Multiple sequence alignment - TraesCS7D01G264300

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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 TraesCS7D01G264300 chr7D 100.000 5638 0 0 1 5638 244957168 244951531 0.000000e+00 10412
1 TraesCS7D01G264300 chr7B 93.749 5695 215 58 2 5637 220871308 220865696 0.000000e+00 8414
2 TraesCS7D01G264300 chr7A 94.561 3328 134 21 2332 5638 261224157 261220856 0.000000e+00 5099
3 TraesCS7D01G264300 chr7A 94.382 2136 74 12 327 2419 261226286 261224154 0.000000e+00 3238
4 TraesCS7D01G264300 chr7A 96.364 330 10 2 1 329 261226727 261226399 4.970000e-150 542
5 TraesCS7D01G264300 chr2A 88.803 1170 105 11 2628 3790 14848713 14847563 0.000000e+00 1411


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 TraesCS7D01G264300 chr7D 244951531 244957168 5637 True 10412.000000 10412 100.000000 1 5638 1 chr7D.!!$R1 5637
1 TraesCS7D01G264300 chr7B 220865696 220871308 5612 True 8414.000000 8414 93.749000 2 5637 1 chr7B.!!$R1 5635
2 TraesCS7D01G264300 chr7A 261220856 261226727 5871 True 2959.666667 5099 95.102333 1 5638 3 chr7A.!!$R1 5637
3 TraesCS7D01G264300 chr2A 14847563 14848713 1150 True 1411.000000 1411 88.803000 2628 3790 1 chr2A.!!$R1 1162

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
694 847 1.204941 CCGCTAACTCACTGCCTAACT 59.795 52.381 0.00 0.00 0.00 2.24 F
734 887 1.953559 GCCACCTCAGCGAAATCATA 58.046 50.000 0.00 0.00 0.00 2.15 F
2287 2484 2.851263 AGCGTCCATTCCTTTGTACA 57.149 45.000 0.00 0.00 0.00 2.90 F
2311 2508 0.752054 CTGATGGTCTCCTCTCCTGC 59.248 60.000 0.00 0.00 0.00 4.85 F
3865 4155 2.423577 GTCCCATTTAGTGTGAACGCT 58.576 47.619 1.64 1.64 40.27 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1787 0.629596 TCAGATCCGAGTACCCCTGT 59.370 55.000 0.0 0.0 0.00 4.00 R
2311 2508 1.350193 CTGATTGTCCGTGAGAACCG 58.650 55.000 0.0 0.0 0.00 4.44 R
4140 4438 0.523072 CGCTGTGCTAACCTGCAAAT 59.477 50.000 0.0 0.0 45.12 2.32 R
4234 4532 3.721706 AAGGCCCCTCCTGAAGCG 61.722 66.667 0.0 0.0 46.94 4.68 R
5603 5924 0.625849 ATGCCCCTTCCTTCGTTGAT 59.374 50.000 0.0 0.0 0.00 2.57 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
540 692 7.753132 TCTCCCGAAAATAAAATCGTGATTTTG 59.247 33.333 23.90 10.69 46.80 2.44
553 705 3.908382 CGTGATTTTGCTCAGCAGTTTAC 59.092 43.478 0.00 0.00 40.61 2.01
616 769 3.254024 ATGTCCCACCGTGTCAGCC 62.254 63.158 0.00 0.00 0.00 4.85
694 847 1.204941 CCGCTAACTCACTGCCTAACT 59.795 52.381 0.00 0.00 0.00 2.24
704 857 2.436115 GCCTAACTGGTCCCACGC 60.436 66.667 0.00 0.00 38.35 5.34
734 887 1.953559 GCCACCTCAGCGAAATCATA 58.046 50.000 0.00 0.00 0.00 2.15
779 932 4.778143 GCCCTCGGTGTTCGGCAT 62.778 66.667 0.00 0.00 39.77 4.40
