Multiple sequence alignment - TraesCS7B01G055900

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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 TraesCS7B01G055900 chr7B 100.000 2498 0 0 1 2498 59070966 59073463 0.000000e+00 4614
1 TraesCS7B01G055900 chr7D 94.947 2533 90 11 1 2498 101736702 101739231 0.000000e+00 3934
2 TraesCS7B01G055900 chr7D 84.879 787 93 13 1683 2446 101732715 101733498 0.000000e+00 771
3 TraesCS7B01G055900 chr7A 94.488 1796 89 5 1 1788 105510413 105512206 0.000000e+00 2760
4 TraesCS7B01G055900 chr7A 96.358 906 25 3 1601 2498 105512391 105513296 0.000000e+00 1483
5 TraesCS7B01G055900 chr7A 82.378 1152 178 13 1 1133 105501901 105503046 0.000000e+00 979
6 TraesCS7B01G055900 chr7A 81.718 815 108 16 1659 2446 105503843 105504643 2.090000e-180 641
7 TraesCS7B01G055900 chr7A 96.354 192 3 1 1601 1788 105512203 105512394 1.870000e-81 313
8 TraesCS7B01G055900 chr5B 79.837 734 122 16 1718 2425 533035342 533034609 1.710000e-141 512
9 TraesCS7B01G055900 chr5B 81.193 553 94 8 1884 2430 532239381 532239929 1.060000e-118 436
10 TraesCS7B01G055900 chr5B 72.806 1151 257 39 1 1105 532548221 532549361 8.560000e-90 340
11 TraesCS7B01G055900 chr5B 72.542 1180 251 47 6 1133 533038033 533036875 1.440000e-82 316
12 TraesCS7B01G055900 chr5D 78.995 776 128 22 1683 2430 437867218 437867986 4.800000e-137 497
13 TraesCS7B01G055900 chr5D 79.201 726 132 12 1718 2425 438438712 438437988 1.040000e-133 486
14 TraesCS7B01G055900 chr5D 76.766 736 139 18 1718 2425 438443276 438442545 1.400000e-102 383
15 TraesCS7B01G055900 chr5D 72.455 1169 262 41 13 1133 438046037 438047193 1.110000e-83 320
16 TraesCS7B01G055900 chr2D 78.947 722 126 16 1725 2425 12632436 12631720 3.760000e-128 468
17 TraesCS7B01G055900 chr2A 78.581 733 133 18 1712 2425 14740577 14739850 1.750000e-126 462
18 TraesCS7B01G055900 chr2A 78.503 735 130 22 1712 2425 14703616 14702889 8.140000e-125 457
19 TraesCS7B01G055900 chr5A 80.645 496 83 10 1937 2425 553538672 553538183 3.030000e-99 372


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 TraesCS7B01G055900 chr7B 59070966 59073463 2497 False 4614.000000 4614 100.000000 1 2498 1 chr7B.!!$F1 2497
1 TraesCS7B01G055900 chr7D 101732715 101739231 6516 False 2352.500000 3934 89.913000 1 2498 2 chr7D.!!$F1 2497
2 TraesCS7B01G055900 chr7A 105510413 105513296 2883 False 1518.666667 2760 95.733333 1 2498 3 chr7A.!!$F2 2497
3 TraesCS7B01G055900 chr7A 105501901 105504643 2742 False 810.000000 979 82.048000 1 2446 2 chr7A.!!$F1 2445
4 TraesCS7B01G055900 chr5B 532239381 532239929 548 False 436.000000 436 81.193000 1884 2430 1 chr5B.!!$F1 546
5 TraesCS7B01G055900 chr5B 533034609 533038033 3424 True 414.000000 512 76.189500 6 2425 2 chr5B.!!$R1 2419
6 TraesCS7B01G055900 chr5B 532548221 532549361 1140 False 340.000000 340 72.806000 1 1105 1 chr5B.!!$F2 1104
7 TraesCS7B01G055900 chr5D 437867218 437867986 768 False 497.000000 497 78.995000 1683 2430 1 chr5D.!!$F1 747
8 TraesCS7B01G055900 chr5D 438437988 438443276 5288 True 434.500000 486 77.983500 1718 2425 2 chr5D.!!$R1 707
9 TraesCS7B01G055900 chr5D 438046037 438047193 1156 False 320.000000 320 72.455000 13 1133 1 chr5D.!!$F2 1120
10 TraesCS7B01G055900 chr2D 12631720 12632436 716 True 468.000000 468 78.947000 1725 2425 1 chr2D.!!$R1 700
11 TraesCS7B01G055900 chr2A 14739850 14740577 727 True 462.000000 462 78.581000 1712 2425 1 chr2A.!!$R2 713
12 TraesCS7B01G055900 chr2A 14702889 14703616 727 True 457.000000 457 78.503000 1712 2425 1 chr2A.!!$R1 713

