Multiple sequence alignment - TraesCS5D01G268800

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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 TraesCS5D01G268800 chr5D 100.000 3578 0 0 1 3578 371861068 371864645 0.000000e+00 6608
1 TraesCS5D01G268800 chr5D 87.213 305 31 6 3268 3568 78505357 78505657 1.230000e-89 340
2 TraesCS5D01G268800 chr5A 93.387 3100 111 22 11 3056 475293797 475296856 0.000000e+00 4503
3 TraesCS5D01G268800 chr5A 90.826 109 6 2 3376 3483 512071635 512071740 3.720000e-30 143
4 TraesCS5D01G268800 chr5A 84.071 113 12 3 4 116 475291932 475292038 1.760000e-18 104
5 TraesCS5D01G268800 chr5B 93.516 1496 71 9 220 1703 441744049 441745530 0.000000e+00 2202
6 TraesCS5D01G268800 chr5B 98.190 884 14 2 1722 2604 441745518 441746400 0.000000e+00 1543
7 TraesCS5D01G268800 chr5B 98.000 200 4 0 2630 2829 441746507 441746706 7.350000e-92 348
8 TraesCS5D01G268800 chr5B 92.857 238 16 1 2820 3056 441747682 441747919 9.510000e-91 344
9 TraesCS5D01G268800 chr7D 81.199 1484 252 19 1088 2563 477641732 477643196 0.000000e+00 1170
10 TraesCS5D01G268800 chr7D 80.067 1485 267 22 1088 2562 78115573 78117038 0.000000e+00 1075
11 TraesCS5D01G268800 chr7D 75.401 1370 287 41 1209 2559 585538299 585539637 5.080000e-173 617
12 TraesCS5D01G268800 chr7D 86.907 527 43 9 3052 3578 577780926 577780426 5.180000e-158 568
13 TraesCS5D01G268800 chr7A 81.098 1476 236 29 1091 2559 518658726 518657287 0.000000e+00 1140
14 TraesCS5D01G268800 chr7A 80.215 1486 263 25 1088 2562 81548325 81549790 0.000000e+00 1086
15 TraesCS5D01G268800 chr7A 96.140 544 5 1 3051 3578 635281433 635281976 0.000000e+00 874
16 TraesCS5D01G268800 chr3A 80.925 1384 246 14 1180 2560 33137245 33138613 0.000000e+00 1077
17 TraesCS5D01G268800 chr2B 80.994 1368 217 35 1220 2564 111359786 111361133 0.000000e+00 1046
18 TraesCS5D01G268800 chr2B 77.600 1250 232 29 1191 2410 7837662 7838893 0.000000e+00 713
19 TraesCS5D01G268800 chr2A 79.479 1496 254 45 1092 2559 72932854 72931384 0.000000e+00 1013
20 TraesCS5D01G268800 chr2A 95.926 540 6 1 3055 3578 5098447 5097908 0.000000e+00 861
21 TraesCS5D01G268800 chr2A 80.374 321 56 5 2242 2559 72811776 72811460 1.660000e-58 237
22 TraesCS5D01G268800 chr2D 79.050 1494 274 31 1092 2564 73454313 73452838 0.000000e+00 989
23 TraesCS5D01G268800 chr2D 96.455 536 6 7 3056 3578 86076336 86075801 0.000000e+00 872
24 TraesCS5D01G268800 chr2D 78.331 1246 227 25 1191 2410 2948474 2947246 0.000000e+00 765
25 TraesCS5D01G268800 chr3D 78.610 1281 236 23 1139 2412 606941038 606942287 0.000000e+00 813
