Multiple sequence alignment - TraesCS1A01G303900

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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 TraesCS1A01G303900 chr1A 100.000 3071 0 0 1 3071 497281202 497284272 0.000000e+00 5672
1 TraesCS1A01G303900 chr1A 82.281 903 103 27 1 857 497516303 497517194 0.000000e+00 728
2 TraesCS1A01G303900 chr1A 80.506 395 64 4 1729 2119 99908326 99907941 1.080000e-74 291
3 TraesCS1A01G303900 chr1B 94.825 3092 119 15 1 3071 539447380 539450451 0.000000e+00 4785
4 TraesCS1A01G303900 chr1B 87.632 1140 137 4 970 2108 539135527 539136663 0.000000e+00 1321
5 TraesCS1A01G303900 chr1B 83.654 520 51 15 1 488 539564687 539565204 2.790000e-125 459
6 TraesCS1A01G303900 chr1B 87.812 320 29 7 544 858 539565474 539565788 1.740000e-97 366
7 TraesCS1A01G303900 chr1D 96.942 2747 56 9 1 2728 401197194 401199931 0.000000e+00 4582
8 TraesCS1A01G303900 chr1D 95.044 343 12 3 2733 3071 401201754 401202095 4.510000e-148 534
9 TraesCS1A01G303900 chr1D 89.362 235 16 3 1 226 401678997 401679231 1.390000e-73 287
10 TraesCS1A01G303900 chr3A 75.823 699 142 19 1379 2057 714738667 714739358 2.280000e-86 329
11 TraesCS1A01G303900 chr3D 76.774 620 119 17 1381 1983 579614809 579615420 1.060000e-84 324
12 TraesCS1A01G303900 chr3B 75.523 621 112 25 1382 1983 735131236 735130637 5.050000e-68 268
13 TraesCS1A01G303900 chr2D 81.065 338 33 13 2318 2652 104272415 104272724 1.100000e-59 241
14 TraesCS1A01G303900 chr2D 79.330 358 35 16 2309 2658 103474909 103475235 6.670000e-52 215
15 TraesCS1A01G303900 chr7D 74.569 464 97 19 1556 2004 504766768 504767225 1.880000e-42 183
16 TraesCS1A01G303900 chr6D 72.320 513 131 7 1557 2062 448159652 448159144 1.910000e-32 150


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 TraesCS1A01G303900 chr1A 497281202 497284272 3070 False 5672.0 5672 100.000 1 3071 1 chr1A.!!$F1 3070
1 TraesCS1A01G303900 chr1A 497516303 497517194 891 False 728.0 728 82.281 1 857 1 chr1A.!!$F2 856
2 TraesCS1A01G303900 chr1B 539447380 539450451 3071 False 4785.0 4785 94.825 1 3071 1 chr1B.!!$F2 3070
3 TraesCS1A01G303900 chr1B 539135527 539136663 1136 False 1321.0 1321 87.632 970 2108 1 chr1B.!!$F1 1138
4 TraesCS1A01G303900 chr1B 539564687 539565788 1101 False 412.5 459 85.733 1 858 2 chr1B.!!$F3 857
5 TraesCS1A01G303900 chr1D 401197194 401202095 4901 False 2558.0 4582 95.993 1 3071 2 chr1D.!!$F2 3070
6 TraesCS1A01G303900 chr3A 714738667 714739358 691 False 329.0 329 75.823 1379 2057 1 chr3A.!!$F1 678
7 TraesCS1A01G303900 chr3D 579614809 579615420 611 False 324.0 324 76.774 1381 1983 1 chr3D.!!$F1 602
8 TraesCS1A01G303900 chr3B 735130637 735131236 599 True 268.0 268 75.523 1382 1983 1 chr3B.!!$R1 601

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
