Multiple sequence alignment - TraesCS5D01G295000

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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 TraesCS5D01G295000 chr5D 100.000 4316 0 0 1 4316 392081622 392077307 0.000000e+00 7971.0
1 TraesCS5D01G295000 chr5B 98.711 2173 26 1 1553 3725 473091292 473089122 0.000000e+00 3856.0
2 TraesCS5D01G295000 chr5B 96.686 1569 36 4 3 1555 473092908 473091340 0.000000e+00 2595.0
3 TraesCS5D01G295000 chr5B 97.475 594 8 2 3723 4316 473089067 473088481 0.000000e+00 1007.0
4 TraesCS5D01G295000 chr5B 77.737 548 88 17 417 933 631547073 631547617 5.420000e-79 305.0
5 TraesCS5D01G295000 chr2A 89.179 536 55 1 43 575 617818196 617817661 0.000000e+00 665.0
6 TraesCS5D01G295000 chr2A 85.771 253 36 0 681 933 617817596 617817344 7.110000e-68 268.0
7 TraesCS5D01G295000 chr3D 79.389 917 162 17 43 934 148222212 148223126 4.740000e-174 621.0
8 TraesCS5D01G295000 chr3B 79.066 707 108 22 259 933 62959773 62959075 2.370000e-122 449.0
9 TraesCS5D01G295000 chr1D 92.683 41 3 0 985 1025 365710905 365710865 4.660000e-05 60.2


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 TraesCS5D01G295000 chr5D 392077307 392081622 4315 True 7971.0 7971 100.000 1 4316 1 chr5D.!!$R1 4315
1 TraesCS5D01G295000 chr5B 473088481 473092908 4427 True 2486.0 3856 97.624 3 4316 3 chr5B.!!$R1 4313
2 TraesCS5D01G295000 chr5B 631547073 631547617 544 False 305.0 305 77.737 417 933 1 chr5B.!!$F1 516
3 TraesCS5D01G295000 chr2A 617817344 617818196 852 True 466.5 665 87.475 43 933 2 chr2A.!!$R1 890
4 TraesCS5D01G295000 chr3D 148222212 148223126 914 False 621.0 621 79.389 43 934 1 chr3D.!!$F1 891
5 TraesCS5D01G295000 chr3B 62959075 62959773 698 True 449.0 449 79.066 259 933 1 chr3B.!!$R1 674

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
843 873 0.107643 TGAGTTCGATGTGCCAACCA 59.892 50.000 0.00 0.0 0.0 3.67 F
1201 1244 1.152839 CCCTCTCGTCTCTCCCTCC 60.153 68.421 0.00 0.0 0.0 4.30 F
2829 2922 1.613437 ACTTGGGTTGCTTGAATTCGG 59.387 47.619 0.04 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 2532 1.019278 CCACGGGGTTCGAATGACAG 61.019 60.000 0.00 0.0 42.43 3.51 R
3023 3116 3.625313 GCTCCCAGTAGCTCTTCAATTTC 59.375 47.826 0.00 0.0 39.50 2.17 R
3991 4141 0.600255 CCAGGACCACGTGTGAAGAC 60.600 60.000 15.65 0.0 0.00 3.01 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
612 633 0.250338 GTGGGCAAAGTCGAGGAAGT 60.250 55.000 0.00 0.00 0.00 3.01
630 651 6.262207 AGGAAGTGTATTACCAAGACCTACT 58.738 40.000 0.00 0.00 0.00 2.57
