Multiple sequence alignment - TraesCS6B01G398900

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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 TraesCS6B01G398900 chr6B 100.000 2703 0 0 1 2703 674457906 674460608 0.000000e+00 4992
1 TraesCS6B01G398900 chr6B 96.043 2704 102 5 1 2703 152497967 152500666 0.000000e+00 4396
2 TraesCS6B01G398900 chr6B 95.786 2705 98 7 1 2703 208206988 208209678 0.000000e+00 4349
3 TraesCS6B01G398900 chr6B 95.528 2706 99 5 1 2703 663070620 663073306 0.000000e+00 4307
4 TraesCS6B01G398900 chr6B 93.151 73 4 1 46 118 244367045 244366974 3.680000e-19 106
5 TraesCS6B01G398900 chr2B 96.724 2656 83 3 51 2703 676210390 676207736 0.000000e+00 4420
6 TraesCS6B01G398900 chr2B 96.163 2658 94 7 51 2703 739865512 739862858 0.000000e+00 4337
7 TraesCS6B01G398900 chr2B 95.180 2552 94 6 154 2701 780648598 780651124 0.000000e+00 4004
8 TraesCS6B01G398900 chr3B 95.259 2721 99 13 1 2703 142225198 142227906 0.000000e+00 4283
9 TraesCS6B01G398900 chr3B 94.594 2719 116 14 1 2703 761535654 761532951 0.000000e+00 4178
10 TraesCS6B01G398900 chr3B 93.680 2674 106 16 1 2658 751892761 751890135 0.000000e+00 3943
11 TraesCS6B01G398900 chr5B 95.631 2655 110 6 51 2703 638201591 638198941 0.000000e+00 4255
12 TraesCS6B01G398900 chr5B 95.715 2567 80 14 154 2703 209178052 209175499 0.000000e+00 4104
13 TraesCS6B01G398900 chr7B 94.944 2670 104 15 51 2703 3657303 3659958 0.000000e+00 4154
14 TraesCS6B01G398900 chr7B 94.131 2658 97 13 48 2703 692774246 692776846 0.000000e+00 3989
15 TraesCS6B01G398900 chr3A 93.394 2755 118 17 1 2703 233468879 233466137 0.000000e+00 4021
16 TraesCS6B01G398900 chr4B 95.982 2389 92 3 51 2437 613134918 613137304 0.000000e+00 3877
17 TraesCS6B01G398900 chr7A 98.000 200 3 1 1 200 579477499 579477301 1.990000e-91 346
18 TraesCS6B01G398900 chr4A 97.959 196 3 1 4 199 525157809 525157615 3.330000e-89 339
19 TraesCS6B01G398900 chr4A 96.512 86 2 1 1 86 677753882 677753798 1.010000e-29 141


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 TraesCS6B01G398900 chr6B 674457906 674460608 2702 False 4992 4992 100.000 1 2703 1 chr6B.!!$F4 2702
1 TraesCS6B01G398900 chr6B 152497967 152500666 2699 False 4396 4396 96.043 1 2703 1 chr6B.!!$F1 2702
2 TraesCS6B01G398900 chr6B 208206988 208209678 2690 False 4349 4349 95.786 1 2703 1 chr6B.!!$F2 2702
3 TraesCS6B01G398900 chr6B 663070620 663073306 2686 False 4307 4307 95.528 1 2703 1 chr6B.!!$F3 2702
4 TraesCS6B01G398900 chr2B 676207736 676210390 2654 True 4420 4420 96.724 51 2703 1 chr2B.!!$R1 2652
5 TraesCS6B01G398900 chr2B 739862858 739865512 2654 True 4337 4337 96.163 51 2703 1 chr2B.!!$R2 2652
6 TraesCS6B01G398900 chr2B 780648598 780651124 2526 False 4004 4004 95.180 154 2701 1 chr2B.!!$F1 2547
7 TraesCS6B01G398900 chr3B 142225198 142227906 2708 False 4283 4283 95.259 1 2703 1 chr3B.!!$F1 2702
8 TraesCS6B01G398900 chr3B 761532951 761535654 2703 True 4178 4178 94.594 1 2703 1 chr3B.!!$R2 2702
9 TraesCS6B01G398900 chr3B 751890135 751892761 2626 True 3943 3943 93.680 1 2658 1 chr3B.!!$R1 2657
10 TraesCS6B01G398900 chr5B 638198941 638201591 2650 True 4255 4255 95.631 51 2703 1 chr5B.!!$R2 2652
11 TraesCS6B01G398900 chr5B 209175499 209178052 2553 True 4104 4104 95.715 154 2703 1 chr5B.!!$R1 2549
12 TraesCS6B01G398900 chr7B 3657303 3659958 2655 False 4154 4154 94.944 51 2703 1 chr7B.!!$F1 2652
13 TraesCS6B01G398900 chr7B 692774246 692776846 2600 False 3989 3989 94.131 48 2703 1 chr7B.!!$F2 2655
14 TraesCS6B01G398900 chr3A 233466137 233468879 2742 True 4021 4021 93.394 1 2703 1 chr3A.!!$R1 2702
15 TraesCS6B01G398900 chr4B 613134918 613137304 2386 False 3877 3877 95.982 51 2437 1 chr4B.!!$F1 2386

