Multiple sequence alignment - TraesCS4B01G147700

Loading Multiple Alignment...

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 TraesCS4B01G147700 chr4B 100.000 2579 0 0 1 2579 209310098 209312676 0.000000e+00 4763
1 TraesCS4B01G147700 chr7A 98.216 2579 46 0 1 2579 60289763 60292341 0.000000e+00 4508
2 TraesCS4B01G147700 chr7A 97.843 1669 36 0 911 2579 708263722 708262054 0.000000e+00 2883
3 TraesCS4B01G147700 chr7A 95.111 225 5 2 816 1034 60341867 60342091 1.470000e-92 350
4 TraesCS4B01G147700 chr2B 96.627 2579 52 14 1 2579 112851667 112854210 0.000000e+00 4248
5 TraesCS4B01G147700 chr2B 96.892 1673 47 4 911 2579 751960902 751959231 0.000000e+00 2796
6 TraesCS4B01G147700 chr2B 97.257 802 22 0 1 802 391184143 391183342 0.000000e+00 1360
7 TraesCS4B01G147700 chr7D 97.790 1674 32 4 911 2579 381946803 381945130 0.000000e+00 2881
8 TraesCS4B01G147700 chr7D 91.123 383 19 3 621 988 382095451 382095833 2.960000e-139 505
9 TraesCS4B01G147700 chr4D 97.788 1673 33 3 911 2579 398050598 398048926 0.000000e+00 2881
10 TraesCS4B01G147700 chr3D 97.129 1672 43 4 912 2579 602854190 602852520 0.000000e+00 2817
11 TraesCS4B01G147700 chr6B 96.950 1672 46 5 912 2578 388166084 388164413 0.000000e+00 2800
12 TraesCS4B01G147700 chr6B 96.655 1674 51 4 911 2579 388358137 388356464 0.000000e+00 2776
13 TraesCS4B01G147700 chrUn 98.644 1401 19 0 1 1401 403079396 403077996 0.000000e+00 2483
14 TraesCS4B01G147700 chrUn 91.123 383 19 3 621 988 325545043 325544661 2.960000e-139 505
15 TraesCS4B01G147700 chrUn 91.123 383 19 3 621 988 325548139 325547757 2.960000e-139 505
16 TraesCS4B01G147700 chr1B 96.950 918 23 1 1 913 339034641 339035558 0.000000e+00 1535
17 TraesCS4B01G147700 chr6A 97.340 827 19 1 1 827 608889745 608890568 0.000000e+00 1402
18 TraesCS4B01G147700 chr7B 98.282 524 9 0 1 524 716899230 716898707 0.000000e+00 918
19 TraesCS4B01G147700 chr7B 98.282 524 9 0 1 524 742999911 743000434 0.000000e+00 918
20 TraesCS4B01G147700 chr7B 98.092 524 10 0 1 524 716863711 716863188 0.000000e+00 913


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 TraesCS4B01G147700 chr4B 209310098 209312676 2578 False 4763 4763 100.000 1 2579 1 chr4B.!!$F1 2578
1 TraesCS4B01G147700 chr7A 60289763 60292341 2578 False 4508 4508 98.216 1 2579 1 chr7A.!!$F1 2578
2 TraesCS4B01G147700 chr7A 708262054 708263722 1668 True 2883 2883 97.843 911 2579 1 chr7A.!!$R1 1668
3 TraesCS4B01G147700 chr2B 112851667 112854210 2543 False 4248 4248 96.627 1 2579 1 chr2B.!!$F1 2578
