Multiple sequence alignment - TraesCS6B01G213800

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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 TraesCS6B01G213800 chr6B 100.000 3260 0 0 1 3260 288792653 288795912 0 6021
1 TraesCS6B01G213800 chr6B 94.109 662 30 8 2605 3260 590563932 590563274 0 998
2 TraesCS6B01G213800 chr6D 97.016 2614 69 5 1 2605 158076160 158073547 0 4386
3 TraesCS6B01G213800 chr6A 95.946 2615 74 12 1 2605 213148040 213150632 0 4213
4 TraesCS6B01G213800 chr4D 85.000 1880 212 40 474 2295 115045350 115047217 0 1845
5 TraesCS6B01G213800 chr4B 85.983 1755 187 35 584 2292 175473909 175475650 0 1823
6 TraesCS6B01G213800 chr4A 84.795 1881 214 41 474 2295 462222217 462220350 0 1823
7 TraesCS6B01G213800 chr4A 91.345 647 53 3 2602 3245 741155120 741155766 0 881
8 TraesCS6B01G213800 chr1B 95.296 659 27 4 2605 3260 134819978 134819321 0 1042
9 TraesCS6B01G213800 chr1B 94.817 656 33 1 2605 3260 476910425 476911079 0 1022
10 TraesCS6B01G213800 chr3B 93.617 658 40 2 2604 3260 684248458 684247802 0 981
11 TraesCS6B01G213800 chr1A 93.231 650 38 6 2603 3250 515836216 515835571 0 952
12 TraesCS6B01G213800 chr7D 90.615 650 51 5 2605 3250 540733361 540732718 0 854
13 TraesCS6B01G213800 chr5D 90.432 648 54 5 2605 3250 285161481 285160840 0 846
14 TraesCS6B01G213800 chr2D 90.865 613 52 4 2605 3214 537404685 537405296 0 819


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 TraesCS6B01G213800 chr6B 288792653 288795912 3259 False 6021 6021 100.000 1 3260 1 chr6B.!!$F1 3259
1 TraesCS6B01G213800 chr6B 590563274 590563932 658 True 998 998 94.109 2605 3260 1 chr6B.!!$R1 655
2 TraesCS6B01G213800 chr6D 158073547 158076160 2613 True 4386 4386 97.016 1 2605 1 chr6D.!!$R1 2604
3 TraesCS6B01G213800 chr6A 213148040 213150632 2592 False 4213 4213 95.946 1 2605 1 chr6A.!!$F1 2604
4 TraesCS6B01G213800 chr4D 115045350 115047217 1867 False 1845 1845 85.000 474 2295 1 chr4D.!!$F1 1821
5 TraesCS6B01G213800 chr4B 175473909 175475650 1741 False 1823 1823 85.983 584 2292 1 chr4B.!!$F1 1708
6 TraesCS6B01G213800 chr4A 462220350 462222217 1867 True 1823 1823 84.795 474 2295 1 chr4A.!!$R1 1821
7 TraesCS6B01G213800 chr4A 741155120 741155766 646 False 881 881 91.345 2602 3245 1 chr4A.!!$F1 643
8 TraesCS6B01G213800 chr1B 134819321 134819978 657 True 1042 1042 95.296 2605 3260 1 chr1B.!!$R1 655
9 TraesCS6B01G213800 chr1B 476910425 476911079 654 False 1022 1022 94.817 2605 3260 1 chr1B.!!$F1 655
10 TraesCS6B01G213800 chr3B 684247802 684248458 656 True 981 981 93.617 2604 3260 1 chr3B.!!$R1 656
11 TraesCS6B01G213800 chr1A 515835571 515836216 645 True 952 952 93.231 2603 3250 1 chr1A.!!$R1 647
12 TraesCS6B01G213800 chr7D 540732718 540733361 643 True 854 854 90.615 2605 3250 1 chr7D.!!$R1 645
13 TraesCS6B01G213800 chr5D 285160840 285161481 641 True 846 846 90.432 2605 3250 1 chr5D.!!$R1 645
14 TraesCS6B01G213800 chr2D 537404685 537405296 611 False 819 819 90.865 2605 3214 1 chr2D.!!$F1 609

