Multiple sequence alignment - TraesCS3A01G115200

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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 TraesCS3A01G115200 chr3A 100.000 6864 0 0 1 6864 83023352 83030215 0 12676
1 TraesCS3A01G115200 chr5A 98.211 6874 85 19 1 6864 9618909 9625754 0 11978
2 TraesCS3A01G115200 chr5A 97.991 6870 94 23 1 6864 294227002 294233833 0 11882
3 TraesCS3A01G115200 chr1A 98.210 6872 87 16 1 6864 127080744 127087587 0 11976
4 TraesCS3A01G115200 chr1A 98.006 6870 102 17 1 6864 255464232 255471072 0 11895
5 TraesCS3A01G115200 chr2A 98.152 6873 90 21 1 6864 687279599 687272755 0 11954
6 TraesCS3A01G115200 chr7A 98.139 6877 82 23 1 6864 23298658 23291815 0 11948
7 TraesCS3A01G115200 chr2B 98.094 6874 86 23 1 6864 741902559 741909397 0 11926
8 TraesCS3A01G115200 chr2B 97.806 6790 94 24 81 6864 99558154 99564894 0 11662
9 TraesCS3A01G115200 chr2B 97.468 6873 100 40 1 6864 608467352 608460545 0 11660
10 TraesCS3A01G115200 chr4B 97.948 6870 101 24 1 6864 261499258 261492423 0 11869
11 TraesCS3A01G115200 chr4B 97.891 6874 94 25 1 6864 14719143 14712311 0 11843
12 TraesCS3A01G115200 chr4B 97.793 6750 98 25 1 6741 149733245 149726538 0 11592
13 TraesCS3A01G115200 chr6A 97.743 4873 73 16 1997 6864 480632509 480637349 0 8355


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 TraesCS3A01G115200 chr3A 83023352 83030215 6863 False 12676 12676 100.000 1 6864 1 chr3A.!!$F1 6863
1 TraesCS3A01G115200 chr5A 9618909 9625754 6845 False 11978 11978 98.211 1 6864 1 chr5A.!!$F1 6863
2 TraesCS3A01G115200 chr5A 294227002 294233833 6831 False 11882 11882 97.991 1 6864 1 chr5A.!!$F2 6863
3 TraesCS3A01G115200 chr1A 127080744 127087587 6843 False 11976 11976 98.210 1 6864 1 chr1A.!!$F1 6863
4 TraesCS3A01G115200 chr1A 255464232 255471072 6840 False 11895 11895 98.006 1 6864 1 chr1A.!!$F2 6863
5 TraesCS3A01G115200 chr2A 687272755 687279599 6844 True 11954 11954 98.152 1 6864 1 chr2A.!!$R1 6863
6 TraesCS3A01G115200 chr7A 23291815 23298658 6843 True 11948 11948 98.139 1 6864 1 chr7A.!!$R1 6863
7 TraesCS3A01G115200 chr2B 741902559 741909397 6838 False 11926 11926 98.094 1 6864 1 chr2B.!!$F2 6863
8 TraesCS3A01G115200 chr2B 99558154 99564894 6740 False 11662 11662 97.806 81 6864 1 chr2B.!!$F1 6783
9 TraesCS3A01G115200 chr2B 608460545 608467352 6807 True 11660 11660 97.468 1 6864 1 chr2B.!!$R1 6863
10 TraesCS3A01G115200 chr4B 261492423 261499258 6835 True 11869 11869 97.948 1 6864 1 chr4B.!!$R3 6863
11 TraesCS3A01G115200 chr4B 14712311 14719143 6832 True 11843 11843 97.891 1 6864 1 chr4B.!!$R1 6863
12 TraesCS3A01G115200 chr4B 149726538 149733245 6707 True 11592 11592 97.793 1 6741 1 chr4B.!!$R2 6740
13 TraesCS3A01G115200 chr6A 480632509 480637349 4840 False 8355 8355 97.743 1997 6864 1 chr6A.!!$F1 4867

