Multiple sequence alignment - TraesCS5A01G514400

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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 TraesCS5A01G514400 chr5A 100.000 3221 0 0 1 3221 678081148 678084368 0.000000e+00 5949.0
1 TraesCS5A01G514400 chr5A 96.809 752 23 1 6 756 174292308 174293059 0.000000e+00 1254.0
2 TraesCS5A01G514400 chr5A 84.881 1217 149 16 1008 2218 691814267 691813080 0.000000e+00 1195.0
3 TraesCS5A01G514400 chr5A 84.418 937 119 17 2293 3219 691813080 691812161 0.000000e+00 896.0
4 TraesCS5A01G514400 chr5A 80.453 353 21 23 757 1104 677951771 677952080 3.230000e-55 226.0
5 TraesCS5A01G514400 chr4D 94.427 2225 114 5 1002 3221 497667742 497665523 0.000000e+00 3413.0
6 TraesCS5A01G514400 chr4D 92.742 248 17 1 1002 1248 497696248 497696001 1.100000e-94 357.0
7 TraesCS5A01G514400 chr4D 82.787 366 24 19 754 1114 497648839 497649170 1.130000e-74 291.0
8 TraesCS5A01G514400 chr4D 94.915 59 3 0 754 812 497657430 497657488 3.420000e-15 93.5
9 TraesCS5A01G514400 chr4B 90.532 2482 180 21 757 3221 638988829 638986386 0.000000e+00 3230.0
10 TraesCS5A01G514400 chr4B 86.517 1068 130 7 1155 2218 654131606 654130549 0.000000e+00 1162.0
11 TraesCS5A01G514400 chr4B 85.620 1064 116 18 1159 2218 654126344 654125314 0.000000e+00 1083.0
12 TraesCS5A01G514400 chr4B 88.341 832 62 21 783 1600 638814594 638815404 0.000000e+00 966.0
13 TraesCS5A01G514400 chr4B 83.847 941 128 13 2293 3218 654125314 654124383 0.000000e+00 874.0
14 TraesCS5A01G514400 chr3D 96.419 754 27 0 1 754 515228863 515229616 0.000000e+00 1243.0
15 TraesCS5A01G514400 chr3D 96.068 763 29 1 5 766 589558832 589558070 0.000000e+00 1242.0
16 TraesCS5A01G514400 chr7D 96.277 752 27 1 5 755 460054679 460053928 0.000000e+00 1232.0
17 TraesCS5A01G514400 chr7D 82.007 289 46 6 1675 1960 25522673 25522958 1.150000e-59 241.0
18 TraesCS5A01G514400 chr6D 96.159 755 28 1 1 754 16201785 16202539 0.000000e+00 1232.0
19 TraesCS5A01G514400 chr6B 96.011 752 26 4 5 754 705610875 705610126 0.000000e+00 1219.0
20 TraesCS5A01G514400 chr5B 95.509 757 31 3 3 756 280594771 280594015 0.000000e+00 1206.0
21 TraesCS5A01G514400 chr1B 95.503 756 32 2 1 755 673882081 673882835 0.000000e+00 1206.0
22 TraesCS5A01G514400 chr2A 95.106 756 34 3 1 755 14452299 14453052 0.000000e+00 1188.0
23 TraesCS5A01G514400 chr2D 86.220 1045 123 9 1158 2198 602009553 602008526 0.000000e+00 1112.0
