Multiple sequence alignment - TraesCS7A01G188500

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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 TraesCS7A01G188500 chr7A 100.000 4046 0 0 1 4046 144612233 144608188 0.000000e+00 7472.0
1 TraesCS7A01G188500 chr7D 97.137 3074 63 13 959 4016 142619227 142616163 0.000000e+00 5166.0
2 TraesCS7A01G188500 chr7D 90.000 70 3 3 3709 3777 98997903 98997837 2.000000e-13 87.9
3 TraesCS7A01G188500 chr7D 100.000 32 0 0 913 944 142619292 142619261 4.370000e-05 60.2
4 TraesCS7A01G188500 chr7B 96.718 2590 77 7 902 3489 106945078 106947661 0.000000e+00 4305.0
5 TraesCS7A01G188500 chr7B 90.788 901 62 6 1 883 645113628 645114525 0.000000e+00 1184.0
6 TraesCS7A01G188500 chr5D 95.383 888 37 3 1 887 124110632 124109748 0.000000e+00 1410.0
7 TraesCS7A01G188500 chr5D 91.597 833 57 9 1 821 175948588 175949419 0.000000e+00 1138.0
8 TraesCS7A01G188500 chr5D 91.304 69 2 3 3714 3781 51229488 51229553 1.550000e-14 91.6
9 TraesCS7A01G188500 chr5D 91.304 69 2 3 3714 3781 51305875 51305940 1.550000e-14 91.6
10 TraesCS7A01G188500 chr3A 91.170 906 62 13 1 891 700937364 700938266 0.000000e+00 1214.0
11 TraesCS7A01G188500 chr1B 91.358 81 5 2 3713 3793 529506318 529506396 4.280000e-20 110.0
12 TraesCS7A01G188500 chr1A 89.535 86 7 2 3708 3793 492198089 492198172 1.540000e-19 108.0
13 TraesCS7A01G188500 chr1D 89.873 79 6 2 3715 3793 393442175 393442099 2.570000e-17 100.0
14 TraesCS7A01G188500 chr4D 88.889 81 4 4 3703 3781 314659623 314659546 1.200000e-15 95.3
15 TraesCS7A01G188500 chr2B 89.474 76 5 3 3714 3788 35362554 35362627 4.310000e-15 93.5


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 TraesCS7A01G188500 chr7A 144608188 144612233 4045 True 7472.0 7472 100.0000 1 4046 1 chr7A.!!$R1 4045
1 TraesCS7A01G188500 chr7D 142616163 142619292 3129 True 2613.1 5166 98.5685 913 4016 2 chr7D.!!$R2 3103
2 TraesCS7A01G188500 chr7B 106945078 106947661 2583 False 4305.0 4305 96.7180 902 3489 1 chr7B.!!$F1 2587
3 TraesCS7A01G188500 chr7B 645113628 645114525 897 False 1184.0 1184 90.7880 1 883 1 chr7B.!!$F2 882
4 TraesCS7A01G188500 chr5D 124109748 124110632 884 True 1410.0 1410 95.3830 1 887 1 chr5D.!!$R1 886
5 TraesCS7A01G188500 chr5D 175948588 175949419 831 False 1138.0 1138 91.5970 1 821 1 chr5D.!!$F3 820
6 TraesCS7A01G188500 chr3A 700937364 700938266 902 False 1214.0 1214 91.1700 1 891 1 chr3A.!!$F1 890

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
965 999 2.132762 CAGTTGAACTCACCACGTACC 58.867 52.381 0.00 0.0 0.0 3.34 F
1378 1421 1.011968 CCTGTTCGACGAAATGCCGA 61.012 55.000 12.67 0.0 0.0 5.54 F
