Multiple sequence alignment - TraesCS3B01G551000

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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 TraesCS3B01G551000 chr3B 100.000 3094 0 0 1 3094 785894708 785891615 0 5714
1 TraesCS3B01G551000 chr2B 95.892 3116 103 9 1 3094 619084698 619087810 0 5022
2 TraesCS3B01G551000 chr5B 95.395 3105 131 9 1 3094 414952073 414948970 0 4931
3 TraesCS3B01G551000 chr2A 94.129 3117 160 3 1 3094 563823886 563820770 0 4721
4 TraesCS3B01G551000 chr2A 93.873 2840 149 4 277 3094 99470058 99467222 0 4257
5 TraesCS3B01G551000 chr2A 94.083 2028 97 3 1089 3094 533367467 533365441 0 3059
6 TraesCS3B01G551000 chr1A 94.069 3119 157 8 1 3094 272664792 272667907 0 4710
7 TraesCS3B01G551000 chr1A 93.967 3116 165 3 1 3094 592367032 592363918 0 4691
8 TraesCS3B01G551000 chr5A 93.782 3120 167 10 1 3094 360444140 360447258 0 4662
9 TraesCS3B01G551000 chr3A 93.934 3099 165 5 1 3077 596937137 596934040 0 4660
10 TraesCS3B01G551000 chr3A 93.837 3099 168 5 1 3077 596886185 596883088 0 4643
11 TraesCS3B01G551000 chr3A 93.419 2872 163 14 246 3094 612655026 612652158 0 4233
12 TraesCS3B01G551000 chr3A 92.978 2848 152 13 277 3094 299191000 299193829 0 4108
13 TraesCS3B01G551000 chr4D 92.359 3128 203 16 1 3094 259449224 259452349 0 4420
14 TraesCS3B01G551000 chr7B 93.910 1724 80 5 1393 3094 659751484 659753204 0 2579


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 TraesCS3B01G551000 chr3B 785891615 785894708 3093 True 5714 5714 100.000 1 3094 1 chr3B.!!$R1 3093
1 TraesCS3B01G551000 chr2B 619084698 619087810 3112 False 5022 5022 95.892 1 3094 1 chr2B.!!$F1 3093
2 TraesCS3B01G551000 chr5B 414948970 414952073 3103 True 4931 4931 95.395 1 3094 1 chr5B.!!$R1 3093
3 TraesCS3B01G551000 chr2A 563820770 563823886 3116 True 4721 4721 94.129 1 3094 1 chr2A.!!$R3 3093
4 TraesCS3B01G551000 chr2A 99467222 99470058 2836 True 4257 4257 93.873 277 3094 1 chr2A.!!$R1 2817
5 TraesCS3B01G551000 chr2A 533365441 533367467 2026 True 3059 3059 94.083 1089 3094 1 chr2A.!!$R2 2005
6 TraesCS3B01G551000 chr1A 272664792 272667907 3115 False 4710 4710 94.069 1 3094 1 chr1A.!!$F1 3093
7 TraesCS3B01G551000 chr1A 592363918 592367032 3114 True 4691 4691 93.967 1 3094 1 chr1A.!!$R1 3093
8 TraesCS3B01G551000 chr5A 360444140 360447258 3118 False 4662 4662 93.782 1 3094 1 chr5A.!!$F1 3093
9 TraesCS3B01G551000 chr3A 596934040 596937137 3097 True 4660 4660 93.934 1 3077 1 chr3A.!!$R2 3076
10 TraesCS3B01G551000 chr3A 596883088 596886185 3097 True 4643 4643 93.837 1 3077 1 chr3A.!!$R1 3076
11 TraesCS3B01G551000 chr3A 612652158 612655026 2868 True 4233 4233 93.419 246 3094 1 chr3A.!!$R3 2848
12 TraesCS3B01G551000 chr3A 299191000 299193829 2829 False 4108 4108 92.978 277 3094 1 chr3A.!!$F1 2817
13 TraesCS3B01G551000 chr4D 259449224 259452349 3125 False 4420 4420 92.359 1 3094 1 chr4D.!!$F1 3093
14 TraesCS3B01G551000 chr7B 659751484 659753204 1720 False 2579 2579 93.910 1393 3094 1 chr7B.!!$F1 1701

