Multiple sequence alignment - TraesCS7A01G213100

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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 TraesCS7A01G213100 chr7A 100.000 4028 0 0 1 4028 176436823 176432796 0.000000e+00 7439
1 TraesCS7A01G213100 chr7B 97.136 4050 91 13 1 4028 138884697 138880651 0.000000e+00 6813
2 TraesCS7A01G213100 chr7D 97.132 3068 76 6 1 3058 174448662 174445597 0.000000e+00 5168
3 TraesCS7A01G213100 chr7D 98.025 709 12 2 3090 3796 174445597 174444889 0.000000e+00 1230
4 TraesCS7A01G213100 chr7D 98.507 268 4 0 3761 4028 174444890 174444623 1.310000e-129 473


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 TraesCS7A01G213100 chr7A 176432796 176436823 4027 True 7439.000000 7439 100.000 1 4028 1 chr7A.!!$R1 4027
1 TraesCS7A01G213100 chr7B 138880651 138884697 4046 True 6813.000000 6813 97.136 1 4028 1 chr7B.!!$R1 4027
2 TraesCS7A01G213100 chr7D 174444623 174448662 4039 True 2290.333333 5168 97.888 1 4028 3 chr7D.!!$R1 4027

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
989 1018 0.459585 TCTAACGTGGAAGATGGCGC 60.460 55.0 0.0 0.0 0.0 6.53 F
1875 1904 0.036388 ATGTGAATGAAGGCGTCGGT 60.036 50.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2394 2423 1.233019 GCTGATCATCCATCCCGTTG 58.767 55.0 0.0 0.0 0.00 4.10 R
3063 3092 0.106519 AGGAAGCCACAGCAAACAGT 60.107 50.0 0.0 0.0 43.56 3.55 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
25 26 2.613223 GGCTTCGTTCTGGTAGCTTCTT 60.613 50.000 0.00 0.00 34.16 2.52
88 89 1.152756 GGGCCGGGCTCATTAATGT 60.153 57.895 28.80 0.00 0.00 2.71
174 175 1.405256 GCAGCAGCTGATCTACTGTGT 60.405 52.381 27.39 3.28 38.25 3.72
228 229 3.744660 AGTTCGGATTCAGCTTGAAAGT 58.255 40.909 3.27 0.00 40.12 2.66
420 432 4.764172 CTTTGGGTTTGTTTTCCACATGA 58.236 39.130 0.00 0.00 34.43 3.07
585 597 8.940768 TGTTCAACGAACATATCATATCTTCA 57.059 30.769 5.47 0.00 45.88 3.02
647 660 3.036091 TGGTAGCCCACTCCTTATGTAC 58.964 50.000 0.00 0.00 35.17 2.90
652 665 2.172717 GCCCACTCCTTATGTACACCAT 59.827 50.000 0.00 0.00 37.58 3.55
684 697 8.623903 TGTAAAATATGGAAATGCTAGCTCAAG 58.376 33.333 17.23 0.00 0.00 3.02
721 739 7.928706 TGTTTTGGTTTATTCATTAACTGGGTG 59.071 33.333 0.00 0.00 0.00 4.61
745 763 7.390718 GTGGTTGAGTTTACCATGAGAATTACT 59.609 37.037 0.00 0.00 46.63 2.24
758 781 9.956720 CCATGAGAATTACTTATGTTCCATTTC 57.043 33.333 0.00 0.00 39.83 2.17
881 910 8.829373 AAAAGATAATAACCTCCAATTGCTCT 57.171 30.769 0.00 0.00 0.00 4.09
943 972 3.056678 TCATCGGGTTTCGTAACAGCTTA 60.057 43.478 7.25 0.00 40.32 3.09
