Multiple sequence alignment - TraesCS6A01G295700

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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 TraesCS6A01G295700 chr6A 100.000 2506 0 0 1 2506 529359990 529362495 0.000000e+00 4628
1 TraesCS6A01G295700 chr6A 94.099 1576 69 11 307 1871 603915985 603917547 0.000000e+00 2374
2 TraesCS6A01G295700 chr6A 96.028 428 17 0 1 428 136655469 136655896 0.000000e+00 697
3 TraesCS6A01G295700 chr6A 94.850 233 12 0 1 233 401364324 401364556 5.090000e-97 364
4 TraesCS6A01G295700 chr2A 93.333 1935 97 11 593 2506 538635086 538633163 0.000000e+00 2830
5 TraesCS6A01G295700 chr2A 94.641 1642 69 3 884 2506 605771413 605773054 0.000000e+00 2527
6 TraesCS6A01G295700 chr2B 93.127 1935 105 6 595 2506 103775503 103773574 0.000000e+00 2811
7 TraesCS6A01G295700 chr2B 92.778 360 25 1 2148 2506 739888190 739887831 1.030000e-143 520
8 TraesCS6A01G295700 chr2B 90.104 384 19 3 2141 2506 676214380 676213998 4.850000e-132 481
9 TraesCS6A01G295700 chr4B 92.853 1931 107 10 597 2506 505038361 505036441 0.000000e+00 2772
10 TraesCS6A01G295700 chr7B 92.802 1931 109 7 597 2506 610765901 610763980 0.000000e+00 2769
11 TraesCS6A01G295700 chr7B 92.031 1945 110 13 595 2506 551208777 551210709 0.000000e+00 2691
12 TraesCS6A01G295700 chr7B 87.784 352 41 2 2156 2506 725304627 725304977 6.450000e-111 411
13 TraesCS6A01G295700 chr3A 94.082 1825 89 5 701 2506 579943192 579941368 0.000000e+00 2754
14 TraesCS6A01G295700 chr3A 94.695 1131 50 2 234 1362 733886976 733885854 0.000000e+00 1748
15 TraesCS6A01G295700 chr3A 94.421 233 11 2 1 233 513294845 513295075 8.520000e-95 357
16 TraesCS6A01G295700 chr3A 93.991 233 14 0 1 233 733887521 733887289 1.100000e-93 353
17 TraesCS6A01G295700 chrUn 92.612 1949 85 18 597 2506 38465374 38467302 0.000000e+00 2747
18 TraesCS6A01G295700 chr4A 91.434 1938 128 17 593 2506 694170082 694172005 0.000000e+00 2625
19 TraesCS6A01G295700 chr4A 90.876 1370 76 14 1166 2506 429489601 429490950 0.000000e+00 1792
20 TraesCS6A01G295700 chr4A 96.646 984 32 1 234 1216 429488562 429489545 0.000000e+00 1633
21 TraesCS6A01G295700 chr4A 92.142 649 34 6 1869 2506 549622144 549622786 0.000000e+00 900
22 TraesCS6A01G295700 chr4A 91.489 658 29 6 1870 2506 523834660 523835311 0.000000e+00 880
23 TraesCS6A01G295700 chr4A 91.033 658 34 3 1869 2506 523835323 523835975 0.000000e+00 865
24 TraesCS6A01G295700 chr4A 95.279 233 11 0 1 233 490340841 490341073 1.090000e-98 370
25 TraesCS6A01G295700 chr4A 95.928 221 9 0 1 221 429488017 429488237 2.370000e-95 359
26 TraesCS6A01G295700 chr1A 92.017 1666 89 12 234 1871 443853781 443855430 0.000000e+00 2300
27 TraesCS6A01G295700 chr1A 91.049 1497 84 17 407 1871 497975696 497977174 0.000000e+00 1977
