Multiple sequence alignment - TraesCS7D01G214900

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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 TraesCS7D01G214900 chr7D 100.000 4781 0 0 1 4781 174441169 174445949 0.000000e+00 8829.0
1 TraesCS7D01G214900 chr7D 100.000 36 0 0 3721 3756 174444855 174444890 3.090000e-07 67.6
2 TraesCS7D01G214900 chr7D 100.000 36 0 0 3687 3722 174444889 174444924 3.090000e-07 67.6
3 TraesCS7D01G214900 chr7A 93.305 3794 148 55 1 3722 176429304 176433063 0.000000e+00 5502.0
4 TraesCS7D01G214900 chr7A 98.025 709 12 2 3721 4429 176433028 176433734 0.000000e+00 1230.0
5 TraesCS7D01G214900 chr7A 98.017 353 7 0 4429 4781 176433766 176434118 8.790000e-172 614.0
6 TraesCS7D01G214900 chr7A 85.294 68 4 4 2871 2935 176432061 176432125 1.110000e-06 65.8
7 TraesCS7D01G214900 chr7B 93.335 3196 115 38 171 3306 138877372 138880529 0.000000e+00 4632.0
8 TraesCS7D01G214900 chr7B 98.449 709 10 1 3721 4429 138880883 138881590 0.000000e+00 1247.0
9 TraesCS7D01G214900 chr7B 98.982 393 3 1 3331 3722 138880526 138880918 0.000000e+00 702.0
10 TraesCS7D01G214900 chr7B 97.734 353 8 0 4429 4781 138881622 138881974 4.090000e-170 608.0
11 TraesCS7D01G214900 chr7B 86.364 66 7 2 2871 2935 138879944 138880008 2.390000e-08 71.3


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 TraesCS7D01G214900 chr7D 174441169 174445949 4780 False 2988.066667 8829 100.00000 1 4781 3 chr7D.!!$F1 4780
1 TraesCS7D01G214900 chr7A 176429304 176434118 4814 False 1852.950000 5502 93.66025 1 4781 4 chr7A.!!$F1 4780
2 TraesCS7D01G214900 chr7B 138877372 138881974 4602 False 1452.060000 4632 94.97280 171 4781 5 chr7B.!!$F1 4610

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
111 112 0.599558 AAGCATGTGCACAATTCGCT 59.400 45.0 25.72 24.0 45.16 4.93 F
1751 1838 0.400213 TTTGGTCAGTCCCTGCGATT 59.600 50.0 0.00 0.0 34.77 3.34 F
1753 1840 0.535335 TGGTCAGTCCCTGCGATTAC 59.465 55.0 0.00 0.0 34.77 1.89 F
3667 3782 0.684805 CCGGTAGGAGCCTGAAGTCT 60.685 60.0 0.00 0.0 41.02 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1901 0.46362 GCCTCAGTTTTGGGTTGCAA 59.536 50.000 0.00 0.0 0.00 4.08 R
3346 3460 1.00358 CTGCCTAAAAGGAGAGGTGCA 59.996 52.381 0.00 0.0 37.67 4.57 R
3725 3840 4.34095 CCTTCAAAGGCCAAAACTAACTGA 59.659 41.667 5.01 0.0 39.76 3.41 R
4577 4724 2.11467 GCCGACATGGGTGTGGATG 61.115 63.158 0.00 0.0 39.09 3.51 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
59 60 1.519408 AACGGTTAAGCGCATTCAGT 58.481 45.000 25.71 2.57 0.00 3.41
89 90 2.545952 CGGAGCCTACAAAGATACGCAT 60.546 50.000 0.00 0.00 0.00 4.73
92 93 4.022242 GGAGCCTACAAAGATACGCATCTA 60.022 45.833 0.00 0.00 40.81 1.98
