Multiple sequence alignment - TraesCS3A01G229200

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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 TraesCS3A01G229200 chr3A 100.000 3121 0 0 1 3121 429244644 429247764 0.000000e+00 5764.0
1 TraesCS3A01G229200 chr3A 92.824 655 42 1 1 650 418910325 418909671 0.000000e+00 944.0
2 TraesCS3A01G229200 chr3A 85.000 120 18 0 647 766 21217439 21217558 4.230000e-24 122.0
3 TraesCS3A01G229200 chr6A 94.561 2482 122 11 647 3121 480617093 480614618 0.000000e+00 3823.0
4 TraesCS3A01G229200 chr2B 92.708 2496 146 16 647 3116 529093226 529095711 0.000000e+00 3568.0
5 TraesCS3A01G229200 chr2B 84.835 1398 159 23 1308 2680 510736769 510738138 0.000000e+00 1358.0
6 TraesCS3A01G229200 chr2B 92.934 651 41 1 1 646 226019427 226020077 0.000000e+00 942.0
7 TraesCS3A01G229200 chr2B 94.262 122 7 0 3000 3121 510751724 510751845 1.480000e-43 187.0
8 TraesCS3A01G229200 chr2B 100.000 29 0 0 1057 1085 706977699 706977671 2.000000e-03 54.7
9 TraesCS3A01G229200 chr6B 91.610 2491 159 22 647 3121 363934056 363931600 0.000000e+00 3397.0
10 TraesCS3A01G229200 chr6B 84.000 1750 191 35 1308 2998 279658891 279660610 0.000000e+00 1598.0
11 TraesCS3A01G229200 chr6B 93.030 660 41 1 1 655 458231630 458232289 0.000000e+00 959.0
12 TraesCS3A01G229200 chr6B 93.098 652 40 1 1 647 236160122 236159471 0.000000e+00 950.0
13 TraesCS3A01G229200 chr6B 88.010 784 68 13 1091 1857 77659918 77659144 0.000000e+00 904.0
14 TraesCS3A01G229200 chr6B 91.063 649 47 4 2478 3121 77659161 77658519 0.000000e+00 867.0
15 TraesCS3A01G229200 chr6B 90.022 461 27 9 647 1089 77660453 77659994 2.090000e-161 579.0
16 TraesCS3A01G229200 chr6B 94.881 293 15 0 2824 3116 603812288 603812580 2.840000e-125 459.0
17 TraesCS3A01G229200 chr6B 79.186 442 48 15 651 1051 279658026 279658464 1.850000e-67 267.0
18 TraesCS3A01G229200 chr6B 90.984 122 11 0 3000 3121 279660660 279660781 6.920000e-37 165.0
19 TraesCS3A01G229200 chr6B 100.000 29 0 0 1057 1085 381191475 381191503 2.000000e-03 54.7
20 TraesCS3A01G229200 chr6D 94.273 1362 64 5 962 2309 145005112 145003751 0.000000e+00 2071.0
21 TraesCS3A01G229200 chr6D 93.869 685 36 4 2443 3121 144999029 144998345 0.000000e+00 1027.0
22 TraesCS3A01G229200 chr6D 93.548 651 37 1 1 646 281907493 281908143 0.000000e+00 965.0
23 TraesCS3A01G229200 chr6D 94.562 331 16 1 647 977 145006298 145005970 7.720000e-141 510.0
24 TraesCS3A01G229200 chr4A 93.599 1156 64 8 1970 3116 715605915 715604761 0.000000e+00 1716.0
25 TraesCS3A01G229200 chr4A 91.945 869 60 3 647 1505 715607135 715606267 0.000000e+00 1208.0
26 TraesCS3A01G229200 chr4A 93.443 183 12 0 1793 1975 715606275 715606093 3.970000e-69 272.0
27 TraesCS3A01G229200 chr4A 83.333 120 20 0 647 766 552223093 552223212 9.150000e-21 111.0
28 TraesCS3A01G229200 chr4A 78.409 176 30 7 2058 2228 520952572 520952744 1.180000e-19 108.0
29 TraesCS3A01G229200 chr1B 93.558 652 37 1 1 647 322054480 322055131 0.000000e+00 966.0
30 TraesCS3A01G229200 chr1B 79.920 503 87 11 1918 2409 641210386 641210885 1.060000e-94 357.0
31 TraesCS3A01G229200 chr2A 93.415 653 38 1 1 648 433685823 433685171 0.000000e+00 963.0
32 TraesCS3A01G229200 chr5D 93.098 652 39 2 1 647 133501240 133500590 0.000000e+00 950.0
33 TraesCS3A01G229200 chr5A 92.945 652 41 1 1 647 363885152 363885803 0.000000e+00 944.0
34 TraesCS3A01G229200 chr5A 95.489 133 5 1 647 779 29062554 29062685 8.770000e-51 211.0
35 TraesCS3A01G229200 chr5B 86.087 115 16 0 1987 2101 503874767 503874653 1.180000e-24 124.0
36 TraesCS3A01G229200 chr5B 95.652 46 2 0 1987 2032 503875793 503875748 1.200000e-09 75.0


