Multiple sequence alignment - TraesCS7D01G069800

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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 TraesCS7D01G069800 chr7D 100.000 4591 0 0 1 4591 40704353 40699763 0 8479
1 TraesCS7D01G069800 chr7D 94.990 4172 192 13 1 4159 396586965 396591132 0 6530
2 TraesCS7D01G069800 chr6D 95.374 4172 175 14 1 4159 292636882 292641048 0 6619
3 TraesCS7D01G069800 chr6D 94.795 4169 205 9 1 4159 140464782 140468948 0 6486
4 TraesCS7D01G069800 chr6D 98.157 434 8 0 4158 4591 175682883 175683316 0 758
5 TraesCS7D01G069800 chr2D 94.922 4175 189 19 1 4159 62117224 62121391 0 6514
6 TraesCS7D01G069800 chr2D 98.848 434 5 0 4158 4591 446340477 446340044 0 774
7 TraesCS7D01G069800 chr2D 98.618 434 6 0 4158 4591 62122020 62122453 0 769
8 TraesCS7D01G069800 chr2D 98.387 434 7 0 4158 4591 47502412 47501979 0 763
9 TraesCS7D01G069800 chr2D 98.387 434 7 0 4158 4591 321213731 321213298 0 763
10 TraesCS7D01G069800 chr4D 94.852 4176 196 15 1 4162 277715352 277711182 0 6503
11 TraesCS7D01G069800 chr1D 94.895 4172 190 18 2 4159 27651593 27655755 0 6503
12 TraesCS7D01G069800 chr1D 94.853 4177 192 19 1 4159 479691821 479695992 0 6501
13 TraesCS7D01G069800 chr1D 98.618 434 6 0 4158 4591 27656384 27656817 0 769
14 TraesCS7D01G069800 chr1D 98.618 434 6 0 4158 4591 479696621 479697054 0 769
15 TraesCS7D01G069800 chr1D 98.157 434 8 0 4158 4591 75750918 75751351 0 758
16 TraesCS7D01G069800 chr5D 94.801 4174 196 17 1 4159 179746763 179750930 0 6486
17 TraesCS7D01G069800 chr5D 98.387 434 6 1 4158 4591 507411383 507410951 0 761
18 TraesCS7D01G069800 chr3D 94.777 4174 199 14 1 4159 192295840 192300009 0 6482


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 TraesCS7D01G069800 chr7D 40699763 40704353 4590 True 8479.0 8479 100.0000 1 4591 1 chr7D.!!$R1 4590
1 TraesCS7D01G069800 chr7D 396586965 396591132 4167 False 6530.0 6530 94.9900 1 4159 1 chr7D.!!$F1 4158
2 TraesCS7D01G069800 chr6D 292636882 292641048 4166 False 6619.0 6619 95.3740 1 4159 1 chr6D.!!$F3 4158
3 TraesCS7D01G069800 chr6D 140464782 140468948 4166 False 6486.0 6486 94.7950 1 4159 1 chr6D.!!$F1 4158
4 TraesCS7D01G069800 chr2D 62117224 62122453 5229 False 3641.5 6514 96.7700 1 4591 2 chr2D.!!$F1 4590
5 TraesCS7D01G069800 chr4D 277711182 277715352 4170 True 6503.0 6503 94.8520 1 4162 1 chr4D.!!$R1 4161
