Multiple sequence alignment - TraesCS3A01G162700

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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 TraesCS3A01G162700 chr3A 100.000 2690 0 0 1 2690 164909707 164912396 0.000000e+00 4968.0
1 TraesCS3A01G162700 chr3A 86.232 1104 135 14 590 1684 164614431 164615526 0.000000e+00 1181.0
2 TraesCS3A01G162700 chr3A 81.916 1117 187 13 576 1684 163793048 163794157 0.000000e+00 929.0
3 TraesCS3A01G162700 chr3A 95.169 207 5 2 1685 1886 164926462 164926668 3.340000e-84 322.0
4 TraesCS3A01G162700 chr3B 96.384 1687 53 3 1 1684 213708234 213709915 0.000000e+00 2771.0
5 TraesCS3A01G162700 chr3B 86.327 1119 141 9 572 1684 207738759 207739871 0.000000e+00 1208.0
6 TraesCS3A01G162700 chr3B 84.057 1129 168 11 562 1684 205775384 205776506 0.000000e+00 1077.0
7 TraesCS3A01G162700 chr3B 82.316 1114 155 25 603 1684 85108140 85107037 0.000000e+00 928.0
8 TraesCS3A01G162700 chr3B 80.321 1123 200 15 576 1684 207291789 207292904 0.000000e+00 830.0
9 TraesCS3A01G162700 chr3B 81.112 1043 161 28 661 1680 85224444 85223415 0.000000e+00 802.0
10 TraesCS3A01G162700 chr3D 91.561 1730 84 21 1 1684 148337388 148335675 0.000000e+00 2329.0
11 TraesCS3A01G162700 chr3D 83.968 1129 169 10 562 1684 148700269 148699147 0.000000e+00 1072.0
12 TraesCS3A01G162700 chr3D 82.585 1114 155 24 600 1684 55742244 55743347 0.000000e+00 946.0
13 TraesCS3A01G162700 chr3D 82.358 1111 157 23 603 1684 55084920 55083820 0.000000e+00 929.0
14 TraesCS3A01G162700 chr3D 81.345 1115 197 10 576 1684 143948655 143949764 0.000000e+00 896.0
15 TraesCS3A01G162700 chr3D 79.515 825 137 24 657 1460 55577503 55578316 2.340000e-155 558.0
16 TraesCS3A01G162700 chr3D 73.770 244 56 8 963 1202 135641574 135641335 3.690000e-14 89.8
17 TraesCS3A01G162700 chr5D 92.537 1005 65 6 1685 2681 159427824 159428826 0.000000e+00 1432.0
18 TraesCS3A01G162700 chr1B 92.224 1016 70 5 1683 2690 325447817 325446803 0.000000e+00 1430.0
19 TraesCS3A01G162700 chr6A 91.807 1013 74 5 1685 2690 617744770 617745780 0.000000e+00 1402.0
20 TraesCS3A01G162700 chr2A 92.773 761 44 6 1684 2436 775608650 775609407 0.000000e+00 1090.0
21 TraesCS3A01G162700 chr2A 85.185 216 29 3 1803 2016 676109470 676109684 4.510000e-53 219.0
22 TraesCS3A01G162700 chr1A 81.959 1031 151 22 1685 2690 310879476 310878456 0.000000e+00 841.0
23 TraesCS3A01G162700 chr1A 79.663 890 173 6 1799 2681 161668109 161667221 3.780000e-178 634.0
24 TraesCS3A01G162700 chr6B 80.868 1014 173 18 1681 2681 592018717 592017712 0.000000e+00 778.0
25 TraesCS3A01G162700 chr5A 82.945 815 125 6 1867 2668 590112041 590112854 0.000000e+00 723.0
26 TraesCS3A01G162700 chr4A 83.005 812 124 10 1867 2670 621676071 621676876 0.000000e+00 723.0
27 TraesCS3A01G162700 chr7A 94.203 276 10 3 1685 1954 52782910 52782635 1.490000e-112 416.0
28 TraesCS3A01G162700 chr7A 92.271 207 11 2 1685 1886 52780390 52780184 3.390000e-74 289.0


