Multiple sequence alignment - TraesCS4B01G336900

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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 TraesCS4B01G336900 chr4B 100.000 3843 0 0 1 3843 629506242 629510084 0 7097
1 TraesCS4B01G336900 chr3B 96.025 3824 137 11 1 3817 646354833 646358648 0 6205
2 TraesCS4B01G336900 chr3B 95.686 3825 153 11 1 3820 656109231 656105414 0 6139
3 TraesCS4B01G336900 chr3B 93.188 3846 219 26 1 3817 664729687 664725856 0 5611
4 TraesCS4B01G336900 chr3B 93.557 1459 92 2 1 1458 420622505 420623962 0 2172
5 TraesCS4B01G336900 chr3B 91.888 678 51 4 1 674 300391203 300391880 0 944
6 TraesCS4B01G336900 chr1B 95.373 3825 159 13 1 3820 575067000 575063189 0 6067
7 TraesCS4B01G336900 chr1B 94.617 3790 165 17 39 3817 413055984 413059745 0 5832
8 TraesCS4B01G336900 chr1B 93.560 3851 210 26 1 3820 84522057 84518214 0 5703
9 TraesCS4B01G336900 chr5B 95.294 3825 169 10 1 3820 519961573 519957755 0 6056
10 TraesCS4B01G336900 chr6B 93.323 3849 213 30 1 3820 42180202 42176369 0 5644
11 TraesCS4B01G336900 chr2B 95.125 3467 151 14 360 3820 35778468 35775014 0 5450
12 TraesCS4B01G336900 chr3A 91.667 1368 108 5 1 1362 417397292 417398659 0 1890
13 TraesCS4B01G336900 chr3A 86.259 1259 138 19 1 1255 84712693 84713920 0 1334


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 TraesCS4B01G336900 chr4B 629506242 629510084 3842 False 7097 7097 100.000 1 3843 1 chr4B.!!$F1 3842
1 TraesCS4B01G336900 chr3B 646354833 646358648 3815 False 6205 6205 96.025 1 3817 1 chr3B.!!$F3 3816
2 TraesCS4B01G336900 chr3B 656105414 656109231 3817 True 6139 6139 95.686 1 3820 1 chr3B.!!$R1 3819
3 TraesCS4B01G336900 chr3B 664725856 664729687 3831 True 5611 5611 93.188 1 3817 1 chr3B.!!$R2 3816
4 TraesCS4B01G336900 chr3B 420622505 420623962 1457 False 2172 2172 93.557 1 1458 1 chr3B.!!$F2 1457
5 TraesCS4B01G336900 chr3B 300391203 300391880 677 False 944 944 91.888 1 674 1 chr3B.!!$F1 673
6 TraesCS4B01G336900 chr1B 575063189 575067000 3811 True 6067 6067 95.373 1 3820 1 chr1B.!!$R2 3819
7 TraesCS4B01G336900 chr1B 413055984 413059745 3761 False 5832 5832 94.617 39 3817 1 chr1B.!!$F1 3778
8 TraesCS4B01G336900 chr1B 84518214 84522057 3843 True 5703 5703 93.560 1 3820 1 chr1B.!!$R1 3819
9 TraesCS4B01G336900 chr5B 519957755 519961573 3818 True 6056 6056 95.294 1 3820 1 chr5B.!!$R1 3819
10 TraesCS4B01G336900 chr6B 42176369 42180202 3833 True 5644 5644 93.323 1 3820 1 chr6B.!!$R1 3819
11 TraesCS4B01G336900 chr2B 35775014 35778468 3454 True 5450 5450 95.125 360 3820 1 chr2B.!!$R1 3460