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
105 106 1.676967 CCAGCCAGAAGCCACTTCC 60.677 63.158 3.77 0.0 45.47 3.46 F
1781 1845 2.294512 TCTCGATCGATGCTGCTAATGT 59.705 45.455 19.78 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2106 0.533032 GTCGAAAGAGTAGGCCAGCT 59.467 55.0 5.01 1.07 43.49 4.24 R
3195 3274 0.468226 TGTCTTCTTTGTGGGCGAGT 59.532 50.0 0.00 0.00 0.00 4.18 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
105 106 1.676967 CCAGCCAGAAGCCACTTCC 60.677 63.158 3.77 0.00 45.47 3.46
202 203 5.876460 GGGCTTTGCTGAATTTGACATTTAT 59.124 36.000 0.00 0.00 0.00 1.40
212 213 6.154877 TGAATTTGACATTTATGGCATGGAGT 59.845 34.615 10.98 3.31 46.90 3.85
215 216 7.473735 TTTGACATTTATGGCATGGAGTTTA 57.526 32.000 10.98 0.00 46.90 2.01
216 217 7.658525 TTGACATTTATGGCATGGAGTTTAT 57.341 32.000 10.98 0.00 46.90 1.40
319 320 8.776061 TTAATAAAATTTGGGCCTGCTATAGT 57.224 30.769 4.53 0.00 0.00 2.12
561 565 5.590259 ACTTTCAGTTACATGGACCATATGC 59.410 40.000 6.67 0.00 0.00 3.14
614 633 5.483685 TGAGTAAAGTGCAGTTCATACCT 57.516 39.130 7.36 0.00 0.00 3.08
678 697 5.465056 GCTGTCCTGCTAGAATACTCAAATC 59.535 44.000 0.00 0.00 0.00 2.17
826 854 8.488764 GCTGTAGTTTATTTTGGACGATCTATC 58.511 37.037 0.00 0.00 0.00 2.08
1318 1382 3.755378 AGATTCACGCTTGCTTTCTGAAT 59.245 39.130 0.00 0.00 34.89 2.57
1419 1483 4.286032 ACTGAGATTACCCACTTACAGCAA 59.714 41.667 0.00 0.00 0.00 3.91
1507 1571 6.954684 ACTTAACAAGGAGTCAGAGGAATCTA 59.045 38.462 0.00 0.00 38.19 1.98
1781 1845 2.294512 TCTCGATCGATGCTGCTAATGT 59.705 45.455 19.78 0.00 0.00 2.71
1953 2017 2.488204 TCTTCGGCAACATGGATCAA 57.512 45.000 0.00 0.00 0.00 2.57
2042 2106 3.495331 AGTCCATATGGTTGTTGCACAA 58.505 40.909 21.28 0.00 35.42 3.33
2097 2161 3.297134 TTCCAAGTGAAGAAGGCAAGT 57.703 42.857 0.00 0.00 0.00 3.16
2240 2304 2.229302 AGTCTCGAGTGTACCTTTCTGC 59.771 50.000 13.13 0.00 0.00 4.26
2268 2332 2.412089 GTGTGCCGACTGATAAGTGTTC 59.588 50.000 0.00 0.00 0.00 3.18
2289 2353 1.004745 GGGTTGCCTGAGAAGATTCCA 59.995 52.381 0.00 0.00 0.00 3.53
2373 2437 9.567848 AAAATGTTATTCGTATGAAATGTGGTC 57.432 29.630 0.55 0.00 37.71 4.02
2392 2456 3.285745 GTCGCAACACCTTTTTCGTAAG 58.714 45.455 0.00 0.00 0.00 2.34
2519 2586 2.228925 TGTCAATGTGGTGTGGATGTG 58.771 47.619 0.00 0.00 0.00 3.21
2521 2588 1.202915 TCAATGTGGTGTGGATGTGCT 60.203 47.619 0.00 0.00 0.00 4.40
2617 2686 6.136857 TCTACTGCCTAACTAGACCATGATT 58.863 40.000 0.00 0.00 0.00 2.57
3026 3101 5.132648 TGCTTGATTCCCATATTGGTAGACT 59.867 40.000 0.00 0.00 35.17 3.24
3044 3119 4.147321 AGACTTTCTCATTGTTGCCATGT 58.853 39.130 0.00 0.00 0.00 3.21