4 TraesCS4B01G147700 chr2B 751959231 751960902 1671 True 2796 2796 96.892 911 2579 1 chr2B.!!$R2 1668
5 TraesCS4B01G147700 chr2B 391183342 391184143 801 True 1360 1360 97.257 1 802 1 chr2B.!!$R1 801
6 TraesCS4B01G147700 chr7D 381945130 381946803 1673 True 2881 2881 97.790 911 2579 1 chr7D.!!$R1 1668
7 TraesCS4B01G147700 chr4D 398048926 398050598 1672 True 2881 2881 97.788 911 2579 1 chr4D.!!$R1 1668
8 TraesCS4B01G147700 chr3D 602852520 602854190 1670 True 2817 2817 97.129 912 2579 1 chr3D.!!$R1 1667
9 TraesCS4B01G147700 chr6B 388164413 388166084 1671 True 2800 2800 96.950 912 2578 1 chr6B.!!$R1 1666
10 TraesCS4B01G147700 chr6B 388356464 388358137 1673 True 2776 2776 96.655 911 2579 1 chr6B.!!$R2 1668
11 TraesCS4B01G147700 chrUn 403077996 403079396 1400 True 2483 2483 98.644 1 1401 1 chrUn.!!$R1 1400
12 TraesCS4B01G147700 chrUn 325544661 325548139 3478 True 505 505 91.123 621 988 2 chrUn.!!$R2 367
13 TraesCS4B01G147700 chr1B 339034641 339035558 917 False 1535 1535 96.950 1 913 1 chr1B.!!$F1 912
14 TraesCS4B01G147700 chr6A 608889745 608890568 823 False 1402 1402 97.340 1 827 1 chr6A.!!$F1 826
15 TraesCS4B01G147700 chr7B 716898707 716899230 523 True 918 918 98.282 1 524 1 chr7B.!!$R2 523
16 TraesCS4B01G147700 chr7B 742999911 743000434 523 False 918 918 98.282 1 524 1 chr7B.!!$F1 523
17 TraesCS4B01G147700 chr7B 716863188 716863711 523 True 913 913 98.092 1 524 1 chr7B.!!$R1 523

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
480 481 0.395724 GGCCAACTTACATCTGGGGG 60.396 60.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 4607 1.408422 GTTGCATCCGCTGTTTCAAC 58.592 50.0 0.0 0.0 39.64 3.18 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
28 29 7.504924 TTGACGTATTCAAAGTGGAAAGAAT 57.495 32.000 0.00 0.00 41.51 2.40
52 53 6.691508 TGAATATCGATTCTCGTGGATGAAT 58.308 36.000 1.71 0.00 41.87 2.57
194 195 2.037901 ACACACCAAATGATGCCACAA 58.962 42.857 0.00 0.00 0.00 3.33
217 218 7.446625 ACAAAAGAGATTGCAGTACAAGAAGAT 59.553 33.333 0.00 0.00 42.87 2.40
366 367 2.884639 GCATTGCCCTTATTGATACCGT 59.115 45.455 0.00 0.00 0.00 4.83
480 481 0.395724 GGCCAACTTACATCTGGGGG 60.396 60.000 0.00 0.00 0.00 5.40
557 558 4.154556 CGGAAGAGTTTCTAGTCGAGAAGT 59.845 45.833 0.00 0.00 45.05 3.01
741 3218 0.839946 AGTGCATTTCCCTAGCGGAT 59.160 50.000 0.00 0.00 41.63 4.18
742 3219 2.037251 GAGTGCATTTCCCTAGCGGATA 59.963 50.000 0.00 0.00 41.63 2.59
769 3246 6.749118 GGTGATTTATGCAAGATCTTGTCAAC 59.251 38.462 30.88 24.13 42.31 3.18