2150 2347 3.420300 TTGTGCAGTTCCCGGTTAATA 57.580 42.857 0.00 0.00 0.00 0.98
2214 2411 5.250543 TGATCTCTGGTAGGTCATGGAAAAA 59.749 40.000 0.00 0.00 40.56 1.94
2287 2484 2.851263 AGCGTCCATTCCTTTGTACA 57.149 45.000 0.00 0.00 0.00 2.90
2296 2493 5.044919 TCCATTCCTTTGTACATGACCTGAT 60.045 40.000 0.00 0.00 0.00 2.90
2311 2508 0.752054 CTGATGGTCTCCTCTCCTGC 59.248 60.000 0.00 0.00 0.00 4.85
2534 2815 3.814842 CGCAGGTTGGCTGATAATGAATA 59.185 43.478 0.00 0.00 0.00 1.75
2538 2819 4.823989 AGGTTGGCTGATAATGAATAGTGC 59.176 41.667 0.00 0.00 0.00 4.40
3453 3743 4.048970 AGGAGTCCTCTAGTTTGCAGTA 57.951 45.455 5.62 0.00 0.00 2.74
3532 3822 5.234466 AGATAATCCAGATACCAGGCAAC 57.766 43.478 0.00 0.00 0.00 4.17
3665 3955 3.329542 ATCCCATCCGCGCACTGTT 62.330 57.895 8.75 0.00 0.00 3.16
3750 4040 3.545703 CCACTTCCTCTTCAGTGTGTTT 58.454 45.455 0.00 0.00 39.09 2.83
3818 4108 6.294731 GGGCAAACATCTTATCTTTGAAGTGT 60.295 38.462 0.00 0.00 0.00 3.55
3823 4113 7.897575 ACATCTTATCTTTGAAGTGTCTGTC 57.102 36.000 0.00 0.00 0.00 3.51
3865 4155 2.423577 GTCCCATTTAGTGTGAACGCT 58.576 47.619 1.64 1.64 40.27 5.07
3968 4259 3.636300 TGGGTCATCTTGTTTCTTTGTGG 59.364 43.478 0.00 0.00 0.00 4.17
4058 4351 7.806690 TGTTTTGCATCATTGTAGAGAAGTAC 58.193 34.615 0.00 0.00 0.00 2.73
4059 4352 7.443879 TGTTTTGCATCATTGTAGAGAAGTACA 59.556 33.333 0.00 0.00 0.00 2.90
4078 4371 5.719085 AGTACAGAGTCTCCATCAGTGAAAT 59.281 40.000 0.00 0.00 0.00 2.17
4276 4574 0.179936 GCTCTTCCCATGACAGAGGG 59.820 60.000 9.06 9.06 46.90 4.30
4604 4902 1.596220 GGCCGTTTTGTCAAGTCGAAC 60.596 52.381 11.29 1.63 0.00 3.95
4681 4983 0.463204 CACGGAGATGACATCCTGCT 59.537 55.000 11.92 0.00 34.45 4.24
4777 5079 4.162320 AGAGGATCATATTCACGGTGTGTT 59.838 41.667 8.17 0.00 37.82 3.32
4778 5080 4.442706 AGGATCATATTCACGGTGTGTTC 58.557 43.478 8.17 3.91 34.79 3.18
4781 5083 5.354234 GGATCATATTCACGGTGTGTTCTTT 59.646 40.000 8.17 0.00 34.79 2.52
4955 5263 4.100189 TGGGTTCCAAATCGACAAACAATT 59.900 37.500 0.00 0.00 0.00 2.32
5035 5349 5.394663 GCTGCTCTTACTCCTAACTGATTGA 60.395 44.000 0.00 0.00 0.00 2.57
5039 5353 7.093333 TGCTCTTACTCCTAACTGATTGATCAA 60.093 37.037 11.26 11.26 36.18 2.57
5264 5578 1.823470 GTTCACCACCAGCTGCACA 60.823 57.895 8.66 0.00 0.00 4.57
5307 5623 1.366854 CCGTCCGTCAGTCGAGATCA 61.367 60.000 0.00 0.00 42.86 2.92
5311 5627 2.092323 TCCGTCAGTCGAGATCAATGT 58.908 47.619 0.00 0.00 42.86 2.71
5313 5629 2.416027 CCGTCAGTCGAGATCAATGTGT 60.416 50.000 0.00 0.00 42.86 3.72
5339 5655 1.725641 GAACACAGATGCATGGACGA 58.274 50.000 2.46 0.00 0.00 4.20
5340 5656 1.662629 GAACACAGATGCATGGACGAG 59.337 52.381 2.46 0.00 0.00 4.18