2261 2304 0.625849 CCTATGTTGCCCCTTGGAGT 59.374 55.000 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2242 0.671781 CTGAAGAGAAGGTGTGCCGG 60.672 60.0 0.0 0.0 40.50 6.13 R
2488 2531 1.173043 ATGTGTGTTGGCATAACCCG 58.827 50.0 0.0 0.0 37.83 5.28 R
3922 3981 0.038526 AGACAAAGCGGTGGTAGACG 60.039 55.0 0.0 0.0 0.00 4.18 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
348 368 7.333423 CCTACCAACAAGAATTCGAAATGACTA 59.667 37.037 0.00 0.00 0.00 2.59
361 381 6.936279 TCGAAATGACTAAAGAATCTCAGGT 58.064 36.000 0.00 0.00 0.00 4.00
419 439 3.240302 ACTTAAGTCTAGGGCGGCATAT 58.760 45.455 12.47 0.00 0.00 1.78
510 530 3.186613 CGGAGCTTGAAAACTTAGTCACC 59.813 47.826 0.00 0.00 0.00 4.02
604 626 3.685139 TCCGAAGCTCTCAGTTTCATT 57.315 42.857 0.00 0.00 35.51 2.57
633 655 5.818678 GTCCCCTACCAATATGTCACATA 57.181 43.478 0.00 0.00 0.00 2.29
746 768 9.066892 GGCTAGAAAATATGACCATGTTCATAA 57.933 33.333 15.88 1.80 40.92 1.90
821 843 9.461312 AAAAGCACTCATATAAAATGTCCACTA 57.539 29.630 0.00 0.00 0.00 2.74
826 848 9.476202 CACTCATATAAAATGTCCACTATCGAA 57.524 33.333 0.00 0.00 0.00 3.71
835 858 9.981114 AAAATGTCCACTATCGAAAATCTTTTT 57.019 25.926 0.00 0.00 0.00 1.94
863 886 5.989168 TCATATTTCGTATTCTCGTGGCAAT 59.011 36.000 0.00 0.00 0.00 3.56
884 907 2.629051 GCACGGGCATTTAACTAGTCT 58.371 47.619 3.77 0.00 40.72 3.24
885 908 3.788937 GCACGGGCATTTAACTAGTCTA 58.211 45.455 3.77 0.00 40.72 2.59
888 911 5.987347 GCACGGGCATTTAACTAGTCTATAA 59.013 40.000 3.77 0.00 40.72 0.98
889 912 6.649557 GCACGGGCATTTAACTAGTCTATAAT 59.350 38.462 3.77 0.00 40.72 1.28
890 913 7.816031 GCACGGGCATTTAACTAGTCTATAATA 59.184 37.037 3.77 0.00 40.72 0.98
891 914 9.136952 CACGGGCATTTAACTAGTCTATAATAC 57.863 37.037 0.00 0.00 0.00 1.89
893 916 9.924650 CGGGCATTTAACTAGTCTATAATACTT 57.075 33.333 0.00 0.00 0.00 2.24
965 999 2.132762 CAGTTGAACTCACCACGTACC 58.867 52.381 0.00 0.00 0.00 3.34
1013 1056 1.413256 ATCCTGATGCGGAGATGGCA 61.413 55.000 0.00 0.00 45.71 4.92
1377 1420 1.419922 CCTGTTCGACGAAATGCCG 59.580 57.895 12.67 0.00 0.00 5.69
1378 1421 1.011968 CCTGTTCGACGAAATGCCGA 61.012 55.000 12.67 0.00 0.00 5.54
2261 2304 0.625849 CCTATGTTGCCCCTTGGAGT 59.374 55.000 0.00 0.00 0.00 3.85
2309 2352 2.159653 CGTTTCTGCCAGATACTGCAAC 60.160 50.000 12.48 4.56 0.00 4.17
2343 2386 5.992217 CCTTATAACAATGTACTCCAGAGGC 59.008 44.000 0.00 0.00 0.00 4.70
2488 2531 1.482593 TCGAAGAAATGAGGAGAGCCC 59.517 52.381 0.00 0.00 33.31 5.19
2634 2677 3.577649 GAGCACTACTCAGCACTTGTA 57.422 47.619 0.00 0.00 45.49 2.41
2802 2845 4.670765 AGGCATTATCCAAGATTGATCCC 58.329 43.478 0.00 0.00 0.00 3.85