28 TraesCS6A01G295700 chr1A 95.708 233 9 1 1 233 580782996 580783227 8.460000e-100 374
29 TraesCS6A01G295700 chr4D 92.430 1321 86 8 561 1873 222629931 222628617 0.000000e+00 1873
30 TraesCS6A01G295700 chr6B 91.351 659 30 5 1869 2506 180276056 180275404 0.000000e+00 876
31 TraesCS6A01G295700 chr5A 95.279 233 11 0 1 233 345672959 345672727 1.090000e-98 370
32 TraesCS6A01G295700 chr5A 94.348 230 13 0 1 230 133817630 133817859 1.100000e-93 353
33 TraesCS6A01G295700 chr5B 89.630 135 8 2 492 626 189704803 189704931 1.540000e-37 167


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 TraesCS6A01G295700 chr6A 529359990 529362495 2505 False 4628.000000 4628 100.000000 1 2506 1 chr6A.!!$F3 2505
1 TraesCS6A01G295700 chr6A 603915985 603917547 1562 False 2374.000000 2374 94.099000 307 1871 1 chr6A.!!$F4 1564
2 TraesCS6A01G295700 chr2A 538633163 538635086 1923 True 2830.000000 2830 93.333000 593 2506 1 chr2A.!!$R1 1913
3 TraesCS6A01G295700 chr2A 605771413 605773054 1641 False 2527.000000 2527 94.641000 884 2506 1 chr2A.!!$F1 1622
4 TraesCS6A01G295700 chr2B 103773574 103775503 1929 True 2811.000000 2811 93.127000 595 2506 1 chr2B.!!$R1 1911
5 TraesCS6A01G295700 chr4B 505036441 505038361 1920 True 2772.000000 2772 92.853000 597 2506 1 chr4B.!!$R1 1909
6 TraesCS6A01G295700 chr7B 610763980 610765901 1921 True 2769.000000 2769 92.802000 597 2506 1 chr7B.!!$R1 1909
7 TraesCS6A01G295700 chr7B 551208777 551210709 1932 False 2691.000000 2691 92.031000 595 2506 1 chr7B.!!$F1 1911
8 TraesCS6A01G295700 chr3A 579941368 579943192 1824 True 2754.000000 2754 94.082000 701 2506 1 chr3A.!!$R1 1805
9 TraesCS6A01G295700 chr3A 733885854 733887521 1667 True 1050.500000 1748 94.343000 1 1362 2 chr3A.!!$R2 1361
10 TraesCS6A01G295700 chrUn 38465374 38467302 1928 False 2747.000000 2747 92.612000 597 2506 1 chrUn.!!$F1 1909
11 TraesCS6A01G295700 chr4A 694170082 694172005 1923 False 2625.000000 2625 91.434000 593 2506 1 chr4A.!!$F3 1913
12 TraesCS6A01G295700 chr4A 429488017 429490950 2933 False 1261.333333 1792 94.483333 1 2506 3 chr4A.!!$F4 2505
13 TraesCS6A01G295700 chr4A 549622144 549622786 642 False 900.000000 900 92.142000 1869 2506 1 chr4A.!!$F2 637
14 TraesCS6A01G295700 chr4A 523834660 523835975 1315 False 872.500000 880 91.261000 1869 2506 2 chr4A.!!$F5 637
15 TraesCS6A01G295700 chr1A 443853781 443855430 1649 False 2300.000000 2300 92.017000 234 1871 1 chr1A.!!$F1 1637
16 TraesCS6A01G295700 chr1A 497975696 497977174 1478 False 1977.000000 1977 91.049000 407 1871 1 chr1A.!!$F2 1464
17 TraesCS6A01G295700 chr4D 222628617 222629931 1314 True 1873.000000 1873 92.430000 561 1873 1 chr4D.!!$R1 1312
