Multiple sequence alignment - TraesCS7B01G388100

Loading Multiple Alignment...

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 TraesCS7B01G388100 chr7B 100.000 3513 0 0 1 3513 654207519 654204007 0 6488
1 TraesCS7B01G388100 chr7B 96.770 3529 93 4 1 3513 578788407 578784884 0 5866
2 TraesCS7B01G388100 chr7B 93.968 3067 145 18 453 3513 34706245 34703213 0 4602
3 TraesCS7B01G388100 chr5B 96.997 3530 86 3 1 3513 410544952 410541426 0 5914
4 TraesCS7B01G388100 chr5B 95.202 792 32 3 2728 3513 60085244 60084453 0 1247
5 TraesCS7B01G388100 chr6B 96.486 3529 104 3 1 3513 360609997 360606473 0 5812
6 TraesCS7B01G388100 chr3A 96.260 3529 95 11 1 3513 738664866 738668373 0 5751
7 TraesCS7B01G388100 chr3A 96.203 3529 96 9 1 3513 738586373 738589879 0 5740
8 TraesCS7B01G388100 chr3A 96.146 3529 99 8 1 3513 738492165 738495672 0 5729
9 TraesCS7B01G388100 chr3A 95.252 1053 30 5 1 1037 738564707 738565755 0 1650
10 TraesCS7B01G388100 chr1D 94.933 3118 139 5 1 3100 49626905 49630021 0 4865
11 TraesCS7B01G388100 chr1D 91.973 598 18 5 2916 3513 2738198 2737631 0 811
12 TraesCS7B01G388100 chr7D 92.392 3089 201 11 4 3070 305154449 305157525 0 4372
13 TraesCS7B01G388100 chrUn 95.397 1021 30 2 1 1005 344735003 344733984 0 1609
14 TraesCS7B01G388100 chr4B 83.137 848 91 33 1 805 635615682 635614844 0 726


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 TraesCS7B01G388100 chr7B 654204007 654207519 3512 True 6488 6488 100.000 1 3513 1 chr7B.!!$R3 3512
1 TraesCS7B01G388100 chr7B 578784884 578788407 3523 True 5866 5866 96.770 1 3513 1 chr7B.!!$R2 3512
2 TraesCS7B01G388100 chr7B 34703213 34706245 3032 True 4602 4602 93.968 453 3513 1 chr7B.!!$R1 3060
3 TraesCS7B01G388100 chr5B 410541426 410544952 3526 True 5914 5914 96.997 1 3513 1 chr5B.!!$R2 3512
4 TraesCS7B01G388100 chr5B 60084453 60085244 791 True 1247 1247 95.202 2728 3513 1 chr5B.!!$R1 785
5 TraesCS7B01G388100 chr6B 360606473 360609997 3524 True 5812 5812 96.486 1 3513 1 chr6B.!!$R1 3512
6 TraesCS7B01G388100 chr3A 738664866 738668373 3507 False 5751 5751 96.260 1 3513 1 chr3A.!!$F4 3512
7 TraesCS7B01G388100 chr3A 738586373 738589879 3506 False 5740 5740 96.203 1 3513 1 chr3A.!!$F3 3512
8 TraesCS7B01G388100 chr3A 738492165 738495672 3507 False 5729 5729 96.146 1 3513 1 chr3A.!!$F1 3512
9 TraesCS7B01G388100 chr3A 738564707 738565755 1048 False 1650 1650 95.252 1 1037 1 chr3A.!!$F2 1036
10 TraesCS7B01G388100 chr1D 49626905 49630021 3116 False 4865 4865 94.933 1 3100 1 chr1D.!!$F1 3099
11 TraesCS7B01G388100 chr1D 2737631 2738198 567 True 811 811 91.973 2916 3513 1 chr1D.!!$R1 597
12 TraesCS7B01G388100 chr7D 305154449 305157525 3076 False 4372 4372 92.392 4 3070 1 chr7D.!!$F1 3066
