Multiple sequence alignment - TraesCS5B01G103800

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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 TraesCS5B01G103800 chr5B 100.000 2633 0 0 1 2633 138558596 138555964 0.000000e+00 4863.0
1 TraesCS5B01G103800 chr5B 89.130 828 62 11 1832 2633 138453697 138452872 0.000000e+00 1005.0
2 TraesCS5B01G103800 chr5D 90.871 1654 67 26 829 2421 125778477 125776847 0.000000e+00 2141.0
3 TraesCS5B01G103800 chr5D 94.595 333 12 3 99 426 125781491 125781160 6.500000e-141 510.0
4 TraesCS5B01G103800 chr5D 92.760 221 15 1 2414 2633 125776162 125775942 4.230000e-83 318.0
5 TraesCS5B01G103800 chr5D 94.972 179 7 1 425 603 125781078 125780902 2.000000e-71 279.0
6 TraesCS5B01G103800 chr5D 94.737 171 6 1 658 828 125779623 125779456 2.010000e-66 263.0
7 TraesCS5B01G103800 chr5D 92.157 51 3 1 44 94 125781624 125781575 1.310000e-08 71.3
8 TraesCS5B01G103800 chr5A 93.801 984 46 10 786 1759 139894182 139893204 0.000000e+00 1465.0
9 TraesCS5B01G103800 chr5A 93.162 351 16 1 411 761 139894629 139894287 2.340000e-140 508.0
10 TraesCS5B01G103800 chr5A 88.441 372 14 11 44 410 139895137 139894790 3.130000e-114 422.0
11 TraesCS5B01G103800 chr6A 80.833 720 95 20 999 1703 581965270 581965961 2.320000e-145 525.0
12 TraesCS5B01G103800 chr6D 80.415 674 94 20 999 1658 434604446 434605095 1.830000e-131 479.0
13 TraesCS5B01G103800 chr6D 94.595 37 1 1 189 224 22113308 22113272 3.660000e-04 56.5
14 TraesCS5B01G103800 chr7D 80.570 561 81 17 1091 1637 549318748 549318202 8.770000e-110 407.0
15 TraesCS5B01G103800 chr7D 80.216 556 81 19 1095 1637 549368854 549368315 8.840000e-105 390.0
16 TraesCS5B01G103800 chr7D 88.119 101 9 1 193 290 549369959 549369859 1.660000e-22 117.0
17 TraesCS5B01G103800 chr7D 94.000 50 3 0 996 1045 549368932 549368883 2.810000e-10 76.8
18 TraesCS5B01G103800 chr7B 87.143 70 6 2 996 1062 593557587 593557518 2.810000e-10 76.8
19 TraesCS5B01G103800 chr4A 88.710 62 4 3 178 236 240370247 240370308 3.640000e-09 73.1


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 TraesCS5B01G103800 chr5B 138555964 138558596 2632 True 4863.000000 4863 100.000000 1 2633 1 chr5B.!!$R2 2632
1 TraesCS5B01G103800 chr5B 138452872 138453697 825 True 1005.000000 1005 89.130000 1832 2633 1 chr5B.!!$R1 801
2 TraesCS5B01G103800 chr5D 125775942 125781624 5682 True 597.050000 2141 93.348667 44 2633 6 chr5D.!!$R1 2589
3 TraesCS5B01G103800 chr5A 139893204 139895137 1933 True 798.333333 1465 91.801333 44 1759 3 chr5A.!!$R1 1715
