Multiple sequence alignment - TraesCS2B01G593700

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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 TraesCS2B01G593700 chr2B 100.000 2747 0 0 1 2747 778449820 778452566 0.000000e+00 5073.0
1 TraesCS2B01G593700 chr2B 96.196 1998 51 11 757 2747 778477205 778475226 0.000000e+00 3245.0
2 TraesCS2B01G593700 chr2B 84.009 938 113 23 824 1746 778293426 778292511 0.000000e+00 867.0
3 TraesCS2B01G593700 chr2B 81.089 973 163 11 803 1762 778778959 778779923 0.000000e+00 758.0
4 TraesCS2B01G593700 chr2A 91.069 1993 106 25 803 2747 778563314 778565282 0.000000e+00 2628.0
5 TraesCS2B01G593700 chr2A 83.790 876 114 16 897 1761 778457598 778456740 0.000000e+00 806.0
6 TraesCS2B01G593700 chr2A 85.154 586 85 2 2163 2747 26933196 26932612 1.410000e-167 599.0
7 TraesCS2B01G593700 chr4A 98.681 758 9 1 1 757 701552839 701553596 0.000000e+00 1343.0
8 TraesCS2B01G593700 chr4A 98.539 753 11 0 4 756 734628775 734628023 0.000000e+00 1330.0
9 TraesCS2B01G593700 chr4A 86.237 574 78 1 2174 2747 69306110 69305538 3.000000e-174 621.0
10 TraesCS2B01G593700 chrUn 98.677 756 9 1 4 758 194093682 194092927 0.000000e+00 1339.0
11 TraesCS2B01G593700 chrUn 98.280 756 12 1 4 758 311874616 311873861 0.000000e+00 1323.0
12 TraesCS2B01G593700 chrUn 82.073 965 135 22 812 1761 217850428 217849487 0.000000e+00 789.0
13 TraesCS2B01G593700 chrUn 82.073 965 135 22 812 1761 331471440 331470499 0.000000e+00 789.0
14 TraesCS2B01G593700 chrUn 82.692 572 85 11 809 1374 345946492 345947055 1.900000e-136 496.0
15 TraesCS2B01G593700 chrUn 82.692 572 85 11 809 1374 345948882 345949445 1.900000e-136 496.0
16 TraesCS2B01G593700 chrUn 82.692 572 85 11 809 1374 436326431 436326994 1.900000e-136 496.0
17 TraesCS2B01G593700 chr6B 98.047 768 11 4 4 769 70698552 70697787 0.000000e+00 1332.0
18 TraesCS2B01G593700 chr6B 98.280 756 11 2 3 757 716423280 716424034 0.000000e+00 1323.0
19 TraesCS2B01G593700 chr6B 98.153 758 13 1 1 757 689057382 689058139 0.000000e+00 1321.0
20 TraesCS2B01G593700 chr5B 98.283 757 11 2 1 756 127859882 127860637 0.000000e+00 1325.0
21 TraesCS2B01G593700 chr5B 97.775 764 15 2 4 766 689149473 689148711 0.000000e+00 1315.0
22 TraesCS2B01G593700 chr5B 86.018 565 76 3 2175 2738 638783200 638783762 1.090000e-168 603.0
23 TraesCS2B01G593700 chr3B 86.620 568 75 1 2171 2738 792853319 792853885 6.460000e-176 627.0
24 TraesCS2B01G593700 chr1B 86.348 564 76 1 2175 2738 453521964 453522526 5.030000e-172 614.0
25 TraesCS2B01G593700 chr6A 85.993 564 78 1 2175 2738 590370890 590371452 1.090000e-168 603.0
26 TraesCS2B01G593700 chr1A 85.689 573 81 1 2175 2747 491376534 491375963 1.090000e-168 603.0
27 TraesCS2B01G593700 chr7A 85.866 566 79 1 2173 2738 10422947 10423511 3.910000e-168 601.0
28 TraesCS2B01G593700 chr1D 100.000 28 0 0 2014 2041 350901223 350901250 5.000000e-03 52.8


