Multiple sequence alignment - TraesCS1A01G146800

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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 TraesCS1A01G146800 chr1A 100.000 2703 0 0 1 2703 253373209 253370507 0.000000e+00 4992
1 TraesCS1A01G146800 chr2D 94.639 1660 84 5 1 1658 60048826 60047170 0.000000e+00 2567
2 TraesCS1A01G146800 chr2D 95.652 69 3 0 1755 1823 60046959 60046891 7.910000e-21 111
3 TraesCS1A01G146800 chr7B 90.027 1825 167 14 1 1823 583697214 583695403 0.000000e+00 2348
4 TraesCS1A01G146800 chr7D 88.621 1828 190 13 1 1823 589288580 589290394 0.000000e+00 2207
5 TraesCS1A01G146800 chr7D 85.285 1665 191 29 1 1660 609917164 609918779 0.000000e+00 1668
6 TraesCS1A01G146800 chr7D 90.226 133 13 0 1690 1822 609919030 609919162 9.950000e-40 174
7 TraesCS1A01G146800 chr4D 85.951 1509 186 16 1 1507 318517390 318518874 0.000000e+00 1589
8 TraesCS1A01G146800 chr4D 90.809 272 19 2 1551 1822 318518875 318519140 2.560000e-95 359
9 TraesCS1A01G146800 chr3A 94.820 888 44 2 1818 2703 498515214 498514327 0.000000e+00 1384
10 TraesCS1A01G146800 chr3A 95.006 881 43 1 1824 2703 437504734 437505614 0.000000e+00 1382
11 TraesCS1A01G146800 chr3A 94.892 881 44 1 1824 2703 674846851 674847731 0.000000e+00 1376
12 TraesCS1A01G146800 chr3A 94.677 883 39 8 1824 2703 430375699 430374822 0.000000e+00 1363
13 TraesCS1A01G146800 chr3A 94.564 883 46 2 1822 2703 606958276 606957395 0.000000e+00 1363
14 TraesCS1A01G146800 chr7A 94.892 881 44 1 1824 2703 606837155 606838035 0.000000e+00 1376
15 TraesCS1A01G146800 chr4A 94.570 884 44 3 1824 2703 77950619 77949736 0.000000e+00 1363
16 TraesCS1A01G146800 chr4A 94.659 880 46 1 1824 2702 494791736 494790857 0.000000e+00 1363
17 TraesCS1A01G146800 chr4A 94.558 882 46 2 1824 2703 343919900 343920781 0.000000e+00 1362
18 TraesCS1A01G146800 chr3B 81.454 1623 266 19 141 1750 571321349 571319749 0.000000e+00 1297
19 TraesCS1A01G146800 chr3B 91.892 74 6 0 1746 1819 571315258 571315185 1.320000e-18 104
20 TraesCS1A01G146800 chr2B 80.638 1694 287 21 141 1822 575338072 575336408 0.000000e+00 1273
21 TraesCS1A01G146800 chr2B 85.958 819 97 13 825 1637 104600104 104599298 0.000000e+00 859
22 TraesCS1A01G146800 chr2B 82.289 734 124 5 51 784 104601004 104600277 4.910000e-177 630
23 TraesCS1A01G146800 chr4B 81.524 1391 221 23 438 1822 672993746 672992386 0.000000e+00 1112


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 TraesCS1A01G146800 chr1A 253370507 253373209 2702 True 4992.0 4992 100.0000 1 2703 1 chr1A.!!$R1 2702
1 TraesCS1A01G146800 chr2D 60046891 60048826 1935 True 1339.0 2567 95.1455 1 1823 2 chr2D.!!$R1 1822
2 TraesCS1A01G146800 chr7B 583695403 583697214 1811 True 2348.0 2348 90.0270 1 1823 1 chr7B.!!$R1 1822
3 TraesCS1A01G146800 chr7D 589288580 589290394 1814 False 2207.0 2207 88.6210 1 1823 1 chr7D.!!$F1 1822