96 97 5.289595 CCTACAAAGATACGCATCTAAGCA 58.710 41.667 0.00 0.00 40.81 3.91
98 99 5.663795 ACAAAGATACGCATCTAAGCATG 57.336 39.130 0.00 0.00 40.81 4.06
106 107 2.223409 CGCATCTAAGCATGTGCACAAT 60.223 45.455 25.72 12.87 45.16 2.71
109 110 3.745332 TCTAAGCATGTGCACAATTCG 57.255 42.857 25.72 14.48 45.16 3.34
111 112 0.599558 AAGCATGTGCACAATTCGCT 59.400 45.000 25.72 24.00 45.16 4.93
137 138 3.647771 GGCCCCACCGAAGTTCCT 61.648 66.667 0.00 0.00 0.00 3.36
160 162 6.347160 CCTGTATTATATTCACGACGAGACGA 60.347 42.308 0.00 0.00 37.03 4.20
314 319 2.547218 GCGAGAGAGAGATAGAGACGGT 60.547 54.545 0.00 0.00 0.00 4.83
371 381 2.495939 CGAAAAAGATGCACAGTACGC 58.504 47.619 0.00 0.00 0.00 4.42
509 529 3.646715 CCCTCTCCCAAACCCGCA 61.647 66.667 0.00 0.00 0.00 5.69
549 587 1.258445 GCACGGGAAGAGGAGGAGAA 61.258 60.000 0.00 0.00 0.00 2.87
904 962 4.154347 CGTGGCAGGAGGAGGAGC 62.154 72.222 0.00 0.00 0.00 4.70
905 963 4.154347 GTGGCAGGAGGAGGAGCG 62.154 72.222 0.00 0.00 0.00 5.03
1368 1444 5.294306 CCACTACAAGTATGTATGGCAACTG 59.706 44.000 0.00 0.00 41.09 3.16
1378 1454 1.035932 ATGGCAACTGCAGCTCCATC 61.036 55.000 22.11 7.14 44.36 3.51
1382 1458 1.077930 AACTGCAGCTCCATCGCAT 60.078 52.632 15.27 0.00 34.63 4.73
1413 1489 4.414852 CCGTTTTCATTTCATAGCTGTGG 58.585 43.478 10.87 0.00 0.00 4.17
1751 1838 0.400213 TTTGGTCAGTCCCTGCGATT 59.600 50.000 0.00 0.00 34.77 3.34
1752 1839 1.271856 TTGGTCAGTCCCTGCGATTA 58.728 50.000 0.00 0.00 34.77 1.75
1753 1840 0.535335 TGGTCAGTCCCTGCGATTAC 59.465 55.000 0.00 0.00 34.77 1.89
1754 1841 0.824759 GGTCAGTCCCTGCGATTACT 59.175 55.000 0.00 0.00 0.00 2.24
1778 1865 7.739444 ACTACTTGATTTGGGGATCCATAGATA 59.261 37.037 15.23 0.00 43.63 1.98
1806 1900 1.856265 CTGGGTTTCGCTCCAACTGC 61.856 60.000 0.00 0.00 31.97 4.40
1807 1901 1.600916 GGGTTTCGCTCCAACTGCT 60.601 57.895 0.00 0.00 0.00 4.24
2059 2153 9.107177 CATTTGACTCTGATAAACTGAGCTATT 57.893 33.333 0.00 0.00 44.70 1.73
2067 2161 9.920133 TCTGATAAACTGAGCTATTATCATGAC 57.080 33.333 17.22 0.00 42.18 3.06
2193 2287 2.866762 GAGTACATGAGCAACGGGAATC 59.133 50.000 0.00 0.00 0.00 2.52
2337 2436 7.013834 TGGGAAGGGAATAAACTAAATGTTGT 58.986 34.615 0.00 0.00 39.13 3.32
2338 2437 7.177744 TGGGAAGGGAATAAACTAAATGTTGTC 59.822 37.037 0.00 0.00 39.13 3.18
2477 2590 1.072266 ACCTGCATGAAGGGGTACAA 58.928 50.000 24.44 0.00 42.11 2.41
2805 2918 3.060736 TGCCGATGGTTTAGCTAAACA 57.939 42.857 37.31 27.29 45.50 2.83
2973 3086 6.751888 GGAAGACGCATGCAACTAAAATAAAT 59.248 34.615 19.57 0.00 0.00 1.40
3047 3161 4.461081 TGCTCTGTTTGTTTTACTTGGTGT 59.539 37.500 0.00 0.00 0.00 4.16
3188 3302 6.619801 AAGAAGAGCGATGTTTACAGTTTT 57.380 33.333 0.00 0.00 0.00 2.43
3310 3424 5.825593 TTCTGACAAGATTTCAGTAGGGT 57.174 39.130 0.00 0.00 41.22 4.34