24 TraesCS5A01G514400 chr2D 84.295 936 130 13 2293 3221 602008506 602007581 0.000000e+00 898.0
25 TraesCS5A01G514400 chr2B 87.110 993 110 6 1209 2198 732224512 732223535 0.000000e+00 1109.0
26 TraesCS5A01G514400 chr2B 83.957 935 135 12 2293 3221 732223515 732222590 0.000000e+00 881.0
27 TraesCS5A01G514400 chr4A 84.081 936 123 14 1203 2137 731002833 731003743 0.000000e+00 880.0
28 TraesCS5A01G514400 chr4A 82.007 289 46 6 1675 1960 709977525 709977810 1.150000e-59 241.0
29 TraesCS5A01G514400 chr3B 74.710 431 89 17 1211 1631 142721895 142722315 1.190000e-39 174.0


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 TraesCS5A01G514400 chr5A 678081148 678084368 3220 False 5949.0 5949 100.0000 1 3221 1 chr5A.!!$F3 3220
1 TraesCS5A01G514400 chr5A 174292308 174293059 751 False 1254.0 1254 96.8090 6 756 1 chr5A.!!$F1 750
2 TraesCS5A01G514400 chr5A 691812161 691814267 2106 True 1045.5 1195 84.6495 1008 3219 2 chr5A.!!$R1 2211
3 TraesCS5A01G514400 chr4D 497665523 497667742 2219 True 3413.0 3413 94.4270 1002 3221 1 chr4D.!!$R1 2219
4 TraesCS5A01G514400 chr4B 638986386 638988829 2443 True 3230.0 3230 90.5320 757 3221 1 chr4B.!!$R1 2464
5 TraesCS5A01G514400 chr4B 654130549 654131606 1057 True 1162.0 1162 86.5170 1155 2218 1 chr4B.!!$R2 1063
6 TraesCS5A01G514400 chr4B 654124383 654126344 1961 True 978.5 1083 84.7335 1159 3218 2 chr4B.!!$R3 2059
7 TraesCS5A01G514400 chr4B 638814594 638815404 810 False 966.0 966 88.3410 783 1600 1 chr4B.!!$F1 817
8 TraesCS5A01G514400 chr3D 515228863 515229616 753 False 1243.0 1243 96.4190 1 754 1 chr3D.!!$F1 753
9 TraesCS5A01G514400 chr3D 589558070 589558832 762 True 1242.0 1242 96.0680 5 766 1 chr3D.!!$R1 761
10 TraesCS5A01G514400 chr7D 460053928 460054679 751 True 1232.0 1232 96.2770 5 755 1 chr7D.!!$R1 750
11 TraesCS5A01G514400 chr6D 16201785 16202539 754 False 1232.0 1232 96.1590 1 754 1 chr6D.!!$F1 753
12 TraesCS5A01G514400 chr6B 705610126 705610875 749 True 1219.0 1219 96.0110 5 754 1 chr6B.!!$R1 749
13 TraesCS5A01G514400 chr5B 280594015 280594771 756 True 1206.0 1206 95.5090 3 756 1 chr5B.!!$R1 753
14 TraesCS5A01G514400 chr1B 673882081 673882835 754 False 1206.0 1206 95.5030 1 755 1 chr1B.!!$F1 754
15 TraesCS5A01G514400 chr2A 14452299 14453052 753 False 1188.0 1188 95.1060 1 755 1 chr2A.!!$F1 754
16 TraesCS5A01G514400 chr2D 602007581 602009553 1972 True 1005.0 1112 85.2575 1158 3221 2 chr2D.!!$R1 2063