2916 2959 0.675633 AAGGTGTTCACAAGCATGCC 59.324 50.000 15.66 0.00 0.00 4.40
3139 3182 7.703621 ACACATGTTTTCTGTCTTTGATTCTTG 59.296 33.333 0.00 0.00 0.00 3.02
3202 3246 7.201821 CCCTACCCAAATCAGCTATTTACAAAG 60.202 40.741 0.00 0.00 35.54 2.77
3386 3432 1.143620 GGCAGTTGCACAAGCCAAA 59.856 52.632 15.48 0.00 46.26 3.28
3464 3510 6.995686 TCTGGTACACATGTGTTTTGATACTT 59.004 34.615 34.66 9.97 41.83 2.24
3545 3602 4.189580 ACGTGTGCAAGGCCTGGT 62.190 61.111 5.69 0.00 0.00 4.00
3556 3613 0.329596 AGGCCTGGTTGAACAGATCC 59.670 55.000 3.11 0.00 40.97 3.36
3597 3654 7.665559 TCAAAGATTGGCACATAAGTTACTCTT 59.334 33.333 0.00 0.00 39.30 2.85
3602 3659 6.852420 TGGCACATAAGTTACTCTTCTAGT 57.148 37.500 0.00 0.00 42.62 2.57
3675 3732 8.844244 GCTTGATTACCTGTTTATGAATCATCT 58.156 33.333 0.00 0.00 36.64 2.90
3711 3768 3.054361 ACACTCGCTCCCCAAATTCTAAT 60.054 43.478 0.00 0.00 0.00 1.73
3713 3770 4.399303 CACTCGCTCCCCAAATTCTAATTT 59.601 41.667 0.00 0.00 39.07 1.82
3714 3771 5.016831 ACTCGCTCCCCAAATTCTAATTTT 58.983 37.500 0.00 0.00 36.52 1.82
3798 3856 7.606839 AGTTTTACAGATAGCCCTCAACTAAAC 59.393 37.037 0.00 0.00 0.00 2.01
3799 3857 6.614694 TTACAGATAGCCCTCAACTAAACA 57.385 37.500 0.00 0.00 0.00 2.83
3813 3872 8.076178 CCTCAACTAAACAGTATTTGACTTTGG 58.924 37.037 0.00 0.00 35.64 3.28
3815 3874 8.962679 TCAACTAAACAGTATTTGACTTTGGTT 58.037 29.630 0.00 0.00 35.64 3.67
3839 3898 9.268268 GTTAAAATCCCATATTGTAGATCGTCA 57.732 33.333 0.00 0.00 0.00 4.35
3841 3900 6.672266 AATCCCATATTGTAGATCGTCACT 57.328 37.500 0.00 0.00 0.00 3.41
3869 3928 9.624697 GTAATTTCAACATGCTATTCTGAAACA 57.375 29.630 0.00 0.00 38.45 2.83
3870 3929 8.752766 AATTTCAACATGCTATTCTGAAACAG 57.247 30.769 0.00 0.00 38.45 3.16
3891 3950 3.499737 CATGCTTCCGTCGCACCC 61.500 66.667 0.00 0.00 40.65 4.61
3922 3981 5.295540 AGCTTTGATCTTTTCTTATCCGCTC 59.704 40.000 0.00 0.00 0.00 5.03
3984 4043 3.215151 TCTATCTTCTCTGGTGCTACGG 58.785 50.000 0.00 0.00 0.00 4.02
3985 4044 2.145397 ATCTTCTCTGGTGCTACGGA 57.855 50.000 0.00 0.00 0.00 4.69
3986 4045 1.919240 TCTTCTCTGGTGCTACGGAA 58.081 50.000 0.00 0.00 0.00 4.30
3987 4046 1.819288 TCTTCTCTGGTGCTACGGAAG 59.181 52.381 0.00 0.00 33.65 3.46
3988 4047 0.895530 TTCTCTGGTGCTACGGAAGG 59.104 55.000 0.00 0.00 0.00 3.46
3989 4048 0.039180 TCTCTGGTGCTACGGAAGGA 59.961 55.000 0.00 0.00 0.00 3.36
3994 4053 3.723554 GTGCTACGGAAGGACAGAG 57.276 57.895 6.78 0.00 45.40 3.35
4016 4075 4.003788 CACCTCGGTTGGGCGAGT 62.004 66.667 0.00 0.00 0.00 4.18
4017 4076 2.283388 ACCTCGGTTGGGCGAGTA 60.283 61.111 0.00 0.00 0.00 2.59
4018 4077 2.348888 ACCTCGGTTGGGCGAGTAG 61.349 63.158 0.00 0.00 0.00 2.57