4 TraesCS5B01G103800 chr6A 581965270 581965961 691 False 525.000000 525 80.833000 999 1703 1 chr6A.!!$F1 704
5 TraesCS5B01G103800 chr6D 434604446 434605095 649 False 479.000000 479 80.415000 999 1658 1 chr6D.!!$F1 659
6 TraesCS5B01G103800 chr7D 549318202 549318748 546 True 407.000000 407 80.570000 1091 1637 1 chr7D.!!$R1 546

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
939 3586 0.172127 TCTGCTCTCTTGCGCTACTG 59.828 55.0 9.73 0.0 35.36 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 5042 0.1078 GGCCTCGAACCTAAACCTCC 60.108 60.0 0.0 0.0 0.0 4.3 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
18 19 3.001576 GATCGTTTGCGCCAAGTTC 57.998 52.632 4.18 0.00 38.14 3.01
19 20 0.517316 GATCGTTTGCGCCAAGTTCT 59.483 50.000 4.18 0.00 38.14 3.01
20 21 1.730064 GATCGTTTGCGCCAAGTTCTA 59.270 47.619 4.18 0.00 38.14 2.10
21 22 1.144969 TCGTTTGCGCCAAGTTCTAG 58.855 50.000 4.18 0.00 38.14 2.43
22 23 1.144969 CGTTTGCGCCAAGTTCTAGA 58.855 50.000 4.18 0.00 0.00 2.43
23 24 1.529438 CGTTTGCGCCAAGTTCTAGAA 59.471 47.619 4.18 0.00 0.00 2.10
24 25 2.159627 CGTTTGCGCCAAGTTCTAGAAT 59.840 45.455 8.75 0.00 0.00 2.40
25 26 3.725010 CGTTTGCGCCAAGTTCTAGAATC 60.725 47.826 8.75 2.88 0.00 2.52
26 27 2.760634 TGCGCCAAGTTCTAGAATCA 57.239 45.000 8.75 0.00 0.00 2.57
27 28 3.266510 TGCGCCAAGTTCTAGAATCAT 57.733 42.857 8.75 0.00 0.00 2.45
28 29 3.198068 TGCGCCAAGTTCTAGAATCATC 58.802 45.455 8.75 0.00 0.00 2.92
29 30 3.198068 GCGCCAAGTTCTAGAATCATCA 58.802 45.455 8.75 0.00 0.00 3.07
30 31 3.623060 GCGCCAAGTTCTAGAATCATCAA 59.377 43.478 8.75 0.00 0.00 2.57
31 32 4.274459 GCGCCAAGTTCTAGAATCATCAAT 59.726 41.667 8.75 0.00 0.00 2.57
32 33 5.745514 CGCCAAGTTCTAGAATCATCAATG 58.254 41.667 8.75 0.04 0.00 2.82
33 34 5.295292 CGCCAAGTTCTAGAATCATCAATGT 59.705 40.000 8.75 0.00 0.00 2.71
34 35 6.479990 CGCCAAGTTCTAGAATCATCAATGTA 59.520 38.462 8.75 0.00 0.00 2.29
35 36 7.011389 CGCCAAGTTCTAGAATCATCAATGTAA 59.989 37.037 8.75 0.00 0.00 2.41
36 37 8.844244 GCCAAGTTCTAGAATCATCAATGTAAT 58.156 33.333 8.75 0.00 0.00 1.89
74 75 3.513680 TGTACATGTCGATGTGGTACC 57.486 47.619 0.00 4.43 43.03 3.34
79 80 0.543410 TGTCGATGTGGTACCCCTGT 60.543 55.000 10.07 0.00 0.00 4.00
87 88 2.106857 TGTGGTACCCCTGTTTGTTAGG 59.893 50.000 10.07 0.00 35.01 2.69
152 231 4.780815 TGTGAGGAGCAATATACTTTGGG 58.219 43.478 0.00 0.00 0.00 4.12
153 232 4.227300 TGTGAGGAGCAATATACTTTGGGT 59.773 41.667 0.00 0.00 0.00 4.51
163 242 1.447099 TACTTTGGGTGGGGTTGCTA 58.553 50.000 0.00 0.00 0.00 3.49
239 318 1.061324 TGTGGGTTACCTTTCCCCGT 61.061 55.000 0.00 0.00 42.80 5.28
255 334 1.545582 CCCGTTGATGGCAATTCACTT 59.454 47.619 0.00 0.00 36.22 3.16
