 0 1 3092 460413467 460416558 0.000000e+00 5710.0
1 TraesCS3D01G348700 chr3A 97.222 3096 71 6 1 3092 602681040 602684124 0.000000e+00 5227.0
2 TraesCS3D01G348700 chr3B 95.894 3093 100 13 1 3092 610492435 610495501 0.000000e+00 4983.0
3 TraesCS3D01G348700 chr1D 82.022 89 16 0 1206 1294 384475044 384474956 3.310000e-10 76.8
4 TraesCS3D01G348700 chr1B 84.722 72 11 0 1223 1294 515913902 515913831 4.280000e-09 73.1


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 TraesCS3D01G348700 chr3D 460413467 460416558 3091 False 5710 5710 100.000 1 3092 1 chr3D.!!$F1 3091
1 TraesCS3D01G348700 chr3A 602681040 602684124 3084 False 5227 5227 97.222 1 3092 1 chr3A.!!$F1 3091
2 TraesCS3D01G348700 chr3B 610492435 610495501 3066 False 4983 4983 95.894 1 3092 1 chr3B.!!$F1 3091

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
970 973 0.185175 ACCAAACCCAGAGACCAACC 59.815 55.0 0.00 0.0 0.00 3.77 F
1248 1251 0.321919 TCTACAAGGGCAAGCTGCTG 60.322 55.0 1.35 0.0 44.28 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 1855 1.205893 AGAGTCATTTGAGCTCGGGAC 59.794 52.381 9.64 13.04 34.69 4.46 R
2973 2979 0.249699 CGCCACCAGTGACTTGTACA 60.250 55.000 0.00 0.00 0.00 2.90 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
177 178 2.037772 ACTGATGTCACCCTCACACTTC 59.962 50.000 0.00 0.00 0.00 3.01
191 192 4.832248 TCACACTTCCATAGGTTGACATC 58.168 43.478 0.00 0.00 0.00 3.06
209 210 9.559958 GTTGACATCGAGATGAAATAAACAAAT 57.440 29.630 18.76 0.00 41.20 2.32
357 359 5.215160 CCACAGAAACTTTGCATACTTCAC 58.785 41.667 0.00 0.00 0.00 3.18
388 390 6.493449 TGCTGAAATCATATTGTTTCACGA 57.507 33.333 7.76 0.00 38.88 4.35
507 509 2.076100 CAGTTCGCATGCTAACCAAGA 58.924 47.619 26.26 8.14 0.00 3.02
540 542 2.327343 GCACATCAGCAGGCGTGAA 61.327 57.895 11.29 0.00 0.00 3.18
606 608 2.044123 AGCACTTAATGGCTACCTGC 57.956 50.000 0.00 0.00 38.90 4.85
678 680 2.233271 ACATGCAAAGGAACAGGTGAG 58.767 47.619 0.00 0.00 28.19 3.51
707 709 0.983467 TCACCTAATGCACTGCAGGA 59.017 50.000 19.93 1.24 43.65 3.86
970 973 0.185175 ACCAAACCCAGAGACCAACC 59.815 55.000 0.00 0.00 0.00 3.77
1248 1251 0.321919 TCTACAAGGGCAAGCTGCTG 60.322 55.000 1.35 0.00 44.28 4.41
1508 1511 4.153835 GTCCAAGAAGCTCAAGTTCATCAG 59.846 45.833 0.00 0.00 0.00 2.90
1821 1824 1.758862 ACGTCATCTGCCTCATCATCA 59.241 47.619 0.00 0.00 0.00 3.07
1852 1855 5.748630 TCTTCGTCAAATTCATCATCCTACG 59.251 40.000 0.00 0.00 0.00 3.51
2031 2034 3.308053 GGTTCATGTCATCATCAGTGTCG 59.692 47.826 0.00 0.00 31.15 4.35
2057 2060 3.908643 AGCTGCAGAATCTGAAGATGA 57.091 42.857 22.01 0.00 39.42 2.92
2082 2085 7.047460 AGAAGACATTTTTGAGATTTGCAGT 57.953 32.000 0.00 0.00 0.00 4.40
2351 2354 8.586879 TCTCTGATCAGTATCCATATTACAGG 57.413 38.462 21.92 0.00 0.00 4.00
2376 2379 4.442893 GCACATGTAGCAAGTCCATACCTA 60.443 45.833 13.27 0.00 0.00 3.08
2393 2396 6.183360 CCATACCTAAAAAGAGATGCAACAGG 60.183 42.308 0.00 0.00 0.00 4.00
2407 2410 4.081406 TGCAACAGGAACAAGCATCTTAT 58.919 39.130 0.00 0.00 0.00 1.73
2436 2439 4.842574 TGCAATGAGCCATAGTTAACAGA 58.157 39.130 8.61 0.00 44.83 3.41
2531 2534 9.643693 AATGCACAAATTAGTTCCTGATTAAAG 57.356 29.630 0.00 0.00 0.00 1.85
2574 2577 6.923508 TGTTGAACACAACACAAAAACATACA 59.076 30.769 10.98 0.00 45.56 2.29
2595 2598 3.853671 CACTCAAAAGCTTGTGTGTCAAC 59.146 43.478 19.11 0.00 45.54 3.18
2635 2638 8.377034 TGTAACATAGGTAAGGAACTAAGCAAA 58.623 33.333 0.00 0.00 38.49 3.68
2636 2639 9.223099 GTAACATAGGTAAGGAACTAAGCAAAA 57.777 33.333 0.00 0.00 38.49 2.44