4019 4078 2.348888 CCTCGGTTGGGCGAGTAGT 61.349 63.158 0.00 0.00 0.00 2.73
4020 4079 1.033746 CCTCGGTTGGGCGAGTAGTA 61.034 60.000 0.00 0.00 0.00 1.82
4021 4080 0.813184 CTCGGTTGGGCGAGTAGTAA 59.187 55.000 0.00 0.00 0.00 2.24
4022 4081 0.527565 TCGGTTGGGCGAGTAGTAAC 59.472 55.000 0.00 0.00 0.00 2.50
4023 4082 0.459063 CGGTTGGGCGAGTAGTAACC 60.459 60.000 0.00 0.00 37.90 2.85
4024 4083 0.459063 GGTTGGGCGAGTAGTAACCG 60.459 60.000 0.00 0.00 32.42 4.44
4025 4084 0.459063 GTTGGGCGAGTAGTAACCGG 60.459 60.000 0.00 0.00 0.00 5.28
4026 4085 0.611618 TTGGGCGAGTAGTAACCGGA 60.612 55.000 9.46 0.00 0.00 5.14
4027 4086 1.033746 TGGGCGAGTAGTAACCGGAG 61.034 60.000 9.46 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
301 321 6.067217 AGGTGGTATAGAATTTGCTCAGTT 57.933 37.500 0.00 0.00 0.00 3.16
302 322 5.700402 AGGTGGTATAGAATTTGCTCAGT 57.300 39.130 0.00 0.00 0.00 3.41
305 325 5.925509 TGGTAGGTGGTATAGAATTTGCTC 58.074 41.667 0.00 0.00 0.00 4.26
311 331 7.504926 TTCTTGTTGGTAGGTGGTATAGAAT 57.495 36.000 0.00 0.00 0.00 2.40
320 340 5.682943 TTTCGAATTCTTGTTGGTAGGTG 57.317 39.130 0.00 0.00 0.00 4.00
419 439 4.567747 GGCTTGATCAAAGAAGAACCCCTA 60.568 45.833 9.88 0.00 38.24 3.53
543 565 4.521146 CCATCAGCTCTCACTTATTGGTT 58.479 43.478 0.00 0.00 0.00 3.67
835 858 6.584942 GCCACGAGAATACGAAATATGATGTA 59.415 38.462 0.00 0.00 37.03 2.29
888 911 7.040409 GGTCAGACCAAAACATTCTCAAAGTAT 60.040 37.037 15.43 0.00 38.42 2.12
889 912 6.262273 GGTCAGACCAAAACATTCTCAAAGTA 59.738 38.462 15.43 0.00 38.42 2.24
890 913 5.067805 GGTCAGACCAAAACATTCTCAAAGT 59.932 40.000 15.43 0.00 38.42 2.66
891 914 5.523369 GGTCAGACCAAAACATTCTCAAAG 58.477 41.667 15.43 0.00 38.42 2.77
1189 1232 0.031721 GAGTTCCAGGTCACGACGTT 59.968 55.000 0.00 0.00 0.00 3.99
2199 2242 0.671781 CTGAAGAGAAGGTGTGCCGG 60.672 60.000 0.00 0.00 40.50 6.13
2261 2304 4.041567 TCTCAATAAGTTGGTGGAGCTGAA 59.958 41.667 0.00 0.00 35.99 3.02
2309 2352 6.639632 ACATTGTTATAAGGGCATTGCTAG 57.360 37.500 8.82 0.00 0.00 3.42
2343 2386 1.648720 CGCATCAGTTATTGCCCCG 59.351 57.895 0.00 0.00 35.41 5.73
2488 2531 1.173043 ATGTGTGTTGGCATAACCCG 58.827 50.000 0.00 0.00 37.83 5.28
2634 2677 6.479972 TTACCATGTCGACCTATGAGATTT 57.520 37.500 14.12 0.00 0.00 2.17
2802 2845 3.724508 ACATATGGAGCAGAACTCTCG 57.275 47.619 7.80 0.00 45.48 4.04
2916 2959 2.332063 AATCAATCCAGCTGTACCCG 57.668 50.000 13.81 0.00 0.00 5.28
2976 3019 8.940012 AATATATCTCCTGGATAAAGGGATGT 57.060 34.615 0.00 0.00 39.94 3.06
3092 3135 7.539436 TGTGTTTGTTTCTACACTGCAAAATA 58.461 30.769 0.00 0.00 43.82 1.40