6 TraesCS7D01G069800 chr1D 27651593 27656817 5224 False 3636.0 6503 96.7565 2 4591 2 chr1D.!!$F2 4589
7 TraesCS7D01G069800 chr1D 479691821 479697054 5233 False 3635.0 6501 96.7355 1 4591 2 chr1D.!!$F3 4590
8 TraesCS7D01G069800 chr5D 179746763 179750930 4167 False 6486.0 6486 94.8010 1 4159 1 chr5D.!!$F1 4158
9 TraesCS7D01G069800 chr3D 192295840 192300009 4169 False 6482.0 6482 94.7770 1 4159 1 chr3D.!!$F1 4158

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
88 91 0.034863 GGATTCTTGGTAACCCGCCA 60.035 55.0 0.00 0.00 0.00 5.69 F
1344 1358 0.178929 ACCTCGGAGAAGAACCCAGT 60.179 55.0 6.58 0.00 34.09 4.00 F
1521 1535 0.389948 GGTTCTACTGCCAGGACACG 60.390 60.0 0.00 0.00 0.00 4.49 F
2503 2520 0.874607 GCGTCAGTCGTCAACCACTT 60.875 55.0 0.00 0.00 42.13 3.16 F
3232 3256 0.178987 TCAAGGGCCGGCTTAAACAA 60.179 50.0 28.56 3.23 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2032 0.467844 TGGCTTTCTTGGCAGCTTCA 60.468 50.000 0.00 0.00 37.59 3.02 R
2541 2558 0.173481 CTGAATTGAGTCGCCGGAGA 59.827 55.000 5.05 3.81 0.00 3.71 R
2832 2851 0.552848 ATCATTTGGATGAGCCGGGT 59.447 50.000 5.45 5.45 45.01 5.28 R
3394 3419 3.865011 TTTGCAAGCAAAGACACTTGA 57.135 38.095 15.59 0.00 44.89 3.02 R
4563 5223 0.252239 GGTCATTTGGGGGCTTCCTT 60.252 55.000 0.00 0.00 35.33 3.36 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
88 91 0.034863 GGATTCTTGGTAACCCGCCA 60.035 55.000 0.00 0.00 0.00 5.69
134 137 3.426191 CGTTTCGTCCAACGTATCTCAAA 59.574 43.478 0.00 0.00 43.72 2.69
135 138 4.084952 CGTTTCGTCCAACGTATCTCAAAA 60.085 41.667 0.00 0.00 43.72 2.44
204 208 4.387598 GCTGGATAATCATGTCTTCAGCT 58.612 43.478 15.46 0.00 41.91 4.24
413 423 2.124983 GCCTCCGCTGCTCATCAA 60.125 61.111 0.00 0.00 0.00 2.57
516 526 2.859165 TTCCTTCGCAGTTCTTCCAT 57.141 45.000 0.00 0.00 0.00 3.41
526 537 0.750546 GTTCTTCCATAACGGCCCCC 60.751 60.000 0.00 0.00 33.14 5.40
539 550 0.684479 GGCCCCCTTGATCCAAGAAC 60.684 60.000 8.16 0.00 43.42 3.01
548 559 4.334759 CCTTGATCCAAGAACAGTGCATAG 59.665 45.833 8.16 0.00 43.42 2.23
579 590 2.496111 AGTCGTTTCACGCCCATTTTA 58.504 42.857 0.00 0.00 42.21 1.52
624 636 4.356405 TGCAAAGAGACCTCATTGAGAA 57.644 40.909 15.36 1.81 39.76 2.87
642 654 5.470368 TGAGAACTTATGAACTTCTCCGTG 58.530 41.667 4.60 0.00 39.40 4.94
810 824 4.039488 AGCCATGCTTTGTGAAATTTCTGA 59.961 37.500 18.64 2.96 33.89 3.27
