Multiple sequence alignment - TraesCS3D01G129000

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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 TraesCS3D01G129000 chr3D 100.000 2580 0 0 579 3158 88094111 88091532 0.000000e+00 4765
1 TraesCS3D01G129000 chr3D 100.000 269 0 0 1 269 88094689 88094421 6.080000e-137 497
2 TraesCS3D01G129000 chr3B 96.838 2024 63 1 579 2602 137604722 137602700 0.000000e+00 3382
3 TraesCS3D01G129000 chr3B 97.211 502 12 1 2619 3118 137602715 137602214 0.000000e+00 848
4 TraesCS3D01G129000 chr3B 93.023 258 15 3 1 256 137605172 137604916 1.070000e-99 374
5 TraesCS3D01G129000 chr3A 96.800 2000 54 4 607 2602 104559198 104557205 0.000000e+00 3330
6 TraesCS3D01G129000 chr3A 90.132 304 18 6 2622 2923 104557217 104556924 4.940000e-103 385
7 TraesCS3D01G129000 chr3A 93.902 246 13 2 1 244 104559441 104559196 1.380000e-98 370
8 TraesCS3D01G129000 chr3A 84.959 246 21 13 2928 3158 104556864 104556620 5.270000e-58 235


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 TraesCS3D01G129000 chr3D 88091532 88094689 3157 True 2631.000000 4765 100.000000 1 3158 2 chr3D.!!$R1 3157
1 TraesCS3D01G129000 chr3B 137602214 137605172 2958 True 1534.666667 3382 95.690667 1 3118 3 chr3B.!!$R1 3117
2 TraesCS3D01G129000 chr3A 104556620 104559441 2821 True 1080.000000 3330 91.448250 1 3158 4 chr3A.!!$R1 3157

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
639 784 0.108138 AAGTTCGAGCTTCCCATCGG 60.108 55.0 8.9 0.0 39.38 4.18 F
658 803 1.160137 GCGCAGAGTTCATGTTTCCT 58.840 50.0 0.3 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2284 0.036952 CTCAGCTCCCACGTGTTGAT 60.037 55.0 15.65 0.0 0.0 2.57 R
2219 2364 0.393402 GATCACCCATCACAGCTGCA 60.393 55.0 15.27 0.0 0.0 4.41 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
33 34 2.618709 GGTCTGCACATACCCAATTAGC 59.381 50.000 0.00 0.00 0.00 3.09
113 115 6.658188 TGGACGAAAATACCCTTTTGAAAT 57.342 33.333 0.00 0.00 0.00 2.17
116 118 7.654116 TGGACGAAAATACCCTTTTGAAATTTC 59.346 33.333 11.41 11.41 0.00 2.17
201 205 6.650120 AGTTCTCTGTAAAGGAGTCAAACAA 58.350 36.000 0.00 0.00 33.06 2.83
597 742 1.967319 GAGTCACTCCTTGGTGCAAA 58.033 50.000 0.00 0.00 37.16 3.68
615 760 4.928615 TGCAAAGTTTGAGTTTCTTGTTGG 59.071 37.500 19.82 0.00 0.00 3.77
639 784 0.108138 AAGTTCGAGCTTCCCATCGG 60.108 55.000 8.90 0.00 39.38 4.18
658 803 1.160137 GCGCAGAGTTCATGTTTCCT 58.840 50.000 0.30 0.00 0.00 3.36
671 816 1.748493 TGTTTCCTGTTGGTGTGAAGC 59.252 47.619 0.00 0.00 34.23 3.86
735 880 2.056223 CGGATCCGGGTAGTGTGGT 61.056 63.158 26.95 0.00 35.56 4.16
782 927 3.100207 GGGACAAATTTCCATCCCTCA 57.900 47.619 18.60 0.00 46.43 3.86
871 1016 5.798132 ACTGAATCTGTTGCTAGAACATGA 58.202 37.500 0.00 2.67 0.00 3.07
875 1020 8.429493 TGAATCTGTTGCTAGAACATGATAAG 57.571 34.615 0.00 0.00 0.00 1.73
879 1024 8.621532 TCTGTTGCTAGAACATGATAAGTTTT 57.378 30.769 0.00 0.00 0.00 2.43
976 1121 6.696198 CAAGTATGCGTCTATAATATTGCCG 58.304 40.000 0.00 0.00 0.00 5.69
1059 1204 2.409870 GCAGTTCCCTTGCATCCCG 61.410 63.158 0.00 0.00 41.17 5.14