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 TraesCS3A01G162700 chr3A 164909707 164912396 2689 False 4968.0 4968 100.000 1 2690 1 chr3A.!!$F3 2689
1 TraesCS3A01G162700 chr3A 164614431 164615526 1095 False 1181.0 1181 86.232 590 1684 1 chr3A.!!$F2 1094
2 TraesCS3A01G162700 chr3A 163793048 163794157 1109 False 929.0 929 81.916 576 1684 1 chr3A.!!$F1 1108
3 TraesCS3A01G162700 chr3B 213708234 213709915 1681 False 2771.0 2771 96.384 1 1684 1 chr3B.!!$F4 1683
4 TraesCS3A01G162700 chr3B 207738759 207739871 1112 False 1208.0 1208 86.327 572 1684 1 chr3B.!!$F3 1112
5 TraesCS3A01G162700 chr3B 205775384 205776506 1122 False 1077.0 1077 84.057 562 1684 1 chr3B.!!$F1 1122
6 TraesCS3A01G162700 chr3B 85107037 85108140 1103 True 928.0 928 82.316 603 1684 1 chr3B.!!$R1 1081
7 TraesCS3A01G162700 chr3B 207291789 207292904 1115 False 830.0 830 80.321 576 1684 1 chr3B.!!$F2 1108
8 TraesCS3A01G162700 chr3B 85223415 85224444 1029 True 802.0 802 81.112 661 1680 1 chr3B.!!$R2 1019
9 TraesCS3A01G162700 chr3D 148335675 148337388 1713 True 2329.0 2329 91.561 1 1684 1 chr3D.!!$R3 1683
10 TraesCS3A01G162700 chr3D 148699147 148700269 1122 True 1072.0 1072 83.968 562 1684 1 chr3D.!!$R4 1122
11 TraesCS3A01G162700 chr3D 55742244 55743347 1103 False 946.0 946 82.585 600 1684 1 chr3D.!!$F2 1084
12 TraesCS3A01G162700 chr3D 55083820 55084920 1100 True 929.0 929 82.358 603 1684 1 chr3D.!!$R1 1081
13 TraesCS3A01G162700 chr3D 143948655 143949764 1109 False 896.0 896 81.345 576 1684 1 chr3D.!!$F3 1108
14 TraesCS3A01G162700 chr3D 55577503 55578316 813 False 558.0 558 79.515 657 1460 1 chr3D.!!$F1 803
15 TraesCS3A01G162700 chr5D 159427824 159428826 1002 False 1432.0 1432 92.537 1685 2681 1 chr5D.!!$F1 996
16 TraesCS3A01G162700 chr1B 325446803 325447817 1014 True 1430.0 1430 92.224 1683 2690 1 chr1B.!!$R1 1007
17 TraesCS3A01G162700 chr6A 617744770 617745780 1010 False 1402.0 1402 91.807 1685 2690 1 chr6A.!!$F1 1005
18 TraesCS3A01G162700 chr2A 775608650 775609407 757 False 1090.0 1090 92.773 1684 2436 1 chr2A.!!$F2 752
19 TraesCS3A01G162700 chr1A 310878456 310879476 1020 True 841.0 841 81.959 1685 2690 1 chr1A.!!$R2 1005
20 TraesCS3A01G162700 chr1A 161667221 161668109 888 True 634.0 634 79.663 1799 2681 1 chr1A.!!$R1 882
21 TraesCS3A01G162700 chr6B 592017712 592018717 1005 True 778.0 778 80.868 1681 2681 1 chr6B.!!$R1 1000
22 TraesCS3A01G162700 chr5A 590112041 590112854 813 False 723.0 723 82.945 1867 2668 1 chr5A.!!$F1 801
23 TraesCS3A01G162700 chr4A 621676071 621676876 805 False 723.0 723 83.005 1867 2670 1 chr4A.!!$F1 803
24 TraesCS3A01G162700 chr7A 52780184 52782910 2726 True 352.5 416 93.237 1685 1954 2 chr7A.!!$R1 269