3346 3460 5.656859 TGTAGTACCAGTCAGTGAGCATTAT 59.343 40.000 0.00 0.00 0.00 1.28
3667 3782 0.684805 CCGGTAGGAGCCTGAAGTCT 60.685 60.000 0.00 0.00 41.02 3.24
3708 3823 6.267471 TGAAATCATCAGTTAGTTTTGGCCTT 59.733 34.615 3.32 0.00 33.04 4.35
3709 3824 6.670695 AATCATCAGTTAGTTTTGGCCTTT 57.329 33.333 3.32 0.00 0.00 3.11
3710 3825 5.452078 TCATCAGTTAGTTTTGGCCTTTG 57.548 39.130 3.32 0.00 0.00 2.77
3711 3826 5.136828 TCATCAGTTAGTTTTGGCCTTTGA 58.863 37.500 3.32 0.00 0.00 2.69
3712 3827 5.596361 TCATCAGTTAGTTTTGGCCTTTGAA 59.404 36.000 3.32 0.00 0.00 2.69
3713 3828 5.514274 TCAGTTAGTTTTGGCCTTTGAAG 57.486 39.130 3.32 0.00 0.00 3.02
3728 3843 6.674694 CCTTTGAAGGTGTCTAATCATCAG 57.325 41.667 1.49 0.00 41.41 2.90
3729 3844 6.176183 CCTTTGAAGGTGTCTAATCATCAGT 58.824 40.000 1.49 0.00 41.41 3.41
3730 3845 6.656693 CCTTTGAAGGTGTCTAATCATCAGTT 59.343 38.462 1.49 0.00 41.41 3.16
3731 3846 7.824289 CCTTTGAAGGTGTCTAATCATCAGTTA 59.176 37.037 1.49 0.00 41.41 2.24
3732 3847 8.777865 TTTGAAGGTGTCTAATCATCAGTTAG 57.222 34.615 0.00 0.00 0.00 2.34
3733 3848 7.482169 TGAAGGTGTCTAATCATCAGTTAGT 57.518 36.000 0.00 0.00 32.35 2.24
3734 3849 7.907389 TGAAGGTGTCTAATCATCAGTTAGTT 58.093 34.615 0.00 0.00 32.35 2.24
3735 3850 8.375506 TGAAGGTGTCTAATCATCAGTTAGTTT 58.624 33.333 0.00 0.00 32.35 2.66
3736 3851 9.220767 GAAGGTGTCTAATCATCAGTTAGTTTT 57.779 33.333 0.00 0.00 32.35 2.43
3737 3852 8.553459 AGGTGTCTAATCATCAGTTAGTTTTG 57.447 34.615 0.00 0.00 32.35 2.44
3738 3853 7.607991 AGGTGTCTAATCATCAGTTAGTTTTGG 59.392 37.037 0.00 0.00 32.35 3.28
3739 3854 7.244192 GTGTCTAATCATCAGTTAGTTTTGGC 58.756 38.462 0.00 0.00 32.35 4.52
3740 3855 6.374333 TGTCTAATCATCAGTTAGTTTTGGCC 59.626 38.462 0.00 0.00 32.35 5.36
3741 3856 6.599638 GTCTAATCATCAGTTAGTTTTGGCCT 59.400 38.462 3.32 0.00 32.35 5.19
3784 3899 7.947890 TGGGTTGGAATAGATGTAAATAATCCC 59.052 37.037 0.00 0.00 0.00 3.85
3891 4006 4.569719 AAGTGTAAATCGATGAAGGGGT 57.430 40.909 0.00 0.00 0.00 4.95
3892 4007 4.569719 AGTGTAAATCGATGAAGGGGTT 57.430 40.909 0.00 0.00 0.00 4.11
3960 4075 8.845227 TGAACTAGACAATAAATTTCACAGCAA 58.155 29.630 0.00 0.00 0.00 3.91
4377 4492 1.016627 GCAGGCATATTCAACGCTCA 58.983 50.000 0.00 0.00 0.00 4.26
4577 4724 2.037847 AAGGAACAGGCCCCATGC 59.962 61.111 0.00 0.00 40.16 4.06
4596 4743 2.601702 ATCCACACCCATGTCGGCA 61.602 57.895 0.00 0.00 36.72 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.479603 CGCTTAACCGTTAACTAGGAATTTTTC 59.520 37.037 3.71 0.00 0.00 2.29
31 32 3.253230 GCGCTTAACCGTTAACTAGGAA 58.747 45.455 0.00 0.00 0.00 3.36
36 37 3.068560 TGAATGCGCTTAACCGTTAACT 58.931 40.909 9.73 0.00 0.00 2.24
59 60 0.540133 TGTAGGCTCCGGTGTGTACA 60.540 55.000 0.00 8.55 0.00 2.90