18 TraesCS6A01G295700 chr6B 180275404 180276056 652 True 876.000000 876 91.351000 1869 2506 1 chr6B.!!$R1 637

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
142 143 0.322456 TGATGTGGTGCTACCTTGCC 60.322 55.0 6.83 0.0 39.58 4.52 F
845 1168 1.108727 CCCCACAAAGTGAAGCTGCA 61.109 55.0 1.02 0.0 35.23 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 1723 0.032130 TAGCAAGATCATCGTCCGCC 59.968 55.0 0.00 0.0 0.0 6.13 R
1939 2486 0.324275 AATGGCGCTGTTTGGGGTAT 60.324 50.0 7.64 0.0 0.0 2.73 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
40 41 2.642311 TCTGTTGATTCCAGCCCAACTA 59.358 45.455 0.00 0.00 40.40 2.24
142 143 0.322456 TGATGTGGTGCTACCTTGCC 60.322 55.000 6.83 0.00 39.58 4.52
143 144 1.369091 GATGTGGTGCTACCTTGCCG 61.369 60.000 6.83 0.00 39.58 5.69
181 182 2.499693 TGTGGTTCTCTTCACAGTGACA 59.500 45.455 1.52 0.00 38.75 3.58
263 576 8.792633 TGTGTTTAAATTGAGAATCTAGGGTTG 58.207 33.333 0.00 0.00 34.92 3.77
578 894 7.181305 TGGTTCTGTTCCTATTTATGTCCAGTA 59.819 37.037 0.00 0.00 0.00 2.74
810 1133 2.413371 GCCTGACAAGTTTGCGAAGATC 60.413 50.000 0.00 0.00 0.00 2.75
845 1168 1.108727 CCCCACAAAGTGAAGCTGCA 61.109 55.000 1.02 0.00 35.23 4.41
982 1312 2.826725 CTCGGGTACTTCCTTGTCTTCT 59.173 50.000 0.00 0.00 36.25 2.85
1093 1423 3.897239 CTCTCTGCCTCTCTTCTTCCTA 58.103 50.000 0.00 0.00 0.00 2.94
1230 1649 3.369892 GGAGCAGCCTATTCTTTCTGACA 60.370 47.826 0.00 0.00 0.00 3.58
1300 1719 3.821421 GGATGACGACCTTTCTATGGT 57.179 47.619 0.00 0.00 41.07 3.55
1301 1720 3.458189 GGATGACGACCTTTCTATGGTG 58.542 50.000 0.00 0.00 38.03 4.17
1302 1721 3.458189 GATGACGACCTTTCTATGGTGG 58.542 50.000 0.00 0.00 38.03 4.61
1303 1722 2.253610 TGACGACCTTTCTATGGTGGT 58.746 47.619 0.41 0.41 46.54 4.16
1304 1723 2.028476 TGACGACCTTTCTATGGTGGTG 60.028 50.000 5.36 0.00 44.50 4.17
1305 1724 1.278127 ACGACCTTTCTATGGTGGTGG 59.722 52.381 0.00 0.00 43.23 4.61
1306 1725 1.751437 GACCTTTCTATGGTGGTGGC 58.249 55.000 0.00 0.00 38.03 5.01
1307 1726 0.035439 ACCTTTCTATGGTGGTGGCG 60.035 55.000 0.00 0.00 36.30 5.69
1308 1727 0.748005 CCTTTCTATGGTGGTGGCGG 60.748 60.000 0.00 0.00 0.00 6.13
1309 1728 0.251916 CTTTCTATGGTGGTGGCGGA 59.748 55.000 0.00 0.00 0.00 5.54
1310 1729 0.035820 TTTCTATGGTGGTGGCGGAC 60.036 55.000 0.00 0.00 0.00 4.79
1311 1730 2.202878 CTATGGTGGTGGCGGACG 60.203 66.667 0.00 0.00 0.00 4.79
1312 1731 2.680707 TATGGTGGTGGCGGACGA 60.681 61.111 0.00 0.00 0.00 4.20
1313 1732 2.028125 CTATGGTGGTGGCGGACGAT 62.028 60.000 0.00 0.00 0.00 3.73
1314 1733 2.304901 TATGGTGGTGGCGGACGATG 62.305 60.000 0.00 0.00 0.00 3.84
1315 1734 4.077184 GGTGGTGGCGGACGATGA 62.077 66.667 0.00 0.00 0.00 2.92
1316 1735 2.186903 GTGGTGGCGGACGATGAT 59.813 61.111 0.00 0.00 0.00 2.45