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
583 588 1.595311 ATCTACCCAATCCACCAGCA 58.405 50.000 0.00 0.0 0.00 4.41 F
742 748 5.451798 GGATGTGGTTGTTTTCATGTGTCTT 60.452 40.000 0.00 0.0 0.00 3.01 F
1687 1707 0.671781 GCTGTCGCATCTTCCACAGT 60.672 55.000 0.00 0.0 38.83 3.55 F
2305 2330 1.200760 TGCAGTCCTACCAGCCACAT 61.201 55.000 0.00 0.0 0.00 3.21 F
2598 2623 1.377725 CCACGGCCTTGAAGCTCAT 60.378 57.895 11.54 0.0 0.00 2.90 F
4226 4277 0.665835 GCTGACGACGATGAGGAGAT 59.334 55.000 0.00 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 1707 3.046283 ACCCACATACCTCAGCATCTA 57.954 47.619 0.00 0.0 0.00 1.98 R
2598 2623 4.141287 CACAAGTCCATAACACTTTGGGA 58.859 43.478 0.00 0.0 31.40 4.37 R
3224 3258 5.504853 TCCTACCAATTGATGCAACACATA 58.495 37.500 7.12 0.0 39.84 2.29 R
4226 4277 3.500343 TCCTCTGATTCATCCGCATCTA 58.500 45.455 0.00 0.0 0.00 1.98 R
4398 4485 3.169099 CTCACCTTCTTCTTCCTCCTCA 58.831 50.000 0.00 0.0 0.00 3.86 R
6221 6310 0.609957 TGCTCCTTTGTGATGCCTGG 60.610 55.000 0.00 0.0 0.00 4.45 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
163 165 3.630312 GGTCAGTTGGCTCACTGTTTTTA 59.370 43.478 14.53 0.0 44.10 1.52
269 271 3.572682 TCCATATAGTACTTGGCTGTCCG 59.427 47.826 0.00 0.0 34.14 4.79
487 491 8.654215 GTTATACACTTTTACTAGTTGGCTGTC 58.346 37.037 0.00 0.0 0.00 3.51
583 588 1.595311 ATCTACCCAATCCACCAGCA 58.405 50.000 0.00 0.0 0.00 4.41
742 748 5.451798 GGATGTGGTTGTTTTCATGTGTCTT 60.452 40.000 0.00 0.0 0.00 3.01
1687 1707 0.671781 GCTGTCGCATCTTCCACAGT 60.672 55.000 0.00 0.0 38.83 3.55
1793 1817 9.934190 GTTTTTCTTGTGTTGCAATATCATTTT 57.066 25.926 0.59 0.0 36.36 1.82
1815 1839 9.840427 ATTTTCTTATTGTTGCACATACACTAC 57.160 29.630 0.00 0.0 0.00 2.73
2305 2330 1.200760 TGCAGTCCTACCAGCCACAT 61.201 55.000 0.00 0.0 0.00 3.21
2598 2623 1.377725 CCACGGCCTTGAAGCTCAT 60.378 57.895 11.54 0.0 0.00 2.90
2990 3019 1.924731 ATCTCTCCTGGTGTGTTCGA 58.075 50.000 0.00 0.0 0.00 3.71
3224 3258 8.413229 ACAGTTTTACTAATCTTTGTTGCACAT 58.587 29.630 0.00 0.0 0.00 3.21
3252 3287 5.304101 TGTTGCATCAATTGGTAGGAACTTT 59.696 36.000 20.92 0.0 41.75 2.66
3379 3418 4.915085 GGTTGTAATGTGTGGTTTCATTCG 59.085 41.667 0.00 0.0 36.06 3.34
3774 3818 4.059511 CAACTTTTGGCAGAAATGCATGA 58.940 39.130 0.00 0.0 36.33 3.07
4226 4277 0.665835 GCTGACGACGATGAGGAGAT 59.334 55.000 0.00 0.0 0.00 2.75
4398 4485 6.126825 ACAAGGAAGAAGATAGTGATGCAGAT 60.127 38.462 0.00 0.0 0.00 2.90
4509 4596 0.535797 CAGCTGATGGCAGTGAGAGA 59.464 55.000 8.42 0.0 44.17 3.10
4520 4607 2.486203 GCAGTGAGAGAGAAGAAGACGA 59.514 50.000 0.00 0.0 0.00 4.20
4521 4608 3.426159 GCAGTGAGAGAGAAGAAGACGAG 60.426 52.174 0.00 0.0 0.00 4.18
4522 4609 3.126858 CAGTGAGAGAGAAGAAGACGAGG 59.873 52.174 0.00 0.0 0.00 4.63
4523 4610 3.008594 AGTGAGAGAGAAGAAGACGAGGA 59.991 47.826 0.00 0.0 0.00 3.71
4524 4611 3.945285 GTGAGAGAGAAGAAGACGAGGAT 59.055 47.826 0.00 0.0 0.00 3.24
4645 4732 1.697432 CTCCTGGTTCTGGTGGTACAA 59.303 52.381 0.00 0.0 44.16 2.41
4975 5063 4.151121 TCAAATTGACATGGAGGAAGCAA 58.849 39.130 0.00 0.0 0.00 3.91
5430 5518 1.228245 GGTGCCAAGTTCTGCCAGA 60.228 57.895 0.00 0.0 0.00 3.86
5530 5619 2.092646 ACAGTCAAAACCACCACAGCTA 60.093 45.455 0.00 0.0 0.00 3.32
5689 5778 6.098409 ACAAGAGGAGGTGTTCGACATTATAT 59.902 38.462 0.00 0.0 0.00 0.86
5764 5853 3.579586 AGTGAATGATGCACCCATGTTTT 59.420 39.130 0.00 0.0 36.95 2.43