17 TraesCS5A01G514400 chr2B 732222590 732224512 1922 True 995.0 1109 85.5335 1209 3221 2 chr2B.!!$R1 2012
18 TraesCS5A01G514400 chr4A 731002833 731003743 910 False 880.0 880 84.0810 1203 2137 1 chr4A.!!$F2 934

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
870 882 0.033796 ACAATGGTGCCCAGATGAGG 60.034 55.0 13.26 0.0 36.75 3.86 F
995 1013 0.540365 ATTGGTGCAGGAAGTGGTGG 60.540 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 1893 1.068753 CGAGCAGGCGGAGATGATT 59.931 57.895 0.0 0.0 0.00 2.57 R
2454 2486 1.229428 CAGGTCGAAGAAAAGCAGCA 58.771 50.000 0.0 0.0 39.69 4.41 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
235 238 4.514401 GCTAGCAAGTAAGTACCCAACAT 58.486 43.478 10.63 0.00 0.00 2.71
313 316 2.009774 GTGGCACTTCTTCGCATGTAT 58.990 47.619 11.13 0.00 0.00 2.29
376 380 1.207329 GAGCTAAGACACCCGTTGGAT 59.793 52.381 0.00 0.00 34.81 3.41
507 512 9.571816 TTTCATGGAGTTGCATCATTGTATATA 57.428 29.630 0.00 0.00 0.00 0.86
583 588 2.259618 CCTGTACACTTCCGTTCATCG 58.740 52.381 0.00 0.00 39.52 3.84
767 772 7.090808 GGCTATGCTAGTTAAAACAAAAAGCT 58.909 34.615 0.00 0.00 0.00 3.74
781 786 6.849588 ACAAAAAGCTGAAGCCTAAAAATG 57.150 33.333 0.00 0.00 43.38 2.32
848 856 1.217779 GAGAGCTGTGGAGGAGCAC 59.782 63.158 0.00 0.00 39.05 4.40
867 879 0.533491 CCAACAATGGTGCCCAGATG 59.467 55.000 0.00 4.69 42.18 2.90
870 882 0.033796 ACAATGGTGCCCAGATGAGG 60.034 55.000 13.26 0.00 36.75 3.86
884 896 5.893255 CCCAGATGAGGGTTCATTTTATCAA 59.107 40.000 0.00 0.00 44.01 2.57
897 909 3.469008 TTTATCAATCGTCGCCTCCAT 57.531 42.857 0.00 0.00 0.00 3.41
916 930 4.880696 TCCATATCAATGCAATCGTGTTGA 59.119 37.500 0.95 0.95 35.33 3.18
931 945 5.757886 TCGTGTTGAAATCTGTTTGATTCC 58.242 37.500 0.00 0.00 43.99 3.01
993 1011 0.773644 AGATTGGTGCAGGAAGTGGT 59.226 50.000 0.00 0.00 0.00 4.16
994 1012 0.883833 GATTGGTGCAGGAAGTGGTG 59.116 55.000 0.00 0.00 0.00 4.17
995 1013 0.540365 ATTGGTGCAGGAAGTGGTGG 60.540 55.000 0.00 0.00 0.00 4.61
996 1014 1.640593 TTGGTGCAGGAAGTGGTGGA 61.641 55.000 0.00 0.00 0.00 4.02
1015 1033 2.286872 GATGGATGGATGGATCATCGC 58.713 52.381 0.00 0.00 41.35 4.58
1024 1042 3.928779 GATCATCGCCCCTCGCCA 61.929 66.667 0.00 0.00 38.27 5.69
1054 1072 0.978146 GCTGGGAGAAGACCTGGCTA 60.978 60.000 0.00 0.00 0.00 3.93
1531 1556 1.066573 AGCTGCTGCGTCTTGAAGTAT 60.067 47.619 10.14 0.00 45.42 2.12
1561 1586 1.745489 GTACCCGAAGCTGCCCTTG 60.745 63.158 0.00 0.00 32.78 3.61
1564 1589 3.121030 CCGAAGCTGCCCTTGACG 61.121 66.667 0.00 0.00 32.78 4.35