841 3318 6.917217 AACGCGTATAGTAAGTAGTCTTCT 57.083 37.500 14.46 0.00 35.36 2.85
972 3459 2.033299 CCTTTCAAAAGTGAGCGAGCAA 59.967 45.455 0.00 0.00 34.49 3.91
1028 3515 6.931840 AGATTTCTTTCTACGGATATGAAGGC 59.068 38.462 0.00 0.00 0.00 4.35
1247 3734 9.892130 ATTCTTCAATCCTAACGAAGTAATTCT 57.108 29.630 0.96 0.00 45.00 2.40
1522 4009 5.047235 ACGTTCAAAGCTTCTACCATAGACT 60.047 40.000 0.00 0.00 33.84 3.24
1559 4046 6.408662 GGCTTGATAGTCCTAAGAAAGGTGAT 60.409 42.308 0.00 0.00 46.62 3.06
1709 4198 3.073209 TGTCATGCCCCACAAGTTAGTTA 59.927 43.478 0.00 0.00 0.00 2.24
2004 4495 2.548057 CCTCAAAGCGCTAACAAAGTCA 59.452 45.455 12.05 0.00 0.00 3.41
2078 4569 4.819105 TGTCTGATGAAGAATAACGGGT 57.181 40.909 0.00 0.00 36.40 5.28
2165 4656 8.399425 TGCATTTCGTTCTTTTGTTCTTTACTA 58.601 29.630 0.00 0.00 0.00 1.82
2190 4681 0.106708 TCGCTTTGGCACTCACTTCT 59.893 50.000 0.00 0.00 38.60 2.85
2242 4733 3.885901 TCATTCCGTTGACCATCAAACAA 59.114 39.130 0.00 0.00 38.22 2.83
2375 4866 7.176690 TCCCTCATTCTTATTGTTTGTTCTTCC 59.823 37.037 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.786441 ACCAAGTTCCCATTTCCTCCA 59.214 47.619 0.00 0.00 0.00 3.86
194 195 7.164122 TCATCTTCTTGTACTGCAATCTCTTT 58.836 34.615 0.00 0.00 36.36 2.52
366 367 8.849168 ACAAATCAATGAATGTACTTGAACTGA 58.151 29.630 3.65 2.39 33.03 3.41
557 558 1.064758 AGGATTTGCTAATGCCCGACA 60.065 47.619 8.64 0.00 38.71 4.35
741 3218 7.828717 TGACAAGATCTTGCATAAATCACCTTA 59.171 33.333 30.95 5.22 44.03 2.69
742 3219 6.660521 TGACAAGATCTTGCATAAATCACCTT 59.339 34.615 30.95 10.28 44.03 3.50
769 3246 3.544834 CGTCGCCAGCTAAATCAATCAAG 60.545 47.826 0.00 0.00 0.00 3.02
841 3318 0.544357 ACACTGGAGGTCCCATCGAA 60.544 55.000 0.00 0.00 45.57 3.71
972 3459 5.966742 GGTAACTCCATCTTTTTCAGCTT 57.033 39.130 0.00 0.00 35.97 3.74
1522 4009 6.098409 AGGACTATCAAGCCTTCTCGAATTAA 59.902 38.462 0.00 0.00 0.00 1.40
1675 4164 2.159057 GGGCATGACATCCCAAATTCAC 60.159 50.000 0.00 0.00 42.18 3.18
1709 4198 3.083997 CCTAGGGAGCGCTTGGGT 61.084 66.667 13.26 0.00 0.00 4.51
1773 4262 5.542635 AGAAAAACCTAAAATGGAGGGGTTC 59.457 40.000 0.00 0.00 39.05 3.62
1813 4302 4.322349 GCTTATCTGGCCGATATGACTTCT 60.322 45.833 22.70 2.49 34.68 2.85
2116 4607 1.408422 GTTGCATCCGCTGTTTCAAC 58.592 50.000 0.00 0.00 39.64 3.18
2165 4656 3.758554 AGTGAGTGCCAAAGCGAAAATAT 59.241 39.130 0.00 0.00 44.31 1.28
2190 4681 9.996554 GAGAAGAAAAATTCCCTTATTCCAAAA 57.003 29.630 0.00 0.00 0.00 2.44
2375 4866 3.425758 GCGAGTTAAAAACAAGGGGATCG 60.426 47.826 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.