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
410 4410 0.467384 GAGCTTCTCCTATGGCTGCA 59.533 55.0 0.5 0.0 35.01 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 7870 1.334869 CTCGCCATACCAAAATCTGCC 59.665 52.381 0.0 0.0 0.0 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
154 4145 3.176411 TGTTCTCTCTGATGGTGATGGT 58.824 45.455 0.00 0.0 0.00 3.55
246 4243 1.070289 GACCGGTAACCTCATCATCCC 59.930 57.143 7.34 0.0 0.00 3.85
338 4335 1.831106 TGCGAATCAGGTACAGGACAT 59.169 47.619 0.00 0.0 0.00 3.06
410 4410 0.467384 GAGCTTCTCCTATGGCTGCA 59.533 55.000 0.50 0.0 35.01 4.41
548 4554 3.603532 CAGCGCCATCATGATATACCTT 58.396 45.455 8.15 0.0 0.00 3.50
641 4647 2.646175 GCTGACCTACTCCGGCACA 61.646 63.158 0.00 0.0 0.00 4.57
757 4817 2.282887 GGTGTTGCCCGTCCCAAT 60.283 61.111 0.00 0.0 0.00 3.16
850 4910 1.301716 GACGGAAAGAGGCACTGCA 60.302 57.895 2.82 0.0 41.55 4.41
893 4956 3.003230 CCGGGGATTAAGCCACCA 58.997 61.111 12.67 0.0 0.00 4.17
944 5013 3.755628 GAGGAGTGTGCGGCGGTA 61.756 66.667 9.78 0.0 0.00 4.02
1145 5219 5.497474 AGCTGGTACCACTTTATTACCTTG 58.503 41.667 11.60 0.0 36.89 3.61
1377 5600 6.435428 CAAAGGTGCGTTTAGTTTACATTCT 58.565 36.000 0.00 0.0 0.00 2.40
1825 7309 9.482627 TTTGGCAAAGTTTACAAGGTAATTATG 57.517 29.630 8.93 0.0 0.00 1.90
2345 7870 1.404391 GCACAGATGAAGCCCAAGATG 59.596 52.381 0.00 0.0 0.00 2.90
2425 7950 1.135489 TGTCGTCGGAACATAGTGAGC 60.135 52.381 0.00 0.0 0.00 4.26
2439 7964 1.670811 AGTGAGCAACTGTTTGAACCG 59.329 47.619 0.00 0.0 37.88 4.44
2446 7971 3.058224 GCAACTGTTTGAACCGATAGCTT 60.058 43.478 0.00 0.0 34.24 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 3999 1.470979 GCCGTTGTACCAGATGTCGAT 60.471 52.381 0.00 0.0 0.00 3.59
15 4003 1.555075 AGATGCCGTTGTACCAGATGT 59.445 47.619 0.00 0.0 0.00 3.06
154 4145 2.867287 TCGTCCAAACAACACGACTA 57.133 45.000 0.00 0.0 37.62 2.59
246 4243 2.358125 TGGTGCCGTTGGATGACG 60.358 61.111 0.00 0.0 42.43 4.35
322 4319 2.677902 CGCACATGTCCTGTACCTGATT 60.678 50.000 0.00 0.0 35.91 2.57
410 4410 1.006813 TGGATAATGGTGGCTGGGTT 58.993 50.000 0.00 0.0 0.00 4.11
460 4460 1.077068 CATGGGGTGGTGCGGTATT 60.077 57.895 0.00 0.0 0.00 1.89
755 4815 1.568612 CGTCGAGGCACTTGCACATT 61.569 55.000 3.15 0.0 41.55 2.71
757 4817 2.661537 CGTCGAGGCACTTGCACA 60.662 61.111 3.15 0.0 41.55 4.57
790 4850 1.694150 CCTTGTTCCACTCCTCTGTGA 59.306 52.381 0.00 0.0 40.12 3.58
850 4910 0.171007 CAAGAAACCATCGCCGCAAT 59.829 50.000 0.00 0.0 0.00 3.56
884 4947 1.414919 ACGAACTTGTCTGGTGGCTTA 59.585 47.619 0.00 0.0 0.00 3.09
893 4956 1.474017 CGACGAACACGAACTTGTCT 58.526 50.000 0.00 0.0 0.00 3.41
1009 5078 0.995024 AAGCACCTTGGCATACCTCT 59.005 50.000 0.00 0.0 36.63 3.69
1213 5287 5.885912 ACAAAGTATTATACACAGCCAAGGG 59.114 40.000 5.11 0.0 0.00 3.95
1222 5296 8.730427 GCGCACATAAAACAAAGTATTATACAC 58.270 33.333 0.30 0.0 0.00 2.90
1255 5345 3.476552 CAGTGCTCCTTGTCCTTTTACA 58.523 45.455 0.00 0.0 0.00 2.41
1377 5600 5.134661 ACTTGAATGTTTCGGGAAGGTAAA 58.865 37.500 0.00 0.0 0.00 2.01
1825 7309 8.450964 TCAGTTAGAATAAAAGCAATGTAGTGC 58.549 33.333 0.00 0.0 45.28 4.40
2345 7870 1.334869 CTCGCCATACCAAAATCTGCC 59.665 52.381 0.00 0.0 0.00 4.85
2425 7950 4.712763 GAAGCTATCGGTTCAAACAGTTG 58.287 43.478 4.44 0.0 44.81 3.16


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

AutoCloner maintained by Alex Coulton.