Multiple sequence alignment - TraesCS4A01G153400

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 TraesCS4A01G153400 chr4A 100.000 3098 0 0 1 3098 309511523 309514620 0 5722
1 TraesCS4A01G153400 chr4A 94.294 3102 155 16 3 3098 310734983 310738068 0 4728
2 TraesCS4A01G153400 chr1D 96.515 3099 88 11 3 3098 254401702 254398621 0 5107
3 TraesCS4A01G153400 chr1D 95.362 1423 60 5 3 1422 51882464 51883883 0 2257
4 TraesCS4A01G153400 chr5D 96.484 3100 90 13 3 3098 6185345 6188429 0 5103
5 TraesCS4A01G153400 chr5D 97.006 2472 63 8 628 3098 503281198 503278737 0 4145
6 TraesCS4A01G153400 chr5D 96.279 1881 54 12 1221 3098 432405875 432404008 0 3072
7 TraesCS4A01G153400 chr5D 96.590 1085 34 3 3 1085 503282895 503281812 0 1796
8 TraesCS4A01G153400 chr2A 95.871 3100 94 13 3 3098 335835048 335838117 0 4985
9 TraesCS4A01G153400 chr6D 95.938 3077 106 14 3 3072 45515973 45519037 0 4972
10 TraesCS4A01G153400 chr4B 94.711 3101 133 20 3 3096 308692882 308695958 0 4789
11 TraesCS4A01G153400 chr3D 96.710 2158 59 8 942 3098 589282199 589280053 0 3581
12 TraesCS4A01G153400 chr5A 95.541 1996 79 7 1101 3095 607271900 607273886 0 3184
13 TraesCS4A01G153400 chr5A 94.879 1035 50 3 72 1104 607216288 607217321 0 1615
14 TraesCS4A01G153400 chr7A 91.918 1262 86 11 427 1686 91617668 91618915 0 1751
15 TraesCS4A01G153400 chr2B 96.767 959 25 4 2137 3095 474906988 474907940 0 1594
16 TraesCS4A01G153400 chr7B 87.477 1094 109 18 1441 2527 719441305 719442377 0 1236


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 TraesCS4A01G153400 chr4A 309511523 309514620 3097 False 5722.0 5722 100.000 1 3098 1 chr4A.!!$F1 3097
1 TraesCS4A01G153400 chr4A 310734983 310738068 3085 False 4728.0 4728 94.294 3 3098 1 chr4A.!!$F2 3095
2 TraesCS4A01G153400 chr1D 254398621 254401702 3081 True 5107.0 5107 96.515 3 3098 1 chr1D.!!$R1 3095
3 TraesCS4A01G153400 chr1D 51882464 51883883 1419 False 2257.0 2257 95.362 3 1422 1 chr1D.!!$F1 1419
4 TraesCS4A01G153400 chr5D 6185345 6188429 3084 False 5103.0 5103 96.484 3 3098 1 chr5D.!!$F1 3095
5 TraesCS4A01G153400 chr5D 432404008 432405875 1867 True 3072.0 3072 96.279 1221 3098 1 chr5D.!!$R1 1877
6 TraesCS4A01G153400 chr5D 503278737 503282895 4158 True 2970.5 4145 96.798 3 3098 2 chr5D.!!$R2 3095
7 TraesCS4A01G153400 chr2A 335835048 335838117 3069 False 4985.0 4985 95.871 3 3098 1 chr2A.!!$F1 3095
8 TraesCS4A01G153400 chr6D 45515973 45519037 3064 False 4972.0 4972 95.938 3 3072 1 chr6D.!!$F1 3069
9 TraesCS4A01G153400 chr4B 308692882 308695958 3076 False 4789.0 4789 94.711 3 3096 1 chr4B.!!$F1 3093