12 TraesCS4B01G336900 chr3A 417397292 417398659 1367 False 1890 1890 91.667 1 1362 1 chr3A.!!$F2 1361
13 TraesCS4B01G336900 chr3A 84712693 84713920 1227 False 1334 1334 86.259 1 1255 1 chr3A.!!$F1 1254

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
941 971 1.476085 CACCATTGCCGCTTCCATTTA 59.524 47.619 0.00 0.0 0.00 1.40 F
1082 1112 0.171007 GTCGACATTAACGTCCCCGA 59.829 55.000 11.55 0.0 37.88 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2628 2674 2.350522 TCTTCTTCTTCATGCCTTCGC 58.649 47.619 0.0 0.0 0.0 4.70 R
3007 3054 3.972502 GCAAACTTGTTGGACGACATAAC 59.027 43.478 0.0 0.0 0.0 1.89 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
338 344 4.319177 ACTAAAACAGCAGGATCAGTCAC 58.681 43.478 0.00 0.00 0.00 3.67
394 401 3.367292 CCCATGCGCTGTTTGAAATTACT 60.367 43.478 9.73 0.00 0.00 2.24
477 484 6.104390 AAAGGCCTAACTTTGGTTGGTACAA 61.104 40.000 5.16 0.00 40.75 2.41
689 714 2.427095 GTGGGATTTGGCAGGTCATAAC 59.573 50.000 4.04 0.00 0.00 1.89
941 971 1.476085 CACCATTGCCGCTTCCATTTA 59.524 47.619 0.00 0.00 0.00 1.40
1082 1112 0.171007 GTCGACATTAACGTCCCCGA 59.829 55.000 11.55 0.00 37.88 5.14
1152 1188 0.681564 AGGAGACGCTGGAGATCGTT 60.682 55.000 0.00 0.00 39.22 3.85
1221 1257 1.449778 GAAGGGAGGCGGCTTGTAC 60.450 63.158 14.76 0.00 0.00 2.90
1471 1508 8.288689 AGTGTGGTTTGTAGTGAAGTATTTTT 57.711 30.769 0.00 0.00 0.00 1.94
1528 1565 4.373156 AACTAAGGACTTGGTGAAGCAT 57.627 40.909 1.72 0.00 34.44 3.79
1541 1578 3.181476 GGTGAAGCATTGGTTCTGTGTTT 60.181 43.478 24.43 0.00 40.24 2.83
1844 1885 7.753309 AGTTACATGCATTTACCAAACTGTA 57.247 32.000 0.00 0.00 0.00 2.74
2167 2209 7.733969 AGAAGTGCATATATCATTGACTCTGT 58.266 34.615 0.00 0.00 0.00 3.41
2302 2345 5.583457 TCTGAACTACATTCATGCATGACTG 59.417 40.000 33.41 33.41 46.37 3.51
2303 2346 4.637091 TGAACTACATTCATGCATGACTGG 59.363 41.667 35.96 26.25 42.62 4.00
2604 2650 0.321653 GACTCCTTGGCCGATGTTGT 60.322 55.000 0.00 0.00 0.00 3.32
2608 2654 0.251916 CCTTGGCCGATGTTGTAGGA 59.748 55.000 0.00 0.00 0.00 2.94
2628 2674 1.097547 GGCGTCATCCACCCATTCTG 61.098 60.000 0.00 0.00 0.00 3.02
2730 2777 2.035961 ACGCAGGAATAGATGCATACGT 59.964 45.455 0.00 0.00 42.68 3.57
2880 2927 4.634012 TGTTGAACCAGCTACCTTATGT 57.366 40.909 0.00 0.00 0.00 2.29
2927 2974 7.542890 TGTTTCAGATTTGTAGTTTGCTTTCA 58.457 30.769 0.00 0.00 0.00 2.69
2983 3030 2.093764 CAGGGTTTGAACAAGTTTGCCA 60.094 45.455 0.00 0.00 0.00 4.92
3003 3050 4.084328 GCCAATGTCTATCAAGTACATCGC 60.084 45.833 0.00 0.00 32.80 4.58
3007 3054 6.834959 ATGTCTATCAAGTACATCGCTTTG 57.165 37.500 0.00 0.00 0.00 2.77
3038 3085 2.622942 CCAACAAGTTTGCTAGCTTCCA 59.377 45.455 17.23 0.00 0.00 3.53