1388 1915 4.457496 CTCGCGATGGTGGTGGCT 62.457 66.667 10.36 0.00 0.00 4.75
1838 2383 0.672401 GACCGCCGTGAAGAAATCCA 60.672 55.000 0.00 0.00 0.00 3.41
1936 2483 3.399181 CGGCTACAAGGAGGGGCA 61.399 66.667 0.00 0.00 0.00 5.36
1937 2484 2.272471 GGCTACAAGGAGGGGCAC 59.728 66.667 0.00 0.00 0.00 5.01
1977 2530 5.008415 GCCATTCCATGTCTATCTCAAAGTG 59.992 44.000 0.00 0.00 0.00 3.16
2071 2624 1.153568 CTTCGGCCGATTCAGCTGA 60.154 57.895 31.56 13.74 43.79 4.26
2114 2668 1.348775 GGTCCTCCATAGCTTGCCCT 61.349 60.000 0.00 0.00 0.00 5.19
2160 2715 1.398390 GCTTCACAGGTAGGCATTTCG 59.602 52.381 0.00 0.00 0.00 3.46
2179 2734 1.125021 CGTCACAGAATCGACAACAGC 59.875 52.381 0.00 0.00 32.24 4.40
2189 2744 2.124320 ACAACAGCTTGGCACGGT 60.124 55.556 0.00 0.00 0.00 4.83
2323 2910 9.410556 CTAGCAAAAATACTAAACTTGCAATGT 57.589 29.630 0.00 0.00 43.77 2.71
2348 3600 4.259253 GGCGTTTTCTTGAAAAAGTGTTCG 60.259 41.667 17.85 13.25 0.00 3.95
2380 3632 6.479972 ACCTACCATGAACGAAGATTCATA 57.520 37.500 0.00 0.00 45.52 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.069227 GGAATCAACAGAACACACGCC 60.069 52.381 0.00 0.0 0.00 5.68
16 17 1.144708 TGGGCTGGAATCAACAGAACA 59.855 47.619 0.00 0.0 38.20 3.18
40 41 3.006859 TGAATATGGTCCAATCGCTCGAT 59.993 43.478 0.00 0.0 36.23 3.59
142 143 1.485066 ACAGGGAAACTAGCATACCCG 59.515 52.381 0.00 0.0 44.57 5.28
143 144 2.421529 CCACAGGGAAACTAGCATACCC 60.422 54.545 0.00 0.0 40.71 3.69
221 222 5.391312 AAACACACCTAGCATCATTTTCC 57.609 39.130 0.00 0.0 0.00 3.13
222 223 8.986477 ATTTAAACACACCTAGCATCATTTTC 57.014 30.769 0.00 0.0 0.00 2.29
263 576 4.009370 AGAACCCAGCACTTAAGAACTC 57.991 45.455 10.09 0.0 0.00 3.01
380 693 7.231317 CCCATGTCTACTATAAATGGCAAACAT 59.769 37.037 0.00 0.0 43.07 2.71
982 1312 1.955495 ATGGTGTCGCCGTCATAGCA 61.955 55.000 0.00 0.0 41.21 3.49
1065 1395 3.943671 AGAGAGGCAGAGAGCTTACTA 57.056 47.619 0.00 0.0 44.79 1.82
1093 1423 3.054065 CAGGTAGAGGAAGCCAAAAGGAT 60.054 47.826 0.00 0.0 0.00 3.24
1223 1642 3.056179 TCATAGCATGGTCGTTGTCAGAA 60.056 43.478 0.00 0.0 0.00 3.02
1224 1643 2.495669 TCATAGCATGGTCGTTGTCAGA 59.504 45.455 0.00 0.0 0.00 3.27
1290 1709 0.251916 TCCGCCACCACCATAGAAAG 59.748 55.000 0.00 0.0 0.00 2.62
1291 1710 0.035820 GTCCGCCACCACCATAGAAA 60.036 55.000 0.00 0.0 0.00 2.52
1292 1711 1.600107 GTCCGCCACCACCATAGAA 59.400 57.895 0.00 0.0 0.00 2.10
1293 1712 2.717044 CGTCCGCCACCACCATAGA 61.717 63.158 0.00 0.0 0.00 1.98
1294 1713 2.028125 ATCGTCCGCCACCACCATAG 62.028 60.000 0.00 0.0 0.00 2.23
1295 1714 2.061578 ATCGTCCGCCACCACCATA 61.062 57.895 0.00 0.0 0.00 2.74
1296 1715 3.399181 ATCGTCCGCCACCACCAT 61.399 61.111 0.00 0.0 0.00 3.55
1297 1716 4.386951 CATCGTCCGCCACCACCA 62.387 66.667 0.00 0.0 0.00 4.17