4 TraesCS1A01G146800 chr7D 609917164 609919162 1998 False 921.0 1668 87.7555 1 1822 2 chr7D.!!$F2 1821
5 TraesCS1A01G146800 chr4D 318517390 318519140 1750 False 974.0 1589 88.3800 1 1822 2 chr4D.!!$F1 1821
6 TraesCS1A01G146800 chr3A 498514327 498515214 887 True 1384.0 1384 94.8200 1818 2703 1 chr3A.!!$R2 885
7 TraesCS1A01G146800 chr3A 437504734 437505614 880 False 1382.0 1382 95.0060 1824 2703 1 chr3A.!!$F1 879
8 TraesCS1A01G146800 chr3A 674846851 674847731 880 False 1376.0 1376 94.8920 1824 2703 1 chr3A.!!$F2 879
9 TraesCS1A01G146800 chr3A 430374822 430375699 877 True 1363.0 1363 94.6770 1824 2703 1 chr3A.!!$R1 879
10 TraesCS1A01G146800 chr3A 606957395 606958276 881 True 1363.0 1363 94.5640 1822 2703 1 chr3A.!!$R3 881
11 TraesCS1A01G146800 chr7A 606837155 606838035 880 False 1376.0 1376 94.8920 1824 2703 1 chr7A.!!$F1 879
12 TraesCS1A01G146800 chr4A 77949736 77950619 883 True 1363.0 1363 94.5700 1824 2703 1 chr4A.!!$R1 879
13 TraesCS1A01G146800 chr4A 494790857 494791736 879 True 1363.0 1363 94.6590 1824 2702 1 chr4A.!!$R2 878
14 TraesCS1A01G146800 chr4A 343919900 343920781 881 False 1362.0 1362 94.5580 1824 2703 1 chr4A.!!$F1 879
15 TraesCS1A01G146800 chr3B 571319749 571321349 1600 True 1297.0 1297 81.4540 141 1750 1 chr3B.!!$R2 1609
16 TraesCS1A01G146800 chr2B 575336408 575338072 1664 True 1273.0 1273 80.6380 141 1822 1 chr2B.!!$R1 1681
17 TraesCS1A01G146800 chr2B 104599298 104601004 1706 True 744.5 859 84.1235 51 1637 2 chr2B.!!$R2 1586
18 TraesCS1A01G146800 chr4B 672992386 672993746 1360 True 1112.0 1112 81.5240 438 1822 1 chr4B.!!$R1 1384

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
908 1052 0.534877 TCCAACGCTCAAGCACACAT 60.535 50.0 2.5 0.0 42.21 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 2239 0.036952 AGGGATGACACTGAAGCACG 60.037 55.0 0.0 0.0 0.0 5.34 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
29 30 7.425606 TGCTTCTTTCATACTTCCAACTTTTC 58.574 34.615 0.00 0.00 0.00 2.29
30 31 6.863645 GCTTCTTTCATACTTCCAACTTTTCC 59.136 38.462 0.00 0.00 0.00 3.13
46 47 0.555769 TTCCCCCTCTGTTTTGCAGT 59.444 50.000 0.00 0.00 45.23 4.40
123 124 4.454504 CACGGCAACTTACAACCTTTCTAT 59.545 41.667 0.00 0.00 0.00 1.98
190 192 4.022676 TGTGTCTGCTCATACGACTAAACA 60.023 41.667 0.00 0.00 0.00 2.83
192 194 5.577164 GTGTCTGCTCATACGACTAAACATT 59.423 40.000 0.00 0.00 0.00 2.71
206 209 5.077564 ACTAAACATTCCAAGAAAGACCCC 58.922 41.667 0.00 0.00 0.00 4.95
509 520 4.495422 ACTCCATTGTTGATACGTCTGAC 58.505 43.478 0.00 0.00 0.00 3.51
556 567 1.342174 CACAAGTTTGGCTGCCTCAAT 59.658 47.619 21.03 2.28 0.00 2.57
630 641 1.505425 GCATGATCGTGCTGCTCATA 58.495 50.000 28.82 0.00 41.82 2.15
708 720 2.366533 CAGTCGGTACTAGGAAGAGCA 58.633 52.381 0.00 0.00 33.48 4.26
754 766 4.502263 CGTGCATCGTCAGGACAT 57.498 55.556 0.00 0.00 34.52 3.06