645 674 3.490348 ACCTACTGCAAATGCTTTCTGT 58.510 40.909 6.97 1.43 42.66 3.41
646 675 3.254166 ACCTACTGCAAATGCTTTCTGTG 59.746 43.478 6.97 0.00 42.66 3.66
672 701 2.689983 AGTTTGCTGGAACTTGTGGAAG 59.310 45.455 0.00 0.00 36.49 3.46
810 840 8.391106 CAACATTTATTTGAGTAGTAGAGTGCC 58.609 37.037 0.00 0.00 0.00 5.01
820 850 2.609747 AGTAGAGTGCCTGAGTTGGAA 58.390 47.619 0.00 0.00 0.00 3.53
821 851 2.300437 AGTAGAGTGCCTGAGTTGGAAC 59.700 50.000 0.00 0.00 35.86 3.62
843 873 0.107643 TGAGTTCGATGTGCCAACCA 59.892 50.000 0.00 0.00 0.00 3.67
957 987 5.240891 TGACTTGCCTTGTAGATTCTCTTG 58.759 41.667 0.00 0.00 0.00 3.02
979 1009 8.786898 TCTTGTATCTGATTTTTCAGTTTCAGG 58.213 33.333 0.00 1.21 38.75 3.86
981 1011 4.853924 TCTGATTTTTCAGTTTCAGGGC 57.146 40.909 3.15 0.00 38.75 5.19
1040 1070 1.672356 CGCCTCCTGTTGTTGAGGG 60.672 63.158 7.60 0.00 46.79 4.30
1052 1084 6.092122 CCTGTTGTTGAGGGAAAAAGAAAAAC 59.908 38.462 0.00 0.00 0.00 2.43
1053 1085 6.764379 TGTTGTTGAGGGAAAAAGAAAAACT 58.236 32.000 0.00 0.00 0.00 2.66
1054 1086 6.871492 TGTTGTTGAGGGAAAAAGAAAAACTC 59.129 34.615 0.00 0.00 0.00 3.01
1128 1171 3.386402 CCCCTCCTGAGATTCAGTTCTAC 59.614 52.174 5.46 0.00 42.80 2.59
1147 1190 3.470645 ACATAGATCGGGCAAGTAACC 57.529 47.619 0.00 0.00 0.00 2.85
1163 1206 2.103339 AACCCACGTGGACCTAACCG 62.103 60.000 36.07 18.20 37.39 4.44
1201 1244 1.152839 CCCTCTCGTCTCTCCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
1395 1438 2.960170 CAGGCAGGAAACAGCAGC 59.040 61.111 0.00 0.00 46.07 5.25
1540 1583 2.159226 ACTGCCTCCTTTTCGTAGATCG 60.159 50.000 0.00 0.00 41.41 3.69
1994 2087 3.760684 CAGAGGCCAAGTTTTAATCTGCT 59.239 43.478 5.01 0.00 0.00 4.24
2083 2176 2.386661 AATGCCAAGTAGAGTGGACG 57.613 50.000 0.00 0.00 38.54 4.79
2439 2532 3.639538 TCTCGCTCAGTTGTACTTGTTC 58.360 45.455 0.00 0.00 0.00 3.18
2451 2544 5.900339 TGTACTTGTTCTGTCATTCGAAC 57.100 39.130 0.00 0.00 39.85 3.95
2552 2645 7.224297 ACATGCGAACTACCCATTATAAATCT 58.776 34.615 0.00 0.00 0.00 2.40
2575 2668 4.406456 TGCACTGGTTTTATCATTGGAGT 58.594 39.130 0.00 0.00 0.00 3.85
2829 2922 1.613437 ACTTGGGTTGCTTGAATTCGG 59.387 47.619 0.04 0.00 0.00 4.30
2851 2944 5.121768 CGGACCAAAGTTCTGTTATGTAAGG 59.878 44.000 0.00 0.00 0.00 2.69
2940 3033 5.116882 GCTGACCTATTGTAGTAACCCAAG 58.883 45.833 0.00 0.00 0.00 3.61
3124 3217 9.177608 CCAAGAATATGGAGTGATGAAGTTAAA 57.822 33.333 0.00 0.00 43.54 1.52
3330 3423 5.338789 GGGAGGTTAGAAGAAGCAAGAAGAT 60.339 44.000 0.00 0.00 0.00 2.40
3449 3542 6.721321 AGTTTAAACACGTCGTTCAATTGAT 58.279 32.000 20.06 0.00 36.59 2.57