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
962 965 0.391661 CTGACCTACACGGCTGCAAT 60.392 55.0 0.5 0.0 35.61 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2616 2674 0.394352 AATGTGGGCATCCGTCCTTC 60.394 55.0 0.0 0.0 37.98 3.46 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
114 115 5.140454 AGCCTTTACTTCTTTGTCACCAAT 58.860 37.500 0.00 0.00 0.00 3.16
140 142 5.700183 TGTAGGGATTTTGCTATGCCATTA 58.300 37.500 7.18 0.00 38.39 1.90
158 160 5.572885 GCCATTATAGACGGGGATTGGTATT 60.573 44.000 0.00 0.00 0.00 1.89
403 406 3.323691 TGACTAGAAGCTTACCTGCACAA 59.676 43.478 0.00 0.00 34.99 3.33
461 464 1.694844 TGTGTGACCTCTTACCGTGA 58.305 50.000 0.00 0.00 0.00 4.35
467 470 3.066481 GTGACCTCTTACCGTGATAGACC 59.934 52.174 0.00 0.00 0.00 3.85
535 538 5.574970 AAGAGGGAACACTTCAGAAAGAT 57.425 39.130 0.00 0.00 36.45 2.40
541 544 6.656693 AGGGAACACTTCAGAAAGATTATGTG 59.343 38.462 0.00 0.00 36.30 3.21
614 617 5.183228 GTGATCGAGTCTTATGGGGAAAAA 58.817 41.667 0.00 0.00 0.00 1.94
624 627 2.231215 TGGGGAAAAATGTGCAAACG 57.769 45.000 0.00 0.00 0.00 3.60
661 664 2.957006 ACTAATCGATTAGCCGTGTCCT 59.043 45.455 34.56 16.87 42.66 3.85
726 729 8.531622 AGCGATCTCATCACTCTTAATTAATG 57.468 34.615 0.00 0.00 0.00 1.90
894 897 8.522003 CACCAGCCATATTGCATGTATAAATAA 58.478 33.333 1.13 0.00 0.00 1.40
962 965 0.391661 CTGACCTACACGGCTGCAAT 60.392 55.000 0.50 0.00 35.61 3.56
1051 1054 1.656652 GATGGTGTTGATGGGACTCG 58.343 55.000 0.00 0.00 0.00 4.18
1057 1060 0.736325 GTTGATGGGACTCGACACCG 60.736 60.000 0.00 0.00 31.02 4.94
1058 1061 0.896479 TTGATGGGACTCGACACCGA 60.896 55.000 0.00 0.00 43.35 4.69
1182 1190 1.924731 TACCGATCCAGGGATAGCAG 58.075 55.000 0.00 0.00 34.60 4.24
1247 1255 5.587844 AGAAATGGTATCAGAGCACATGTTC 59.412 40.000 0.00 0.00 38.68 3.18
1339 1350 6.758254 GGAATTTTCCCTCATCTTTTGAACA 58.242 36.000 0.00 0.00 41.62 3.18
1340 1351 6.870439 GGAATTTTCCCTCATCTTTTGAACAG 59.130 38.462 0.00 0.00 41.62 3.16
1457 1482 4.030216 TCATGGTATTGGTCAGACTGCTA 58.970 43.478 0.00 0.00 0.00 3.49
1472 1497 2.027561 ACTGCTAAAGTTGCCGATACCA 60.028 45.455 0.00 0.00 34.57 3.25
1844 1870 2.110901 AGGAAGCACTGCATGAAGAG 57.889 50.000 8.02 0.00 0.00 2.85
1881 1907 2.584835 AGAGGTAACCAAGCATGCAA 57.415 45.000 21.98 0.00 37.17 4.08
2298 2354 5.709164 GGACCCAATAGATGATGAATGAAGG 59.291 44.000 0.00 0.00 0.00 3.46
2320 2376 2.094700 TGGACTCAAATTCTCGAGACCG 60.095 50.000 16.36 3.92 44.05 4.79
2470 2526 4.406326 TGGAAAATGCATCAAGCCATACAT 59.594 37.500 0.00 0.00 44.83 2.29
2614 2672 6.725834 AGAAATTGGACACACCCATAAAGAAT 59.274 34.615 0.00 0.00 35.87 2.40
2616 2674 7.645058 AATTGGACACACCCATAAAGAATAG 57.355 36.000 0.00 0.00 35.87 1.73
2692 2750 4.156008 CCTGGCAGGTTACATGTTTCTTAC 59.844 45.833 25.74 0.00 0.00 2.34
2788 2846 3.010696 GGAAGGAATGAAGGAAACCCTCT 59.989 47.826 0.00 0.00 32.44 3.69