5948 6037 2.958818 TGAGTGTGAGTTAGACCCAGT 58.041 47.619 0.00 0.0 0.00 4.00
5971 6060 4.197750 AGCTGTGAATGAAGGATGTGATC 58.802 43.478 0.00 0.0 0.00 2.92
6364 6453 2.158682 TGCACAGAACAGGGCTTTTAGA 60.159 45.455 0.00 0.0 0.00 2.10
6450 6541 9.030301 GCTAACTTGTCTTTTTATTGCTTTCAA 57.970 29.630 0.00 0.0 36.51 2.69
6673 6769 6.894339 TCTTTTTACCCTCATCTTTGTTCC 57.106 37.500 0.00 0.0 0.00 3.62
6695 6791 3.423123 CGTAGCACTTTTCGTTGACCATC 60.423 47.826 0.00 0.0 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 165 0.899019 TCAGCCAATGCATTGCACAT 59.101 45.000 30.15 14.32 43.04 3.21
583 588 1.531365 CCACCACAGCCACCACAAT 60.531 57.895 0.00 0.00 0.00 2.71
742 748 3.056107 CGTCCCTAGTTGAACATGAAGGA 60.056 47.826 0.00 0.00 0.00 3.36
1687 1707 3.046283 ACCCACATACCTCAGCATCTA 57.954 47.619 0.00 0.00 0.00 1.98
1815 1839 4.757149 AGACCTAGCAGCTACAAAAAGTTG 59.243 41.667 0.00 0.00 40.84 3.16
2034 2059 8.812329 GCATTACACAAACATTAAACACAAAGA 58.188 29.630 0.00 0.00 0.00 2.52
2035 2060 8.816144 AGCATTACACAAACATTAAACACAAAG 58.184 29.630 0.00 0.00 0.00 2.77
2036 2061 8.709386 AGCATTACACAAACATTAAACACAAA 57.291 26.923 0.00 0.00 0.00 2.83
2305 2330 4.733077 TGGGAAAACCATTTCAGAGGTA 57.267 40.909 3.97 0.00 46.80 3.08
2598 2623 4.141287 CACAAGTCCATAACACTTTGGGA 58.859 43.478 0.00 0.00 31.40 4.37
3224 3258 5.504853 TCCTACCAATTGATGCAACACATA 58.495 37.500 7.12 0.00 39.84 2.29
4023 4074 3.725895 CGTCATCAATCTTGGCAACTTCG 60.726 47.826 0.00 0.00 37.61 3.79
4226 4277 3.500343 TCCTCTGATTCATCCGCATCTA 58.500 45.455 0.00 0.00 0.00 1.98
4398 4485 3.169099 CTCACCTTCTTCTTCCTCCTCA 58.831 50.000 0.00 0.00 0.00 3.86
4509 4596 5.013547 TCTTCTTCATCCTCGTCTTCTTCT 58.986 41.667 0.00 0.00 0.00 2.85
4520 4607 3.636679 TCATCCTCGTCTTCTTCATCCT 58.363 45.455 0.00 0.00 0.00 3.24
4521 4608 4.098654 TCTTCATCCTCGTCTTCTTCATCC 59.901 45.833 0.00 0.00 0.00 3.51
4522 4609 5.255710 TCTTCATCCTCGTCTTCTTCATC 57.744 43.478 0.00 0.00 0.00 2.92
4523 4610 5.420421 TCTTCTTCATCCTCGTCTTCTTCAT 59.580 40.000 0.00 0.00 0.00 2.57
4524 4611 4.767409 TCTTCTTCATCCTCGTCTTCTTCA 59.233 41.667 0.00 0.00 0.00 3.02
4645 4732 0.037303 CTCCTGGATGTGTTGCCACT 59.963 55.000 0.00 0.00 42.34 4.00
4975 5063 1.821088 ACCCAGTCAAGACCCTTTCT 58.179 50.000 0.00 0.00 35.32 2.52
5430 5518 1.531423 CAGTCTGAGTTGGCAGCAAT 58.469 50.000 3.63 0.00 35.86 3.56
5530 5619 1.757306 CAGTGGTGCCTTCCTGACT 59.243 57.895 0.00 0.00 0.00 3.41
5711 5800 2.482336 CGCAATAGTGTTGTAGTTGGCA 59.518 45.455 1.33 0.00 0.00 4.92
5764 5853 2.751436 GGCATCTCCTTGCGGCAA 60.751 61.111 15.55 15.55 43.71 4.52
5888 5977 2.293677 GCTTCCGCTGTATCTACTGCTA 59.706 50.000 14.63 3.47 45.37 3.49
5914 6003 5.205759 TCACACTCATCGATGCTAATCAT 57.794 39.130 20.81 0.00 38.32 2.45
5948 6037 4.824479 TCACATCCTTCATTCACAGCTA 57.176 40.909 0.00 0.00 0.00 3.32
5971 6060 1.888018 CCTTGCCAACATCAGCAGG 59.112 57.895 0.00 0.00 40.73 4.85
6123 6212 4.836825 TGAATGGAGACCTTTGAGATGTC 58.163 43.478 0.00 0.00 0.00 3.06
6221 6310 0.609957 TGCTCCTTTGTGATGCCTGG 60.610 55.000 0.00 0.00 0.00 4.45
6673 6769 1.862201 TGGTCAACGAAAAGTGCTACG 59.138 47.619 0.00 0.00 0.00 3.51
6695 6791 1.204113 AGGTGAAAGGCCTCCCTCAG 61.204 60.000 5.23 0.00 41.90 3.35


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

AutoCloner maintained by Alex Coulton.