5341 5657 0.742281 ACACAGATGCATGGACGAGC 60.742 55.000 2.46 0.00 0.00 5.03
5342 5658 0.741927 CACAGATGCATGGACGAGCA 60.742 55.000 2.46 0.00 45.92 4.26
5346 5662 2.988800 TGCATGGACGAGCATGGA 59.011 55.556 0.00 0.00 35.51 3.41
5347 5663 1.450134 TGCATGGACGAGCATGGAC 60.450 57.895 0.00 0.00 35.51 4.02
5348 5664 2.528743 GCATGGACGAGCATGGACG 61.529 63.158 0.00 0.00 0.00 4.79
5583 5904 0.179004 AGCAGACGGGAGATCGAGAT 60.179 55.000 0.00 0.00 0.00 2.75
5618 5939 2.094762 ACGAATCAACGAAGGAAGGG 57.905 50.000 0.00 0.00 37.03 3.95
5625 5946 2.045045 CGAAGGAAGGGGCATGCA 60.045 61.111 21.36 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
540 692 1.067495 AGGACTCGTAAACTGCTGAGC 60.067 52.381 0.00 0.00 31.64 4.26
553 705 4.083110 TGGAAAGAACTTACGTAGGACTCG 60.083 45.833 12.14 0.00 0.00 4.18
583 736 1.568504 GACATGAGTAGTGGGTCCCA 58.431 55.000 6.47 6.47 0.00 4.37
1527 1718 2.930562 AGCGCTTCCCCCTTGAGT 60.931 61.111 2.64 0.00 0.00 3.41
1596 1787 0.629596 TCAGATCCGAGTACCCCTGT 59.370 55.000 0.00 0.00 0.00 4.00
1853 2044 9.661563 ATTTGTTTGCATATCATTCTCATGTTT 57.338 25.926 0.00 0.00 0.00 2.83
2214 2411 6.112734 TGTTATTCATCTGAACGCCAATAGT 58.887 36.000 0.00 0.00 36.80 2.12
2311 2508 1.350193 CTGATTGTCCGTGAGAACCG 58.650 55.000 0.00 0.00 0.00 4.44
2437 2718 6.008696 TCTACTCCCCTTTCAAGTTGAAAA 57.991 37.500 26.60 14.26 44.69 2.29
2534 2815 2.906389 TGTTGGTAGAGGAGAATGCACT 59.094 45.455 0.00 0.00 0.00 4.40
2538 2819 3.265791 GCACTGTTGGTAGAGGAGAATG 58.734 50.000 0.00 0.00 0.00 2.67
3453 3743 9.271828 CAAAGGAATAAAAACCAATAACAGCTT 57.728 29.630 0.00 0.00 0.00 3.74
3665 3955 7.913789 TGGAAAGTTAATAGCTAAGAGGAACA 58.086 34.615 0.00 0.00 0.00 3.18
3750 4040 3.263170 TGAATTAGGAACACAGCAGCCTA 59.737 43.478 0.00 0.00 32.04 3.93
3818 4108 2.092429 AGCCAACTTTCACAAGGACAGA 60.092 45.455 0.00 0.00 33.82 3.41
3823 4113 4.949856 ACCATATAGCCAACTTTCACAAGG 59.050 41.667 0.00 0.00 33.82 3.61
3865 4155 3.244422 ACCGTGATTGAGAGCACCTAAAA 60.244 43.478 0.00 0.00 38.95 1.52
3968 4259 6.398935 GCTGACAAAATTGCGACTTAATGTTC 60.399 38.462 0.00 0.00 0.00 3.18
3974 4265 2.227865 GGGCTGACAAAATTGCGACTTA 59.772 45.455 0.00 0.00 0.00 2.24
3978 4269 0.597568 CAGGGCTGACAAAATTGCGA 59.402 50.000 0.00 0.00 0.00 5.10
3979 4270 0.597568 TCAGGGCTGACAAAATTGCG 59.402 50.000 0.00 0.00 34.14 4.85
4058 4351 6.654161 AGAAAATTTCACTGATGGAGACTCTG 59.346 38.462 8.55 0.00 0.00 3.35
4059 4352 6.654161 CAGAAAATTTCACTGATGGAGACTCT 59.346 38.462 15.69 0.00 34.07 3.24
4140 4438 0.523072 CGCTGTGCTAACCTGCAAAT 59.477 50.000 0.00 0.00 45.12 2.32
4234 4532 3.721706 AAGGCCCCTCCTGAAGCG 61.722 66.667 0.00 0.00 46.94 4.68