388 472 2.941860 GCTGCTTTCCTTAGTTCCTCCC 60.942 54.545 0.00 0.00 0.00 4.30
409 650 3.128242 CCTTTCAATCCTGCTAGCTTGTG 59.872 47.826 17.23 7.15 0.00 3.33
493 817 4.790937 TCACCAACCATGCATATACACAT 58.209 39.130 0.00 0.00 0.00 3.21
539 863 3.066380 TCTTGTGATGTGATGTGGTTCG 58.934 45.455 0.00 0.00 0.00 3.95
587 911 3.736224 CCATCAGGGCAGGCAGGT 61.736 66.667 0.00 0.00 0.00 4.00
588 912 2.377810 CCATCAGGGCAGGCAGGTA 61.378 63.158 0.00 0.00 0.00 3.08
589 913 1.147824 CATCAGGGCAGGCAGGTAG 59.852 63.158 0.00 0.00 0.00 3.18
590 914 2.074948 ATCAGGGCAGGCAGGTAGG 61.075 63.158 0.00 0.00 0.00 3.18
591 915 4.496336 CAGGGCAGGCAGGTAGGC 62.496 72.222 0.00 0.00 44.61 3.93
678 2244 4.401519 AGAGAAAAGCATGATGGTTGATGG 59.598 41.667 10.93 0.00 38.20 3.51
791 2357 7.402054 ACCAAAGTTCATATCATCAAGTGGTA 58.598 34.615 0.00 0.00 32.86 3.25
878 3517 2.668625 TGTACTACCACTCACACACCA 58.331 47.619 0.00 0.00 0.00 4.17
897 3544 2.224719 CCATAAATCTCAGGCCCTCAGG 60.225 54.545 0.00 0.00 0.00 3.86
939 3586 0.172127 TCTGCTCTCTTGCGCTACTG 59.828 55.000 9.73 0.00 35.36 2.74
992 3639 2.362369 CGGGGCACTCCATCTCTGT 61.362 63.158 0.00 0.00 37.22 3.41
1077 3724 2.520458 CACCACCACCACCACCAT 59.480 61.111 0.00 0.00 0.00 3.55
1497 4159 2.444706 AGGCTGCGCATAGAGGGA 60.445 61.111 12.24 0.00 0.00 4.20
1500 4162 3.120105 CTGCGCATAGAGGGACGA 58.880 61.111 12.24 0.00 0.00 4.20
1717 4389 7.025485 ACGTCTTTGTAAGTAGCTATAGGAC 57.975 40.000 0.00 0.00 0.00 3.85
1738 4410 3.635373 ACAAGATCGACGGGATTAGCTTA 59.365 43.478 0.00 0.00 34.82 3.09
1852 4529 3.740044 AATGCTACATCCACGAAAACG 57.260 42.857 0.00 0.00 0.00 3.60
1875 4552 8.031848 ACGTACATTGGAATTTTACGTAATGT 57.968 30.769 9.18 11.06 40.25 2.71
1927 4629 2.039624 TGGTGGAGGAGAGAGGGC 59.960 66.667 0.00 0.00 0.00 5.19
1930 4632 0.469144 GGTGGAGGAGAGAGGGCTAG 60.469 65.000 0.00 0.00 0.00 3.42
1941 4643 4.283337 AGAGAGGGCTAGTAAGGAAGTTC 58.717 47.826 0.00 0.00 0.00 3.01
1950 4652 5.989777 GCTAGTAAGGAAGTTCACAAAGACA 59.010 40.000 5.01 0.00 0.00 3.41
1965 4667 8.771920 TCACAAAGACAATATACTTCGACAAT 57.228 30.769 0.00 0.00 0.00 2.71
2045 4748 2.945668 ACTTGGTGACTTCAACTTGCTC 59.054 45.455 0.00 0.00 33.92 4.26
2095 4807 7.174426 TGCCATGATCAATAGAAGAATGATGAC 59.826 37.037 0.00 0.00 34.10 3.06
2256 4969 3.550842 GCTGTTTCCAACATGTCAACTCC 60.551 47.826 0.00 0.00 41.26 3.85
2272 4985 4.447342 CCCGGCTTTGGGCTCCAT 62.447 66.667 0.00 0.00 43.70 3.41
2309 5022 2.459934 CCGCTTTTGTTGGACTTGAAC 58.540 47.619 0.00 0.00 0.00 3.18
2311 5024 1.852280 GCTTTTGTTGGACTTGAACGC 59.148 47.619 0.00 0.00 0.00 4.84