1720 1746 1.482621 CGCGGTGGATGATGTTCTCG 61.483 60.000 0.00 0.00 0.00 4.04
1906 1932 1.659954 GCAGTAGCCGATGAGCGAG 60.660 63.158 0.00 0.00 44.57 5.03
2258 2287 1.935327 CTCCTTGTCCTCCGTCGACC 61.935 65.000 10.58 0.00 0.00 4.79
2318 2347 2.786564 GAAAAAGCAGAGCACCGCGG 62.787 60.000 26.86 26.86 0.00 6.46
2359 2388 4.415332 ACCGTCGCGAGCACGATT 62.415 61.111 18.89 4.10 45.06 3.34
2364 2396 0.498927 GTCGCGAGCACGATTATGAC 59.501 55.000 10.24 2.93 45.06 3.06
2406 2438 1.668101 GACCCCGTCGAGCTCAGATT 61.668 60.000 15.40 0.00 0.00 2.40
2412 2444 1.202154 CGTCGAGCTCAGATTAACGGT 60.202 52.381 15.40 0.00 0.00 4.83
2434 2466 1.134189 TGCAGCTTCATGATCTCCAGG 60.134 52.381 0.00 0.00 0.00 4.45
2453 2485 1.449601 CCGTTCAGTATGCCGCCTT 60.450 57.895 0.00 0.00 34.76 4.35
2454 2486 1.024579 CCGTTCAGTATGCCGCCTTT 61.025 55.000 0.00 0.00 34.76 3.11
2465 2497 1.662044 CCGCCTTTGCTGCTTTTCT 59.338 52.632 0.00 0.00 34.43 2.52
2466 2498 0.032540 CCGCCTTTGCTGCTTTTCTT 59.967 50.000 0.00 0.00 34.43 2.52
2530 2562 1.370172 GGCCGCGTAGTCGATGTAG 60.370 63.158 4.92 0.00 39.71 2.74
2844 2882 1.290324 CGTAGATGATCGGGCTGGG 59.710 63.158 0.00 0.00 0.00 4.45
2891 2932 2.758737 CGCCGAAGAGGTAGGGGT 60.759 66.667 0.00 0.00 43.70 4.95
2937 2978 1.068417 TGTCGTTCCCGTTGGTCAG 59.932 57.895 0.00 0.00 35.01 3.51
2940 2981 2.317609 CGTTCCCGTTGGTCAGCAG 61.318 63.158 0.00 0.00 0.00 4.24
3016 3057 1.379916 CAGGTCATTGCTCCCCACA 59.620 57.895 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
183 186 1.413008 GAATTTTCATGCCCGTGCGC 61.413 55.000 0.00 0.0 41.78 6.09
261 264 5.571784 ATCATTGCATATTATCGCCAAGG 57.428 39.130 0.00 0.0 0.00 3.61
313 316 0.404426 TCTCTCTGAGGACGTTGGGA 59.596 55.000 4.59 0.0 0.00 4.37
376 380 4.270008 GCTTTTGCAAATCCCTCTACCTA 58.730 43.478 13.65 0.0 46.58 3.08
583 588 6.573664 TTGCAGCCATGTATGATAAATACC 57.426 37.500 0.00 0.0 0.00 2.73
767 772 7.324935 TGTACTATCGTCATTTTTAGGCTTCA 58.675 34.615 0.00 0.0 0.00 3.02
781 786 4.041740 TGCAGTTCCATGTACTATCGTC 57.958 45.455 0.00 0.0 0.00 4.20
812 817 5.182001 AGCTCTCAAACATGTGTAATTGTCC 59.818 40.000 0.00 0.0 0.00 4.02
867 879 5.738370 CGACGATTGATAAAATGAACCCTC 58.262 41.667 0.00 0.0 0.00 4.30
870 882 4.035208 AGGCGACGATTGATAAAATGAACC 59.965 41.667 0.00 0.0 0.00 3.62
871 883 5.156804 AGGCGACGATTGATAAAATGAAC 57.843 39.130 0.00 0.0 0.00 3.18
872 884 4.272504 GGAGGCGACGATTGATAAAATGAA 59.727 41.667 0.00 0.0 0.00 2.57
873 885 3.807622 GGAGGCGACGATTGATAAAATGA 59.192 43.478 0.00 0.0 0.00 2.57