3450 3543 7.853524 AGTTTAAACACGTCGTTCAATTGATA 58.146 30.769 20.06 0.00 36.59 2.15
3578 3671 5.393027 GGATGTGTGTATTCGATTGCCTTTT 60.393 40.000 0.00 0.00 0.00 2.27
3627 3720 5.413309 TTGGATTTTGTTCAAGTGGTGTT 57.587 34.783 0.00 0.00 0.00 3.32
3700 3793 4.571919 TGCACCTGTTACATACTACAACC 58.428 43.478 0.00 0.00 0.00 3.77
3840 3990 3.722147 TCAGAGTGCTCTTTTCAGACAC 58.278 45.455 0.00 0.00 37.98 3.67
3841 3991 3.132824 TCAGAGTGCTCTTTTCAGACACA 59.867 43.478 0.00 0.00 37.98 3.72
3991 4141 7.589587 TGTTTACAGTTAGAATGCAACAATTCG 59.410 33.333 0.00 0.00 40.75 3.34
4059 4209 0.248661 AGTAGTGCAGCGTGCTATCG 60.249 55.000 10.54 0.00 45.31 2.92
4072 4222 2.431454 TGCTATCGTTTGCACAATCCA 58.569 42.857 0.00 0.00 33.94 3.41
4194 4344 2.340337 GTGCTGCATGTCCATTTTTCC 58.660 47.619 5.27 0.00 0.00 3.13
4284 4434 6.742109 TCGAGTTACTTGTAACAGTTTAGCT 58.258 36.000 21.10 0.00 32.63 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 196 3.514706 CAGTCTATCCCAGAGATGGATGG 59.485 52.174 2.10 0.00 43.56 3.51
451 452 4.530161 AGGTAGCAAACTGAAGTCTGATCT 59.470 41.667 0.00 0.00 0.00 2.75
612 633 5.748670 TTGCAGTAGGTCTTGGTAATACA 57.251 39.130 0.00 0.00 0.00 2.29
630 651 2.309613 AGGACACAGAAAGCATTTGCA 58.690 42.857 5.20 0.00 39.27 4.08
645 674 3.118038 ACAAGTTCCAGCAAACTAGGACA 60.118 43.478 0.00 0.00 38.52 4.02
646 675 3.251004 CACAAGTTCCAGCAAACTAGGAC 59.749 47.826 0.00 0.00 38.52 3.85
672 701 2.355010 ATACCCTGCCATTTCTCTGC 57.645 50.000 0.00 0.00 0.00 4.26
810 840 2.135933 GAACTCACCGTTCCAACTCAG 58.864 52.381 0.00 0.00 45.00 3.35
820 850 1.374252 GGCACATCGAACTCACCGT 60.374 57.895 0.00 0.00 0.00 4.83
821 851 0.948623 TTGGCACATCGAACTCACCG 60.949 55.000 0.00 0.00 39.30 4.94
957 987 6.151817 AGCCCTGAAACTGAAAAATCAGATAC 59.848 38.462 12.46 4.12 41.38 2.24
979 1009 4.568152 TTCAGCTCAGTAACAAAAAGCC 57.432 40.909 0.00 0.00 33.43 4.35
981 1011 8.633075 TTTTCATTCAGCTCAGTAACAAAAAG 57.367 30.769 0.00 0.00 0.00 2.27
1040 1070 7.650104 TCTCTCTCTCTCGAGTTTTTCTTTTTC 59.350 37.037 13.13 0.00 38.45 2.29
1052 1084 0.179084 AGCGGTCTCTCTCTCTCGAG 60.179 60.000 5.93 5.93 38.67 4.04
1053 1085 0.461163 CAGCGGTCTCTCTCTCTCGA 60.461 60.000 0.00 0.00 0.00 4.04
1054 1086 0.742990 ACAGCGGTCTCTCTCTCTCG 60.743 60.000 0.00 0.00 0.00 4.04
1067 1110 2.047844 CACCACAGAGGACAGCGG 60.048 66.667 0.00 0.00 41.22 5.52
1128 1171 2.767505 GGGTTACTTGCCCGATCTATG 58.232 52.381 0.00 0.00 36.30 2.23
1147 1190 1.080298 GACGGTTAGGTCCACGTGG 60.080 63.158 29.26 29.26 39.95 4.94
1540 1583 2.537328 GCTCTTCTAGCGACGACAGTAC 60.537 54.545 0.00 0.00 42.53 2.73