2329 5042 2.008268 GCTGATTTGGTCATGGGGCG 62.008 60.000 0.00 0.00 35.97 6.13
2397 5110 4.864334 CGGTGGAGGAGGCATGGC 62.864 72.222 12.14 12.14 0.00 4.40
2407 5120 2.440065 GGCATGGCAATCGGTCCA 60.440 61.111 15.47 0.00 36.70 4.02
2426 5831 3.299503 CCATAGTTATGGCAGCCCTTTT 58.700 45.455 9.64 0.00 45.92 2.27
2496 5901 0.739561 GAGTGACCGACGAATAGGCT 59.260 55.000 0.00 0.00 0.00 4.58
2500 5905 0.659711 GACCGACGAATAGGCTACGC 60.660 60.000 0.00 0.00 0.00 4.42
2520 5925 2.234414 GCCAAGCTTCAAATTGGGATCA 59.766 45.455 0.00 0.00 45.08 2.92
2567 5972 0.682209 AAGCCATGGATGACAGGCAC 60.682 55.000 18.40 0.00 42.35 5.01
2608 6014 5.759059 TGATTGCAGAGAACCCTCAATAAT 58.241 37.500 0.00 0.00 41.87 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.517316 AGAACTTGGCGCAAACGATC 59.483 50.000 10.83 3.02 43.93 3.69
1 2 1.732259 CTAGAACTTGGCGCAAACGAT 59.268 47.619 10.83 0.00 43.93 3.73
2 3 1.144969 CTAGAACTTGGCGCAAACGA 58.855 50.000 10.83 0.00 43.93 3.85
3 4 1.144969 TCTAGAACTTGGCGCAAACG 58.855 50.000 10.83 0.61 44.07 3.60
4 5 3.188460 TGATTCTAGAACTTGGCGCAAAC 59.812 43.478 10.83 0.00 0.00 2.93
5 6 3.407698 TGATTCTAGAACTTGGCGCAAA 58.592 40.909 10.83 2.19 0.00 3.68
6 7 3.052455 TGATTCTAGAACTTGGCGCAA 57.948 42.857 10.83 0.00 0.00 4.85
7 8 2.760634 TGATTCTAGAACTTGGCGCA 57.239 45.000 10.83 0.00 0.00 6.09
8 9 3.198068 TGATGATTCTAGAACTTGGCGC 58.802 45.455 7.48 0.00 0.00 6.53
9 10 5.295292 ACATTGATGATTCTAGAACTTGGCG 59.705 40.000 7.48 0.00 0.00 5.69
10 11 6.690194 ACATTGATGATTCTAGAACTTGGC 57.310 37.500 7.48 0.00 0.00 4.52
35 36 9.859427 CATGTACATGTTAAAATTGGAGTCAAT 57.141 29.630 24.91 0.00 38.27 2.57
93 94 8.903820 GCCATAGGAACTTTGATACATAGTTTT 58.096 33.333 8.43 4.65 39.79 2.43
152 231 0.107945 CTCTCAGCTAGCAACCCCAC 60.108 60.000 18.83 0.00 0.00 4.61
153 232 1.267574 CCTCTCAGCTAGCAACCCCA 61.268 60.000 18.83 0.00 0.00 4.96
163 242 0.337773 TCACTCATCCCCTCTCAGCT 59.662 55.000 0.00 0.00 0.00 4.24
239 318 3.081061 AGCGTAAGTGAATTGCCATCAA 58.919 40.909 0.00 0.00 41.68 2.57
255 334 1.671845 GTTGTTTGGGTGTGAAGCGTA 59.328 47.619 0.00 0.00 0.00 4.42
388 472 3.755378 ACACAAGCTAGCAGGATTGAAAG 59.245 43.478 18.83 10.17 36.29 2.62
409 650 5.746307 TGAAGCTAGATTGCAATCATCAC 57.254 39.130 34.59 22.43 37.89 3.06
493 817 0.889994 AAGCCGCAATGAAAGATGCA 59.110 45.000 0.00 0.00 42.68 3.96
501 825 2.042686 AGATGCTAAAGCCGCAATGA 57.957 45.000 0.00 0.00 41.26 2.57
591 915 4.798344 CCTCTGCCTGCCTGCCTG 62.798 72.222 0.00 0.00 0.00 4.85
594 918 4.357279 AACCCTCTGCCTGCCTGC 62.357 66.667 0.00 0.00 0.00 4.85
678 2244 0.670162 TCTTGCTTTGCTTGGTGCTC 59.330 50.000 0.00 0.00 43.37 4.26