89 90 2.159531 GCGAATTGTGCACATGCTTAGA 60.160 45.455 22.39 3.59 42.66 2.10
92 93 0.599558 AGCGAATTGTGCACATGCTT 59.400 45.000 22.39 14.46 42.66 3.91
96 97 1.198408 CTGTCAGCGAATTGTGCACAT 59.802 47.619 22.39 6.49 33.85 3.21
98 99 0.110056 CCTGTCAGCGAATTGTGCAC 60.110 55.000 10.75 10.75 33.85 4.57
125 126 7.096189 CGTGAATATAATACAGGAACTTCGGTG 60.096 40.741 0.00 0.00 34.60 4.94
126 127 6.921857 CGTGAATATAATACAGGAACTTCGGT 59.078 38.462 0.00 0.00 34.60 4.69
132 133 7.323177 GTCTCGTCGTGAATATAATACAGGAAC 59.677 40.741 0.00 0.00 31.94 3.62
133 134 7.358066 GTCTCGTCGTGAATATAATACAGGAA 58.642 38.462 0.00 0.00 31.94 3.36
137 138 6.529463 TCGTCTCGTCGTGAATATAATACA 57.471 37.500 0.00 0.00 0.00 2.29
271 276 4.671250 GCTCGCTTCCTCTTTGATCTTTTG 60.671 45.833 0.00 0.00 0.00 2.44
371 381 5.807520 ACTGAGAGTAATTAATGTCTGCGTG 59.192 40.000 14.15 3.04 0.00 5.34
509 529 3.660111 GGCTGTTGCTTTCGCCGT 61.660 61.111 0.00 0.00 39.59 5.68
555 593 4.847585 CGACGACGACGCGAGAGG 62.848 72.222 15.93 6.49 43.96 3.69
784 842 4.360405 GCGCCAGGGGGAAGGAAA 62.360 66.667 5.50 0.00 35.59 3.13
846 904 3.420943 GGAATCAATCCCGCACCG 58.579 61.111 0.00 0.00 43.00 4.94
984 1060 4.796495 ATTCCCGCCGTGCCTTCC 62.796 66.667 0.00 0.00 0.00 3.46
1005 1081 1.299165 CACGACCTTCGCCCTATCG 60.299 63.158 0.00 0.00 45.12 2.92
1368 1444 1.505477 GAGGAATGCGATGGAGCTGC 61.505 60.000 0.00 0.00 38.13 5.25
1413 1489 5.028549 TGATAGCTTCTGGAACTGGAATC 57.971 43.478 0.00 0.00 0.00 2.52
1745 1832 4.080807 TCCCCAAATCAAGTAGTAATCGCA 60.081 41.667 0.00 0.00 0.00 5.10
1778 1865 1.032114 GCGAAACCCAGCTGGCTATT 61.032 55.000 28.39 19.99 37.83 1.73
1806 1900 1.538849 GCCTCAGTTTTGGGTTGCAAG 60.539 52.381 0.00 0.00 0.00 4.01
1807 1901 0.463620 GCCTCAGTTTTGGGTTGCAA 59.536 50.000 0.00 0.00 0.00 4.08
1870 1964 6.256321 GCACAACCAAAATTAAGATATGCCAG 59.744 38.462 0.00 0.00 0.00 4.85
2059 2153 4.332543 GCAAATGAAGACGTGGTCATGATA 59.667 41.667 10.49 0.00 34.70 2.15
2067 2161 1.238439 ACCTGCAAATGAAGACGTGG 58.762 50.000 0.00 0.00 0.00 4.94
2193 2287 3.340814 ACCATACAGAAGAGTTGCCAG 57.659 47.619 0.00 0.00 0.00 4.85
2315 2413 9.573133 CATGACAACATTTAGTTTATTCCCTTC 57.427 33.333 0.00 0.00 38.74 3.46
2317 2415 8.877864 TCATGACAACATTTAGTTTATTCCCT 57.122 30.769 0.00 0.00 38.74 4.20
2477 2590 5.583457 GGTACGTGTTTAATAGCCATCAACT 59.417 40.000 0.00 0.00 0.00 3.16
2777 2890 2.128771 AAACCATCGGCATTAGCACT 57.871 45.000 0.00 0.00 44.61 4.40
2778 2891 2.287009 GCTAAACCATCGGCATTAGCAC 60.287 50.000 18.85 0.20 44.09 4.40
2805 2918 7.392494 TGAACTCGTGATAGAGACAATACTT 57.608 36.000 0.62 0.00 40.57 2.24
2973 3086 7.560991 ACAATTTTCTGCCATGGAACTGATATA 59.439 33.333 18.40 0.00 0.00 0.86
3310 3424 7.737869 TGACTGGTACTACAAGGTAAATTTCA 58.262 34.615 0.00 0.00 0.00 2.69