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
428 465 1.613437 GGCTTAATTGTGCCTGTGTGT 59.387 47.619 13.99 0.0 45.26 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2376 0.175989 CCTCACCCTTACGCTCTTCC 59.824 60.0 0.0 0.0 0.0 3.46 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
58 59 3.313012 TCACATCTTTCCAGTGGTACG 57.687 47.619 9.54 0.00 34.17 3.67
428 465 1.613437 GGCTTAATTGTGCCTGTGTGT 59.387 47.619 13.99 0.00 45.26 3.72
690 728 6.989659 TGGTGTACAAGAAGGTAGAAGTTAG 58.010 40.000 0.00 0.00 0.00 2.34
814 852 4.705023 ACAAGACTGTTAAGGTGCAAACTT 59.295 37.500 9.54 9.54 28.57 2.66
926 965 4.761975 TGTTTATACGAGGCACTAAAGGG 58.238 43.478 0.00 0.00 41.55 3.95
959 999 3.185455 AGAGGCCTGGTGTTAAGAAGAT 58.815 45.455 12.00 0.00 0.00 2.40
1226 1272 0.260816 AGCATGGATGGAAGTGGCAT 59.739 50.000 0.00 0.00 0.00 4.40
1283 1329 1.561076 TGAAGCAGGCACTATCCACAT 59.439 47.619 0.00 0.00 36.02 3.21
1348 1394 6.767423 TGTCATCAATGAAGAAGAACAACAGA 59.233 34.615 0.00 0.00 38.75 3.41
1374 1420 3.745975 TGCTTCAATCAGGTAAGTTGACG 59.254 43.478 0.00 0.00 32.10 4.35
1413 1459 8.855110 TCTTTTACTAGTGCATTTTCCAAATGA 58.145 29.630 5.39 0.18 0.00 2.57
1754 1804 7.667043 TGTTGTAAGCTACTTGTTTCATAGG 57.333 36.000 0.00 0.00 0.00 2.57
1888 1938 2.356135 AGACCGCGTGCAAAGATATTT 58.644 42.857 4.92 0.00 0.00 1.40
2075 2127 7.174772 TCTCTGCTTTGTTTGATGCTTTATGTA 59.825 33.333 0.00 0.00 0.00 2.29
2259 2326 8.172484 CGTTTGATCCTCGTTGAATAACATTTA 58.828 33.333 0.00 0.00 36.58 1.40
2331 2398 0.331954 AGAGCGTAAGGGTGAGGAGA 59.668 55.000 0.00 0.00 38.28 3.71
2388 2455 0.941542 CAAGAAGCACGGGTTTTCGA 59.058 50.000 0.00 0.00 0.00 3.71
2402 2469 1.497991 TTTCGAAGCCAGTCAAGACG 58.502 50.000 0.00 0.00 36.20 4.18
2517 2584 0.599558 TTCACAGCCAGCTTTGATGC 59.400 50.000 9.16 0.00 33.46 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.732259 GCACGTACCACTGGAAAGATG 59.268 52.381 0.71 0.00 0.00 2.90
58 59 2.420628 TGCACTAAACAAGCATGCAC 57.579 45.000 21.98 0.00 41.18 4.57
369 406 6.807720 TGCAACAATACATTTCACTTAGCATG 59.192 34.615 0.00 0.00 0.00 4.06
390 427 3.359033 AGCCAGCTTATTCAGATTGCAA 58.641 40.909 0.00 0.00 0.00 4.08
428 465 8.877195 AGTTATTCAGGTAAGGAAGACTAACAA 58.123 33.333 0.00 0.00 0.00 2.83
690 728 2.904434 TCCACTACCTTCTTGAACCTCC 59.096 50.000 0.00 0.00 0.00 4.30
814 852 0.538057 CAGCCCTCCAAGCAAGACAA 60.538 55.000 0.00 0.00 0.00 3.18
926 965 1.611491 CAGGCCTCTTCGTCCTAGATC 59.389 57.143 0.00 0.00 0.00 2.75
959 999 4.526262 AGCTCTTCTTCTTCTTGCTGACTA 59.474 41.667 0.00 0.00 0.00 2.59
1226 1272 2.768527 CCTCCTTCATCTAGGCAGACAA 59.231 50.000 0.00 0.00 35.15 3.18
1283 1329 1.071699 GTGCAACAGGGTTGAGGTCTA 59.928 52.381 12.90 0.00 36.32 2.59
1365 1411 3.980646 AGCATTGCAAACGTCAACTTA 57.019 38.095 11.91 0.00 0.00 2.24
1374 1420 7.218963 GCACTAGTAAAAGATAGCATTGCAAAC 59.781 37.037 11.91 0.00 0.00 2.93
1413 1459 7.087409 TCGACAAAAGCATACATGATCATTT 57.913 32.000 5.16 1.90 0.00 2.32
1469 1515 6.361748 GCATCTGAAAATGAAACTGAACTCAC 59.638 38.462 0.00 0.00 0.00 3.51
1478 1524 7.274250 GGTAGTCATTGCATCTGAAAATGAAAC 59.726 37.037 12.50 12.78 40.85 2.78
1888 1938 7.431084 GCGTCTGTTCTTTGAATTTTTCTACAA 59.569 33.333 0.00 0.00 0.00 2.41
2309 2376 0.175989 CCTCACCCTTACGCTCTTCC 59.824 60.000 0.00 0.00 0.00 3.46
2331 2398 5.106555 CCTTAAACAAGTCAATCGCAGACAT 60.107 40.000 0.00 0.00 42.51 3.06
2388 2455 1.276622 ATACCCGTCTTGACTGGCTT 58.723 50.000 10.45 0.00 0.00 4.35
2402 2469 4.589374 AGCATGGAGTGACTTACTATACCC 59.411 45.833 0.00 0.00 40.53 3.69
2404 2471 7.042335 ACAAAGCATGGAGTGACTTACTATAC 58.958 38.462 0.00 0.00 40.53 1.47


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

AutoCloner maintained by Alex Coulton.