874 886 3.559655 TGGAGGCGACGATTGATAAAATG 59.440 43.478 0.00 0.0 0.00 2.32
875 887 3.804036 TGGAGGCGACGATTGATAAAAT 58.196 40.909 0.00 0.0 0.00 1.82
876 888 3.254470 TGGAGGCGACGATTGATAAAA 57.746 42.857 0.00 0.0 0.00 1.52
877 889 2.971660 TGGAGGCGACGATTGATAAA 57.028 45.000 0.00 0.0 0.00 1.40
878 890 4.219725 TGATATGGAGGCGACGATTGATAA 59.780 41.667 0.00 0.0 0.00 1.75
880 892 2.562738 TGATATGGAGGCGACGATTGAT 59.437 45.455 0.00 0.0 0.00 2.57
884 896 2.932622 GCATTGATATGGAGGCGACGAT 60.933 50.000 0.00 0.0 32.15 3.73
897 909 6.968335 CAGATTTCAACACGATTGCATTGATA 59.032 34.615 0.00 0.0 31.45 2.15
916 930 6.656693 AGATGTTCTCGGAATCAAACAGATTT 59.343 34.615 0.00 0.0 46.76 2.17
931 945 5.587043 ACCACTAGAGTAGAAGATGTTCTCG 59.413 44.000 8.63 0.0 42.40 4.04
993 1011 2.237893 CGATGATCCATCCATCCATCCA 59.762 50.000 0.00 0.0 37.57 3.41
994 1012 2.915349 CGATGATCCATCCATCCATCC 58.085 52.381 0.00 0.0 37.57 3.51
995 1013 2.286872 GCGATGATCCATCCATCCATC 58.713 52.381 0.00 0.0 37.57 3.51
996 1014 1.064906 GGCGATGATCCATCCATCCAT 60.065 52.381 0.00 0.0 37.57 3.41
1054 1072 2.833582 ATGACCGACCTCGCCGAT 60.834 61.111 0.00 0.0 38.18 4.18
1063 1081 2.512515 GGCCTGAGCATGACCGAC 60.513 66.667 0.00 0.0 42.56 4.79
1720 1746 2.510238 CTGCACAGCGGCTACTCC 60.510 66.667 0.26 0.0 34.04 3.85
1867 1893 1.068753 CGAGCAGGCGGAGATGATT 59.931 57.895 0.00 0.0 0.00 2.57
2406 2438 2.499197 TCATGAAGCTGCAAACCGTTA 58.501 42.857 0.00 0.0 0.00 3.18
2412 2444 3.014623 CTGGAGATCATGAAGCTGCAAA 58.985 45.455 18.84 0.0 29.59 3.68
2434 2466 3.573491 GGCGGCATACTGAACGGC 61.573 66.667 3.07 0.0 44.25 5.68
2453 2485 1.603802 CAGGTCGAAGAAAAGCAGCAA 59.396 47.619 0.00 0.0 39.69 3.91
2454 2486 1.229428 CAGGTCGAAGAAAAGCAGCA 58.771 50.000 0.00 0.0 39.69 4.41
2465 2497 2.125552 CAGCATCGGCAGGTCGAA 60.126 61.111 0.00 0.0 44.61 3.71
2466 2498 3.068064 TCAGCATCGGCAGGTCGA 61.068 61.111 0.00 0.0 44.61 4.20
2510 2542 1.449726 TACATCGACTACGCGGCCAT 61.450 55.000 12.47 0.0 39.58 4.40
2524 2556 1.404391 TCGAACGAGGCCTTCTACATC 59.596 52.381 6.77 0.0 0.00 3.06
2530 2562 2.095252 GCAGTCGAACGAGGCCTTC 61.095 63.158 6.77 0.0 0.00 3.46
2561 2599 3.057547 CTCCAGACCTCACGCCGAG 62.058 68.421 0.00 0.0 41.89 4.63
2872 2910 4.570663 CCCTACCTCTTCGGCGCG 62.571 72.222 0.00 0.0 35.61 6.86
3106 3156 4.011517 GTCAGGTTCGCCCCGGAA 62.012 66.667 0.73 0.0 38.27 4.30


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

AutoCloner maintained by Alex Coulton.