Multiple sequence alignment - TraesCS1A01G318100

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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 TraesCS1A01G318100 chr1A 100.000 2697 0 0 1 2697 509542952 509540256 0.000000e+00 4981
1 TraesCS1A01G318100 chr1A 96.492 2708 83 3 1 2697 510110555 510113261 0.000000e+00 4464
2 TraesCS1A01G318100 chr1A 85.075 938 110 15 979 1894 509914025 509913096 0.000000e+00 929
3 TraesCS1A01G318100 chr1B 92.656 1171 73 4 979 2138 556834856 556836024 0.000000e+00 1674
4 TraesCS1A01G318100 chr1B 92.656 1171 73 4 979 2138 556863277 556864445 0.000000e+00 1674
5 TraesCS1A01G318100 chr1B 91.722 1196 80 10 979 2163 556252183 556253370 0.000000e+00 1642
6 TraesCS1A01G318100 chr1B 93.093 333 18 4 1811 2142 556666532 556666860 1.450000e-132 483
7 TraesCS1A01G318100 chr1B 95.333 150 7 0 2150 2299 556666917 556667066 3.470000e-59 239
8 TraesCS1A01G318100 chr1B 93.210 162 9 2 2139 2299 556253411 556253571 1.250000e-58 237
9 TraesCS1A01G318100 chr1B 91.358 162 12 2 2138 2299 556836082 556836241 1.260000e-53 220
10 TraesCS1A01G318100 chr1B 91.358 162 12 2 2138 2299 556864503 556864662 1.260000e-53 220
11 TraesCS1A01G318100 chr1D 91.201 1182 68 12 979 2149 412684831 412685987 0.000000e+00 1574
12 TraesCS1A01G318100 chr1D 90.758 1201 66 16 979 2163 412898525 412899696 0.000000e+00 1561
13 TraesCS1A01G318100 chr1D 85.760 934 108 15 979 1894 412642991 412643917 0.000000e+00 965
14 TraesCS1A01G318100 chr1D 84.958 944 106 17 979 1894 412746969 412747904 0.000000e+00 926
15 TraesCS1A01G318100 chr1D 85.959 876 98 15 979 1836 412764132 412765000 0.000000e+00 913
16 TraesCS1A01G318100 chr1D 88.296 769 77 6 979 1739 412855549 412856312 0.000000e+00 909
17 TraesCS1A01G318100 chr1D 93.333 150 9 1 2150 2299 412816315 412816463 1.260000e-53 220
18 TraesCS1A01G318100 chr1D 91.333 150 10 3 2150 2299 412899750 412899896 4.550000e-48 202
19 TraesCS1A01G318100 chr1D 90.667 150 11 2 2150 2299 412686049 412686195 2.120000e-46 196
20 TraesCS1A01G318100 chr4D 93.712 986 58 2 1 982 93109073 93110058 0.000000e+00 1474
21 TraesCS1A01G318100 chr4D 91.228 399 35 0 2299 2697 191750870 191751268 6.570000e-151 544
22 TraesCS1A01G318100 chr6B 93.712 986 57 3 1 982 274184008 274183024 0.000000e+00 1472
23 TraesCS1A01G318100 chr6B 93.408 986 60 3 1 982 200000501 199999517 0.000000e+00 1456
24 TraesCS1A01G318100 chr5D 93.617 987 57 4 1 982 247544470 247545455 0.000000e+00 1469
25 TraesCS1A01G318100 chr5D 90.955 398 35 1 2300 2697 75812770 75813166 3.950000e-148 534
26 TraesCS1A01G318100 chr2B 93.509 986 60 2 1 982 113311123 113312108 0.000000e+00 1463
27 TraesCS1A01G318100 chr2B 84.146 246 38 1 1893 2138 800495480 800495236 1.250000e-58 237
28 TraesCS1A01G318100 chr7D 93.414 987 59 4 1 982 312530042 312529057 0.000000e+00 1458
29 TraesCS1A01G318100 chr7D 91.479 399 32 2 2300 2697 605492140 605492537 5.080000e-152 547
30 TraesCS1A01G318100 chr7D 91.067 403 32 4 2296 2697 335879097 335878698 2.360000e-150 542
31 TraesCS1A01G318100 chr7D 90.977 399 36 0 2299 2697 43891159 43890761 3.060000e-149 538
32 TraesCS1A01G318100 chr7D 84.047 257 38 3 1893 2148 21096411 21096665 7.460000e-61 244