3087 3134 2.361483 TTGATGGCTGCCACGCAT 60.361 55.556 25.99 8.09 38.13 4.73
3131 3179 8.940768 AAAAATAACACATGGATATTTTCGGG 57.059 30.769 17.94 0.00 37.93 5.14
3165 3214 5.047306 GGCAGACTAAATAAAGGCCAAAAGT 60.047 40.000 5.01 0.00 39.66 2.66
3206 3255 5.355596 GCTCAGTACAGCTTAGACATGAAT 58.644 41.667 0.00 0.00 36.38 2.57
3224 3273 8.631480 ACATGAATGGTAGTACTATCACGATA 57.369 34.615 18.06 5.94 0.00 2.92
3265 3316 8.981724 AGTTTCAGAAAAACACTAAAAAGACC 57.018 30.769 0.00 0.00 32.81 3.85
3273 3324 7.806149 AAAACACTAAAAAGACCAAGTTTCG 57.194 32.000 0.00 0.00 0.00 3.46
3301 3352 7.119262 CCGAGGACAACATTCAGTACTAAAAAT 59.881 37.037 0.00 0.00 0.00 1.82
3371 3422 3.838244 AGCAAGAGAAACACCAGTACA 57.162 42.857 0.00 0.00 0.00 2.90
3399 3450 4.604050 TCCTAGTCACTAGCATCCTAGGAT 59.396 45.833 19.18 19.18 45.46 3.24
3490 3541 4.759516 TCAGTTCGCATTCCTTAAAACC 57.240 40.909 0.00 0.00 0.00 3.27
3598 3654 1.072965 CTGGAGAAGAACCACAGCCTT 59.927 52.381 0.00 0.00 33.57 4.35
3661 3720 7.410485 AGTTCGACAAAAGAGAAAAATCTCAC 58.590 34.615 8.42 0.00 39.12 3.51
3833 3892 9.597999 AGTTTTAAACGTAGCTAATTTAAACCG 57.402 29.630 23.74 12.90 37.45 4.44
3834 3893 8.839914 GTTTTAAACGTAGCTAATTTAAACCGG 58.160 33.333 23.74 0.00 37.45 5.28
3835 3894 7.665561 TTAAACGTAGCTAATTTAAACCGGT 57.334 32.000 16.41 0.00 0.00 5.28
3836 3895 8.764524 TTAAACGTAGCTAATTTAAACCGGTA 57.235 30.769 8.00 0.00 0.00 4.02
3837 3896 6.647212 AACGTAGCTAATTTAAACCGGTAC 57.353 37.500 8.00 0.00 0.00 3.34
3838 3897 5.965922 ACGTAGCTAATTTAAACCGGTACT 58.034 37.500 8.00 0.00 0.00 2.73
3839 3898 6.398095 ACGTAGCTAATTTAAACCGGTACTT 58.602 36.000 8.00 1.02 0.00 2.24
3840 3899 6.873605 ACGTAGCTAATTTAAACCGGTACTTT 59.126 34.615 8.00 0.09 0.00 2.66
3841 3900 8.032451 ACGTAGCTAATTTAAACCGGTACTTTA 58.968 33.333 8.00 0.00 0.00 1.85
3842 3901 8.868916 CGTAGCTAATTTAAACCGGTACTTTAA 58.131 33.333 8.00 6.70 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 224 2.673368 GACCAGATCATTCGTTGTGGTC 59.327 50.000 9.85 9.85 43.85 4.02
394 401 9.772973 ATGTTTTAGTACTGTGTGAACTGAATA 57.227 29.630 5.39 0.00 0.00 1.75
689 714 5.048364 ACTGACTAGTCTTGTCAAGCTGTAG 60.048 44.000 23.01 9.91 42.85 2.74
941 971 0.034574 TGGAGGTTTGTGTGCAGTGT 60.035 50.000 0.00 0.00 0.00 3.55
1082 1112 1.154263 GTGTACTCGCGCTTCTCGT 60.154 57.895 5.56 0.00 41.07 4.18
1152 1188 1.891919 GTCTGGTTCGCTGGTGCAA 60.892 57.895 0.00 0.00 39.64 4.08
1221 1257 1.089920 CAACTCCGATGAAGCTTGGG 58.910 55.000 2.10 0.00 0.00 4.12
1528 1565 7.093727 TGTTGAAATAGGAAAACACAGAACCAA 60.094 33.333 0.00 0.00 0.00 3.67