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 TraesCS2B01G593700 chr2B 778449820 778452566 2746 False 5073 5073 100.000 1 2747 1 chr2B.!!$F1 2746
1 TraesCS2B01G593700 chr2B 778475226 778477205 1979 True 3245 3245 96.196 757 2747 1 chr2B.!!$R2 1990
2 TraesCS2B01G593700 chr2B 778292511 778293426 915 True 867 867 84.009 824 1746 1 chr2B.!!$R1 922
3 TraesCS2B01G593700 chr2B 778778959 778779923 964 False 758 758 81.089 803 1762 1 chr2B.!!$F2 959
4 TraesCS2B01G593700 chr2A 778563314 778565282 1968 False 2628 2628 91.069 803 2747 1 chr2A.!!$F1 1944
5 TraesCS2B01G593700 chr2A 778456740 778457598 858 True 806 806 83.790 897 1761 1 chr2A.!!$R2 864
6 TraesCS2B01G593700 chr2A 26932612 26933196 584 True 599 599 85.154 2163 2747 1 chr2A.!!$R1 584
7 TraesCS2B01G593700 chr4A 701552839 701553596 757 False 1343 1343 98.681 1 757 1 chr4A.!!$F1 756
8 TraesCS2B01G593700 chr4A 734628023 734628775 752 True 1330 1330 98.539 4 756 1 chr4A.!!$R2 752
9 TraesCS2B01G593700 chr4A 69305538 69306110 572 True 621 621 86.237 2174 2747 1 chr4A.!!$R1 573
10 TraesCS2B01G593700 chrUn 194092927 194093682 755 True 1339 1339 98.677 4 758 1 chrUn.!!$R1 754
11 TraesCS2B01G593700 chrUn 311873861 311874616 755 True 1323 1323 98.280 4 758 1 chrUn.!!$R3 754
12 TraesCS2B01G593700 chrUn 217849487 217850428 941 True 789 789 82.073 812 1761 1 chrUn.!!$R2 949
13 TraesCS2B01G593700 chrUn 331470499 331471440 941 True 789 789 82.073 812 1761 1 chrUn.!!$R4 949
14 TraesCS2B01G593700 chrUn 345946492 345949445 2953 False 496 496 82.692 809 1374 2 chrUn.!!$F2 565
15 TraesCS2B01G593700 chrUn 436326431 436326994 563 False 496 496 82.692 809 1374 1 chrUn.!!$F1 565
16 TraesCS2B01G593700 chr6B 70697787 70698552 765 True 1332 1332 98.047 4 769 1 chr6B.!!$R1 765
17 TraesCS2B01G593700 chr6B 716423280 716424034 754 False 1323 1323 98.280 3 757 1 chr6B.!!$F2 754
18 TraesCS2B01G593700 chr6B 689057382 689058139 757 False 1321 1321 98.153 1 757 1 chr6B.!!$F1 756
19 TraesCS2B01G593700 chr5B 127859882 127860637 755 False 1325 1325 98.283 1 756 1 chr5B.!!$F1 755
20 TraesCS2B01G593700 chr5B 689148711 689149473 762 True 1315 1315 97.775 4 766 1 chr5B.!!$R1 762
21 TraesCS2B01G593700 chr5B 638783200 638783762 562 False 603 603 86.018 2175 2738 1 chr5B.!!$F2 563
22 TraesCS2B01G593700 chr3B 792853319 792853885 566 False 627 627 86.620 2171 2738 1 chr3B.!!$F1 567
23 TraesCS2B01G593700 chr1B 453521964 453522526 562 False 614 614 86.348 2175 2738 1 chr1B.!!$F1 563
24 TraesCS2B01G593700 chr6A 590370890 590371452 562 False 603 603 85.993 2175 2738 1 chr6A.!!$F1 563
25 TraesCS2B01G593700 chr1A 491375963 491376534 571 True 603 603 85.689 2175 2747 1 chr1A.!!$R1 572
26 TraesCS2B01G593700 chr7A 10422947 10423511 564 False 601 601 85.866 2173 2738 1 chr7A.!!$F1 565