26 TraesCS5D01G268800 chr3D 89.302 215 15 4 3368 3578 451225739 451225529 2.740000e-66 263
27 TraesCS5D01G268800 chr7B 74.966 1478 321 36 1091 2551 502316812 502318257 5.040000e-178 634
28 TraesCS5D01G268800 chr7B 80.603 763 124 18 1806 2562 25340433 25341177 5.180000e-158 568
29 TraesCS5D01G268800 chr1B 87.616 323 33 5 3258 3578 563963282 563963599 5.640000e-98 368
30 TraesCS5D01G268800 chr1B 87.500 320 32 4 3261 3578 399000610 399000297 2.630000e-96 363
31 TraesCS5D01G268800 chr1B 83.974 156 23 2 3057 3211 399001125 399000971 8.000000e-32 148
32 TraesCS5D01G268800 chr4A 87.540 313 33 4 3268 3578 646535075 646534767 1.220000e-94 357
33 TraesCS5D01G268800 chr4B 82.353 170 26 4 3052 3221 12139377 12139212 1.040000e-30 145


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 TraesCS5D01G268800 chr5D 371861068 371864645 3577 False 6608.00 6608 100.00000 1 3578 1 chr5D.!!$F2 3577
1 TraesCS5D01G268800 chr5A 475291932 475296856 4924 False 2303.50 4503 88.72900 4 3056 2 chr5A.!!$F2 3052
2 TraesCS5D01G268800 chr5B 441744049 441747919 3870 False 1109.25 2202 95.64075 220 3056 4 chr5B.!!$F1 2836
3 TraesCS5D01G268800 chr7D 477641732 477643196 1464 False 1170.00 1170 81.19900 1088 2563 1 chr7D.!!$F2 1475
4 TraesCS5D01G268800 chr7D 78115573 78117038 1465 False 1075.00 1075 80.06700 1088 2562 1 chr7D.!!$F1 1474
5 TraesCS5D01G268800 chr7D 585538299 585539637 1338 False 617.00 617 75.40100 1209 2559 1 chr7D.!!$F3 1350
6 TraesCS5D01G268800 chr7D 577780426 577780926 500 True 568.00 568 86.90700 3052 3578 1 chr7D.!!$R1 526
7 TraesCS5D01G268800 chr7A 518657287 518658726 1439 True 1140.00 1140 81.09800 1091 2559 1 chr7A.!!$R1 1468
8 TraesCS5D01G268800 chr7A 81548325 81549790 1465 False 1086.00 1086 80.21500 1088 2562 1 chr7A.!!$F1 1474
9 TraesCS5D01G268800 chr7A 635281433 635281976 543 False 874.00 874 96.14000 3051 3578 1 chr7A.!!$F2 527
10 TraesCS5D01G268800 chr3A 33137245 33138613 1368 False 1077.00 1077 80.92500 1180 2560 1 chr3A.!!$F1 1380
11 TraesCS5D01G268800 chr2B 111359786 111361133 1347 False 1046.00 1046 80.99400 1220 2564 1 chr2B.!!$F2 1344
12 TraesCS5D01G268800 chr2B 7837662 7838893 1231 False 713.00 713 77.60000 1191 2410 1 chr2B.!!$F1 1219
13 TraesCS5D01G268800 chr2A 72931384 72932854 1470 True 1013.00 1013 79.47900 1092 2559 1 chr2A.!!$R3 1467
14 TraesCS5D01G268800 chr2A 5097908 5098447 539 True 861.00 861 95.92600 3055 3578 1 chr2A.!!$R1 523
15 TraesCS5D01G268800 chr2D 73452838 73454313 1475 True 989.00 989 79.05000 1092 2564 1 chr2D.!!$R2 1472
16 TraesCS5D01G268800 chr2D 86075801 86076336 535 True 872.00 872 96.45500 3056 3578 1 chr2D.!!$R3 522