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
247 248 0.956633 TCTGCCTCTTTGCTTTGCTG 59.043 50.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2383 0.464554 GGGTGCTACTGGATGAAGGC 60.465 60.0 0.0 0.0 0.0 4.35 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
247 248 0.956633 TCTGCCTCTTTGCTTTGCTG 59.043 50.000 0.00 0.00 0.00 4.41
685 744 4.082523 CTTTCCCTCCGCTGCCGA 62.083 66.667 0.00 0.00 36.29 5.54
768 827 1.443194 CAACTACCCGTCCGTCGTG 60.443 63.158 0.00 0.00 37.94 4.35
1567 1644 0.668535 TCTGCTCGGTATCGACATGG 59.331 55.000 0.00 0.00 40.88 3.66
1789 1873 3.054287 ACCGACCTTCTCTGTATCTCTCA 60.054 47.826 0.00 0.00 0.00 3.27
2025 2383 1.361668 CCTCGTCATCCACCTTTGCG 61.362 60.000 0.00 0.00 0.00 4.85
2062 2423 1.383799 CAAGCCATGTCCCTTGGGA 59.616 57.895 3.91 3.91 35.86 4.37
2173 2534 2.124860 TCGATCCGACGAGCCAGA 60.125 61.111 0.00 0.00 37.37 3.86
2229 2592 3.118592 GGAAGGAGGAACAGATCGTCAAT 60.119 47.826 3.15 0.00 43.26 2.57
2289 2652 2.108075 TCAAGGTTTTCTGATGGGCTCA 59.892 45.455 0.00 0.00 0.00 4.26
2322 2685 1.152984 CCTTGCACAGGTGGTCACA 60.153 57.895 1.10 0.00 37.99 3.58
2352 2715 4.564110 GTGGAGGTATGGGCCGCC 62.564 72.222 0.00 0.00 46.86 6.13
2360 2723 0.823356 GTATGGGCCGCCATTCATGT 60.823 55.000 12.58 0.00 0.00 3.21
2362 2725 2.124151 GGGCCGCCATTCATGTCT 60.124 61.111 12.58 0.00 0.00 3.41
2369 2732 2.489329 CCGCCATTCATGTCTCTTTTGT 59.511 45.455 0.00 0.00 0.00 2.83
2448 2811 4.647564 AGGAAACCTGAACATGACAGAT 57.352 40.909 19.98 6.10 37.54 2.90
2475 2838 4.621068 TGCCAAAATTAAGATGCTCTCG 57.379 40.909 0.00 0.00 0.00 4.04
2505 2869 3.925630 ATGCACAGGAGCGGGGTTG 62.926 63.158 0.00 0.00 37.31 3.77
2623 4775 6.256053 ACTGTCCAGGAATTATTCAACCAAT 58.744 36.000 7.29 0.00 0.00 3.16
2681 4852 3.000727 GGATGAACGTTCGTCAATCCTT 58.999 45.455 37.86 9.55 43.39 3.36
2684 4855 2.056577 GAACGTTCGTCAATCCTTCGT 58.943 47.619 13.36 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 248 3.642778 TTCGTCGGCTAGTGGCTGC 62.643 63.158 1.68 0.00 46.32 5.25
1401 1478 1.306642 CGTACTCCAGCGTCCACTCT 61.307 60.000 0.00 0.00 0.00 3.24
1567 1644 2.639286 CACAACCTTGCGAGCACC 59.361 61.111 0.00 0.00 0.00 5.01
1734 1816 8.532819 GGAGTTAGACAGAAGAAAGGATAGAAA 58.467 37.037 0.00 0.00 0.00 2.52
1789 1873 9.722056 GCTTACAAAATGATCGATAGTTTGATT 57.278 29.630 23.97 12.19 34.16 2.57
1807 1895 4.148079 TGGATGTTGTCATGGCTTACAAA 58.852 39.130 9.34 0.00 37.35 2.83
2010 2368 1.244019 AAGGCGCAAAGGTGGATGAC 61.244 55.000 10.83 0.00 0.00 3.06
2025 2383 0.464554 GGGTGCTACTGGATGAAGGC 60.465 60.000 0.00 0.00 0.00 4.35
2062 2423 0.839946 AGCTTCTCTTGTGGTGGTGT 59.160 50.000 0.00 0.00 0.00 4.16
2229 2592 2.192861 CCAGAGGTGGCGTGCAAAA 61.193 57.895 0.00 0.00 36.89 2.44
2289 2652 1.804372 GCAAGGATCTCGCGAGACAAT 60.804 52.381 38.89 24.93 40.75 2.71
2322 2685 1.376424 CTCCACTGGCGTCTGCAAT 60.376 57.895 0.00 0.00 45.35 3.56
2352 2715 4.240096 GGGCAACAAAAGAGACATGAATG 58.760 43.478 0.00 0.00 39.74 2.67
2369 2732 0.689080 TTGGGCTTGAGTTTGGGCAA 60.689 50.000 0.00 0.00 0.00 4.52
2438 2801 6.839124 TTTTGGCAAGATAATCTGTCATGT 57.161 33.333 0.00 0.00 0.00 3.21
2475 2838 1.485838 CTGTGCATGCGATCTCGTCC 61.486 60.000 14.09 0.00 42.22 4.79
2500 2864 2.615227 ATCTCTGCATCGCCCAACCC 62.615 60.000 0.00 0.00 0.00 4.11
2501 2865 1.153086 ATCTCTGCATCGCCCAACC 60.153 57.895 0.00 0.00 0.00 3.77
2509 2873 1.035923 TGGGAGACGATCTCTGCATC 58.964 55.000 13.00 0.00 42.95 3.91
2514 2878 2.955660 GAGAACATGGGAGACGATCTCT 59.044 50.000 12.62 0.00 42.95 3.10
2611 4763 6.876789 TCGAAGCTGAGTAATTGGTTGAATAA 59.123 34.615 0.00 0.00 0.00 1.40
2623 4775 1.214589 GGGCGTCGAAGCTGAGTAA 59.785 57.895 22.38 0.00 37.29 2.24


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

AutoCloner maintained by Alex Coulton.