Multiple sequence alignment - TraesCS1A01G191700

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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 TraesCS1A01G191700 chr1A 100.000 2840 0 0 1 2840 346680510 346683349 0.000000e+00 5245.0
1 TraesCS1A01G191700 chr1D 94.288 2101 79 25 752 2840 274254290 274256361 0.000000e+00 3177.0
2 TraesCS1A01G191700 chr1D 86.290 744 86 13 1 740 274253577 274254308 0.000000e+00 795.0
3 TraesCS1A01G191700 chr1D 84.416 77 12 0 610 686 411544716 411544640 3.030000e-10 76.8
4 TraesCS1A01G191700 chr1B 92.854 2071 58 27 752 2774 373628041 373630069 0.000000e+00 2922.0
5 TraesCS1A01G191700 chr1B 88.636 748 70 10 1 740 373627319 373628059 0.000000e+00 896.0
6 TraesCS1A01G191700 chr3A 81.115 323 45 12 1350 1664 145667466 145667780 7.860000e-61 244.0
7 TraesCS1A01G191700 chr3D 80.864 324 44 14 1350 1664 132275352 132275666 3.660000e-59 239.0
8 TraesCS1A01G191700 chr3B 80.864 324 44 12 1350 1664 188877448 188877762 3.660000e-59 239.0


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 TraesCS1A01G191700 chr1A 346680510 346683349 2839 False 5245 5245 100.000 1 2840 1 chr1A.!!$F1 2839
1 TraesCS1A01G191700 chr1D 274253577 274256361 2784 False 1986 3177 90.289 1 2840 2 chr1D.!!$F1 2839
2 TraesCS1A01G191700 chr1B 373627319 373630069 2750 False 1909 2922 90.745 1 2774 2 chr1B.!!$F1 2773

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
143 144 0.743688 CTATGCACCGACTCTGCTCT 59.256 55.0 0.00 0.0 35.53 4.09 F
674 680 0.813184 TACTCGGCGGTTTACTCCTG 59.187 55.0 7.21 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1603 1.073964 CGACGACGTAGGACTCAAGA 58.926 55.000 0.0 0.00 34.56 3.02 R
2626 2693 1.337167 TGCTGCTACTGTGCTACTGTG 60.337 52.381 0.0 2.46 32.45 3.66 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
66 67 1.268743 GCCAGATTTTACGCATCCAGC 60.269 52.381 0.00 0.00 40.87 4.85
67 68 1.334869 CCAGATTTTACGCATCCAGCC 59.665 52.381 0.00 0.00 41.38 4.85
68 69 2.016318 CAGATTTTACGCATCCAGCCA 58.984 47.619 0.00 0.00 41.38 4.75
69 70 2.032550 CAGATTTTACGCATCCAGCCAG 59.967 50.000 0.00 0.00 41.38 4.85
112 113 2.403561 TCATGGATTGGACGGGTATCA 58.596 47.619 0.00 0.00 0.00 2.15
137 138 2.071688 CATAGCCTATGCACCGACTC 57.928 55.000 0.00 0.00 41.13 3.36
138 139 1.615883 CATAGCCTATGCACCGACTCT 59.384 52.381 0.00 0.00 41.13 3.24
141 142 1.819229 CCTATGCACCGACTCTGCT 59.181 57.895 0.00 0.00 35.53 4.24
143 144 0.743688 CTATGCACCGACTCTGCTCT 59.256 55.000 0.00 0.00 35.53 4.09