4348 4646 1.010574 CGTCTCGCTGTCGATCCTC 60.011 63.158 0.00 0.00 44.56 3.71
4369 4667 1.671054 GCTGTCCCTGTTTAGCGCA 60.671 57.895 11.47 0.00 0.00 6.09
4681 4983 1.671979 GCATCATGCTTAGGTGCAGA 58.328 50.000 1.02 0.00 46.71 4.26
4724 5026 4.435917 CGATGCTGAAAATGATGACGACAA 60.436 41.667 0.00 0.00 0.00 3.18
4781 5083 7.574607 AGAAAAGGAGAGGTCTCTTACAAAAA 58.425 34.615 6.94 0.00 42.48 1.94
4798 5100 4.982241 ATGTGTTCTGAGGAGAAAAGGA 57.018 40.909 0.00 0.00 40.00 3.36
4799 5101 7.693969 ATTTATGTGTTCTGAGGAGAAAAGG 57.306 36.000 0.00 0.00 40.00 3.11
4934 5242 6.921307 AGTAAATTGTTTGTCGATTTGGAACC 59.079 34.615 0.00 0.00 39.60 3.62
4936 5244 7.013846 AGGAGTAAATTGTTTGTCGATTTGGAA 59.986 33.333 0.00 0.00 39.60 3.53
4943 5251 7.929785 AGTTCTTAGGAGTAAATTGTTTGTCGA 59.070 33.333 0.00 0.00 0.00 4.20
4991 5301 4.701651 CAGCACCTTGATATGTTCCAAAGA 59.298 41.667 0.00 0.00 0.00 2.52
4996 5306 2.615912 GAGCAGCACCTTGATATGTTCC 59.384 50.000 0.00 0.00 0.00 3.62
5035 5349 2.514592 CGCCGGCCAGACATTGAT 60.515 61.111 23.46 0.00 0.00 2.57
5228 5542 2.048597 CTACAGACGGCGGCAACA 60.049 61.111 18.30 0.00 0.00 3.33
5264 5578 1.593006 CGTCGTTCTCTGCTTTGTTGT 59.407 47.619 0.00 0.00 0.00 3.32
5313 5629 0.813210 TGCATCTGTGTTCGTGCACA 60.813 50.000 18.64 12.52 45.85 4.57
5339 5655 2.667470 AGTAGACCATACGTCCATGCT 58.333 47.619 0.00 0.00 43.08 3.79
5340 5656 3.612004 GCTAGTAGACCATACGTCCATGC 60.612 52.174 0.00 0.00 43.08 4.06
5341 5657 3.821600 AGCTAGTAGACCATACGTCCATG 59.178 47.826 0.00 0.00 43.08 3.66
5342 5658 4.101645 AGCTAGTAGACCATACGTCCAT 57.898 45.455 0.00 0.00 43.08 3.41
5343 5659 3.572632 AGCTAGTAGACCATACGTCCA 57.427 47.619 0.00 0.00 43.08 4.02
5344 5660 5.303971 TCTAAGCTAGTAGACCATACGTCC 58.696 45.833 0.00 0.00 43.08 4.79
5345 5661 6.128227 CCATCTAAGCTAGTAGACCATACGTC 60.128 46.154 0.00 0.00 42.32 4.34
5346 5662 5.706369 CCATCTAAGCTAGTAGACCATACGT 59.294 44.000 0.00 0.00 32.97 3.57
5347 5663 5.938710 TCCATCTAAGCTAGTAGACCATACG 59.061 44.000 0.00 0.00 32.97 3.06
5348 5664 7.948034 ATCCATCTAAGCTAGTAGACCATAC 57.052 40.000 0.00 0.00 32.97 2.39
5375 5693 6.072342 ACGTACGGCAAGAAGGAAAAATAAAT 60.072 34.615 21.06 0.00 0.00 1.40
5379 5697 3.143728 ACGTACGGCAAGAAGGAAAAAT 58.856 40.909 21.06 0.00 0.00 1.82
5568 5889 2.915775 TCGATCTCGATCTCCCGTC 58.084 57.895 0.00 0.00 44.22 4.79
5583 5904 7.059147 CGTTGATTCGTTAATTAGATCGATCGA 59.941 37.037 21.86 21.86 32.54 3.59
5596 5917 3.998341 CCCTTCCTTCGTTGATTCGTTAA 59.002 43.478 0.00 0.00 0.00 2.01
5603 5924 0.625849 ATGCCCCTTCCTTCGTTGAT 59.374 50.000 0.00 0.00 0.00 2.57
5605 5926 1.937546 GCATGCCCCTTCCTTCGTTG 61.938 60.000 6.36 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.