17 TraesCS5D01G268800 chr2D 2947246 2948474 1228 True 765.00 765 78.33100 1191 2410 1 chr2D.!!$R1 1219
18 TraesCS5D01G268800 chr3D 606941038 606942287 1249 False 813.00 813 78.61000 1139 2412 1 chr3D.!!$F1 1273
19 TraesCS5D01G268800 chr7B 502316812 502318257 1445 False 634.00 634 74.96600 1091 2551 1 chr7B.!!$F2 1460
20 TraesCS5D01G268800 chr7B 25340433 25341177 744 False 568.00 568 80.60300 1806 2562 1 chr7B.!!$F1 756
21 TraesCS5D01G268800 chr1B 399000297 399001125 828 True 255.50 363 85.73700 3057 3578 2 chr1B.!!$R1 521

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
77 1936 0.034059 ACGTTGAAGCTCACAGGGAG 59.966 55.0 0.00 0.00 46.93 4.30 F
781 2688 1.102154 TAGAACCGTTCGCCCGATTA 58.898 50.0 5.62 0.00 34.02 1.75 F
952 2859 1.298602 ATAAATGCATGCAGACGCGA 58.701 45.0 26.69 8.15 42.97 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 3749 2.039624 ATCAGGTCCTCCGGCAGT 59.960 61.111 0.00 0.00 39.05 4.40 R
2568 4523 0.103755 TGCTGATCGATCACCTGCTC 59.896 55.000 27.98 14.08 32.50 4.26 R
2937 5959 1.363443 CCCACACAATTGCGCAAGT 59.637 52.632 28.62 23.97 41.68 3.16 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
19 20 1.478631 CTCCAAATCAAAGGAGGCCC 58.521 55.000 0.00 0.00 46.11 5.80
25 26 3.303351 AATCAAAGGAGGCCCTACATG 57.697 47.619 0.00 0.00 43.48 3.21
26 27 0.255890 TCAAAGGAGGCCCTACATGC 59.744 55.000 0.00 0.00 43.48 4.06
41 1900 4.453478 CCTACATGCGGACTATAGTCGTTA 59.547 45.833 23.35 13.57 45.65 3.18
69 1928 3.597377 ACGGTAAAAACGTTGAAGCTC 57.403 42.857 0.00 0.00 42.70 4.09
71 1930 3.242511 ACGGTAAAAACGTTGAAGCTCAC 60.243 43.478 0.00 0.00 42.70 3.51
77 1936 0.034059 ACGTTGAAGCTCACAGGGAG 59.966 55.000 0.00 0.00 46.93 4.30
89 1948 4.982241 TCACAGGGAGAGAAAAATGTCT 57.018 40.909 0.00 0.00 0.00 3.41
91 1950 6.433847 TCACAGGGAGAGAAAAATGTCTAA 57.566 37.500 0.00 0.00 0.00 2.10
92 1951 6.837312 TCACAGGGAGAGAAAAATGTCTAAA 58.163 36.000 0.00 0.00 0.00 1.85
93 1952 6.710744 TCACAGGGAGAGAAAAATGTCTAAAC 59.289 38.462 0.00 0.00 0.00 2.01
94 1953 5.701290 ACAGGGAGAGAAAAATGTCTAAACG 59.299 40.000 0.00 0.00 0.00 3.60
95 1954 5.122396 CAGGGAGAGAAAAATGTCTAAACGG 59.878 44.000 0.00 0.00 0.00 4.44
98 1957 4.981812 AGAGAAAAATGTCTAAACGGGGT 58.018 39.130 0.00 0.00 0.00 4.95
117 1976 4.519350 GGGGTAGGAGTTTTCAACTGAAAG 59.481 45.833 5.13 0.00 43.90 2.62
120 1979 6.017026 GGGTAGGAGTTTTCAACTGAAAGAAG 60.017 42.308 5.13 0.00 43.90 2.85
162 2022 1.428448 GCATGTCAGCGACAGTACAA 58.572 50.000 14.80 0.00 46.04 2.41
164 2024 2.403259 CATGTCAGCGACAGTACAACA 58.597 47.619 14.80 0.00 46.04 3.33
345 2240 2.887152 ACTGCAAACACAATCTCCTTCC 59.113 45.455 0.00 0.00 0.00 3.46