1721 1814 5.733620 ATTTGTCTCTAACGTACTTGGGA 57.266 39.130 0.00 0.00 0.00 4.37
2078 2171 2.029964 GACCTCGGTTTGCGTCCA 59.970 61.111 0.00 0.00 0.00 4.02
2083 2176 4.695217 TGATAAAATGACCTCGGTTTGC 57.305 40.909 0.00 0.00 0.00 3.68
2439 2532 1.019278 CCACGGGGTTCGAATGACAG 61.019 60.000 0.00 0.00 42.43 3.51
2451 2544 3.995506 GATGGCAAGTCCCACGGGG 62.996 68.421 0.00 0.00 46.11 5.73
2463 2556 5.085219 TGGCATATCCATAAATTGATGGCA 58.915 37.500 16.34 7.55 45.31 4.92
2464 2557 5.664294 TGGCATATCCATAAATTGATGGC 57.336 39.130 16.34 4.89 45.31 4.40
2552 2645 4.832266 ACTCCAATGATAAAACCAGTGCAA 59.168 37.500 0.00 0.00 0.00 4.08
2829 2922 7.506328 AACCTTACATAACAGAACTTTGGTC 57.494 36.000 0.00 0.00 0.00 4.02
2851 2944 7.095649 GCATGAAAAATTGTAAGAGTGGGAAAC 60.096 37.037 0.00 0.00 0.00 2.78
2940 3033 3.950395 AGGATTGGCAATAGCTTCAGTTC 59.050 43.478 13.65 0.00 41.70 3.01
3023 3116 3.625313 GCTCCCAGTAGCTCTTCAATTTC 59.375 47.826 0.00 0.00 39.50 2.17
3124 3217 8.501580 CGTGCATAAATCAGATCAGAATAACAT 58.498 33.333 0.00 0.00 0.00 2.71
3129 3222 6.051074 TGACGTGCATAAATCAGATCAGAAT 58.949 36.000 0.00 0.00 0.00 2.40
3176 3269 5.099042 TGTACCTCTATTTTCCTCCTTGC 57.901 43.478 0.00 0.00 0.00 4.01
3330 3423 2.103373 GTCTGACCTGCTCATGACCTA 58.897 52.381 0.00 0.00 0.00 3.08
3450 3543 9.492973 AATGCAACTGTTTAAAGCAGATTAATT 57.507 25.926 18.56 12.03 38.75 1.40
3505 3598 4.646945 TGAGTTGCCAAATTAACAACCTCA 59.353 37.500 12.14 11.85 43.68 3.86
3578 3671 3.243569 CGGGTACAAGGTTCAATTGCAAA 60.244 43.478 1.71 0.00 0.00 3.68
3598 3691 5.685511 CACTTGAACAAAATCCAAACTACGG 59.314 40.000 0.00 0.00 0.00 4.02
3739 3889 9.788960 GTATAGGAACTTTCATGGAATTCAAAC 57.211 33.333 7.93 0.00 41.75 2.93
3840 3990 5.237996 ACAGAAATCACAATCACAGACACTG 59.762 40.000 0.00 0.00 37.52 3.66
3841 3991 5.237996 CACAGAAATCACAATCACAGACACT 59.762 40.000 0.00 0.00 0.00 3.55
3991 4141 0.600255 CCAGGACCACGTGTGAAGAC 60.600 60.000 15.65 0.00 0.00 3.01
4059 4209 3.989817 GGATTTCAGTGGATTGTGCAAAC 59.010 43.478 0.00 0.00 0.00 2.93
4068 4218 4.446889 GCAGGGATTAGGATTTCAGTGGAT 60.447 45.833 0.00 0.00 0.00 3.41
4069 4219 3.117888 GCAGGGATTAGGATTTCAGTGGA 60.118 47.826 0.00 0.00 0.00 4.02
4070 4220 3.217626 GCAGGGATTAGGATTTCAGTGG 58.782 50.000 0.00 0.00 0.00 4.00
4071 4221 3.889815 TGCAGGGATTAGGATTTCAGTG 58.110 45.455 0.00 0.00 0.00 3.66
4072 4222 4.467769 CATGCAGGGATTAGGATTTCAGT 58.532 43.478 0.00 0.00 0.00 3.41
4215 4365 5.031578 GTGTGATTAGACTAGCTCAACTCG 58.968 45.833 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.