869 1133 2.280628 CAGTATTTTCTCCAGTCGCCC 58.719 52.381 0.0 0.0 0.00 6.13 F
1373 1637 0.532115 GGTAAGCAAATGTGGGGCTG 59.468 55.000 0.0 0.0 38.04 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2233 0.523072 CATGCCTTCTTCAACCCGTG 59.477 55.000 0.00 0.00 0.0 4.94 R
2682 3008 1.884579 CCCAAGGACTATCATGCATGC 59.115 52.381 22.25 11.82 0.0 4.06 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
103 105 5.028549 TCCATCAAGAATAGAAGAGTGGC 57.971 43.478 0.00 0.00 0.00 5.01
429 644 8.859156 CAAAAACCTTGTATTGATTTCATACCG 58.141 33.333 0.00 0.00 0.00 4.02
869 1133 2.280628 CAGTATTTTCTCCAGTCGCCC 58.719 52.381 0.00 0.00 0.00 6.13
1053 1317 2.512896 GGATCCGCCTCTGCCATT 59.487 61.111 0.00 0.00 0.00 3.16
1065 1329 2.359850 GCCATTGTCGCCACCTCA 60.360 61.111 0.00 0.00 0.00 3.86
1104 1368 2.186076 CTCAAGATCGACGGTTACTGC 58.814 52.381 0.00 0.00 0.00 4.40
1155 1419 5.261040 TCCTCCAATCCAGTCAATTCTTT 57.739 39.130 0.00 0.00 0.00 2.52
1262 1526 1.202177 CGATGAAATTGCAACCGAGGG 60.202 52.381 0.00 0.00 0.00 4.30
1373 1637 0.532115 GGTAAGCAAATGTGGGGCTG 59.468 55.000 0.00 0.00 38.04 4.85
1384 1648 1.228124 TGGGGCTGTCCAAAGTTCG 60.228 57.895 0.00 0.00 37.22 3.95
2060 2366 1.001248 AGCTGATTGCCATGCCCTT 59.999 52.632 0.00 0.00 44.23 3.95
2170 2476 3.520290 ATGTGTACTGGTATGTGGACG 57.480 47.619 0.00 0.00 0.00 4.79
2286 2592 3.181418 ACCCCCAAGACATGATTGTTCTT 60.181 43.478 0.00 0.00 35.79 2.52
2303 2609 7.903995 TTGTTCTTTCAGCATTTTGTTTTCT 57.096 28.000 0.00 0.00 0.00 2.52
2304 2610 7.903995 TGTTCTTTCAGCATTTTGTTTTCTT 57.096 28.000 0.00 0.00 0.00 2.52
2305 2611 8.994429 TGTTCTTTCAGCATTTTGTTTTCTTA 57.006 26.923 0.00 0.00 0.00 2.10
2328 2634 8.500753 TTATTACAATGCTTTGGACGAGTAAT 57.499 30.769 15.92 11.28 37.15 1.89
2399 2705 9.727859 AAGTTTTAACCCTGTTTTTATGTTTGT 57.272 25.926 0.00 0.00 0.00 2.83
2454 2760 7.038729 ACTCCAAGAATACTCTGTCATTTCTCA 60.039 37.037 0.00 0.00 30.03 3.27
2549 2856 1.753073 CTTTCCATGTTGCCATCTCCC 59.247 52.381 0.00 0.00 0.00 4.30
2552 2859 1.108776 CCATGTTGCCATCTCCCTTG 58.891 55.000 0.00 0.00 0.00 3.61
2568 2875 3.999663 TCCCTTGTGCACAAAACAAAAAG 59.000 39.130 30.62 17.28 37.10 2.27
2569 2876 3.999663 CCCTTGTGCACAAAACAAAAAGA 59.000 39.130 30.62 7.03 37.10 2.52
2570 2877 4.453819 CCCTTGTGCACAAAACAAAAAGAA 59.546 37.500 30.62 6.50 37.10 2.52
2571 2878 5.049129 CCCTTGTGCACAAAACAAAAAGAAA 60.049 36.000 30.62 6.30 37.10 2.52
2654 2961 0.839946 CTGTAGGGCCTACCAAGCAT 59.160 55.000 34.70 1.00 43.89 3.79
2660 2986 2.110296 GCCTACCAAGCATTCAGGC 58.890 57.895 0.00 0.00 44.54 4.85
2682 3008 3.869065 TGCTTACTGATTAAACTCCGGG 58.131 45.455 0.00 0.00 0.00 5.73
2700 3026 1.884579 GGGCATGCATGATAGTCCTTG 59.115 52.381 30.64 1.04 0.00 3.61
2717 3043 4.022849 GTCCTTGGGTCATTCTGTTTTCTG 60.023 45.833 0.00 0.00 0.00 3.02