779 791 1.512926 ATGTGTCTGCGTCAACCTTC 58.487 50.000 0.00 0.00 0.00 3.46
908 1052 0.534877 TCCAACGCTCAAGCACACAT 60.535 50.000 2.50 0.00 42.21 3.21
1001 1146 3.096852 TGCCTATCGATATTCCGGACAT 58.903 45.455 1.83 0.00 0.00 3.06
1097 1242 1.560860 GCAGCGTCTCTTGGTGTGAC 61.561 60.000 0.00 0.00 37.18 3.67
1134 1279 0.107654 GCGAGTTCAGGCACCCTATT 60.108 55.000 0.00 0.00 29.64 1.73
1163 1309 2.915659 ACCACCGTTCAGCCTCGA 60.916 61.111 0.00 0.00 0.00 4.04
1230 1376 3.006940 GTCTTATGCATTCCCGTCACAA 58.993 45.455 3.54 0.00 0.00 3.33
1609 1772 1.336517 GCACACGCTACCACTTCTGTA 60.337 52.381 0.00 0.00 34.30 2.74
1734 2118 3.127895 AGCAACAACAAGCACTTTACGAA 59.872 39.130 0.00 0.00 0.00 3.85
1759 2143 1.240256 TAGGCGTTTTGGAAATGCGT 58.760 45.000 14.63 14.63 0.00 5.24
1804 2188 6.981762 ATGCAATCAGAGAGTAAGTTTCTG 57.018 37.500 0.00 0.00 39.69 3.02
1839 2223 1.466025 TTGTGTAGCGACCCGACCTT 61.466 55.000 0.00 0.00 0.00 3.50
1855 2239 3.397849 ACCTTAAACGGTCAAGTCTCC 57.602 47.619 0.00 0.00 29.14 3.71
1926 2310 8.522542 ACTCGAAGGATTTATAACAGAGTAGT 57.477 34.615 0.00 0.00 35.06 2.73
1965 2349 8.777865 TTACATCGAATGTCTCAAAAGAGAAT 57.222 30.769 4.15 0.00 43.67 2.40
2006 2390 5.355350 GCTTAAGGCCATCTAATGCGATAAT 59.645 40.000 5.01 0.00 34.27 1.28
2174 2560 9.104965 GAATATGCTACCAATGTAACACAGTAA 57.895 33.333 0.00 0.00 0.00 2.24
2253 2639 9.005777 TCTATGGTTATAGTTTTTGCGAAAAGT 57.994 29.630 20.64 20.64 40.54 2.66
2340 2726 4.010349 GAGAAGGTAACCCCAACTCAATG 58.990 47.826 0.00 0.00 37.50 2.82
2444 2831 1.305129 TCCATAACCGGGGACACGA 60.305 57.895 6.32 0.00 35.47 4.35
2452 2839 1.080298 CGGGGACACGACTAACCAC 60.080 63.158 0.00 0.00 35.47 4.16
2468 2855 6.927416 ACTAACCACGATTAGATTGTACACA 58.073 36.000 0.00 0.00 35.96 3.72
2469 2856 7.553334 ACTAACCACGATTAGATTGTACACAT 58.447 34.615 0.00 0.00 35.96 3.21
2487 2874 0.796312 ATTACAGAGGTTTGCGCACG 59.204 50.000 11.12 0.00 0.00 5.34
2518 2905 0.389948 GACTTGATCGCCTCCGTTGT 60.390 55.000 0.00 0.00 35.54 3.32
2519 2906 0.389948 ACTTGATCGCCTCCGTTGTC 60.390 55.000 0.00 0.00 35.54 3.18
2534 2921 2.153247 CGTTGTCTTTCTCGCACTACAC 59.847 50.000 0.00 0.00 0.00 2.90
2646 3035 0.179089 CCTGCTGATCCACCTCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 6.834451 TGTGGTGTAAAATGAAGGTTAAAGGA 59.166 34.615 0.00 0.00 0.00 3.36
82 83 3.684305 CCGTGCATGAAAGTCATAAGTGA 59.316 43.478 7.72 0.00 34.28 3.41
83 84 3.728864 GCCGTGCATGAAAGTCATAAGTG 60.729 47.826 7.72 0.00 34.28 3.16
123 124 7.604927 CCTGCATGTAAGTAAGGTAGTAACAAA 59.395 37.037 0.00 0.00 0.00 2.83
190 192 2.158325 TGCAAGGGGTCTTTCTTGGAAT 60.158 45.455 0.00 0.00 38.15 3.01
192 194 0.850100 TGCAAGGGGTCTTTCTTGGA 59.150 50.000 0.00 0.00 40.31 3.53
493 504 4.699637 AGGTTTGTCAGACGTATCAACAA 58.300 39.130 4.09 4.09 33.43 2.83
509 520 8.936864 CAATCTTTACCTACTGACTAAGGTTTG 58.063 37.037 0.00 0.00 43.77 2.93
556 567 2.167487 GGACCCTTGTTTTGAACAGCAA 59.833 45.455 0.00 0.00 43.27 3.91