989 1018 0.459585 TCTAACGTGGAAGATGGCGC 60.460 55.000 0.00 0.00 0.00 6.53
1009 1038 0.813184 CCGTTGCCTGATGATTGCTT 59.187 50.000 0.00 0.00 0.00 3.91
1072 1101 3.760684 AGAATTTGAAAGGCGCAAGAGAT 59.239 39.130 10.83 0.00 43.02 2.75
1087 1116 5.166398 GCAAGAGATCAATTCCTTTGTTGG 58.834 41.667 0.00 0.00 36.65 3.77
1196 1225 2.874457 GCAAAACTAGAAGCGAGGGGAA 60.874 50.000 0.00 0.00 0.00 3.97
1478 1507 2.165167 CAAGGATCTCCAGCAGCAAAA 58.835 47.619 0.00 0.00 38.89 2.44
1484 1513 3.719268 TCTCCAGCAGCAAAAGGATAA 57.281 42.857 0.00 0.00 0.00 1.75
1875 1904 0.036388 ATGTGAATGAAGGCGTCGGT 60.036 50.000 0.00 0.00 0.00 4.69
1996 2025 2.619074 GGCACTTCAAGCTTCCCTGTAT 60.619 50.000 0.00 0.00 0.00 2.29
2268 2297 2.687700 AAGATGCTGAGATGCTTCGT 57.312 45.000 0.00 0.00 40.58 3.85
2394 2423 3.814283 GTGAGATGATGAGCAGGGAATTC 59.186 47.826 0.00 0.00 0.00 2.17
2459 2488 4.232310 GGCAAGGAGGCTAGCAAG 57.768 61.111 18.24 0.08 40.24 4.01
2564 2593 0.104671 CCAAAAACACCACCAGCCTG 59.895 55.000 0.00 0.00 0.00 4.85
2745 2774 2.548875 CTATCAACCTCACTGAGCAGC 58.451 52.381 0.00 0.00 0.00 5.25
2790 2819 0.464554 GTCAGGTGCCTGCTATTCCC 60.465 60.000 13.12 0.00 43.31 3.97
2799 2828 0.034186 CTGCTATTCCCAAGGGTGCA 60.034 55.000 4.80 10.47 36.47 4.57
2847 2876 2.372172 CCAAGTTGGTAACTGGAGGACT 59.628 50.000 14.21 0.00 41.91 3.85
3063 3092 2.634940 AGAGAAGTCAGTTTGGCTGCTA 59.365 45.455 0.00 0.00 38.31 3.49
3205 3234 4.585879 TGGCCTTTCCTGTACATAGTTTC 58.414 43.478 3.32 0.00 35.26 2.78
3207 3236 4.324331 GGCCTTTCCTGTACATAGTTTCCT 60.324 45.833 0.00 0.00 0.00 3.36
3209 3238 5.354513 GCCTTTCCTGTACATAGTTTCCTTC 59.645 44.000 0.00 0.00 0.00 3.46
3210 3239 6.712276 CCTTTCCTGTACATAGTTTCCTTCT 58.288 40.000 0.00 0.00 0.00 2.85
3212 3241 7.334671 CCTTTCCTGTACATAGTTTCCTTCTTC 59.665 40.741 0.00 0.00 0.00 2.87
3336 3367 9.763465 CATTCAAAGATGCCATTCAAATAAAAC 57.237 29.630 0.00 0.00 0.00 2.43
3528 3559 6.367686 TGCACTCTATTATTGATGCAGTTG 57.632 37.500 0.00 0.00 38.11 3.16
3731 3762 2.334977 TCCTGCCAAACTCTACCTTCA 58.665 47.619 0.00 0.00 0.00 3.02
3793 3858 4.892934 TCAAAGGCCAAAACTAACTGATGT 59.107 37.500 5.01 0.00 0.00 3.06
4017 4082 1.376683 GTTGATGCACCGGTAGGCA 60.377 57.895 20.56 20.56 45.23 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 1.814394 TGAGCTACGCGTAAGGAAAGA 59.186 47.619 20.97 0.00 38.28 2.52
174 175 1.135660 CGAGTACAAGCTTCGCTCAGA 60.136 52.381 16.71 0.00 38.25 3.27
210 211 3.074412 GGAACTTTCAAGCTGAATCCGA 58.926 45.455 0.00 0.00 36.11 4.55
324 335 2.948979 ACAATCGTGCAGTTTTCTTCCA 59.051 40.909 0.00 0.00 0.00 3.53