170 171 1.889829 CGGTATGGCCTCCTTCTCTAG 59.110 57.143 3.32 0.00 34.25 2.43
172 173 2.894765 GGTATGGCCTCCTTCTCTAGTC 59.105 54.545 3.32 0.00 0.00 2.59
196 197 1.338769 TGGATCTCACTCGTCGACTGA 60.339 52.381 14.70 9.79 0.00 3.41
278 279 4.500116 GCTCCTCGCTGTCGGTCC 62.500 72.222 0.00 0.00 36.13 4.46
282 283 2.487428 CTCGCTGTCGGTCCTCAG 59.513 66.667 6.58 6.58 36.13 3.35
331 332 1.646540 CCAAGTTTCGAGCACGCAA 59.353 52.632 0.00 0.00 39.58 4.85
334 335 2.384382 CAAGTTTCGAGCACGCAAAAT 58.616 42.857 0.00 0.00 39.58 1.82
477 482 0.895530 TCGGTTCTCTTGGCGAAGAT 59.104 50.000 11.86 0.00 37.58 2.40
481 486 3.074412 GGTTCTCTTGGCGAAGATTTGA 58.926 45.455 11.86 3.34 37.58 2.69
514 519 3.676646 ACTACGGTGTTTTAAGATGACGC 59.323 43.478 0.00 0.00 0.00 5.19
631 637 7.333423 CAGTTAGGTCCGATCAAAATTTAGTGA 59.667 37.037 0.00 0.00 0.00 3.41
672 678 2.094545 TCTTTACTCGGCGGTTTACTCC 60.095 50.000 7.21 0.00 0.00 3.85
674 680 0.813184 TACTCGGCGGTTTACTCCTG 59.187 55.000 7.21 0.00 0.00 3.86
675 681 1.810030 CTCGGCGGTTTACTCCTGC 60.810 63.158 7.21 0.00 0.00 4.85
708 720 7.334858 AGGGAGATGCTCTTAGTTTAGAAAAG 58.665 38.462 0.00 0.00 0.00 2.27
715 727 8.336801 TGCTCTTAGTTTAGAAAAGGATTTCC 57.663 34.615 0.00 0.00 44.96 3.13
1228 1264 2.515523 CCAGGCCAATGCTCCTCG 60.516 66.667 5.01 0.00 37.74 4.63
1441 1477 4.200283 GAGCGCCTCGACCTCCTG 62.200 72.222 2.29 0.00 0.00 3.86
1567 1603 1.154016 CGAGATCTGCACCGTCGTT 60.154 57.895 0.00 0.00 0.00 3.85
1570 1606 0.603569 AGATCTGCACCGTCGTTCTT 59.396 50.000 0.00 0.00 0.00 2.52
2041 2077 3.543680 TCATACTCTAGCCCTTGTTGC 57.456 47.619 0.00 0.00 0.00 4.17
2043 2079 4.286707 TCATACTCTAGCCCTTGTTGCTA 58.713 43.478 0.00 0.00 40.23 3.49
2055 2091 5.735354 GCCCTTGTTGCTAAATGATGATGAG 60.735 44.000 0.00 0.00 0.00 2.90
2059 2095 6.628919 TGTTGCTAAATGATGATGAGGATG 57.371 37.500 0.00 0.00 0.00 3.51
2060 2096 6.358991 TGTTGCTAAATGATGATGAGGATGA 58.641 36.000 0.00 0.00 0.00 2.92
2061 2097 7.002276 TGTTGCTAAATGATGATGAGGATGAT 58.998 34.615 0.00 0.00 0.00 2.45
2062 2098 7.040686 TGTTGCTAAATGATGATGAGGATGATG 60.041 37.037 0.00 0.00 0.00 3.07
2063 2099 6.775708 TGCTAAATGATGATGAGGATGATGA 58.224 36.000 0.00 0.00 0.00 2.92
2064 2100 7.402862 TGCTAAATGATGATGAGGATGATGAT 58.597 34.615 0.00 0.00 0.00 2.45
2084 2120 6.110543 TGATGAATTAGCACTTGTTGATCG 57.889 37.500 0.00 0.00 0.00 3.69
2284 2347 3.127533 GTGTGCTCCGGGATGCAC 61.128 66.667 29.08 29.08 45.89 4.57
2401 2465 1.909781 CCCAGGCCACACTGCAAAT 60.910 57.895 5.01 0.00 37.16 2.32