761 2327 7.492669 ACTTGATGATATGAACTTTGGTACGAG 59.507 37.037 0.00 0.00 0.00 4.18
762 2328 7.277760 CACTTGATGATATGAACTTTGGTACGA 59.722 37.037 0.00 0.00 0.00 3.43
763 2329 7.401860 CACTTGATGATATGAACTTTGGTACG 58.598 38.462 0.00 0.00 0.00 3.67
836 3465 9.803315 GTACAATCAGTGTAAGTCTCAATCATA 57.197 33.333 0.00 0.00 44.38 2.15
951 3598 1.958902 GCTGACTAGCTGAGCTGCCT 61.959 60.000 18.79 0.00 46.57 4.75
992 3639 2.768527 GTGATGAGGGACATGGAGAGAA 59.231 50.000 0.00 0.00 39.56 2.87
1377 4033 3.983420 CCCTGGGCCTGCTGGAAA 61.983 66.667 14.77 0.00 34.57 3.13
1407 4063 2.754658 GACGAGAGGGAGGCGGAA 60.755 66.667 0.00 0.00 0.00 4.30
1497 4159 2.203596 ACCTTCCACCGGAGTCGT 60.204 61.111 9.46 0.00 31.21 4.34
1500 4162 3.637273 GCCACCTTCCACCGGAGT 61.637 66.667 9.46 0.00 31.21 3.85
1717 4389 2.802787 AGCTAATCCCGTCGATCTTG 57.197 50.000 0.00 0.00 0.00 3.02
1738 4410 7.062957 ACAAGAATAGCCCTGTAATTAAGCAT 58.937 34.615 0.00 0.00 0.00 3.79
1852 4529 9.485591 CAGACATTACGTAAAATTCCAATGTAC 57.514 33.333 12.81 5.33 36.89 2.90
1900 4577 3.706594 CTCTCCTCCACCACTAATGCTAA 59.293 47.826 0.00 0.00 0.00 3.09
1927 4629 8.608844 ATTGTCTTTGTGAACTTCCTTACTAG 57.391 34.615 0.00 0.00 0.00 2.57
1965 4667 5.263599 ACCAACTCCTGCATGAATTCAATA 58.736 37.500 13.09 0.99 0.00 1.90
2025 4728 2.032549 CGAGCAAGTTGAAGTCACCAAG 60.033 50.000 7.16 0.00 0.00 3.61
2045 4748 1.881591 TTTTGTCCTCCGGGTTTACG 58.118 50.000 0.00 0.00 0.00 3.18
2065 4777 7.504574 TCATTCTTCTATTGATCATGGCATTGT 59.495 33.333 0.00 0.00 0.00 2.71
2095 4807 0.938713 TAACTTGGCACGAAACCACG 59.061 50.000 0.00 0.00 36.76 4.94
2193 4906 5.163426 TGCTGAACATGTGGTCAATCTTTTT 60.163 36.000 0.00 0.00 41.85 1.94
2256 4969 1.526917 CTATGGAGCCCAAAGCCGG 60.527 63.158 0.00 0.00 45.47 6.13
2309 5022 2.008268 GCCCCATGACCAAATCAGCG 62.008 60.000 0.00 0.00 41.91 5.18
2311 5024 1.386525 CCGCCCCATGACCAAATCAG 61.387 60.000 0.00 0.00 41.91 2.90
2329 5042 0.107800 GGCCTCGAACCTAAACCTCC 60.108 60.000 0.00 0.00 0.00 4.30
2407 5120 3.701040 CACAAAAGGGCTGCCATAACTAT 59.299 43.478 22.05 0.00 0.00 2.12
2460 5865 4.094146 GTCACTCCATTGCTTTAGCTTCTC 59.906 45.833 0.00 0.00 42.66 2.87
2496 5901 1.543802 CCCAATTTGAAGCTTGGCGTA 59.456 47.619 2.10 0.00 40.51 4.42
2500 5905 3.674138 CGTGATCCCAATTTGAAGCTTGG 60.674 47.826 2.10 0.00 41.34 3.61
2520 5925 1.224592 GGGCAATCACCTCCATCGT 59.775 57.895 0.00 0.00 0.00 3.73
2567 5972 2.426522 TCAATCTCTTGCACCGAAAGG 58.573 47.619 0.00 0.00 44.29 3.11
2608 6014 3.013921 CGAGCAAAGCCCCAATAACTTA 58.986 45.455 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.