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
1261 1270 0.387239 TGTCGTGATCAGTGAGCGTG 60.387 55.0 3.57 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 3579 0.31702 GGTTGTTGCTCTTGTGCGTC 60.317 55.0 0.0 0.0 35.36 5.19 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
1261 1270 0.387239 TGTCGTGATCAGTGAGCGTG 60.387 55.000 3.57 0.00 0.00 5.34
1481 2566 3.395702 CATCGTGGGGTTCGGGGA 61.396 66.667 0.00 0.00 0.00 4.81
1726 2826 3.196469 CCTCACTAACATGCTCAAGGAGA 59.804 47.826 0.00 0.00 0.00 3.71
1894 3057 1.209747 GGTGTGGTTAGATCCCAGTCC 59.790 57.143 0.00 0.00 31.13 3.85
1980 3145 1.134521 TGCCCACATCACGTAAGATCC 60.135 52.381 0.00 0.00 43.62 3.36
1996 3161 6.419116 CGTAAGATCCCATGAATATAGCATCG 59.581 42.308 0.00 0.00 43.02 3.84
2088 3258 5.977635 TGGTGGGATCTAGATATAATTGCG 58.022 41.667 4.89 0.00 0.00 4.85
2267 3438 5.920193 AAATTACAACCACATCCATGGAG 57.080 39.130 21.33 14.28 43.02 3.86
2401 3579 0.746923 GCTAAGGCCCCAAAGTACCG 60.747 60.000 0.00 0.00 0.00 4.02
2408 3586 1.301087 CCCAAAGTACCGACGCACA 60.301 57.895 0.00 0.00 0.00 4.57
2440 3747 2.034685 CCATCGCCGATGAAGAGAGTTA 59.965 50.000 27.59 0.00 42.09 2.24
2490 3797 5.804979 CCACACGAAAGAAGACAAACAAAAT 59.195 36.000 0.00 0.00 0.00 1.82
2603 3910 3.550431 ACATCATCGAGGCGGGGG 61.550 66.667 0.00 0.00 0.00 5.40
2677 3984 3.221771 CTCCAACCAAGACATTGAACCA 58.778 45.455 0.00 0.00 38.83 3.67
2730 4037 2.123251 GGGGCCGAGATCCTCTGA 60.123 66.667 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 5.306678 AGGAAGATGAGATACTGGTTCCATC 59.693 44.000 0.00 0.00 35.44 3.51
571 572 3.502123 TTTCTTGAACCGATCACCCTT 57.498 42.857 0.00 0.00 37.92 3.95
572 573 3.072476 TCTTTTCTTGAACCGATCACCCT 59.928 43.478 0.00 0.00 37.92 4.34
573 574 3.408634 TCTTTTCTTGAACCGATCACCC 58.591 45.455 0.00 0.00 37.92 4.61
725 728 1.975680 ACGGTGATTGGGTGAGTACTT 59.024 47.619 0.00 0.00 0.00 2.24
732 735 2.351350 GCTGTTTTACGGTGATTGGGTG 60.351 50.000 0.00 0.00 0.00 4.61
1481 2566 1.178276 CAGTGTAGTCTTCCCGAGCT 58.822 55.000 0.00 0.00 0.00 4.09
1617 2702 3.369546 ACTTTTGGCTTCACGATTTGG 57.630 42.857 0.00 0.00 0.00 3.28
1726 2826 7.770897 GTGTATTTACCTCATGTCCTTCAGAAT 59.229 37.037 0.00 0.00 0.00 2.40
1980 3145 5.107824 CCTCTGTCGATGCTATATTCATGG 58.892 45.833 0.00 0.00 0.00 3.66
1996 3161 5.703130 AGTTGACTTTAATCAAGCCTCTGTC 59.297 40.000 0.00 0.00 39.25 3.51
2088 3258 8.657712 AGGGTAATTAGTGTGGGTAATCTAATC 58.342 37.037 0.00 0.00 33.69 1.75
2145 3315 7.857734 TTGTGAACTAACAAATTCTCAGACA 57.142 32.000 0.00 0.00 37.12 3.41
2148 3318 8.997323 AGAGATTGTGAACTAACAAATTCTCAG 58.003 33.333 16.81 0.00 42.93 3.35
2200 3371 9.710900 CTATGTACTGCCATGATTTATGAGTAA 57.289 33.333 0.00 0.00 39.21 2.24
2208 3379 6.418101 AGTGTTCTATGTACTGCCATGATTT 58.582 36.000 0.00 0.00 0.00 2.17
2247 3418 3.290710 GCTCCATGGATGTGGTTGTAAT 58.709 45.455 16.63 0.00 40.27 1.89
2257 3428 5.873712 GTCATAACTAGATGCTCCATGGATG 59.126 44.000 16.63 10.72 0.00 3.51
2267 3438 4.149046 GCGCTTGTAGTCATAACTAGATGC 59.851 45.833 0.00 1.91 43.40 3.91
2401 3579 0.317020 GGTTGTTGCTCTTGTGCGTC 60.317 55.000 0.00 0.00 35.36 5.19
2408 3586 1.577328 CGGCGATGGTTGTTGCTCTT 61.577 55.000 0.00 0.00 0.00 2.85
2440 3747 9.178758 GTTACAGGTTTGATCTTTCCATTCTAT 57.821 33.333 0.00 0.00 0.00 1.98
2603 3910 6.831976 AGAAATAATGTCTCCCACATCCTAC 58.168 40.000 0.00 0.00 45.77 3.18
2677 3984 7.888021 GGAGGGATCCCATTTTAATTTTTGTTT 59.112 33.333 32.69 5.16 38.92 2.83


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

AutoCloner maintained by Alex Coulton.