907 921 9.613428 TTAATCATATATCATTAGGCCCTTTCG 57.387 33.333 0.00 0.00 0.00 3.46
919 933 1.029947 CCCTTTCGTAAGCCGCCATT 61.030 55.000 0.00 0.00 36.19 3.16
957 971 7.384932 ACTGAAATTTTTCTCCGGCTTAAATTG 59.615 33.333 0.00 0.00 38.02 2.32
1045 1059 1.067425 CCATCACATGCAACTGGGTTG 60.067 52.381 6.10 6.10 45.24 3.77
1068 1082 1.492873 CAACGTCACCGACAGCATG 59.507 57.895 0.00 0.00 39.09 4.06
1165 1179 1.213296 GAGGCCTCAACCCAAGGATA 58.787 55.000 28.43 0.00 35.83 2.59
1242 1256 6.820656 GCTCAAAATTCTTCAGAGATGTCCTA 59.179 38.462 0.00 0.00 0.00 2.94
1314 1328 3.701040 ACATCTGCAACTTCCAAGTGTTT 59.299 39.130 0.00 0.00 39.66 2.83
1318 1332 4.702612 TCTGCAACTTCCAAGTGTTTTGTA 59.297 37.500 0.00 0.00 39.66 2.41
1344 1358 0.178929 ACCTCGGAGAAGAACCCAGT 60.179 55.000 6.58 0.00 34.09 4.00
1359 1373 2.106511 ACCCAGTTTGCTGCTCTTTAGA 59.893 45.455 0.00 0.00 41.26 2.10
1521 1535 0.389948 GGTTCTACTGCCAGGACACG 60.390 60.000 0.00 0.00 0.00 4.49
1545 1559 2.883572 GGCTGACGAGAACCCTCTA 58.116 57.895 0.00 0.00 37.28 2.43
1662 1676 4.328118 AATCAAAGCTCTTCTGGGGAAT 57.672 40.909 0.00 0.00 0.00 3.01
1716 1730 2.123248 TTGCCTGGCGAGTGATTCCA 62.123 55.000 14.98 0.00 0.00 3.53
2333 2350 9.466497 TTTCACATCCTTTAGCTTATCAAGATT 57.534 29.630 0.00 0.00 0.00 2.40
2416 2433 1.684049 AGACCTCTCCTCCGGCTTG 60.684 63.158 0.00 0.00 0.00 4.01
2490 2507 3.976701 ATCCTTTGGCGGGCGTCAG 62.977 63.158 0.00 0.00 0.00 3.51
2503 2520 0.874607 GCGTCAGTCGTCAACCACTT 60.875 55.000 0.00 0.00 42.13 3.16
2541 2558 3.053826 ACTACCAGGGAACTTCACCTTT 58.946 45.455 0.00 0.00 40.21 3.11
2557 2574 1.676014 CCTTTCTCCGGCGACTCAATT 60.676 52.381 9.30 0.00 0.00 2.32
2658 2676 6.942532 TTGCACTAACTCTTTGACTTTCAT 57.057 33.333 0.00 0.00 0.00 2.57
2829 2848 2.011122 TCTGATAACCCGGAGATCCC 57.989 55.000 0.73 0.00 0.00 3.85
2832 2851 1.344598 TGATAACCCGGAGATCCCCAA 60.345 52.381 0.73 0.00 0.00 4.12
2846 2865 2.354729 CCAACCCGGCTCATCCAA 59.645 61.111 0.00 0.00 34.01 3.53
2936 2955 2.234143 GCTCTGCCAAGGAAGAACTTT 58.766 47.619 0.00 0.00 27.71 2.66
3030 3049 6.148948 GCTATGTTAATCAAGTGCACAACAA 58.851 36.000 21.04 9.17 30.48 2.83
3089 3108 5.065731 CAGCAAAAATCTGAGGTATGACTCC 59.934 44.000 0.00 0.00 36.66 3.85
3100 3119 4.104831 AGGTATGACTCCCTTGCTTACTT 58.895 43.478 0.00 0.00 0.00 2.24
3232 3256 0.178987 TCAAGGGCCGGCTTAAACAA 60.179 50.000 28.56 3.23 0.00 2.83
