Multiple sequence alignment - TraesCS6B01G031000

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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 TraesCS6B01G031000 chr6B 100.000 2231 0 0 1 2231 18400236 18398006 0.000000e+00 4120.0
1 TraesCS6B01G031000 chr6B 96.106 2234 75 5 1 2231 18241397 18243621 0.000000e+00 3633.0
2 TraesCS6B01G031000 chr6B 77.475 1283 185 52 695 1925 18431553 18432783 0.000000e+00 673.0
3 TraesCS6B01G031000 chr6B 78.592 696 120 20 604 1284 18268850 18269531 1.220000e-117 433.0
4 TraesCS6B01G031000 chr6B 76.770 805 145 24 604 1388 18167406 18168188 1.590000e-111 412.0
5 TraesCS6B01G031000 chr6B 77.733 494 84 17 751 1234 17726512 17726035 1.690000e-71 279.0
6 TraesCS6B01G031000 chr6B 83.007 306 49 2 944 1249 18229317 18229619 7.850000e-70 274.0
7 TraesCS6B01G031000 chr6B 76.448 518 91 13 5 505 18814450 18814953 3.680000e-63 252.0
8 TraesCS6B01G031000 chr6B 96.875 32 1 0 1 32 17727364 17727333 1.000000e-03 54.7
9 TraesCS6B01G031000 chrUn 75.661 1475 241 72 770 2209 71131226 71132617 5.230000e-176 627.0
10 TraesCS6B01G031000 chrUn 75.048 525 105 12 1 505 240893549 240894067 1.040000e-53 220.0
11 TraesCS6B01G031000 chrUn 75.000 528 106 12 1 508 268930351 268929830 1.040000e-53 220.0
12 TraesCS6B01G031000 chrUn 95.455 44 2 0 1641 1684 71132267 71132310 1.110000e-08 71.3
13 TraesCS6B01G031000 chr6D 81.775 631 101 8 620 1243 9858101 9857478 1.180000e-142 516.0
14 TraesCS6B01G031000 chr6D 75.983 1145 176 61 604 1713 10308177 10307097 1.190000e-137 499.0
15 TraesCS6B01G031000 chr6D 75.676 925 167 38 589 1501 9915429 9916307 2.060000e-110 409.0
16 TraesCS6B01G031000 chr6D 74.699 498 62 35 1729 2200 10307293 10306834 1.770000e-36 163.0
17 TraesCS6B01G031000 chr6A 73.671 1580 286 71 95 1612 11730939 11729428 5.530000e-136 494.0
18 TraesCS6B01G031000 chr6A 76.316 1026 167 43 604 1612 11678883 11677917 1.550000e-131 479.0
19 TraesCS6B01G031000 chr6A 78.707 634 92 21 682 1282 11477568 11478191 1.250000e-102 383.0
20 TraesCS6B01G031000 chr6A 81.046 153 17 9 1508 1658 11764572 11764430 6.510000e-21 111.0
21 TraesCS6B01G031000 chr2D 97.436 39 0 1 2 39 15516505 15516467 5.140000e-07 65.8
22 TraesCS6B01G031000 chr2A 96.875 32 1 0 1 32 17413245 17413214 1.000000e-03 54.7


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 TraesCS6B01G031000 chr6B 18398006 18400236 2230 True 4120.00 4120 100.000 1 2231 1 chr6B.!!$R1 2230
1 TraesCS6B01G031000 chr6B 18241397 18243621 2224 False 3633.00 3633 96.106 1 2231 1 chr6B.!!$F3 2230
2 TraesCS6B01G031000 chr6B 18431553 18432783 1230 False 673.00 673 77.475 695 1925 1 chr6B.!!$F5 1230
3 TraesCS6B01G031000 chr6B 18268850 18269531 681 False 433.00 433 78.592 604 1284 1 chr6B.!!$F4 680
4 TraesCS6B01G031000 chr6B 18167406 18168188 782 False 412.00 412 76.770 604 1388 1 chr6B.!!$F1 784
5 TraesCS6B01G031000 chr6B 18814450 18814953 503 False 252.00 252 76.448 5 505 1 chr6B.!!$F6 500