1401 1546 2.956964 GATTCTGCCGAGTCCGCG 60.957 66.667 0.00 0.00 0.00 6.46
1506 1651 4.569865 GGGGATGTTAAAGGATGGACTGTT 60.570 45.833 0.00 0.00 0.00 3.16
1911 2056 4.851639 AGGTAGTTTGGATGAGAGCATT 57.148 40.909 0.00 0.00 34.11 3.56
1926 2071 1.284198 AGCATTGACTTCCTGGCATCT 59.716 47.619 0.00 0.00 31.11 2.90
2051 2196 5.618236 TGATTCTTCTGATATCCAGCAAGG 58.382 41.667 0.00 0.00 42.62 3.61
2058 2203 2.846206 TGATATCCAGCAAGGTCCAGTT 59.154 45.455 0.00 0.00 39.02 3.16
2139 2284 2.092323 CCTATGGTGACTCACGTGAGA 58.908 52.381 43.55 26.03 44.74 3.27
2142 2287 1.616159 TGGTGACTCACGTGAGATCA 58.384 50.000 43.55 35.81 44.74 2.92
2179 2324 1.277842 GGTTTTAAACTGCCATGGGGG 59.722 52.381 15.13 0.00 40.85 5.40
2219 2364 3.127895 TGCGCGAGTTAGGCAAAAATAAT 59.872 39.130 12.10 0.00 33.01 1.28
2234 2379 2.742428 ATAATGCAGCTGTGATGGGT 57.258 45.000 16.64 0.00 0.00 4.51
2235 2380 1.753930 TAATGCAGCTGTGATGGGTG 58.246 50.000 16.64 0.00 35.58 4.61
2238 2383 0.393402 TGCAGCTGTGATGGGTGATC 60.393 55.000 16.64 0.00 34.56 2.92
2310 2459 1.290324 GAGACGGCAGCAACAGAGA 59.710 57.895 0.00 0.00 0.00 3.10
2502 2651 5.206587 ACTATGGACGGGTTGTTATCTAGT 58.793 41.667 0.00 0.00 0.00 2.57
2582 2731 1.595489 CCGCGAGCTTGTTATTCATGC 60.595 52.381 8.23 0.00 44.29 4.06
2602 2751 4.331968 TGCGTGGATCTTCTTTATGGTTT 58.668 39.130 0.00 0.00 0.00 3.27
2603 2752 4.764823 TGCGTGGATCTTCTTTATGGTTTT 59.235 37.500 0.00 0.00 0.00 2.43
2604 2753 5.242838 TGCGTGGATCTTCTTTATGGTTTTT 59.757 36.000 0.00 0.00 0.00 1.94
2631 2780 5.929697 TTGCGCATAGATCTTCTTTATGG 57.070 39.130 12.75 0.00 0.00 2.74
2632 2781 4.960938 TGCGCATAGATCTTCTTTATGGT 58.039 39.130 5.66 0.00 0.00 3.55
2633 2782 5.368145 TGCGCATAGATCTTCTTTATGGTT 58.632 37.500 5.66 0.00 0.00 3.67
2638 2787 9.081997 CGCATAGATCTTCTTTATGGTTCTATC 57.918 37.037 0.00 0.00 0.00 2.08
2949 3158 6.759272 ACTTGCGTATTCATACCTGACATAT 58.241 36.000 0.00 0.00 0.00 1.78
2998 3217 7.553881 ACAGCTAACACATGGTTATACATTC 57.446 36.000 0.00 0.00 41.00 2.67
3076 3298 4.494091 AGATTGGATATTAGGATGGCCG 57.506 45.455 0.00 0.00 39.96 6.13
3098 3320 6.293462 GCCGTACTTTCAATCATCTTTATCCC 60.293 42.308 0.00 0.00 0.00 3.85
3135 3357 3.018423 ACTCTGTTTGCTTTGGAGGTT 57.982 42.857 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 7.883311 AGGGTATTTTCGTCCATCCATATAAAG 59.117 37.037 0.00 0.00 0.00 1.85
113 115 0.690762 GGCACACACCCCTAGAGAAA 59.309 55.000 0.00 0.00 0.00 2.52
116 118 1.541310 TTCGGCACACACCCCTAGAG 61.541 60.000 0.00 0.00 0.00 2.43
166 169 8.881262 TCCTTTACAGAGAACTTCCTTTTAGAT 58.119 33.333 0.00 0.00 0.00 1.98
174 178 5.470047 TGACTCCTTTACAGAGAACTTCC 57.530 43.478 0.00 0.00 35.27 3.46
201 205 6.182627 TGCTCTTTACTGATGAATCATGGTT 58.817 36.000 0.00 0.00 36.02 3.67
591 736 5.163963 CCAACAAGAAACTCAAACTTTGCAC 60.164 40.000 0.00 0.00 0.00 4.57
597 742 4.764823 TCACACCAACAAGAAACTCAAACT 59.235 37.500 0.00 0.00 0.00 2.66
639 784 1.135859 CAGGAAACATGAACTCTGCGC 60.136 52.381 0.00 0.00 0.00 6.09
671 816 4.543590 ATCTCCAAGCCTTATATCCGTG 57.456 45.455 0.00 0.00 0.00 4.94
708 853 0.748005 ACCCGGATCCGATGCTTTTG 60.748 55.000 35.42 15.32 42.83 2.44
