Multiple sequence alignment - TraesCS7B01G486100

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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 TraesCS7B01G486100 chr7B 100.000 2333 0 0 1 2333 742265003 742267335 0.000000e+00 4309
1 TraesCS7B01G486100 chr7B 89.356 404 25 15 2 397 459113970 459114363 2.080000e-135 492
2 TraesCS7B01G486100 chr6B 93.956 1853 76 24 491 2333 261460622 261462448 0.000000e+00 2769
3 TraesCS7B01G486100 chr6B 95.275 1545 53 13 799 2333 78311193 78309659 0.000000e+00 2431
4 TraesCS7B01G486100 chr6B 95.951 494 19 1 2 494 261454661 261455154 0.000000e+00 800
5 TraesCS7B01G486100 chr3B 96.975 1587 46 2 748 2333 420779573 420777988 0.000000e+00 2663
6 TraesCS7B01G486100 chr1B 96.348 1588 55 3 747 2333 312242742 312244327 0.000000e+00 2608
7 TraesCS7B01G486100 chr2A 95.760 1533 55 7 805 2333 759091975 759093501 0.000000e+00 2462
8 TraesCS7B01G486100 chr4B 95.889 1508 53 7 830 2333 451906171 451904669 0.000000e+00 2433
9 TraesCS7B01G486100 chr4B 91.202 682 49 10 2 678 622317303 622316628 0.000000e+00 917
10 TraesCS7B01G486100 chr1D 94.395 1588 74 11 749 2333 471792917 471794492 0.000000e+00 2425
11 TraesCS7B01G486100 chr2B 94.777 1570 58 16 776 2333 619941890 619943447 0.000000e+00 2423
12 TraesCS7B01G486100 chr2D 94.430 1580 68 15 763 2333 16242399 16240831 0.000000e+00 2412
13 TraesCS7B01G486100 chr2D 89.691 388 36 4 1 386 420561577 420561962 2.080000e-135 492
14 TraesCS7B01G486100 chr7A 94.084 1589 84 8 748 2333 102371337 102372918 0.000000e+00 2405
15 TraesCS7B01G486100 chr7A 84.389 647 65 25 17 643 75910351 75909721 9.220000e-169 603
16 TraesCS7B01G486100 chr7A 89.567 393 29 10 1 390 113456495 113456112 2.690000e-134 488
17 TraesCS7B01G486100 chr4A 86.068 646 56 23 17 643 318037871 318037241 0.000000e+00 664
18 TraesCS7B01G486100 chr7D 90.979 388 26 7 4 390 384068086 384067707 4.450000e-142 514
19 TraesCS7B01G486100 chrUn 89.974 389 34 5 1 386 108425390 108425776 4.480000e-137 497
20 TraesCS7B01G486100 chr5A 90.323 93 8 1 522 614 698860374 698860465 1.130000e-23 121


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 TraesCS7B01G486100 chr7B 742265003 742267335 2332 False 4309 4309 100.000 1 2333 1 chr7B.!!$F2 2332
1 TraesCS7B01G486100 chr6B 261460622 261462448 1826 False 2769 2769 93.956 491 2333 1 chr6B.!!$F2 1842
2 TraesCS7B01G486100 chr6B 78309659 78311193 1534 True 2431 2431 95.275 799 2333 1 chr6B.!!$R1 1534
3 TraesCS7B01G486100 chr3B 420777988 420779573 1585 True 2663 2663 96.975 748 2333 1 chr3B.!!$R1 1585
4 TraesCS7B01G486100 chr1B 312242742 312244327 1585 False 2608 2608 96.348 747 2333 1 chr1B.!!$F1 1586
5 TraesCS7B01G486100 chr2A 759091975 759093501 1526 False 2462 2462 95.760 805 2333 1 chr2A.!!$F1 1528
6 TraesCS7B01G486100 chr4B 451904669 451906171 1502 True 2433 2433 95.889 830 2333 1 chr4B.!!$R1 1503
7 TraesCS7B01G486100 chr4B 622316628 622317303 675 True 917 917 91.202 2 678 1 chr4B.!!$R2 676
8 TraesCS7B01G486100 chr1D 471792917 471794492 1575 False 2425 2425 94.395 749 2333 1 chr1D.!!$F1 1584
9 TraesCS7B01G486100 chr2B 619941890 619943447 1557 False 2423 2423 94.777 776 2333 1 chr2B.!!$F1 1557
10 TraesCS7B01G486100 chr2D 16240831 16242399 1568 True 2412 2412 94.430 763 2333 1 chr2D.!!$R1 1570
11 TraesCS7B01G486100 chr7A 102371337 102372918 1581 False 2405 2405 94.084 748 2333 1 chr7A.!!$F1 1585
12 TraesCS7B01G486100 chr7A 75909721 75910351 630 True 603 603 84.389 17 643 1 chr7A.!!$R1 626
13 TraesCS7B01G486100 chr4A 318037241 318037871 630 True 664 664 86.068 17 643 1 chr4A.!!$R1 626