10 TraesCS4A01G153400 chr3D 589280053 589282199 2146 True 3581.0 3581 96.710 942 3098 1 chr3D.!!$R1 2156
11 TraesCS4A01G153400 chr5A 607271900 607273886 1986 False 3184.0 3184 95.541 1101 3095 1 chr5A.!!$F2 1994
12 TraesCS4A01G153400 chr5A 607216288 607217321 1033 False 1615.0 1615 94.879 72 1104 1 chr5A.!!$F1 1032
13 TraesCS4A01G153400 chr7A 91617668 91618915 1247 False 1751.0 1751 91.918 427 1686 1 chr7A.!!$F1 1259
14 TraesCS4A01G153400 chr2B 474906988 474907940 952 False 1594.0 1594 96.767 2137 3095 1 chr2B.!!$F1 958
15 TraesCS4A01G153400 chr7B 719441305 719442377 1072 False 1236.0 1236 87.477 1441 2527 1 chr7B.!!$F1 1086

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
55 57 0.896940 TCGATACCATAGTCCCCGCC 60.897 60.000 0.0 0.0 0.0 6.13 F
758 1291 1.543358 GACTAGTTCCGGGTTCGAGTT 59.457 52.381 0.0 0.0 39.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1381 2462 0.594602 CTACGTTCCCACTCACGACA 59.405 55.0 0.0 0.0 39.76 4.35 R
2626 3722 1.656652 CCTTGATCCACTTGGCTACG 58.343 55.0 0.0 0.0 34.44 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
55 57 0.896940 TCGATACCATAGTCCCCGCC 60.897 60.000 0.00 0.00 0.00 6.13
117 119 4.242811 ACTGGATCAGGGCATCCTATTAA 58.757 43.478 4.22 0.00 42.67 1.40
134 136 9.897040 ATCCTATTAATAAACCCATTTGGACAT 57.103 29.630 0.00 0.00 37.39 3.06
367 371 5.505173 TGGAAGAAGAGCAAGTTTTTCTG 57.495 39.130 0.00 0.00 30.77 3.02
372 376 6.705863 AGAAGAGCAAGTTTTTCTGTGATT 57.294 33.333 0.00 0.00 0.00 2.57
394 398 9.712305 TGATTTTCACCAAAACAACTCTTTTTA 57.288 25.926 0.00 0.00 34.24 1.52
400 406 9.936759 TCACCAAAACAACTCTTTTTATTTCTT 57.063 25.926 0.00 0.00 0.00 2.52
642 1175 8.139989 CCTCTTTGGAATAGAAATTGGCTATTG 58.860 37.037 14.96 4.82 38.35 1.90
658 1191 5.104109 TGGCTATTGCTACATAGGGAAAGTT 60.104 40.000 0.00 0.00 39.59 2.66
758 1291 1.543358 GACTAGTTCCGGGTTCGAGTT 59.457 52.381 0.00 0.00 39.00 3.01
906 1985 8.094548 TGGTTGACATTGGTATATAGTCTATGC 58.905 37.037 2.37 0.00 0.00 3.14
1031 2110 7.223971 TGCAATTTTAGATAGACGCGAAAGTAT 59.776 33.333 15.93 3.37 0.00 2.12
1076 2155 5.163814 GCAACTGGATAACTAGCACTGAAAG 60.164 44.000 0.00 0.00 42.29 2.62
1143 2222 4.946784 ATTGACCGCAACTTCTGTATTC 57.053 40.909 0.00 0.00 36.72 1.75
1149 2228 6.597672 TGACCGCAACTTCTGTATTCATTATT 59.402 34.615 0.00 0.00 0.00 1.40
1258 2337 6.860034 TCTGGTGCTATTATCCCTACTTCTA 58.140 40.000 0.00 0.00 0.00 2.10
1377 2458 6.704937 ACTTCTTACTTGGTGTAGCTTGTTAC 59.295 38.462 0.00 0.00 32.08 2.50
1381 2462 4.714632 ACTTGGTGTAGCTTGTTACATGT 58.285 39.130 2.69 2.69 36.08 3.21
1397 2478 0.319555 ATGTGTCGTGAGTGGGAACG 60.320 55.000 0.00 0.00 41.11 3.95