3139 3182 9.102757 ACATGAATGAGATATGTACAAGTCAAC 57.897 33.333 0.00 1.16 33.57 3.18
3386 3432 2.750814 CCTGGCTTATCCCCATGTTTT 58.249 47.619 0.00 0.00 0.00 2.43
3545 3602 2.174639 ACCTGTTGTGGGATCTGTTCAA 59.825 45.455 0.00 0.00 0.00 2.69
3556 3613 2.361757 TCTTTGAATGCACCTGTTGTGG 59.638 45.455 0.00 0.00 45.55 4.17
3567 3624 5.413499 ACTTATGTGCCAATCTTTGAATGC 58.587 37.500 0.00 0.00 0.00 3.56
3597 3654 9.851686 AGGCATAAACAAAATGATGATACTAGA 57.148 29.630 0.00 0.00 0.00 2.43
3675 3732 2.423892 GCGAGTGTTATGTCAGAGGAGA 59.576 50.000 0.00 0.00 0.00 3.71
3677 3734 2.423892 GAGCGAGTGTTATGTCAGAGGA 59.576 50.000 0.00 0.00 0.00 3.71
3721 3778 4.552572 GCAAATCTTTTGCCTCCGTTTTTG 60.553 41.667 12.74 0.00 39.38 2.44
3722 3779 3.559655 GCAAATCTTTTGCCTCCGTTTTT 59.440 39.130 12.74 0.00 39.38 1.94
3723 3780 3.130633 GCAAATCTTTTGCCTCCGTTTT 58.869 40.909 12.74 0.00 39.38 2.43
3761 3819 9.863845 GGCTATCTGTAAAACTCTATTATCTCC 57.136 37.037 0.00 0.00 0.00 3.71
3766 3824 8.777578 TGAGGGCTATCTGTAAAACTCTATTA 57.222 34.615 0.00 0.00 0.00 0.98
3798 3856 8.364142 TGGGATTTTAACCAAAGTCAAATACTG 58.636 33.333 0.00 0.00 38.88 2.74
3799 3857 8.485578 TGGGATTTTAACCAAAGTCAAATACT 57.514 30.769 0.00 0.00 41.49 2.12
3813 3872 9.268268 TGACGATCTACAATATGGGATTTTAAC 57.732 33.333 0.00 0.00 0.00 2.01
3815 3874 8.647796 AGTGACGATCTACAATATGGGATTTTA 58.352 33.333 0.00 0.00 0.00 1.52
3839 3898 9.013229 TCAGAATAGCATGTTGAAATTACAAGT 57.987 29.630 0.00 0.00 0.00 3.16
3869 3928 1.153745 GCGACGGAAGCATGTCTCT 60.154 57.895 0.00 0.00 32.93 3.10
3870 3929 1.446099 TGCGACGGAAGCATGTCTC 60.446 57.895 0.00 0.00 40.01 3.36
3891 3950 0.883833 AAAGATCAAAGCTGGCGTGG 59.116 50.000 0.00 0.00 0.00 4.94
3922 3981 0.038526 AGACAAAGCGGTGGTAGACG 60.039 55.000 0.00 0.00 0.00 4.18
3984 4043 1.446966 GGTGAGCGCTCTGTCCTTC 60.447 63.158 35.27 16.81 0.00 3.46
3985 4044 1.882989 GAGGTGAGCGCTCTGTCCTT 61.883 60.000 35.27 21.99 0.00 3.36
3986 4045 2.283532 AGGTGAGCGCTCTGTCCT 60.284 61.111 35.27 31.75 0.00 3.85
3987 4046 2.183046 GAGGTGAGCGCTCTGTCC 59.817 66.667 35.27 30.36 0.00 4.02
3988 4047 2.202544 CGAGGTGAGCGCTCTGTC 60.203 66.667 35.27 25.86 0.00 3.51
3989 4048 3.753434 CCGAGGTGAGCGCTCTGT 61.753 66.667 35.27 20.90 0.00 3.41
4016 4075 0.749454 GTCCTCGCCTCCGGTTACTA 60.749 60.000 0.00 0.00 34.56 1.82
4017 4076 2.050934 GTCCTCGCCTCCGGTTACT 61.051 63.158 0.00 0.00 34.56 2.24
4018 4077 2.493501 GTCCTCGCCTCCGGTTAC 59.506 66.667 0.00 0.00 34.56 2.50
4019 4078 2.757099 GGTCCTCGCCTCCGGTTA 60.757 66.667 0.00 0.00 34.56 2.85


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

AutoCloner maintained by Alex Coulton.