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
265 278 1.137086 CTTGTTCCTCGGTGGATCGAT 59.863 52.381 0.0 0.0 45.68 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1529 0.314618 TGCCGTGCGTCAAAGTAGTA 59.685 50.0 0.0 0.0 0.0 1.82 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
265 278 1.137086 CTTGTTCCTCGGTGGATCGAT 59.863 52.381 0.00 0.00 45.68 3.59
340 353 6.013379 AGGTGATTGTCTGGTTGATCTAGAAA 60.013 38.462 0.00 0.00 35.50 2.52
397 410 1.292992 GGAATCGGAAAATACGGCGT 58.707 50.000 19.64 19.64 0.00 5.68
430 443 1.609932 CGTCGAGCAGCGTTTAGTTA 58.390 50.000 0.00 0.00 41.80 2.24
485 500 2.095750 CTGCAGCAGTAGCATGTGG 58.904 57.895 14.90 0.00 45.49 4.17
599 614 2.048503 AGGTTCGGCGGTTTCTCG 60.049 61.111 7.21 0.00 0.00 4.04
793 812 2.418197 CGGCGGAAGGAAAAGTCTATCA 60.418 50.000 0.00 0.00 0.00 2.15
859 894 3.166489 AGTTGCGCTAGTATTGGAGTC 57.834 47.619 9.73 0.00 0.00 3.36
1049 1093 3.869246 GTGGAGAAGTTCAACGAAACTGA 59.131 43.478 5.50 0.00 39.40 3.41
1091 1135 4.030216 ACAAGGGTGAAAGATTTGTTGGT 58.970 39.130 0.00 0.00 0.00 3.67
1371 1419 7.417911 GGTCAGATCTTGTGGAGTATATGAACA 60.418 40.741 0.00 0.00 0.00 3.18
1481 1529 5.479375 GCCATCATCCTATGACCATTTGATT 59.521 40.000 0.00 0.00 43.01 2.57
1530 1578 7.724506 AGACCGTCAAGAATGAGGATATTACTA 59.275 37.037 0.40 0.00 42.66 1.82
2146 2194 1.208293 GATTGGAGAGAGGACGGCTTT 59.792 52.381 0.00 0.00 0.00 3.51
2216 2264 2.202756 GGAGTTGCGGGAGTAGCG 60.203 66.667 0.00 0.00 37.44 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.877071 GTCCGACTCCGACACTACAA 59.123 55.000 0.00 0.00 38.22 2.41
17 18 1.232621 GGCCAAGGGTACAACGTGTC 61.233 60.000 0.00 0.00 0.00 3.67
135 138 0.245539 CGAGATACCACAACACCGGT 59.754 55.000 0.00 0.00 39.41 5.28
145 158 1.152525 GCTCCTCCCCGAGATACCA 60.153 63.158 0.00 0.00 30.97 3.25
340 353 2.503356 CCTTCTGCAGTATCTCCACCTT 59.497 50.000 14.67 0.00 0.00 3.50
414 427 3.061797 CGAATCTAACTAAACGCTGCTCG 60.062 47.826 0.00 0.00 45.38 5.03
599 614 1.934463 CTGTATCCGATTGCACCGC 59.066 57.895 2.41 0.00 0.00 5.68
658 677 0.178958 ACGAGTTCCACCAGGACTCT 60.179 55.000 0.00 0.00 45.73 3.24
739 758 3.594134 TGTTTTTGCCTCTGTTTGGTTG 58.406 40.909 0.00 0.00 0.00 3.77
743 762 2.861935 CTGCTGTTTTTGCCTCTGTTTG 59.138 45.455 0.00 0.00 0.00 2.93
793 812 1.473677 CGATGGATGCACACCACAAAT 59.526 47.619 15.29 1.60 40.36 2.32
859 894 1.302832 AAAGTGCTCCCTTGGCTCG 60.303 57.895 0.00 0.00 0.00 5.03
1049 1093 2.562738 GTCTGCCATAACCCAAAGCTTT 59.437 45.455 5.69 5.69 0.00 3.51
1091 1135 2.879756 GCCTTCAAGCATCCCTGTTGTA 60.880 50.000 0.00 0.00 0.00 2.41
1371 1419 3.006110 TCCGTCACGACTTGATTAAAGGT 59.994 43.478 0.00 0.00 40.51 3.50
1450 1498 5.014858 GGTCATAGGATGATGGCAATGAAT 58.985 41.667 0.00 0.00 42.04 2.57
1481 1529 0.314618 TGCCGTGCGTCAAAGTAGTA 59.685 50.000 0.00 0.00 0.00 1.82
1530 1578 6.643388 TCATATCATAAGATAGCAATGCCGT 58.357 36.000 0.00 0.00 39.94 5.68
1807 1855 1.202758 ACATCCACGCTTCACCTTTGA 60.203 47.619 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.