420 432 7.998964 TGAGACAGGGAAATCTCTTAAACTTTT 59.001 33.333 3.17 0.00 41.69 2.27
678 691 1.151668 ACACTTCGCATGACTTGAGC 58.848 50.000 0.00 0.00 0.00 4.26
684 697 2.774439 ACCAAAACACTTCGCATGAC 57.226 45.000 0.00 0.00 0.00 3.06
721 739 7.923414 AGTAATTCTCATGGTAAACTCAACC 57.077 36.000 0.00 0.00 37.53 3.77
758 781 8.993121 ACCGATTCTTGCTCTGTAATAAATATG 58.007 33.333 0.00 0.00 0.00 1.78
837 866 6.852664 TCTTTTTCTCAAGTCAGAAACAACC 58.147 36.000 0.00 0.00 41.20 3.77
943 972 1.678101 GCAACAGAAAGCTTCAGTGGT 59.322 47.619 0.00 0.00 29.27 4.16
969 998 1.278238 CGCCATCTTCCACGTTAGAC 58.722 55.000 0.00 0.00 0.00 2.59
989 1018 1.033746 AGCAATCATCAGGCAACGGG 61.034 55.000 0.00 0.00 46.39 5.28
1009 1038 1.006571 GCGAGAAAGGTGTCACGGA 60.007 57.895 0.00 0.00 32.99 4.69
1072 1101 1.344114 GGCAGCCAACAAAGGAATTGA 59.656 47.619 6.55 0.00 41.85 2.57
1087 1116 1.580845 AAGTTGCGAGACATGGCAGC 61.581 55.000 11.57 11.57 41.48 5.25
1196 1225 0.110486 ACGTTTCCATCCAACAGCCT 59.890 50.000 0.00 0.00 0.00 4.58
1478 1507 3.197983 TCAATTGGACCACCCTTATCCT 58.802 45.455 5.42 0.00 35.38 3.24
1484 1513 3.328535 AAACTTCAATTGGACCACCCT 57.671 42.857 5.42 0.00 35.38 4.34
1875 1904 4.141482 ACAGAAGCCTTCTTGTTGGTAGAA 60.141 41.667 3.68 0.00 38.11 2.10
1996 2025 5.894298 ATACCAATCCTGTGAATAGCAGA 57.106 39.130 0.00 0.00 36.12 4.26
2268 2297 1.827344 CGGATCATAGGCAGCTCCATA 59.173 52.381 0.00 0.00 37.29 2.74
2394 2423 1.233019 GCTGATCATCCATCCCGTTG 58.767 55.000 0.00 0.00 0.00 4.10
2459 2488 3.807622 TGTGGAACATTCTTCTCGTTCAC 59.192 43.478 0.00 0.00 45.67 3.18
2745 2774 2.158449 GCTTTTGTCCATGAGACTGACG 59.842 50.000 13.32 0.00 46.46 4.35
2790 2819 2.189594 TCACAGAATCTGCACCCTTG 57.810 50.000 10.62 0.00 34.37 3.61
2799 2828 6.603201 TGTTTTCAGAGGTTTTCACAGAATCT 59.397 34.615 0.00 0.00 0.00 2.40
2847 2876 1.340889 GTTGGGAGCTGTTCATTTGCA 59.659 47.619 0.00 0.00 0.00 4.08
3063 3092 0.106519 AGGAAGCCACAGCAAACAGT 60.107 50.000 0.00 0.00 43.56 3.55
3319 3350 6.314400 GCATGTCTGTTTTATTTGAATGGCAT 59.686 34.615 0.00 0.00 0.00 4.40
3336 3367 5.461078 CCAGAAACTTTTTCTTGCATGTCTG 59.539 40.000 0.00 3.17 0.00 3.51
3528 3559 3.761752 ACCTAGCAGAGACAGAAGAGTTC 59.238 47.826 0.00 0.00 0.00 3.01
3731 3762 8.732854 TGGGTTGGAATAGATGTAAATAATCCT 58.267 33.333 0.00 0.00 0.00 3.24
3793 3858 6.011628 AGTCCCTCCTTCCTATTTGATGAAAA 60.012 38.462 0.00 0.00 0.00 2.29
3807 3872 0.539518 GAGCCTGAAGTCCCTCCTTC 59.460 60.000 0.00 0.00 41.01 3.46


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

AutoCloner maintained by Alex Coulton.