3071 3146 1.923909 GGGAGTTAGGCAGTGGGGT 60.924 63.158 0.00 0.00 0.00 4.95
3195 3274 5.840693 TGGAGATATTAGCCAGACAAGATGA 59.159 40.000 0.00 0.00 0.00 2.92
3197 3276 6.014669 GGAGATATTAGCCAGACAAGATGACT 60.015 42.308 0.00 0.00 0.00 3.41
3227 3306 5.180492 ACAAAGAAGACACGACTTTCACAAA 59.820 36.000 0.00 0.00 32.59 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.440173 GGCTTTTAGTGATGCTTGCTGTA 59.560 43.478 0.00 0.00 0.00 2.74
105 106 0.806492 GGGCGTCTAAAGCTTCTCCG 60.806 60.000 0.00 1.26 34.52 4.63
202 203 4.038763 CCGTCTACTATAAACTCCATGCCA 59.961 45.833 0.00 0.00 0.00 4.92
212 213 7.643569 TCATGTACCAACCGTCTACTATAAA 57.356 36.000 0.00 0.00 0.00 1.40
215 216 5.068723 CCTTCATGTACCAACCGTCTACTAT 59.931 44.000 0.00 0.00 0.00 2.12
216 217 4.400251 CCTTCATGTACCAACCGTCTACTA 59.600 45.833 0.00 0.00 0.00 1.82
561 565 5.126545 TGCCATGAGAAGATTCATTTCAAGG 59.873 40.000 0.00 0.77 35.67 3.61
614 633 3.118629 CCAGTCGATCTCCCAAGATGAAA 60.119 47.826 0.00 0.00 42.46 2.69
678 697 4.578516 TCAACCCATCACAAACAGTACAAG 59.421 41.667 0.00 0.00 0.00 3.16
1318 1382 2.104792 ACAAGTTCTGCTGCTCCTGTAA 59.895 45.455 0.00 0.00 0.00 2.41
1419 1483 0.958822 GTTTGGCCTCATCGGTTTGT 59.041 50.000 3.32 0.00 34.25 2.83
2042 2106 0.533032 GTCGAAAGAGTAGGCCAGCT 59.467 55.000 5.01 1.07 43.49 4.24
2097 2161 3.118992 CCATGTGAATCTCCGAGAACTCA 60.119 47.826 1.27 5.89 0.00 3.41
2240 2304 2.148916 TCAGTCGGCACACTTTACAG 57.851 50.000 0.00 0.00 0.00 2.74
2268 2332 1.373570 GAATCTTCTCAGGCAACCCG 58.626 55.000 0.00 0.00 35.76 5.28
2289 2353 1.593787 CAGGATGTGTGAGACGCCT 59.406 57.895 0.00 0.00 33.42 5.52
2373 2437 3.595709 TCTTACGAAAAAGGTGTTGCG 57.404 42.857 0.00 0.00 0.00 4.85
2519 2586 5.462405 GCTGTACAGTCACCATATAGTAGC 58.538 45.833 23.44 0.88 0.00 3.58
2521 2588 5.451354 TGGCTGTACAGTCACCATATAGTA 58.549 41.667 25.90 0.00 38.26 1.82
2860 2934 9.138062 GCTATTGACTATCATGTATGTTCTCTG 57.862 37.037 0.00 0.00 0.00 3.35
3044 3119 1.972198 CCTAACTCCCTCACGTGCA 59.028 57.895 11.67 0.00 0.00 4.57
3071 3146 1.100463 AGCGCCACACAACATTGACA 61.100 50.000 2.29 0.00 0.00 3.58
3093 3169 2.052237 GTTGCTCGTGTTGGCGTG 60.052 61.111 0.00 0.00 0.00 5.34
3118 3196 5.365403 TTGCAATAGACGGTGGTTTTTAG 57.635 39.130 0.00 0.00 0.00 1.85
3178 3257 3.739519 GCGAGTCATCTTGTCTGGCTAAT 60.740 47.826 0.00 0.00 35.29 1.73
3195 3274 0.468226 TGTCTTCTTTGTGGGCGAGT 59.532 50.000 0.00 0.00 0.00 4.18
3197 3276 0.878523 CGTGTCTTCTTTGTGGGCGA 60.879 55.000 0.00 0.00 0.00 5.54
3227 3306 7.112122 TGATAGTAATGTTGAGGCTCACAATT 58.888 34.615 18.55 20.26 0.00 2.32


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

AutoCloner maintained by Alex Coulton.