2402 2466 1.474332 CCCAGGCCACACTGCAAATT 61.474 55.000 5.01 0.00 37.16 1.82
2422 2486 8.348507 GCAAATTTTTGGTGAATTTATGTCCAA 58.651 29.630 5.28 0.00 38.57 3.53
2527 2591 6.965607 AGCCATCCATATCATGTGATGAATA 58.034 36.000 5.78 0.00 43.50 1.75
2611 2678 5.559770 TGGTGCTTAAAGATTCAGACATGA 58.440 37.500 0.00 0.00 0.00 3.07
2626 2693 3.442977 AGACATGAATGAAGAAAGCCAGC 59.557 43.478 0.00 0.00 0.00 4.85
2632 2699 2.928801 TGAAGAAAGCCAGCACAGTA 57.071 45.000 0.00 0.00 0.00 2.74
2633 2700 2.771089 TGAAGAAAGCCAGCACAGTAG 58.229 47.619 0.00 0.00 0.00 2.57
2634 2701 1.466558 GAAGAAAGCCAGCACAGTAGC 59.533 52.381 0.00 0.00 0.00 3.58
2635 2702 0.397941 AGAAAGCCAGCACAGTAGCA 59.602 50.000 0.00 0.00 36.85 3.49
2636 2703 0.519077 GAAAGCCAGCACAGTAGCAC 59.481 55.000 0.00 0.00 36.85 4.40
2637 2704 0.179020 AAAGCCAGCACAGTAGCACA 60.179 50.000 0.00 0.00 36.85 4.57
2638 2705 0.604780 AAGCCAGCACAGTAGCACAG 60.605 55.000 0.00 0.00 36.85 3.66
2639 2706 1.302033 GCCAGCACAGTAGCACAGT 60.302 57.895 0.00 0.00 36.85 3.55
2792 2865 4.499174 AAGCTTTCGCGAAAAACAAAAG 57.501 36.364 31.68 20.42 42.32 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.227999 ATCCGCCGATTTATGTGCCG 61.228 55.000 0.00 0.00 0.00 5.69
55 56 3.398310 TGGCTGGCTGGATGCGTA 61.398 61.111 2.00 0.00 44.05 4.42
131 132 1.665448 CGATATGCAGAGCAGAGTCGG 60.665 57.143 0.00 0.00 43.65 4.79
137 138 2.614779 CCATACCGATATGCAGAGCAG 58.385 52.381 0.00 0.00 43.65 4.24
138 139 1.338105 GCCATACCGATATGCAGAGCA 60.338 52.381 0.00 0.00 44.86 4.26
141 142 1.550524 GAGGCCATACCGATATGCAGA 59.449 52.381 5.01 0.00 46.52 4.26
143 144 0.613260 GGAGGCCATACCGATATGCA 59.387 55.000 5.01 0.00 46.52 3.96
170 171 0.171455 ACGAGTGAGATCCAAGCGAC 59.829 55.000 0.00 0.00 0.00 5.19
172 173 0.863538 CGACGAGTGAGATCCAAGCG 60.864 60.000 0.00 0.00 0.00 4.68
196 197 2.577059 CGTGGCTATGACGGTGGT 59.423 61.111 0.00 0.00 33.08 4.16
222 223 4.133796 GCCAAGCCCATCCAACGC 62.134 66.667 0.00 0.00 0.00 4.84
305 306 0.238289 CTCGAAACTTGGCGCAACAT 59.762 50.000 10.83 0.00 0.00 2.71
331 332 0.038166 ACACCCACGCTGGATGATTT 59.962 50.000 5.51 0.00 40.96 2.17
334 335 1.003839 GAACACCCACGCTGGATGA 60.004 57.895 5.51 0.00 40.96 2.92
456 461 2.097036 TCTTCGCCAAGAGAACCGATA 58.903 47.619 0.00 0.00 33.38 2.92
477 482 6.403049 ACACCGTAGTACATGATTCATCAAA 58.597 36.000 0.00 0.00 40.69 2.69
481 486 8.780846 TTAAAACACCGTAGTACATGATTCAT 57.219 30.769 0.00 0.00 0.00 2.57