735 880 2.021723 GCAAGTGTTGGGAAGTGGTCA 61.022 52.381 0.00 0.00 0.00 4.02
875 1020 8.976986 AGCAACAGATCAAATAATCAGAAAAC 57.023 30.769 0.00 0.00 0.00 2.43
879 1024 7.012989 CCATGAGCAACAGATCAAATAATCAGA 59.987 37.037 0.00 0.00 30.64 3.27
1003 1148 4.752101 AGATAGCCAATAAGTTAAGCAGCG 59.248 41.667 5.91 0.00 0.00 5.18
1055 1200 3.090790 GCCATAACTTTAAAACCCGGGA 58.909 45.455 32.02 0.00 0.00 5.14
1059 1204 5.830000 ATCTCGCCATAACTTTAAAACCC 57.170 39.130 0.00 0.00 0.00 4.11
1401 1546 3.157087 TGGAGAAAATGGAAGGTTCAGC 58.843 45.455 0.00 0.00 0.00 4.26
1404 1549 5.163457 TGTGTTTGGAGAAAATGGAAGGTTC 60.163 40.000 0.00 0.00 0.00 3.62
1506 1651 3.289128 CTGACGAGCAGGTTCAACA 57.711 52.632 0.00 0.00 41.07 3.33
1794 1939 5.818887 TCCAAGTCAAATTCATCTCCATCA 58.181 37.500 0.00 0.00 0.00 3.07
1911 2056 4.706476 CCAAATAAAGATGCCAGGAAGTCA 59.294 41.667 0.00 0.00 0.00 3.41
1926 2071 1.882989 GCCTGCCACGGCCAAATAAA 61.883 55.000 2.24 0.00 44.41 1.40
2051 2196 3.146847 CCCCTTTGAGTGTTAACTGGAC 58.853 50.000 7.22 0.00 36.52 4.02
2058 2203 0.251165 GCTGCCCCCTTTGAGTGTTA 60.251 55.000 0.00 0.00 0.00 2.41
2139 2284 0.036952 CTCAGCTCCCACGTGTTGAT 60.037 55.000 15.65 0.00 0.00 2.57
2142 2287 2.743718 CCTCAGCTCCCACGTGTT 59.256 61.111 15.65 0.00 0.00 3.32
2179 2324 2.225019 CGCATGGATAGAATGAACAGGC 59.775 50.000 0.00 0.00 35.73 4.85
2219 2364 0.393402 GATCACCCATCACAGCTGCA 60.393 55.000 15.27 0.00 0.00 4.41
2234 2379 0.687757 CCTCGGAGAACCAGGGATCA 60.688 60.000 6.58 0.00 34.09 2.92
2235 2380 0.688087 ACCTCGGAGAACCAGGGATC 60.688 60.000 6.58 0.00 38.15 3.36
2238 2383 2.359967 GGACCTCGGAGAACCAGGG 61.360 68.421 6.58 0.00 38.15 4.45
2310 2459 1.779061 ATCCCAGTCCAACCTGCGTT 61.779 55.000 0.00 0.00 0.00 4.84
2379 2528 1.914764 ACTGCTTTGGCCCCCAATG 60.915 57.895 0.00 1.85 43.55 2.82
2502 2651 5.963176 ACAAATGACACATGTAGCAATCA 57.037 34.783 0.00 0.00 0.00 2.57
2606 2755 7.148086 ACCATAAAGAAGATCTATGCGCAAAAA 60.148 33.333 17.11 2.09 0.00 1.94
2607 2756 6.318648 ACCATAAAGAAGATCTATGCGCAAAA 59.681 34.615 17.11 4.61 0.00 2.44
2608 2757 5.822519 ACCATAAAGAAGATCTATGCGCAAA 59.177 36.000 17.11 2.99 0.00 3.68
2609 2758 5.368145 ACCATAAAGAAGATCTATGCGCAA 58.632 37.500 17.11 0.00 0.00 4.85
2610 2759 4.960938 ACCATAAAGAAGATCTATGCGCA 58.039 39.130 14.96 14.96 0.00 6.09
2611 2760 5.698545 AGAACCATAAAGAAGATCTATGCGC 59.301 40.000 0.00 0.00 0.00 6.09
2612 2761 8.994429 ATAGAACCATAAAGAAGATCTATGCG 57.006 34.615 0.00 0.00 29.90 4.73
2613 2762 9.081997 CGATAGAACCATAAAGAAGATCTATGC 57.918 37.037 0.00 0.00 39.76 3.14
2620 2769 9.909644 GCTAATACGATAGAACCATAAAGAAGA 57.090 33.333 0.00 0.00 41.38 2.87
2621 2770 9.915629 AGCTAATACGATAGAACCATAAAGAAG 57.084 33.333 0.00 0.00 41.38 2.85
2626 2775 9.582431 GCAATAGCTAATACGATAGAACCATAA 57.418 33.333 0.00 0.00 37.59 1.90
2975 3184 7.792374 AGAATGTATAACCATGTGTTAGCTG 57.208 36.000 0.00 0.00 42.50 4.24
2998 3217 4.198028 TGACTCTGGATGACATGACAAG 57.802 45.455 0.00 0.00 0.00 3.16
3098 3320 8.697067 CAAACAGAGTAAATGCAATGAAGAAAG 58.303 33.333 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.