13 TraesCS7B01G388100 chrUn 344733984 344735003 1019 True 1609 1609 95.397 1 1005 1 chrUn.!!$R1 1004
14 TraesCS7B01G388100 chr4B 635614844 635615682 838 True 726 726 83.137 1 805 1 chr4B.!!$R1 804

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
100 102 1.007734 CCTTATAAGCTCGCGCGGA 60.008 57.895 31.69 15.73 42.32 5.54 F
1061 1144 0.179163 CAGATGCAGTACGACGAGCA 60.179 55.000 0.00 6.68 38.11 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1433 1.017177 GCCGCACACCGAATGTTCTA 61.017 55.0 0.00 0.0 40.64 2.10 R
2735 2824 0.320946 GTTGGATTCCACGGTTCCGA 60.321 55.0 18.28 0.0 30.78 4.55 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
100 102 1.007734 CCTTATAAGCTCGCGCGGA 60.008 57.895 31.69 15.73 42.32 5.54
273 276 3.068448 GGCTCCAAAACGGGAAAAGTAAA 59.932 43.478 0.00 0.00 36.27 2.01
282 285 4.884247 ACGGGAAAAGTAAACTCTCTCAG 58.116 43.478 0.00 0.00 0.00 3.35
332 335 8.031848 ACGCTTTTGATTTGATGCATTATTTT 57.968 26.923 0.00 0.00 0.00 1.82
889 966 4.202131 TGCTTGATCATGCTTTTGACAACA 60.202 37.500 27.81 6.91 33.23 3.33
916 993 1.734163 CGCCCGTTTTATGGAGAACT 58.266 50.000 0.00 0.00 0.00 3.01
930 1007 3.056821 TGGAGAACTGAGTGGTAATGTCG 60.057 47.826 0.00 0.00 0.00 4.35
1005 1088 5.240623 TCCGTTTACATTCTGACAAATGCTT 59.759 36.000 9.08 0.00 39.72 3.91
1061 1144 0.179163 CAGATGCAGTACGACGAGCA 60.179 55.000 0.00 6.68 38.11 4.26
1113 1196 3.127895 TGTTGGGTTTCGTTCTTCAGTTG 59.872 43.478 0.00 0.00 0.00 3.16
1501 1584 4.115199 ACTGCTCGGGGGATTGCC 62.115 66.667 0.00 0.00 0.00 4.52
1760 1844 0.331278 AATTTGGATGTGGGAGCGGA 59.669 50.000 0.00 0.00 0.00 5.54
1991 2078 6.817765 TCCGCAACTTTCATTCTTCTTAAT 57.182 33.333 0.00 0.00 0.00 1.40
2385 2473 2.291346 TGTGGGACGAGAGAAGGTATCA 60.291 50.000 0.00 0.00 0.00 2.15
2726 2815 0.517316 GATGGCTCGAACGTGCTTTT 59.483 50.000 17.86 6.18 35.28 2.27
2735 2824 3.805422 TCGAACGTGCTTTTGTATGAAGT 59.195 39.130 0.00 0.00 0.00 3.01
2855 2944 9.927668 ATCCTTATTATGTTTTTGGTTGTTCAG 57.072 29.630 0.00 0.00 0.00 3.02
2982 3071 1.741401 CTTCATCAAGCCACGCCGA 60.741 57.895 0.00 0.00 0.00 5.54
3118 3231 2.244769 AGAAGAAGAGGAGGAGGAGGAG 59.755 54.545 0.00 0.00 0.00 3.69
3119 3232 0.933700 AGAAGAGGAGGAGGAGGAGG 59.066 60.000 0.00 0.00 0.00 4.30
3120 3233 0.930726 GAAGAGGAGGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
3250 3363 2.050714 GTTCCTCGTCGTCGCACA 60.051 61.111 0.00 0.00 36.96 4.57
3375 3488 6.992715 ACTAGTTGTGAGCAAGAACTTGTATT 59.007 34.615 14.62 3.12 42.31 1.89
3402 3515 5.914033 TGCTAGTGATGTCTATTTGGTACC 58.086 41.667 4.43 4.43 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 123 1.749258 GAAGATGGTGGCGGGTTCC 60.749 63.158 0.00 0.00 0.00 3.62