3237 3262 1.819903 GGGCCGGCTTAAACAACATAA 59.180 47.619 28.56 0.00 0.00 1.90
3351 3376 4.912586 TGGGACTTATTTTCATGAACCGA 58.087 39.130 7.89 0.00 0.00 4.69
3394 3419 2.686715 GCATACATTAGCCCCCAAGTGT 60.687 50.000 0.00 0.00 0.00 3.55
3588 3614 6.822667 TTGAATTCAGTGTATCTGCACAAT 57.177 33.333 8.41 0.00 43.32 2.71
3740 3766 2.765135 CCATGTGTCTCAGATGGTCTCT 59.235 50.000 14.95 0.00 46.19 3.10
4339 4999 3.724732 AGGTTAAGCCGGTGGAATTAA 57.275 42.857 1.90 0.00 43.70 1.40
4363 5023 5.982890 ACCACCCTTGAATACTTTTGATG 57.017 39.130 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 152 7.469456 GCGCCTCAATTTTTGGGATAGTTATTA 60.469 37.037 0.00 0.00 30.85 0.98
204 208 2.431942 GGCGCGAGAAACGAGGAA 60.432 61.111 12.10 0.00 45.77 3.36
259 263 2.041350 AGGGAAGAGTGACGAAGACCTA 59.959 50.000 0.00 0.00 0.00 3.08
413 423 1.874345 CGGCGAGGACTTACTGGTGT 61.874 60.000 0.00 0.00 0.00 4.16
516 526 1.208844 TTGGATCAAGGGGGCCGTTA 61.209 55.000 0.00 0.00 0.00 3.18
526 537 4.201891 GCTATGCACTGTTCTTGGATCAAG 60.202 45.833 0.00 1.53 42.25 3.02
539 550 2.528743 CCGCCGAAGCTATGCACTG 61.529 63.158 0.00 0.00 36.60 3.66
548 559 1.681025 GAAACGACTACCGCCGAAGC 61.681 60.000 0.00 0.00 43.32 3.86
579 590 5.760131 AGCAAAAGGGATCTGCTAGTATTT 58.240 37.500 4.69 0.00 44.44 1.40
599 611 2.555325 CAATGAGGTCTCTTTGCAAGCA 59.445 45.455 11.78 0.00 37.73 3.91
624 636 4.281182 ACTGACACGGAGAAGTTCATAAGT 59.719 41.667 5.50 0.00 0.00 2.24
907 921 4.095782 TCAGTATTCAAAATGGCGGCTTAC 59.904 41.667 11.43 0.00 0.00 2.34
942 956 2.718563 GGTTCCAATTTAAGCCGGAGA 58.281 47.619 5.05 0.00 0.00 3.71
957 971 5.834169 TGACAAAATAAAGTTTCCGGTTCC 58.166 37.500 0.00 0.00 0.00 3.62
1165 1179 9.125026 GTGATCAATAAATATGACAACTTCCCT 57.875 33.333 0.00 0.00 0.00 4.20
1242 1256 1.583054 GTCGCAGGTCAAAGAAGTGT 58.417 50.000 0.00 0.00 0.00 3.55
1359 1373 4.259356 GGCGGTTCAGGTAAAATAACTCT 58.741 43.478 0.00 0.00 0.00 3.24
1521 1535 1.153997 GTTCTCGTCAGCCGGAGAC 60.154 63.158 5.05 11.87 37.11 3.36
1662 1676 5.765510 ACCAGATCAATACCATTTAAGCCA 58.234 37.500 0.00 0.00 0.00 4.75
1753 1767 3.068732 CGTAGAGGATCATCTTTCTGGCA 59.931 47.826 16.10 0.00 37.82 4.92
2015 2030 2.094675 GGCTTTCTTGGCAGCTTCATA 58.905 47.619 0.00 0.00 36.20 2.15
2017 2032 0.467844 TGGCTTTCTTGGCAGCTTCA 60.468 50.000 0.00 0.00 37.59 3.02
2333 2350 7.099266 TCTGTTGCTTCAAAAGAAATTGAGA 57.901 32.000 0.00 0.00 40.21 3.27