33 TraesCS1A01G318100 chr7B 93.408 986 61 2 1 982 103026068 103025083 0.000000e+00 1458
34 TraesCS1A01G318100 chr4B 93.414 987 59 4 1 982 44195981 44196966 0.000000e+00 1458
35 TraesCS1A01G318100 chr4B 93.182 132 9 0 1763 1894 633468427 633468558 7.620000e-46 195
36 TraesCS1A01G318100 chr6D 93.500 400 25 1 2298 2697 93891362 93890964 6.430000e-166 593
37 TraesCS1A01G318100 chr7A 92.211 398 31 0 2300 2697 635867568 635867965 5.040000e-157 564
38 TraesCS1A01G318100 chr3A 90.750 400 37 0 2298 2697 328061957 328061558 3.950000e-148 534
39 TraesCS1A01G318100 chr6A 84.462 251 38 1 1892 2142 216006979 216006730 2.070000e-61 246


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 TraesCS1A01G318100 chr1A 509540256 509542952 2696 True 4981.0 4981 100.0000 1 2697 1 chr1A.!!$R1 2696
1 TraesCS1A01G318100 chr1A 510110555 510113261 2706 False 4464.0 4464 96.4920 1 2697 1 chr1A.!!$F1 2696
2 TraesCS1A01G318100 chr1A 509913096 509914025 929 True 929.0 929 85.0750 979 1894 1 chr1A.!!$R2 915
3 TraesCS1A01G318100 chr1B 556834856 556836241 1385 False 947.0 1674 92.0070 979 2299 2 chr1B.!!$F3 1320
4 TraesCS1A01G318100 chr1B 556863277 556864662 1385 False 947.0 1674 92.0070 979 2299 2 chr1B.!!$F4 1320
5 TraesCS1A01G318100 chr1B 556252183 556253571 1388 False 939.5 1642 92.4660 979 2299 2 chr1B.!!$F1 1320
6 TraesCS1A01G318100 chr1B 556666532 556667066 534 False 361.0 483 94.2130 1811 2299 2 chr1B.!!$F2 488
7 TraesCS1A01G318100 chr1D 412642991 412643917 926 False 965.0 965 85.7600 979 1894 1 chr1D.!!$F1 915
8 TraesCS1A01G318100 chr1D 412746969 412747904 935 False 926.0 926 84.9580 979 1894 1 chr1D.!!$F2 915
9 TraesCS1A01G318100 chr1D 412764132 412765000 868 False 913.0 913 85.9590 979 1836 1 chr1D.!!$F3 857
10 TraesCS1A01G318100 chr1D 412855549 412856312 763 False 909.0 909 88.2960 979 1739 1 chr1D.!!$F5 760
11 TraesCS1A01G318100 chr1D 412684831 412686195 1364 False 885.0 1574 90.9340 979 2299 2 chr1D.!!$F6 1320
12 TraesCS1A01G318100 chr1D 412898525 412899896 1371 False 881.5 1561 91.0455 979 2299 2 chr1D.!!$F7 1320
13 TraesCS1A01G318100 chr4D 93109073 93110058 985 False 1474.0 1474 93.7120 1 982 1 chr4D.!!$F1 981
14 TraesCS1A01G318100 chr6B 274183024 274184008 984 True 1472.0 1472 93.7120 1 982 1 chr6B.!!$R2 981
15 TraesCS1A01G318100 chr6B 199999517 200000501 984 True 1456.0 1456 93.4080 1 982 1 chr6B.!!$R1 981
16 TraesCS1A01G318100 chr5D 247544470 247545455 985 False 1469.0 1469 93.6170 1 982 1 chr5D.!!$F2 981
17 TraesCS1A01G318100 chr2B 113311123 113312108 985 False 1463.0 1463 93.5090 1 982 1 chr2B.!!$F1 981
18 TraesCS1A01G318100 chr7D 312529057 312530042 985 True 1458.0 1458 93.4140 1 982 1 chr7D.!!$R2 981
19 TraesCS1A01G318100 chr7B 103025083 103026068 985 True 1458.0 1458 93.4080 1 982 1 chr7B.!!$R1 981
20 TraesCS1A01G318100 chr4B 44195981 44196966 985 False 1458.0 1458 93.4140 1 982 1 chr4B.!!$F1 981

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
723 730 7.083062 AGATCTTGATGCCCAATATGTAAGA 57.917 36.0 0.0 0.0 33.68 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2402 2532 0.815615 GTAGCACTGCCCATACCAGC 60.816 60.0 0.0 0.0 33.65 4.85 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