347 2242 3.565307 TGCAAACACAATCTCCTTCCTT 58.435 40.909 0.00 0.00 0.00 3.36
376 2271 3.476552 TGCGGGGAAATACAATCTGATC 58.523 45.455 0.00 0.00 0.00 2.92
434 2329 6.934645 TCGTTATTCCATCCTGATTGATTACC 59.065 38.462 0.00 0.00 0.00 2.85
463 2358 8.814038 AGTTAGAATATGAATTTGTCCAAGCT 57.186 30.769 0.00 0.00 0.00 3.74
464 2359 9.905713 AGTTAGAATATGAATTTGTCCAAGCTA 57.094 29.630 0.00 0.00 0.00 3.32
614 2516 3.012518 GTGACAGTGCCATGCTTATCTT 58.987 45.455 0.00 0.00 0.00 2.40
781 2688 1.102154 TAGAACCGTTCGCCCGATTA 58.898 50.000 5.62 0.00 34.02 1.75
839 2746 5.645497 AGATAGCTGACCATGACTTTTCAAC 59.355 40.000 0.00 0.00 34.61 3.18
843 2750 1.880027 GACCATGACTTTTCAACGCCT 59.120 47.619 0.00 0.00 34.61 5.52
900 2807 4.735132 CGTCGGCCGCTTTCAGGA 62.735 66.667 23.51 0.00 0.00 3.86
952 2859 1.298602 ATAAATGCATGCAGACGCGA 58.701 45.000 26.69 8.15 42.97 5.87
2568 4523 1.142314 CATCCCGCCATTTGCCAAG 59.858 57.895 0.00 0.00 36.24 3.61
2659 4695 7.269297 GCTAGCTACGCATTTATCTTTATTTGC 59.731 37.037 7.70 0.00 0.00 3.68
2875 5897 5.243954 ACATTTTGGCCTAAAAAGGAGAGAC 59.756 40.000 16.33 0.00 41.29 3.36
2947 5969 3.672293 CAGGGTGACTTGCGCAAT 58.328 55.556 25.26 13.90 0.00 3.56
2971 5993 2.616376 TGTGGGCGATGTAATAATGTGC 59.384 45.455 0.00 0.00 0.00 4.57
2980 6002 6.353582 GCGATGTAATAATGTGCGTTACTTTC 59.646 38.462 0.00 0.00 31.37 2.62
2988 6010 1.719780 GTGCGTTACTTTCGGAGTGAG 59.280 52.381 3.10 0.00 39.48 3.51
3025 6048 8.772705 GGAGAATTAGCTGATCTGTTATGAAAG 58.227 37.037 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.084018 AGGGCCTCCTTTGATTTGGA 58.916 50.000 0.00 0.00 41.56 3.53
7 8 0.255890 GCATGTAGGGCCTCCTTTGA 59.744 55.000 10.74 0.00 41.56 2.69
19 20 4.485024 AACGACTATAGTCCGCATGTAG 57.515 45.455 24.01 11.74 41.86 2.74
25 26 3.549625 CCAAGGTAACGACTATAGTCCGC 60.550 52.174 24.01 12.76 41.86 5.54
26 27 3.879295 TCCAAGGTAACGACTATAGTCCG 59.121 47.826 24.01 20.39 41.86 4.79
41 1900 2.642427 ACGTTTTTACCGTTCCAAGGT 58.358 42.857 0.00 0.00 45.28 3.50
69 1928 6.347725 CGTTTAGACATTTTTCTCTCCCTGTG 60.348 42.308 0.00 0.00 0.00 3.66
71 1930 5.122396 CCGTTTAGACATTTTTCTCTCCCTG 59.878 44.000 0.00 0.00 0.00 4.45
77 1936 5.353400 CCTACCCCGTTTAGACATTTTTCTC 59.647 44.000 0.00 0.00 0.00 2.87
79 1938 5.247862 TCCTACCCCGTTTAGACATTTTTC 58.752 41.667 0.00 0.00 0.00 2.29
80 1939 5.221986 ACTCCTACCCCGTTTAGACATTTTT 60.222 40.000 0.00 0.00 0.00 1.94
81 1940 4.287845 ACTCCTACCCCGTTTAGACATTTT 59.712 41.667 0.00 0.00 0.00 1.82
82 1941 3.842436 ACTCCTACCCCGTTTAGACATTT 59.158 43.478 0.00 0.00 0.00 2.32
83 1942 3.447950 ACTCCTACCCCGTTTAGACATT 58.552 45.455 0.00 0.00 0.00 2.71
84 1943 3.111741 ACTCCTACCCCGTTTAGACAT 57.888 47.619 0.00 0.00 0.00 3.06