2416 2433 1.997928 GCTTCCTTGATGCTTCGGGC 61.998 60.000 6.56 0.00 42.22 6.13
2490 2507 5.694910 TCAGAAGAATTAAGTGGTTGACGAC 59.305 40.000 0.00 0.00 0.00 4.34
2503 2520 7.829211 CCCTGGTAGTTTGAATCAGAAGAATTA 59.171 37.037 0.00 0.00 0.00 1.40
2541 2558 0.173481 CTGAATTGAGTCGCCGGAGA 59.827 55.000 5.05 3.81 0.00 3.71
2658 2676 3.216187 TGCTGGGCTTTACTTGTACAA 57.784 42.857 8.28 8.28 0.00 2.41
2714 2732 1.062275 AGCCTCAGGATCAGTCAGGAT 60.062 52.381 0.00 0.00 0.00 3.24
2829 2848 0.684153 ATTTGGATGAGCCGGGTTGG 60.684 55.000 8.00 0.00 40.66 3.77
2832 2851 0.552848 ATCATTTGGATGAGCCGGGT 59.447 50.000 5.45 5.45 45.01 5.28
2846 2865 3.869246 GTGATTACAACGTCCGGATCATT 59.131 43.478 7.81 0.00 0.00 2.57
2995 3014 7.831193 ACTTGATTAACATAGCCAGAGACAATT 59.169 33.333 0.00 0.00 0.00 2.32
3030 3049 0.999712 ATCAATTTCCAGGTCCCGGT 59.000 50.000 0.00 0.00 0.00 5.28
3089 3108 9.262358 GTAAGGATAACTATGAAGTAAGCAAGG 57.738 37.037 0.00 0.00 33.75 3.61
3100 3119 5.513094 GCTGGCATGGTAAGGATAACTATGA 60.513 44.000 4.06 0.00 37.87 2.15
3232 3256 3.617284 GAAAGGACCGGGTCAATTATGT 58.383 45.455 27.32 7.91 33.68 2.29
3237 3262 1.073098 AAGGAAAGGACCGGGTCAAT 58.927 50.000 27.32 13.39 33.68 2.57
3351 3376 5.997746 TGCTGAAAAGCTCTATTTACAGTGT 59.002 36.000 0.00 0.00 35.49 3.55
3394 3419 3.865011 TTTGCAAGCAAAGACACTTGA 57.135 38.095 15.59 0.00 44.89 3.02
3485 3510 9.933723 AGATCAAAGATTTCCGATTCAAATTTT 57.066 25.926 0.00 0.00 0.00 1.82
3505 3530 3.973206 TCAGGCGGTTCTTTAGATCAA 57.027 42.857 0.00 0.00 0.00 2.57
3588 3614 8.519526 TGCTTCAAACTTTTTCTTCAGTTTCTA 58.480 29.630 0.00 0.00 40.52 2.10
3740 3766 5.165961 AGAGTAGCTTACCAAAGATTGCA 57.834 39.130 0.00 0.00 34.37 4.08
3784 3810 9.850628 CAATTGAGATGCTCTTTGAAAAAGATA 57.149 29.630 0.00 0.00 31.20 1.98
3792 3818 5.311265 AGTGACAATTGAGATGCTCTTTGA 58.689 37.500 13.59 0.00 32.69 2.69
3795 3821 4.874966 GCTAGTGACAATTGAGATGCTCTT 59.125 41.667 13.59 0.00 0.00 2.85
3876 3906 5.570234 GGTATAAACCGCCTTCAATTTGA 57.430 39.130 0.00 0.00 35.62 2.69
4339 4999 6.326323 ACATCAAAAGTATTCAAGGGTGGTTT 59.674 34.615 0.00 0.00 0.00 3.27
4363 5023 6.645700 TTGCAAACAAGTTCTTTTGATCAC 57.354 33.333 0.00 0.00 35.13 3.06
4563 5223 0.252239 GGTCATTTGGGGGCTTCCTT 60.252 55.000 0.00 0.00 35.33 3.36


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

AutoCloner maintained by Alex Coulton.