590 596 9.765795 CGGACCTAACTGATCTTCTAAATTTAT 57.234 33.333 0.00 0.00 0.00 1.40
646 652 2.884894 ACCGCCGAGTAAAGATTAGG 57.115 50.000 0.00 0.00 0.00 2.69
647 653 5.346522 AGTAAACCGCCGAGTAAAGATTAG 58.653 41.667 0.00 0.00 0.00 1.73
743 755 9.748708 CAACACTTTGATGGATTTTCTCTAAAA 57.251 29.630 0.00 0.00 35.54 1.52
744 756 9.130661 TCAACACTTTGATGGATTTTCTCTAAA 57.869 29.630 0.00 0.00 36.79 1.85
745 757 8.690203 TCAACACTTTGATGGATTTTCTCTAA 57.310 30.769 0.00 0.00 36.79 2.10
770 782 7.454225 AGTGTCTTTGCTTAAAACTAGAGGAT 58.546 34.615 0.00 0.00 0.00 3.24
1288 1324 2.205749 TACACCTGGGGGCAGTCA 59.794 61.111 0.00 0.00 35.63 3.41
1567 1603 1.073964 CGACGACGTAGGACTCAAGA 58.926 55.000 0.00 0.00 34.56 3.02
1570 1606 2.449548 GTCGACGACGTAGGACTCA 58.550 57.895 12.94 0.00 40.69 3.41
2041 2077 9.449719 TTCATCATCATCCTCATCATCATTTAG 57.550 33.333 0.00 0.00 0.00 1.85
2043 2079 8.885693 ATTCATCATCATCCTCATCATCATTT 57.114 30.769 0.00 0.00 0.00 2.32
2055 2091 6.630444 ACAAGTGCTAATTCATCATCATCC 57.370 37.500 0.00 0.00 0.00 3.51
2059 2095 6.849811 CGATCAACAAGTGCTAATTCATCATC 59.150 38.462 0.00 0.00 0.00 2.92
2060 2096 6.539826 TCGATCAACAAGTGCTAATTCATCAT 59.460 34.615 0.00 0.00 0.00 2.45
2061 2097 5.874261 TCGATCAACAAGTGCTAATTCATCA 59.126 36.000 0.00 0.00 0.00 3.07
2062 2098 6.349973 TCGATCAACAAGTGCTAATTCATC 57.650 37.500 0.00 0.00 0.00 2.92
2063 2099 6.932356 ATCGATCAACAAGTGCTAATTCAT 57.068 33.333 0.00 0.00 0.00 2.57
2064 2100 7.841915 TTATCGATCAACAAGTGCTAATTCA 57.158 32.000 0.00 0.00 0.00 2.57
2284 2347 3.899734 TCCAAACAGAAACAATGATGCG 58.100 40.909 0.00 0.00 0.00 4.73
2401 2465 8.043710 ACAAGTTGGACATAAATTCACCAAAAA 58.956 29.630 7.96 0.00 41.29 1.94
2402 2466 7.493971 CACAAGTTGGACATAAATTCACCAAAA 59.506 33.333 7.96 0.00 41.29 2.44
2422 2486 9.783081 TGATAACATATTCAGATATGCACAAGT 57.217 29.630 0.00 0.00 45.94 3.16
2547 2611 8.771521 TGGATTGATCATGAAAAATATGAGGT 57.228 30.769 0.00 0.00 37.91 3.85
2611 2678 2.590821 ACTGTGCTGGCTTTCTTCATT 58.409 42.857 0.00 0.00 0.00 2.57
2613 2680 2.771089 CTACTGTGCTGGCTTTCTTCA 58.229 47.619 0.00 0.00 0.00 3.02
2626 2693 1.337167 TGCTGCTACTGTGCTACTGTG 60.337 52.381 0.00 2.46 32.45 3.66
2632 2699 2.082231 CATTCTTGCTGCTACTGTGCT 58.918 47.619 0.00 0.00 0.00 4.40
2633 2700 1.467035 GCATTCTTGCTGCTACTGTGC 60.467 52.381 0.00 2.80 45.77 4.57
2634 2701 2.539346 GCATTCTTGCTGCTACTGTG 57.461 50.000 0.00 0.00 45.77 3.66


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

AutoCloner maintained by Alex Coulton.