85 1944 2.610438 ACTCCTACCCCGTTTAGACA 57.390 50.000 0.00 0.00 0.00 3.41
86 1945 3.969287 AAACTCCTACCCCGTTTAGAC 57.031 47.619 0.00 0.00 0.00 2.59
87 1946 3.903090 TGAAAACTCCTACCCCGTTTAGA 59.097 43.478 0.00 0.00 31.25 2.10
89 1948 4.388485 GTTGAAAACTCCTACCCCGTTTA 58.612 43.478 0.00 0.00 45.32 2.01
90 1949 3.216800 GTTGAAAACTCCTACCCCGTTT 58.783 45.455 0.00 0.00 45.32 3.60
91 1950 2.854963 GTTGAAAACTCCTACCCCGTT 58.145 47.619 0.00 0.00 45.32 4.44
92 1951 2.556144 GTTGAAAACTCCTACCCCGT 57.444 50.000 0.00 0.00 45.32 5.28
117 1976 4.199432 TCTTCTTCTCATGACTGGCTTC 57.801 45.455 0.00 0.00 0.00 3.86
120 1979 4.183101 CTCTTCTTCTTCTCATGACTGGC 58.817 47.826 0.00 0.00 0.00 4.85
212 2072 6.315393 GTCAGTCAAATATATTGGACGGTGTT 59.685 38.462 24.02 8.73 43.82 3.32
345 2240 5.293560 TGTATTTCCCCGCAAAAGAAAAAG 58.706 37.500 0.00 0.00 33.53 2.27
347 2242 4.939052 TGTATTTCCCCGCAAAAGAAAA 57.061 36.364 0.00 0.00 33.53 2.29
376 2271 3.885297 TCCAAAAGTCAGAGCAAAAGGAG 59.115 43.478 0.00 0.00 0.00 3.69
463 2358 2.942376 CGGTCAGCATAAAACTGCCATA 59.058 45.455 0.00 0.00 43.33 2.74
464 2359 1.745087 CGGTCAGCATAAAACTGCCAT 59.255 47.619 0.00 0.00 43.33 4.40
466 2361 1.130561 GACGGTCAGCATAAAACTGCC 59.869 52.381 2.62 0.00 43.33 4.85
473 2368 0.541392 ATGCAGGACGGTCAGCATAA 59.459 50.000 27.75 10.66 45.09 1.90
543 2438 0.181587 TTGGACTTTTGGACAGGCGA 59.818 50.000 0.00 0.00 0.00 5.54
614 2516 0.394762 GCAGGTCATCCTTGCATGGA 60.395 55.000 22.42 22.42 43.07 3.41
653 2555 3.151912 AGCAAGAAAGTTCTCATGGCT 57.848 42.857 0.00 0.00 36.28 4.75
843 2750 4.007644 CACGCCACTCCAGCTGGA 62.008 66.667 33.04 33.04 43.08 3.86
952 2859 1.227999 CGTGTTGCATGGTTCGGAGT 61.228 55.000 0.00 0.00 0.00 3.85
1013 2920 3.627690 GCACTAGGCTGGAGCTCT 58.372 61.111 14.64 0.00 41.70 4.09
1833 3749 2.039624 ATCAGGTCCTCCGGCAGT 59.960 61.111 0.00 0.00 39.05 4.40
2568 4523 0.103755 TGCTGATCGATCACCTGCTC 59.896 55.000 27.98 14.08 32.50 4.26
2659 4695 9.636879 TCAAACCAATATCAACAAATACATGTG 57.363 29.630 9.11 0.00 32.81 3.21
2875 5897 4.625028 TCTATCTGTCCGCAAATCATCAG 58.375 43.478 0.00 0.00 0.00 2.90
2937 5959 1.363443 CCCACACAATTGCGCAAGT 59.637 52.632 28.62 23.97 41.68 3.16
2947 5969 4.095632 CACATTATTACATCGCCCACACAA 59.904 41.667 0.00 0.00 0.00 3.33
2971 5993 4.734917 AGATTCTCACTCCGAAAGTAACG 58.265 43.478 0.00 0.00 36.07 3.18
2980 6002 4.081972 TCTCCTTTCAAGATTCTCACTCCG 60.082 45.833 0.00 0.00 0.00 4.63
2988 6010 7.856145 TCAGCTAATTCTCCTTTCAAGATTC 57.144 36.000 0.00 0.00 0.00 2.52
3025 6048 6.715347 ATTCCCAAATGCTGAAACTATACC 57.285 37.500 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.