630 641 0.100503 GCTTTGGAAACAGTGTGCGT 59.899 50.000 0.00 0.00 44.54 5.24
708 720 2.693069 CTGATCAGCTTTGTTCCGAGT 58.307 47.619 10.38 0.00 0.00 4.18
754 766 1.842052 TGACGCAGACACATACCCTA 58.158 50.000 0.00 0.00 0.00 3.53
804 817 5.106277 ACATTTGTCTGAACTAGATCGACGA 60.106 40.000 0.00 0.00 37.83 4.20
1001 1146 2.678934 AAGTAGGGCGCGGAGTCA 60.679 61.111 8.83 0.00 0.00 3.41
1097 1242 1.760268 GCGCTCATTCTGCTTCTCGG 61.760 60.000 0.00 0.00 0.00 4.63
1101 1246 1.080995 ACTCGCGCTCATTCTGCTTC 61.081 55.000 5.56 0.00 0.00 3.86
1134 1279 2.473760 CGGTGGTGGCGTGAAAACA 61.474 57.895 0.00 0.00 0.00 2.83
1163 1309 4.563140 ATTGGCTGGCTCAAATCAATTT 57.437 36.364 2.00 0.00 0.00 1.82
1208 1354 1.593006 GTGACGGGAATGCATAAGACG 59.407 52.381 0.00 5.53 0.00 4.18
1230 1376 2.507944 GCCATCATCTGCTCCGGT 59.492 61.111 0.00 0.00 0.00 5.28
1421 1582 4.497473 TTGTAAACAGCCATGCAGTTAC 57.503 40.909 0.00 0.00 37.29 2.50
1609 1772 1.376942 GGCACTGCTCTGCACATCT 60.377 57.895 0.00 0.00 39.08 2.90
1676 1839 3.515502 TGGAGGTTCATAGTCCACTTCTG 59.484 47.826 0.00 0.00 35.36 3.02
1734 2118 4.869861 GCATTTCCAAAACGCCTAATGATT 59.130 37.500 0.00 0.00 0.00 2.57
1759 2143 6.443792 CATTCATATGCTTGCTATTGCTTCA 58.556 36.000 0.00 0.00 40.48 3.02
1804 2188 2.354259 CACAAGAAGTGGAGGATGAGC 58.646 52.381 0.00 0.00 44.69 4.26
1855 2239 0.036952 AGGGATGACACTGAAGCACG 60.037 55.000 0.00 0.00 0.00 5.34
1926 2310 9.594478 ACATTCGATGTAATAAGTGTGTGATTA 57.406 29.630 0.00 0.00 42.78 1.75
2006 2390 4.224370 ACTTATCTTCCAAGCCTTCCGTTA 59.776 41.667 0.00 0.00 0.00 3.18
2158 2544 6.312399 TCTTGCTTTACTGTGTTACATTGG 57.688 37.500 0.00 0.00 0.00 3.16
2174 2560 7.555554 AGTGATAGCATTATTCTGTTCTTGCTT 59.444 33.333 0.13 0.00 40.60 3.91
2253 2639 7.425224 TTCCTTTGTTGTAGGGAAAAATTGA 57.575 32.000 0.00 0.00 35.27 2.57
2298 2684 6.968263 TCTCAATATTTGTTCAACCACCAA 57.032 33.333 0.00 0.00 0.00 3.67
2340 2726 7.873505 TGTTGGGTTGTTAATTACTTAATTGGC 59.126 33.333 4.74 0.00 36.62 4.52
2444 2831 6.927416 TGTGTACAATCTAATCGTGGTTAGT 58.073 36.000 0.00 0.00 34.16 2.24
2452 2839 7.921214 ACCTCTGTAATGTGTACAATCTAATCG 59.079 37.037 0.00 0.00 0.00 3.34
2468 2855 0.796312 CGTGCGCAAACCTCTGTAAT 59.204 50.000 14.00 0.00 0.00 1.89
2469 2856 0.531090 ACGTGCGCAAACCTCTGTAA 60.531 50.000 14.00 0.00 0.00 2.41
2487 2874 2.484264 CGATCAAGTCTTGTGGGGAAAC 59.516 50.000 12.30 0.00 0.00 2.78
2518 2905 0.956633 ACCGTGTAGTGCGAGAAAGA 59.043 50.000 0.00 0.00 0.00 2.52
2519 2906 1.060713 CACCGTGTAGTGCGAGAAAG 58.939 55.000 0.00 0.00 0.00 2.62
2534 2921 2.096417 GTCATCCGTTTCTCAAACACCG 60.096 50.000 0.40 0.00 41.44 4.94
2569 2956 6.970043 CGGAGTAGAGAGTTAATGTTTCTGAG 59.030 42.308 0.00 0.00 0.00 3.35
2646 3035 5.044428 TGAGTAAGTTACGTGAAGCTCTC 57.956 43.478 7.38 0.58 0.00 3.20


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

AutoCloner maintained by Alex Coulton.