1431 2512 0.304705 GTATGCGTCCTTGGATTGCG 59.695 55.000 10.68 3.83 0.00 4.85
1505 2587 4.528206 CCCTATTGGTCAAGGAAGCTTTTT 59.472 41.667 0.00 0.00 34.58 1.94
1584 2666 3.012518 AGAGCACAACATCCTTATGCAC 58.987 45.455 0.00 0.00 38.79 4.57
1653 2735 3.199727 TCAGTGCTATGCATGGTTCCTTA 59.800 43.478 10.16 0.00 41.91 2.69
1668 2750 8.755977 CATGGTTCCTTAGTAACCTCTAGTTTA 58.244 37.037 8.17 0.00 45.53 2.01
1915 2999 4.508662 TGGTTTCAATTTCAACCACAACC 58.491 39.130 12.46 0.00 46.16 3.77
1916 3000 4.020218 TGGTTTCAATTTCAACCACAACCA 60.020 37.500 12.46 0.00 46.16 3.67
1917 3001 4.938226 GGTTTCAATTTCAACCACAACCAA 59.062 37.500 9.76 0.00 41.97 3.67
1918 3002 5.588246 GGTTTCAATTTCAACCACAACCAAT 59.412 36.000 9.76 0.00 41.97 3.16
1919 3003 6.763610 GGTTTCAATTTCAACCACAACCAATA 59.236 34.615 9.76 0.00 41.97 1.90
1920 3004 7.254624 GGTTTCAATTTCAACCACAACCAATAC 60.255 37.037 9.76 0.00 41.97 1.89
1940 3026 7.255569 CAATACGTAGTTGATAGTCAAGGTCA 58.744 38.462 0.08 0.00 37.78 4.02
1958 3044 6.549433 AGGTCACGTTATTAATACTTGGGA 57.451 37.500 0.00 0.00 0.00 4.37
2247 3337 8.470002 AGTATCCTTTCTTGCATTTTCATAACC 58.530 33.333 0.00 0.00 0.00 2.85
2289 3379 0.530288 AATTCCCCCAATTTGCGACG 59.470 50.000 0.00 0.00 29.60 5.12
2312 3402 8.652810 ACGTACCATAGGATTTGTTATGTAAC 57.347 34.615 0.00 0.00 36.74 2.50
2384 3474 2.370189 GTGGGTAGAATGCTAGATGCCT 59.630 50.000 0.00 0.00 42.00 4.75
2410 3500 6.650390 GGGACCACGTTACTATTGTTTCTTTA 59.350 38.462 0.00 0.00 0.00 1.85
2415 3505 8.943002 CCACGTTACTATTGTTTCTTTATCCTT 58.057 33.333 0.00 0.00 0.00 3.36
2626 3722 1.119574 TAGCTGGATAAGGGGCGGAC 61.120 60.000 0.00 0.00 0.00 4.79
2746 3842 8.815565 TGCAATTTTCCATATTCCTAGTTACA 57.184 30.769 0.00 0.00 0.00 2.41
3004 4105 2.489985 CCCAACATTACCCACTTGTCCA 60.490 50.000 0.00 0.00 0.00 4.02
3012 4113 1.005450 ACCCACTTGTCCAACTGTTGT 59.995 47.619 18.38 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 143 9.440773 CAAATCGATCAAGAATATCCCAATCTA 57.559 33.333 0.00 0.00 0.00 1.98
301 304 4.680440 GCCGAACCCAATCTTTGCATAAAT 60.680 41.667 0.00 0.00 0.00 1.40
311 314 4.340617 TCTAAAAATGCCGAACCCAATCT 58.659 39.130 0.00 0.00 0.00 2.40
367 371 7.595311 AAAGAGTTGTTTTGGTGAAAATCAC 57.405 32.000 1.88 1.88 46.23 3.06
394 398 4.217118 GCTCAGTGTGTGATCCAAAGAAAT 59.783 41.667 0.00 0.00 33.51 2.17
400 406 0.392706 ACGCTCAGTGTGTGATCCAA 59.607 50.000 12.42 0.00 38.09 3.53
642 1175 3.127030 GCACACAACTTTCCCTATGTAGC 59.873 47.826 0.00 0.00 0.00 3.58
1031 2110 2.180159 GAAGCGACCCCACAGGCTTA 62.180 60.000 0.00 0.00 45.04 3.09
1076 2155 3.160777 ACCATCCGATGTAAAGACGAC 57.839 47.619 7.60 0.00 0.00 4.34