2815 4968 2.358957 TCTCTGGTTTGATGATTGGCG 58.641 47.619 0.00 0.00 0.00 5.69
2871 5024 6.542821 AGAATTACCTTGTGATCTCACCAAA 58.457 36.000 7.81 0.00 45.88 3.28
2915 5068 5.989168 TCACATAGCTTGATATTTACCCACG 59.011 40.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 119 1.002134 GTATGGTGCTGGCCACACT 60.002 57.895 26.82 16.61 46.50 3.55
119 121 0.915364 TATGTATGGTGCTGGCCACA 59.085 50.000 0.00 1.92 46.50 4.17
429 644 5.673337 TCTAGACATGAAAACAACAGTGC 57.327 39.130 0.00 0.00 0.00 4.40
869 1133 0.532573 TACTGGAGGAAGAAGCAGCG 59.467 55.000 0.00 0.00 0.00 5.18
1065 1329 3.748645 AGGGTATGATATCCTCTCGCT 57.251 47.619 0.00 0.00 32.53 4.93
1262 1526 7.576750 TTAATAGTGAACATCGTCTTCACAC 57.423 36.000 18.29 0.00 46.77 3.82
1373 1637 2.143925 CCCTCTTGACGAACTTTGGAC 58.856 52.381 0.00 0.00 0.00 4.02
1384 1648 2.840651 TCTCCAAATCCTCCCTCTTGAC 59.159 50.000 0.00 0.00 0.00 3.18
1660 1961 0.179000 GTGTCGCCCTCCTTCATCAT 59.821 55.000 0.00 0.00 0.00 2.45
1927 2233 0.523072 CATGCCTTCTTCAACCCGTG 59.477 55.000 0.00 0.00 0.00 4.94
2060 2366 1.764571 AACACTCGGCTAAGGTGGCA 61.765 55.000 0.00 0.00 35.53 4.92
2170 2476 5.643777 ACTGCCTGATAACATAAGTCACAAC 59.356 40.000 0.00 0.00 0.00 3.32
2303 2609 7.908827 TTACTCGTCCAAAGCATTGTAATAA 57.091 32.000 0.43 0.00 34.60 1.40
2304 2610 7.466725 GCATTACTCGTCCAAAGCATTGTAATA 60.467 37.037 0.43 0.00 34.60 0.98
2305 2611 6.677920 GCATTACTCGTCCAAAGCATTGTAAT 60.678 38.462 0.43 0.00 34.60 1.89
2391 2697 6.701340 AGTAGAGATGCAGTCAACAAACATA 58.299 36.000 0.00 0.00 0.00 2.29
2399 2705 4.381398 GCAGAGAAGTAGAGATGCAGTCAA 60.381 45.833 0.00 0.00 33.92 3.18
2549 2856 7.905031 TTTTTCTTTTTGTTTTGTGCACAAG 57.095 28.000 29.50 17.05 35.57 3.16
2612 2919 7.015877 ACAGAAAGGTAATGGACTACTAACACA 59.984 37.037 0.00 0.00 0.00 3.72
2654 2961 5.560724 AGTTTAATCAGTAAGCAGCCTGAA 58.439 37.500 0.00 0.00 40.81 3.02
2660 2986 3.871594 CCCGGAGTTTAATCAGTAAGCAG 59.128 47.826 0.73 0.00 0.00 4.24
2682 3008 1.884579 CCCAAGGACTATCATGCATGC 59.115 52.381 22.25 11.82 0.00 4.06
2700 3026 6.881602 AGTATTCTCAGAAAACAGAATGACCC 59.118 38.462 0.00 0.00 39.28 4.46
2731 3057 2.281762 CGCCTCGCATTACTGTCTAAAC 59.718 50.000 0.00 0.00 0.00 2.01
2732 3058 2.536365 CGCCTCGCATTACTGTCTAAA 58.464 47.619 0.00 0.00 0.00 1.85
2733 3059 2.203800 CGCCTCGCATTACTGTCTAA 57.796 50.000 0.00 0.00 0.00 2.10
2734 3060 3.938653 CGCCTCGCATTACTGTCTA 57.061 52.632 0.00 0.00 0.00 2.59
2735 3061 4.814900 CGCCTCGCATTACTGTCT 57.185 55.556 0.00 0.00 0.00 3.41
2809 4962 6.000219 AGAGAAGTATAATGCATTCGCCAAT 59.000 36.000 16.86 6.03 37.32 3.16
2815 4968 5.762218 ACAGGCAGAGAAGTATAATGCATTC 59.238 40.000 16.86 1.35 38.63 2.67
2915 5068 3.421844 AGTTTGACTTCTTACATGGGGC 58.578 45.455 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.