1298 1717 3.385749 ATCATCGTCCGCCACCACC 62.386 63.158 0.00 0.0 0.00 4.61
1299 1718 1.883084 GATCATCGTCCGCCACCAC 60.883 63.158 0.00 0.0 0.00 4.16
1300 1719 1.613317 AAGATCATCGTCCGCCACCA 61.613 55.000 0.00 0.0 0.00 4.17
1301 1720 1.144057 AAGATCATCGTCCGCCACC 59.856 57.895 0.00 0.0 0.00 4.61
1302 1721 1.766143 GCAAGATCATCGTCCGCCAC 61.766 60.000 0.00 0.0 0.00 5.01
1303 1722 1.521457 GCAAGATCATCGTCCGCCA 60.521 57.895 0.00 0.0 0.00 5.69
1304 1723 0.032130 TAGCAAGATCATCGTCCGCC 59.968 55.000 0.00 0.0 0.00 6.13
1305 1724 1.723542 CATAGCAAGATCATCGTCCGC 59.276 52.381 0.00 0.0 0.00 5.54
1306 1725 2.288457 ACCATAGCAAGATCATCGTCCG 60.288 50.000 0.00 0.0 0.00 4.79
1307 1726 3.062763 CACCATAGCAAGATCATCGTCC 58.937 50.000 0.00 0.0 0.00 4.79
1308 1727 3.062763 CCACCATAGCAAGATCATCGTC 58.937 50.000 0.00 0.0 0.00 4.20
1309 1728 2.435805 ACCACCATAGCAAGATCATCGT 59.564 45.455 0.00 0.0 0.00 3.73
1310 1729 2.804527 CACCACCATAGCAAGATCATCG 59.195 50.000 0.00 0.0 0.00 3.84
1311 1730 3.144506 CCACCACCATAGCAAGATCATC 58.855 50.000 0.00 0.0 0.00 2.92
1312 1731 2.750807 GCCACCACCATAGCAAGATCAT 60.751 50.000 0.00 0.0 0.00 2.45
1313 1732 1.408683 GCCACCACCATAGCAAGATCA 60.409 52.381 0.00 0.0 0.00 2.92
1314 1733 1.312815 GCCACCACCATAGCAAGATC 58.687 55.000 0.00 0.0 0.00 2.75
1315 1734 0.464373 CGCCACCACCATAGCAAGAT 60.464 55.000 0.00 0.0 0.00 2.40
1316 1735 1.078497 CGCCACCACCATAGCAAGA 60.078 57.895 0.00 0.0 0.00 3.02
1388 1915 0.609957 CAAGCTGTGGGATTGCAGGA 60.610 55.000 0.00 0.0 34.50 3.86
1448 1977 0.321564 CAGAGTGGCGAATCCCAACA 60.322 55.000 0.00 0.0 36.46 3.33
1801 2346 1.004200 CGTCCGTGGCTAGGGTTTT 60.004 57.895 8.77 0.0 33.55 2.43
1830 2375 5.113383 GTTTTCAAAAACCGGTGGATTTCT 58.887 37.500 8.52 0.0 41.77 2.52
1936 2483 1.677633 GCGCTGTTTGGGGTATGGT 60.678 57.895 0.00 0.0 0.00 3.55
1937 2484 2.414785 GGCGCTGTTTGGGGTATGG 61.415 63.158 7.64 0.0 0.00 2.74
1938 2485 1.037030 ATGGCGCTGTTTGGGGTATG 61.037 55.000 7.64 0.0 0.00 2.39
1939 2486 0.324275 AATGGCGCTGTTTGGGGTAT 60.324 50.000 7.64 0.0 0.00 2.73
1940 2487 0.963355 GAATGGCGCTGTTTGGGGTA 60.963 55.000 7.64 0.0 0.00 3.69
1977 2530 1.482182 ACCGTCCGTAAAATAGGGTCC 59.518 52.381 0.00 0.0 35.31 4.46
2071 2624 3.243401 GCAGTTCAAATTCCAGTCGGTTT 60.243 43.478 0.00 0.0 0.00 3.27
2160 2715 2.408050 AGCTGTTGTCGATTCTGTGAC 58.592 47.619 0.00 0.0 35.67 3.67
2189 2744 1.270625 CGTCTGTGGCTAGGGTTTGAA 60.271 52.381 0.00 0.0 0.00 2.69
2253 2809 2.202932 CGCGGAGGTCTCCCATTG 60.203 66.667 11.08 0.0 46.96 2.82
2323 2910 3.119779 ACACTTTTTCAAGAAAACGCCGA 60.120 39.130 7.44 0.0 39.70 5.54
2348 3600 3.561503 GTTCATGGTAGGTCGTTTTTGC 58.438 45.455 0.00 0.0 0.00 3.68


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

AutoCloner maintained by Alex Coulton.