6 TraesCS6B01G031000 chrUn 71131226 71132617 1391 False 349.15 627 85.558 770 2209 2 chrUn.!!$F2 1439
7 TraesCS6B01G031000 chrUn 240893549 240894067 518 False 220.00 220 75.048 1 505 1 chrUn.!!$F1 504
8 TraesCS6B01G031000 chrUn 268929830 268930351 521 True 220.00 220 75.000 1 508 1 chrUn.!!$R1 507
9 TraesCS6B01G031000 chr6D 9857478 9858101 623 True 516.00 516 81.775 620 1243 1 chr6D.!!$R1 623
10 TraesCS6B01G031000 chr6D 9915429 9916307 878 False 409.00 409 75.676 589 1501 1 chr6D.!!$F1 912
11 TraesCS6B01G031000 chr6D 10306834 10308177 1343 True 331.00 499 75.341 604 2200 2 chr6D.!!$R2 1596
12 TraesCS6B01G031000 chr6A 11729428 11730939 1511 True 494.00 494 73.671 95 1612 1 chr6A.!!$R2 1517
13 TraesCS6B01G031000 chr6A 11677917 11678883 966 True 479.00 479 76.316 604 1612 1 chr6A.!!$R1 1008
14 TraesCS6B01G031000 chr6A 11477568 11478191 623 False 383.00 383 78.707 682 1282 1 chr6A.!!$F1 600

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
837 934 1.194781 CCATATGGGGGAGAGACCGG 61.195 65.0 14.52 0.0 40.11 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 2120 0.169672 CACATGGCAGGAAAGCTTCG 59.83 55.0 5.99 0.0 34.17 3.79 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
92 93 5.620206 CATTAGCACCACCTCACCATATAA 58.380 41.667 0.00 0.00 0.00 0.98
279 286 4.928601 TCGATATGTGTACTGCAGTTACC 58.071 43.478 27.06 13.85 0.00 2.85
699 766 6.317140 GCTTTGATTATCTGGACACATTCTGA 59.683 38.462 0.00 0.00 0.00 3.27
837 934 1.194781 CCATATGGGGGAGAGACCGG 61.195 65.000 14.52 0.00 40.11 5.28
1047 1177 1.216990 GGATCAGGGGATGTTGGAGT 58.783 55.000 0.00 0.00 32.67 3.85
1064 1194 2.439701 TCTCAGGCGTCTACCGGG 60.440 66.667 6.32 0.00 36.94 5.73
1074 1204 2.999063 CTACCGGGGGTTGGACGT 60.999 66.667 6.32 0.00 37.09 4.34
1075 1205 3.305177 CTACCGGGGGTTGGACGTG 62.305 68.421 6.32 0.00 37.09 4.49
1077 1207 3.712907 CCGGGGGTTGGACGTGAT 61.713 66.667 0.00 0.00 0.00 3.06
1404 1576 7.936847 TCAGTCATACATAACTGAACCTTGTTT 59.063 33.333 2.88 0.00 46.59 2.83
1405 1577 8.017373 CAGTCATACATAACTGAACCTTGTTTG 58.983 37.037 0.00 0.00 44.54 2.93
1406 1578 7.719633 AGTCATACATAACTGAACCTTGTTTGT 59.280 33.333 0.00 0.00 0.00 2.83
1407 1579 8.349983 GTCATACATAACTGAACCTTGTTTGTT 58.650 33.333 0.00 0.00 0.00 2.83
1408 1580 8.908903 TCATACATAACTGAACCTTGTTTGTTT 58.091 29.630 0.00 0.00 0.00 2.83
1409 1581 8.967218 CATACATAACTGAACCTTGTTTGTTTG 58.033 33.333 0.00 0.00 0.00 2.93
1460 1632 3.260632 TCTTCCGTGGATTGATGTTGAGA 59.739 43.478 0.00 0.00 0.00 3.27
1484 1658 7.592533 AGATTATTTCAACGCAATATGCATGAC 59.407 33.333 10.16 0.00 45.36 3.06
1536 1710 0.394938 TGAAGCTTTCCTGCCGTGTA 59.605 50.000 0.00 0.00 0.00 2.90
1540 1714 1.202770 AGCTTTCCTGCCGTGTAACTT 60.203 47.619 0.00 0.00 31.75 2.66
1573 1949 0.109132 GCTTCCCGCTTGATTGGTTG 60.109 55.000 0.00 0.00 35.14 3.77
1628 2004 1.153706 GCGGTGCGGCTTCTAGTTA 60.154 57.895 0.00 0.00 0.00 2.24