3346 3460 1.003580 CTGCCTAAAAGGAGAGGTGCA 59.996 52.381 0.00 0.00 37.67 4.57
3708 3823 7.907389 ACTAACTGATGATTAGACACCTTCAA 58.093 34.615 0.00 0.00 34.36 2.69
3709 3824 7.482169 ACTAACTGATGATTAGACACCTTCA 57.518 36.000 0.00 0.00 34.36 3.02
3710 3825 8.779354 AAACTAACTGATGATTAGACACCTTC 57.221 34.615 0.00 0.00 34.36 3.46
3711 3826 9.003658 CAAAACTAACTGATGATTAGACACCTT 57.996 33.333 0.00 0.00 34.36 3.50
3712 3827 7.607991 CCAAAACTAACTGATGATTAGACACCT 59.392 37.037 0.00 0.00 34.36 4.00
3713 3828 7.626452 GCCAAAACTAACTGATGATTAGACACC 60.626 40.741 0.00 0.00 34.36 4.16
3714 3829 7.244192 GCCAAAACTAACTGATGATTAGACAC 58.756 38.462 0.00 0.00 34.36 3.67
3715 3830 6.374333 GGCCAAAACTAACTGATGATTAGACA 59.626 38.462 0.00 0.00 34.36 3.41
3716 3831 6.599638 AGGCCAAAACTAACTGATGATTAGAC 59.400 38.462 5.01 0.00 34.36 2.59
3717 3832 6.721318 AGGCCAAAACTAACTGATGATTAGA 58.279 36.000 5.01 0.00 34.36 2.10
3718 3833 7.396540 AAGGCCAAAACTAACTGATGATTAG 57.603 36.000 5.01 0.00 36.01 1.73
3719 3834 7.450014 TCAAAGGCCAAAACTAACTGATGATTA 59.550 33.333 5.01 0.00 0.00 1.75
3720 3835 6.267471 TCAAAGGCCAAAACTAACTGATGATT 59.733 34.615 5.01 0.00 0.00 2.57
3721 3836 5.774690 TCAAAGGCCAAAACTAACTGATGAT 59.225 36.000 5.01 0.00 0.00 2.45
3722 3837 5.136828 TCAAAGGCCAAAACTAACTGATGA 58.863 37.500 5.01 0.00 0.00 2.92
3723 3838 5.452078 TCAAAGGCCAAAACTAACTGATG 57.548 39.130 5.01 0.00 0.00 3.07
3724 3839 5.011023 CCTTCAAAGGCCAAAACTAACTGAT 59.989 40.000 5.01 0.00 39.76 2.90
3725 3840 4.340950 CCTTCAAAGGCCAAAACTAACTGA 59.659 41.667 5.01 0.00 39.76 3.41
3726 3841 4.620982 CCTTCAAAGGCCAAAACTAACTG 58.379 43.478 5.01 0.00 39.76 3.16
3727 3842 4.937201 CCTTCAAAGGCCAAAACTAACT 57.063 40.909 5.01 0.00 39.76 2.24
3739 3854 6.155666 AACCCAAGTTAGACACCTTCAAAGG 61.156 44.000 7.25 7.25 42.66 3.11
3740 3855 4.461198 ACCCAAGTTAGACACCTTCAAAG 58.539 43.478 0.00 0.00 0.00 2.77
3741 3856 4.513406 ACCCAAGTTAGACACCTTCAAA 57.487 40.909 0.00 0.00 0.00 2.69
3784 3899 1.275291 TCCTGCCAAACTCTACCTTCG 59.725 52.381 0.00 0.00 0.00 3.79
3891 4006 7.339212 ACATAAGGTCAGCATGCAGTTTAATAA 59.661 33.333 21.98 0.00 34.76 1.40
3892 4007 6.828273 ACATAAGGTCAGCATGCAGTTTAATA 59.172 34.615 21.98 5.03 34.76 0.98
3960 4075 5.265191 TCTTCTGTCTCTGCTAGGTTATGT 58.735 41.667 0.00 0.00 0.00 2.29
4304 4419 8.617290 TTTCCTGTACATAGTTTTCCTTCTTC 57.383 34.615 0.00 0.00 0.00 2.87
4377 4492 5.206905 AGCCATCCTTTACAATAGGGTTT 57.793 39.130 0.00 0.00 33.41 3.27
4417 4532 4.706842 AGTCAGTTTGGTCAAGGTATGT 57.293 40.909 0.00 0.00 0.00 2.29
4577 4724 2.114670 GCCGACATGGGTGTGGATG 61.115 63.158 0.00 0.00 39.09 3.51


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

AutoCloner maintained by Alex Coulton.