2920 2980 3.641437 TTTCACAGTATTGCACCAAGC 57.359 42.857 0.00 0.00 45.96 4.01
3024 3084 1.079336 GTCCCCGAAGAGGAAACGG 60.079 63.158 0.00 0.00 34.92 4.44
3063 3123 7.732593 AGTAACCTAATATCTGCAGAGAAGGAT 59.267 37.037 27.94 21.03 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 3.699038 GGCATAGCAAAATCCCTACAACA 59.301 43.478 0.00 0.00 0.00 3.33
140 142 4.905456 TCTCAAATACCAATCCCCGTCTAT 59.095 41.667 0.00 0.00 0.00 1.98
158 160 4.152938 CACTCGCAACTTTCATGATCTCAA 59.847 41.667 0.00 0.00 0.00 3.02
403 406 2.780010 AGAGCCCATAATAGCTTGTGGT 59.220 45.455 0.00 0.00 40.92 4.16
467 470 9.794685 CACCTACATATATAACTACATCTGCTG 57.205 37.037 0.00 0.00 0.00 4.41
624 627 5.862323 TCGATTAGTTTTACACTCTGCAGAC 59.138 40.000 13.74 0.45 36.88 3.51
661 664 3.680490 TGCTCAAATTGTCCATAACCGA 58.320 40.909 0.00 0.00 0.00 4.69
894 897 7.120285 CACACCACAAGAGATGAATAAATGTCT 59.880 37.037 0.00 0.00 31.84 3.41
962 965 9.811995 GTCGGATAATACCTGCAACATAATATA 57.188 33.333 0.00 0.00 0.00 0.86
1051 1054 2.030363 TGGAAACATGCAAATCGGTGTC 60.030 45.455 0.00 0.00 33.40 3.67
1057 1060 4.771590 TCTCAGTGGAAACATGCAAATC 57.228 40.909 0.00 0.00 46.14 2.17
1058 1061 5.479375 AGAATCTCAGTGGAAACATGCAAAT 59.521 36.000 0.00 0.00 46.14 2.32
1182 1190 5.992729 GACGGTCAAGTCTCTATGTATCTC 58.007 45.833 2.62 0.00 38.09 2.75
1247 1255 1.743958 CTAGGGTCACGTCCTACAGTG 59.256 57.143 0.00 0.00 39.55 3.66
1339 1350 8.753497 AGAAATAAGAAGAGTTTTGGTCAACT 57.247 30.769 0.00 0.00 39.84 3.16
1387 1398 0.681733 GTGCTCTCTGGTGTTCAGGA 59.318 55.000 0.00 0.00 43.53 3.86
1457 1482 3.197766 TGATCTCTGGTATCGGCAACTTT 59.802 43.478 0.00 0.00 0.00 2.66
1472 1497 6.015918 TCTTCTCTTCTTCACCTTGATCTCT 58.984 40.000 0.00 0.00 0.00 3.10
1844 1870 2.094675 TCTAGCTTTTGGGCATTGAGC 58.905 47.619 0.00 0.00 44.65 4.26
1881 1907 6.432225 GTTTCCGAACTTCAAGGTCTTCCTT 61.432 44.000 0.00 0.00 42.10 3.36
2298 2354 3.254892 GGTCTCGAGAATTTGAGTCCAC 58.745 50.000 18.55 0.00 40.66 4.02
2320 2376 1.887198 TCGGTCTCCAACTGAGTCTTC 59.113 52.381 0.00 0.00 42.12 2.87
2470 2526 2.309755 AGTCTTTGCTCCATTCCATCCA 59.690 45.455 0.00 0.00 0.00 3.41
2614 2672 0.616395 TGTGGGCATCCGTCCTTCTA 60.616 55.000 0.00 0.00 37.98 2.10
2616 2674 0.394352 AATGTGGGCATCCGTCCTTC 60.394 55.000 0.00 0.00 37.98 3.46
2692 2750 2.527100 GTAGTGATCCGTTCCTTCACG 58.473 52.381 0.00 0.00 43.49 4.35
2788 2846 5.306937 TCACAGGTTCTTTCATACCTTCTCA 59.693 40.000 0.00 0.00 42.01 3.27
2920 2980 8.572855 AAGTATCCTGGATTCTCTTTTCTTTG 57.427 34.615 15.55 0.00 0.00 2.77
3024 3084 3.331718 AGGTTACTCTGGGGAGGTATC 57.668 52.381 0.00 0.00 43.46 2.24
3063 3123 6.070596 ACCTGAAACATGTGATATGACTCAGA 60.071 38.462 18.80 0.00 35.41 3.27


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

AutoCloner maintained by Alex Coulton.