1689 2073 2.370349 CTCGGAGCTCTTGAGGAACTA 58.630 52.381 21.60 0.00 41.55 2.24
1762 2151 1.202817 CTGCCATGTGTGCATTGCTTA 59.797 47.619 10.49 0.00 42.30 3.09
1975 2406 2.419324 GTGTGGTGTTGTTTGTTACGGA 59.581 45.455 0.00 0.00 0.00 4.69
1999 2430 3.054434 TGAAGTTGTGGGATATGGACTGG 60.054 47.826 0.00 0.00 0.00 4.00
2007 2438 3.136443 TGGGATATGGACTGGTTGTGATC 59.864 47.826 0.00 0.00 0.00 2.92
2189 2624 8.408601 GTTTTATACATGCTCATTGTTCCATCT 58.591 33.333 0.00 0.00 0.00 2.90
2209 2645 3.691118 TCTTGTATTTGGAGCTGATGTGC 59.309 43.478 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 2.061061 CCTCCCCTCCATAAGCTGAAT 58.939 52.381 0.00 0.00 0.00 2.57
447 466 8.050778 TGATAACCTTTATGAAACATGTCCAC 57.949 34.615 0.00 0.00 0.00 4.02
699 766 3.768922 GAGAGCAGCTGGGACGCT 61.769 66.667 17.12 5.36 38.56 5.07
837 934 2.028876 GTCTCCAGGCTAGAGAAGGTC 58.971 57.143 14.29 0.00 41.88 3.85
923 1047 2.445525 AGCTTGGGGAAAACTAGAACCA 59.554 45.455 0.00 0.00 0.00 3.67
1047 1177 2.439701 CCCGGTAGACGCCTGAGA 60.440 66.667 0.00 0.00 42.52 3.27
1064 1194 1.734163 CTTGGTATCACGTCCAACCC 58.266 55.000 2.48 0.00 38.57 4.11
1074 1204 0.331278 CCTTGGGTGGCTTGGTATCA 59.669 55.000 0.00 0.00 0.00 2.15
1075 1205 0.331616 ACCTTGGGTGGCTTGGTATC 59.668 55.000 0.00 0.00 32.98 2.24
1077 1207 4.011690 ACCTTGGGTGGCTTGGTA 57.988 55.556 0.00 0.00 32.98 3.25
1404 1576 6.127591 ACCTACAGCATACAAACAAACAAACA 60.128 34.615 0.00 0.00 0.00 2.83
1405 1577 6.270064 ACCTACAGCATACAAACAAACAAAC 58.730 36.000 0.00 0.00 0.00 2.93
1406 1578 6.458232 ACCTACAGCATACAAACAAACAAA 57.542 33.333 0.00 0.00 0.00 2.83
1407 1579 7.569639 TTACCTACAGCATACAAACAAACAA 57.430 32.000 0.00 0.00 0.00 2.83
1408 1580 7.445707 TGATTACCTACAGCATACAAACAAACA 59.554 33.333 0.00 0.00 0.00 2.83
1409 1581 7.812648 TGATTACCTACAGCATACAAACAAAC 58.187 34.615 0.00 0.00 0.00 2.93
1536 1710 0.805711 GCAAGGCAACGCACAAAGTT 60.806 50.000 0.00 0.00 46.39 2.66
1540 1714 1.065600 GAAGCAAGGCAACGCACAA 59.934 52.632 0.00 0.00 46.39 3.33
1573 1949 1.533625 TATGCAGCAAGAACACCACC 58.466 50.000 0.00 0.00 0.00 4.61
1616 1992 5.651530 TCAGATCAAACTAACTAGAAGCCG 58.348 41.667 0.00 0.00 0.00 5.52
1628 2004 6.484364 AACCAAACCAAATCAGATCAAACT 57.516 33.333 0.00 0.00 0.00 2.66
1689 2073 2.039480 TGAATGCTCACTCTGCTTCCTT 59.961 45.455 0.00 0.00 0.00 3.36
1732 2120 0.169672 CACATGGCAGGAAAGCTTCG 59.830 55.000 5.99 0.00 34.17 3.79
1762 2151 1.131928 ACCAAAGCGGGAAGTAGGGT 61.132 55.000 0.00 0.00 40.22 4.34
1840 2229 7.967890 AAGATGATCAAACCAAACCAAATTC 57.032 32.000 0.00 0.00 0.00 2.17
1975 2406 5.195940 CAGTCCATATCCCACAACTTCATT 58.804 41.667 0.00 0.00 0.00 2.57
1999 2430 8.236586 TCATTGTTTATGCTTACAGATCACAAC 58.763 33.333 0.00 0.00 34.06 3.32
2007 2438 9.577110 AATCACAATCATTGTTTATGCTTACAG 57.423 29.630 0.00 0.00 43.23 2.74
2189 2624 3.689347 AGCACATCAGCTCCAAATACAA 58.311 40.909 0.00 0.00 42.18 2.41
2209 2645 3.257393 CCTTACAAGTGACAGCAGCTAG 58.743 50.000 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.