2637 2640 8.700439 AACATAGGTAAGGAACTAAGCAAAAA 57.300 30.769 0.00 0.00 38.49 1.94
2678 2681 7.609097 AGATATTATCAGAGAAGGCAAGACA 57.391 36.000 6.46 0.00 0.00 3.41
2696 2699 7.315142 GCAAGACAATGAACCTTTTATCATGA 58.685 34.615 0.00 0.00 36.44 3.07
2925 2928 1.204704 CTCATGGCTCTACGTCAACCA 59.795 52.381 0.00 0.00 34.28 3.67
3008 3014 0.108851 GGCGGGCACTTAAAACATGG 60.109 55.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 178 4.590850 TCATCTCGATGTCAACCTATGG 57.409 45.455 6.78 0.00 39.72 2.74
191 192 7.697691 ACCTGCTATTTGTTTATTTCATCTCG 58.302 34.615 0.00 0.00 0.00 4.04
357 359 5.163723 ACAATATGATTTCAGCAAGACACGG 60.164 40.000 0.00 0.00 0.00 4.94
525 527 1.978712 CTGCTTCACGCCTGCTGATG 61.979 60.000 0.00 0.00 38.05 3.07
537 539 0.937304 GTGACTCGCAAACTGCTTCA 59.063 50.000 0.00 0.00 42.25 3.02
540 542 2.526304 TAAGTGACTCGCAAACTGCT 57.474 45.000 0.00 0.00 42.25 4.24
606 608 9.912634 ATTTGTTTGTTTGATGTGTAGGATTAG 57.087 29.630 0.00 0.00 0.00 1.73
678 680 6.073003 GCAGTGCATTAGGTGATTAGGTTATC 60.073 42.308 11.09 0.00 0.00 1.75
970 973 0.754957 TGGCCTTGTGTTTCTGGTGG 60.755 55.000 3.32 0.00 0.00 4.61
1077 1080 3.259425 GACCACCTTTGCAGCTGCG 62.259 63.158 32.11 20.61 45.83 5.18
1338 1341 0.454600 ACGACTGGTATGGTGTAGCG 59.545 55.000 0.00 0.00 0.00 4.26
1341 1344 0.533491 GGCACGACTGGTATGGTGTA 59.467 55.000 0.00 0.00 33.09 2.90
1508 1511 3.703001 TGAGACCAAGGTTGAGATTCC 57.297 47.619 0.00 0.00 0.00 3.01
1726 1729 4.268884 GCCGTACTCATCTTCTTTAAGCTG 59.731 45.833 0.00 0.00 31.45 4.24
1803 1806 4.004196 TGATGATGATGAGGCAGATGAC 57.996 45.455 0.00 0.00 0.00 3.06
1821 1824 5.587443 TGATGAATTTGACGAAGAGCATGAT 59.413 36.000 0.00 0.00 0.00 2.45
1852 1855 1.205893 AGAGTCATTTGAGCTCGGGAC 59.794 52.381 9.64 13.04 34.69 4.46
2031 2034 5.599732 TCTTCAGATTCTGCAGCTATCTTC 58.400 41.667 21.52 8.24 0.00 2.87
2057 2060 7.495055 ACTGCAAATCTCAAAAATGTCTTCTT 58.505 30.769 0.00 0.00 0.00 2.52
2161 2164 6.603599 AGTTTTTAAGGGGATAGCATGTCTTC 59.396 38.462 0.00 0.00 0.00 2.87
2351 2354 1.522668 TGGACTTGCTACATGTGCAC 58.477 50.000 18.50 10.75 40.40 4.57
2376 2379 5.594926 CTTGTTCCTGTTGCATCTCTTTTT 58.405 37.500 0.00 0.00 0.00 1.94
2393 2396 5.032863 GCATGTGACATAAGATGCTTGTTC 58.967 41.667 0.00 0.00 38.53 3.18
2407 2410 1.842052 ATGGCTCATTGCATGTGACA 58.158 45.000 8.50 8.50 44.86 3.58
2436 2439 6.186420 ACCCAAAAATAATTGGCTGTCTTT 57.814 33.333 0.49 0.00 46.97 2.52
2531 2534 2.230660 ACAAACAGAAAGCAGGTAGGC 58.769 47.619 0.00 0.00 0.00 3.93
2574 2577 3.758554 AGTTGACACACAAGCTTTTGAGT 59.241 39.130 19.17 16.66 39.30 3.41
2595 2598 7.492524 ACCTATGTTACATCATAGACACACAG 58.507 38.462 0.00 0.00 45.76 3.66
2657 2660 7.795047 TCATTGTCTTGCCTTCTCTGATAATA 58.205 34.615 0.00 0.00 0.00 0.98
2678 2681 8.306761 GTCAGGTTTCATGATAAAAGGTTCATT 58.693 33.333 0.00 0.00 30.24 2.57
2696 2699 5.133221 AGTATTCAAGTTGCAGTCAGGTTT 58.867 37.500 0.00 0.00 0.00 3.27
2970 2976 2.036733 GCCACCAGTGACTTGTACAGTA 59.963 50.000 0.00 0.00 35.01 2.74
2971 2977 1.202651 GCCACCAGTGACTTGTACAGT 60.203 52.381 0.00 0.00 39.07 3.55
2972 2978 1.512926 GCCACCAGTGACTTGTACAG 58.487 55.000 0.00 0.00 0.00 2.74
2973 2979 0.249699 CGCCACCAGTGACTTGTACA 60.250 55.000 0.00 0.00 0.00 2.90
2974 2980 0.949105 CCGCCACCAGTGACTTGTAC 60.949 60.000 0.00 0.00 0.00 2.90
3008 3014 3.222603 TCACCTTTCCTCTTTTGCCTTC 58.777 45.455 0.00 0.00 0.00 3.46
3044 3050 5.640732 CACTACTGCTTTTTGTTTGTCACT 58.359 37.500 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.