723 730 7.083062 AGATCTTGATGCCCAATATGTAAGA 57.917 36.000 0.00 0.00 33.68 2.10
1015 1022 2.352814 CCGACTCTACAACTTCACCAGG 60.353 54.545 0.00 0.00 0.00 4.45
1144 1152 1.610624 CCGGCAGCTTTAAGACCTTCA 60.611 52.381 0.00 0.00 0.00 3.02
1225 1233 1.481056 CCTCACCGACCCTTTCACCT 61.481 60.000 0.00 0.00 0.00 4.00
1288 1296 1.227704 TTCTTCGCCAACTTCGCCA 60.228 52.632 0.00 0.00 0.00 5.69
1303 1311 1.442526 CGCCACCTCCATGATCAAGC 61.443 60.000 0.00 0.00 0.00 4.01
1312 1320 1.179152 CATGATCAAGCTGGGCAACA 58.821 50.000 0.00 0.00 39.74 3.33
1686 1720 8.706936 CCTCAGAGAATATCATAATGTTTCACG 58.293 37.037 0.00 0.00 0.00 4.35
1900 1947 3.759618 CGATAGATCCAAGGTACTCCCTC 59.240 52.174 0.00 0.00 40.80 4.30
2316 2446 4.070009 CACAACACTACTAGGGAAAACCC 58.930 47.826 0.00 0.00 41.63 4.11
2361 2491 2.571757 CAGTAGCGCTCGGTCCAA 59.428 61.111 16.34 0.00 0.00 3.53
2402 2532 6.233073 CTACAGCTAAGTTGTAGCAGTAGCG 61.233 48.000 18.79 4.70 46.14 4.26
2482 2612 4.468643 GCTACTGCTAACTATCTGTAGCG 58.531 47.826 12.88 0.00 44.58 4.26
2503 2633 2.778659 CTTGTTTATCTGAAGCGCTGC 58.221 47.619 12.58 10.71 0.00 5.25
2522 2652 4.421952 GCTAAGCCAGCGGTACTC 57.578 61.111 0.00 0.00 41.37 2.59
2557 2687 2.159099 AGCGCTACTGCTAATGTTGCTA 60.159 45.455 8.99 0.00 45.14 3.49
2566 2696 3.756434 TGCTAATGTTGCTACTTTCACCC 59.244 43.478 2.85 0.00 0.00 4.61
2682 2812 5.926214 TCATAGACATACAGTAGTCTCGC 57.074 43.478 13.07 0.00 43.59 5.03
2683 2813 4.755629 TCATAGACATACAGTAGTCTCGCC 59.244 45.833 13.07 0.00 43.59 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 5.528043 TTGTGACAATACTGGTGCAATTT 57.472 34.783 0.00 0.00 0.00 1.82
467 474 3.483808 TGGAATGTTGTGCACTAGACA 57.516 42.857 19.41 18.95 0.00 3.41
593 600 1.603739 AGAAAGGGTTCTTGCCGGC 60.604 57.895 22.73 22.73 41.55 6.13
723 730 3.297134 TGAAAGACCTTGGTGAAGCTT 57.703 42.857 0.00 0.00 0.00 3.74
794 801 9.903682 GGATGACATATTGTTGATTGGAAATAG 57.096 33.333 0.00 0.00 0.00 1.73
1015 1022 1.522580 GTCGCTGGGCTTCTCCATC 60.523 63.158 0.00 0.00 36.05 3.51
1144 1152 5.068198 TCACTAACTTGAAGTAGTCGGTGTT 59.932 40.000 0.00 0.00 34.78 3.32
1218 1226 0.034337 GGACGTAGGCACAGGTGAAA 59.966 55.000 3.10 0.00 0.00 2.69
1288 1296 0.549950 CCCAGCTTGATCATGGAGGT 59.450 55.000 14.30 3.76 36.09 3.85
1303 1311 3.294493 CGGGTTGGTGTTGCCCAG 61.294 66.667 0.00 0.00 42.44 4.45
1331 1339 3.190383 TCTTCCTGATCTCACCTTGGA 57.810 47.619 0.00 0.00 0.00 3.53
1434 1443 9.601217 GAGAAAGGAGCTATAACAATCTTACAA 57.399 33.333 0.00 0.00 0.00 2.41
1900 1947 8.744652 CCTTAGATGACTTATACACCTAGATGG 58.255 40.741 0.00 0.00 42.93 3.51
2316 2446 5.920840 TGCATATTTCAAGCGCTACTACTAG 59.079 40.000 12.05 0.00 0.00 2.57
2395 2525 1.595382 GCCCATACCAGCGCTACTG 60.595 63.158 10.99 4.10 46.77 2.74
2402 2532 0.815615 GTAGCACTGCCCATACCAGC 60.816 60.000 0.00 0.00 33.65 4.85
2482 2612 2.778659 CAGCGCTTCAGATAAACAAGC 58.221 47.619 7.50 0.00 39.38 4.01
2517 2647 4.608951 CGCTGTAAATCACCTAGGAGTAC 58.391 47.826 17.98 7.13 0.00 2.73
2522 2652 2.604046 AGCGCTGTAAATCACCTAGG 57.396 50.000 10.39 7.41 0.00 3.02
2557 2687 1.774300 GGTGGGGATGGGTGAAAGT 59.226 57.895 0.00 0.00 0.00 2.66
2566 2696 2.415983 TACATAGAGGGGTGGGGATG 57.584 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.