1143 2222 2.606308 GGCAGCGATGAAGGCAATAATG 60.606 50.000 4.02 0.00 0.00 1.90
1149 2228 4.802051 GGGGCAGCGATGAAGGCA 62.802 66.667 4.02 0.00 0.00 4.75
1258 2337 2.852495 AAGTGCAATCCGATCGCCGT 62.852 55.000 10.32 0.00 36.31 5.68
1377 2458 1.148310 GTTCCCACTCACGACACATG 58.852 55.000 0.00 0.00 0.00 3.21
1381 2462 0.594602 CTACGTTCCCACTCACGACA 59.405 55.000 0.00 0.00 39.76 4.35
1397 2478 2.547826 GCATACCCAGACGGAAACTAC 58.452 52.381 0.00 0.00 34.64 2.73
1431 2512 2.648059 ACAGGAGCTGAATATGCAACC 58.352 47.619 0.00 0.00 35.18 3.77
1505 2587 6.101734 AGAGATTCCTAAAGGCATACCATCAA 59.898 38.462 0.00 0.00 39.06 2.57
1561 2643 3.012518 GCATAAGGATGTTGTGCTCTGT 58.987 45.455 0.00 0.00 35.30 3.41
1584 2666 3.085952 ACACCTAACATGTGGAATGGG 57.914 47.619 9.12 2.82 38.05 4.00
1653 2735 8.319881 GTTTCCCTGATTAAACTAGAGGTTACT 58.680 37.037 0.00 0.00 37.12 2.24
1668 2750 8.655935 ATTCATTTTCAGTAGTTTCCCTGATT 57.344 30.769 0.00 0.00 37.54 2.57
1840 2924 3.618690 AGCAGTGAACCAGATTCCTAC 57.381 47.619 0.00 0.00 36.36 3.18
1911 2995 7.010183 CCTTGACTATCAACTACGTATTGGTTG 59.990 40.741 16.14 16.14 40.87 3.77
1912 2996 7.039882 CCTTGACTATCAACTACGTATTGGTT 58.960 38.462 13.93 5.66 32.21 3.67
1913 2997 6.154021 ACCTTGACTATCAACTACGTATTGGT 59.846 38.462 13.93 11.09 32.21 3.67
1914 2998 6.570692 ACCTTGACTATCAACTACGTATTGG 58.429 40.000 13.93 0.46 32.21 3.16
1915 2999 7.220300 GTGACCTTGACTATCAACTACGTATTG 59.780 40.741 0.00 3.74 32.21 1.90
1916 3000 7.256286 GTGACCTTGACTATCAACTACGTATT 58.744 38.462 0.00 0.00 32.21 1.89
1917 3001 6.457934 CGTGACCTTGACTATCAACTACGTAT 60.458 42.308 0.00 0.00 32.21 3.06
1918 3002 5.163824 CGTGACCTTGACTATCAACTACGTA 60.164 44.000 0.00 0.00 32.21 3.57
1919 3003 4.379186 CGTGACCTTGACTATCAACTACGT 60.379 45.833 0.00 0.00 32.21 3.57
1920 3004 4.096311 CGTGACCTTGACTATCAACTACG 58.904 47.826 0.00 0.00 32.21 3.51
1958 3044 4.997395 GGTTAGCACGGTTGATGATATCAT 59.003 41.667 18.21 18.21 39.39 2.45
2096 3183 8.533569 TGGGTATTTCTGTCTTTTCTTTCTTT 57.466 30.769 0.00 0.00 0.00 2.52
2247 3337 2.677971 CCTACTCGGCATTTCACGG 58.322 57.895 0.00 0.00 0.00 4.94
2384 3474 4.040706 AGAAACAATAGTAACGTGGTCCCA 59.959 41.667 0.00 0.00 0.00 4.37
2626 3722 1.656652 CCTTGATCCACTTGGCTACG 58.343 55.000 0.00 0.00 34.44 3.51
2746 3842 7.781548 ATTCTTCGTTGCCGTAAGTAAATAT 57.218 32.000 0.00 0.00 35.01 1.28
2944 4045 1.000052 GGTAGAGCCGGATCTAAGTGC 60.000 57.143 29.95 17.47 33.66 4.40
3012 4113 6.149807 CCGTTTAGTATCCCAAAACTGCTTAA 59.850 38.462 0.00 0.00 32.25 1.85


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

AutoCloner maintained by Alex Coulton.