1574 1611 7.607607 TCAGTAATGCTGTATGTTCTTCATTGT 59.392 33.333 0.00 0.00 45.23 2.71
1614 1653 8.454106 AGTACATCATGTTATTCTTCTTGTTGC 58.546 33.333 0.00 0.00 0.00 4.17
1834 1874 6.153680 TGAAACAATCCACTTTACAGTTTGGT 59.846 34.615 0.00 0.00 0.00 3.67
1836 1877 6.475402 GGTGAAACAATCCACTTTACAGTTTG 59.525 38.462 0.00 0.00 39.98 2.93
1844 1885 6.294731 GCTAATCTGGTGAAACAATCCACTTT 60.295 38.462 0.00 0.00 39.98 2.66
1890 1932 5.622770 ATTTGGTGTATCAAGTTCGGAAC 57.377 39.130 12.91 12.91 0.00 3.62
1894 1936 9.840427 AGAAATTAATTTGGTGTATCAAGTTCG 57.160 29.630 17.98 0.00 30.92 3.95
2052 2094 9.625747 TGTGCATTAATTCTATATCAAGGTCAA 57.374 29.630 0.00 0.00 0.00 3.18
2053 2095 9.625747 TTGTGCATTAATTCTATATCAAGGTCA 57.374 29.630 0.00 0.00 0.00 4.02
2144 2186 9.836864 TTAACAGAGTCAATGATATATGCACTT 57.163 29.630 0.00 0.00 0.00 3.16
2574 2620 2.608090 GCCAAGGAGTCGTAGTATTTGC 59.392 50.000 0.00 0.00 0.00 3.68
2604 2650 3.950232 GGTGGATGACGCCTCCTA 58.050 61.111 0.00 0.00 46.52 2.94
2628 2674 2.350522 TCTTCTTCTTCATGCCTTCGC 58.649 47.619 0.00 0.00 0.00 4.70
2730 2777 5.456548 TGTCTTCCATGACTTGTACGTTA 57.543 39.130 0.00 0.00 37.79 3.18
2880 2927 6.116806 ACAACAATACTAAGGACACACACAA 58.883 36.000 0.00 0.00 0.00 3.33
2927 2974 6.263168 GCATAAGGTAGCTGGTTCAACATAAT 59.737 38.462 0.00 0.00 0.00 1.28
2983 3030 6.818644 ACAAAGCGATGTACTTGATAGACATT 59.181 34.615 0.00 0.00 33.99 2.71
3003 3050 5.418310 ACTTGTTGGACGACATAACAAAG 57.582 39.130 15.80 13.06 41.91 2.77
3007 3054 3.972502 GCAAACTTGTTGGACGACATAAC 59.027 43.478 0.00 0.00 0.00 1.89
3038 3085 9.563748 AACTTCAAATCATGGATGAACAAAATT 57.436 25.926 0.00 0.00 40.69 1.82
3110 3157 7.889873 TTTCCCGAAAATATCCATGTGTTAT 57.110 32.000 0.00 0.00 0.00 1.89
3250 3301 6.327154 CCGAAACTTGGTCTTTTTAGTGTTT 58.673 36.000 0.00 0.00 0.00 2.83
3265 3316 0.882927 TTGTCCTCGGCCGAAACTTG 60.883 55.000 30.53 16.93 0.00 3.16
3273 3324 0.321653 ACTGAATGTTGTCCTCGGCC 60.322 55.000 0.00 0.00 0.00 6.13
3301 3352 8.821147 TTTCTAACTACTTTTTAGCACGATGA 57.179 30.769 0.00 0.00 0.00 2.92
3371 3422 8.588290 CTAGGATGCTAGTGACTAGGAAATAT 57.412 38.462 17.67 1.20 37.89 1.28
3399 3450 5.941058 TGTTCAACTGTACCAGAACTTTCAA 59.059 36.000 14.00 0.00 40.62 2.69
3490 3541 7.464178 GCCACTGTTAATTCTTAGTATGTCACG 60.464 40.741 0.00 0.00 0.00 4.35
3658 3717 2.601314 CGTCTTCTGTTGTGTTTCGTGA 59.399 45.455 0.00 0.00 0.00 4.35
3661 3720 3.795101 AGTACGTCTTCTGTTGTGTTTCG 59.205 43.478 0.00 0.00 0.00 3.46
3813 3872 6.873605 AGTACCGGTTTAAATTAGCTACGTTT 59.126 34.615 15.04 0.60 0.00 3.60


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

AutoCloner maintained by Alex Coulton.