131 133 1.512735 GGCTAGGGGAAGAAGATGGT 58.487 55.000 0.00 0.00 0.00 3.55
273 276 2.938428 ATTGGAGGGACTGAGAGAGT 57.062 50.000 0.00 0.00 41.55 3.24
282 285 4.643784 TCGAGTAGAACTAATTGGAGGGAC 59.356 45.833 0.00 0.00 0.00 4.46
332 335 7.777095 AGTAAAAAGATAGGTTTGTTTGCACA 58.223 30.769 0.00 0.00 0.00 4.57
486 507 6.734137 TCAATCACATCACCACTTGTTTAAC 58.266 36.000 0.00 0.00 0.00 2.01
489 510 5.302568 ACATCAATCACATCACCACTTGTTT 59.697 36.000 0.00 0.00 0.00 2.83
637 660 5.820131 TCACCAACATTCATCATTTATCGC 58.180 37.500 0.00 0.00 0.00 4.58
889 966 0.321298 ATAAAACGGGCGCAGTGACT 60.321 50.000 10.83 0.00 0.00 3.41
916 993 2.750712 TGACGATCGACATTACCACTCA 59.249 45.455 24.34 7.89 0.00 3.41
977 1054 7.753132 GCATTTGTCAGAATGTAAACGGAATTA 59.247 33.333 8.54 0.00 38.86 1.40
999 1076 3.619938 CGCAATGGGGGAAGCATT 58.380 55.556 0.00 0.00 0.00 3.56
1061 1144 4.597004 TCTCCTGAAATACGGAGTGTAGT 58.403 43.478 5.34 0.00 45.73 2.73
1178 1261 5.196341 AGTGAGATGAAAACTGTACGTCA 57.804 39.130 0.00 0.00 0.00 4.35
1183 1266 5.680619 ACCACAAGTGAGATGAAAACTGTA 58.319 37.500 0.94 0.00 0.00 2.74
1350 1433 1.017177 GCCGCACACCGAATGTTCTA 61.017 55.000 0.00 0.00 40.64 2.10
1358 1441 3.923864 ACTTGAGCCGCACACCGA 61.924 61.111 0.00 0.00 40.02 4.69
1501 1584 2.092323 TCCGAGATACATCCATAGGCG 58.908 52.381 0.00 0.00 0.00 5.52
1502 1585 4.442192 GGAATCCGAGATACATCCATAGGC 60.442 50.000 0.00 0.00 0.00 3.93
2276 2364 1.753073 GCAAGGCATAGGAAGCAATGT 59.247 47.619 0.00 0.00 0.00 2.71
2385 2473 1.543802 CTCTCCTCTCGCTGTCTTTGT 59.456 52.381 0.00 0.00 0.00 2.83
2498 2586 3.056821 TCCTCCAATTAGGCGATATCGTG 60.057 47.826 24.99 14.29 42.22 4.35
2510 2598 2.103094 CGCTGTCATCCTCCTCCAATTA 59.897 50.000 0.00 0.00 0.00 1.40
2693 2782 3.608707 CGAGCCATCAATAATGCTTCTGC 60.609 47.826 0.00 0.00 40.20 4.26
2726 2815 1.067425 CCACGGTTCCGACTTCATACA 60.067 52.381 18.28 0.00 0.00 2.29
2735 2824 0.320946 GTTGGATTCCACGGTTCCGA 60.321 55.000 18.28 0.00 30.78 4.55
2855 2944 3.063997 CGGGTGATGAACTTCTGCAATAC 59.936 47.826 0.00 0.00 0.00 1.89
2894 2983 1.450312 GAGCGCACCCAAGCATACT 60.450 57.895 11.47 0.00 35.48 2.12
2982 3071 2.028130 CATGAGTAGAGGAAGCTCCGT 58.972 52.381 0.00 0.00 42.75 4.69
3118 3231 1.428620 GTCGTACTCCTCTGCGTCC 59.571 63.158 0.00 0.00 0.00 4.79
3119 3232 1.060622 CGTCGTACTCCTCTGCGTC 59.939 63.158 0.00 0.00 0.00 5.19
3120 3233 1.375140 TCGTCGTACTCCTCTGCGT 60.375 57.895 0.00 0.00 0.00 5.24
3250 3363 0.887836 GGGTTTCGTCCGGCTTCTTT 60.888 55.000 0.00 0.00 0.00 2.52
3375 3488 7.603180 ACCAAATAGACATCACTAGCATAGA 57.397 36.000 0.00 0.00 42.77 1.98
3402 3515 4.293415 GACATCACCAACAAAGCTTGAAG 58.707 43.478 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.