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 TraesCS3A01G229200 chr3A 429244644 429247764 3120 False 5764.000000 5764 100.000000 1 3121 1 chr3A.!!$F2 3120
1 TraesCS3A01G229200 chr3A 418909671 418910325 654 True 944.000000 944 92.824000 1 650 1 chr3A.!!$R1 649
2 TraesCS3A01G229200 chr6A 480614618 480617093 2475 True 3823.000000 3823 94.561000 647 3121 1 chr6A.!!$R1 2474
3 TraesCS3A01G229200 chr2B 529093226 529095711 2485 False 3568.000000 3568 92.708000 647 3116 1 chr2B.!!$F4 2469
4 TraesCS3A01G229200 chr2B 510736769 510738138 1369 False 1358.000000 1358 84.835000 1308 2680 1 chr2B.!!$F2 1372
5 TraesCS3A01G229200 chr2B 226019427 226020077 650 False 942.000000 942 92.934000 1 646 1 chr2B.!!$F1 645
6 TraesCS3A01G229200 chr6B 363931600 363934056 2456 True 3397.000000 3397 91.610000 647 3121 1 chr6B.!!$R2 2474
7 TraesCS3A01G229200 chr6B 458231630 458232289 659 False 959.000000 959 93.030000 1 655 1 chr6B.!!$F2 654
8 TraesCS3A01G229200 chr6B 236159471 236160122 651 True 950.000000 950 93.098000 1 647 1 chr6B.!!$R1 646
9 TraesCS3A01G229200 chr6B 77658519 77660453 1934 True 783.333333 904 89.698333 647 3121 3 chr6B.!!$R3 2474
10 TraesCS3A01G229200 chr6B 279658026 279660781 2755 False 676.666667 1598 84.723333 651 3121 3 chr6B.!!$F4 2470
11 TraesCS3A01G229200 chr6D 145003751 145006298 2547 True 1290.500000 2071 94.417500 647 2309 2 chr6D.!!$R2 1662
12 TraesCS3A01G229200 chr6D 144998345 144999029 684 True 1027.000000 1027 93.869000 2443 3121 1 chr6D.!!$R1 678
13 TraesCS3A01G229200 chr6D 281907493 281908143 650 False 965.000000 965 93.548000 1 646 1 chr6D.!!$F1 645
14 TraesCS3A01G229200 chr4A 715604761 715607135 2374 True 1065.333333 1716 92.995667 647 3116 3 chr4A.!!$R1 2469
15 TraesCS3A01G229200 chr1B 322054480 322055131 651 False 966.000000 966 93.558000 1 647 1 chr1B.!!$F1 646
16 TraesCS3A01G229200 chr2A 433685171 433685823 652 True 963.000000 963 93.415000 1 648 1 chr2A.!!$R1 647
17 TraesCS3A01G229200 chr5D 133500590 133501240 650 True 950.000000 950 93.098000 1 647 1 chr5D.!!$R1 646
18 TraesCS3A01G229200 chr5A 363885152 363885803 651 False 944.000000 944 92.945000 1 647 1 chr5A.!!$F2 646

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
752 758 0.395173 ATACGGGACCAACCAATGCC 60.395 55.000 0.0 0.0 41.20 4.40 F
1349 2445 1.063972 TGTTTGTGAGCAAGCACGC 59.936 52.632 0.0 0.0 40.14 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 3361 1.686110 CTGGAGGGCCCGTAGAAGT 60.686 63.158 18.44 0.0 37.93 3.01 R
2849 4230 1.207089 CCCAATGGCTCAGTAAGACGA 59.793 52.381 0.00 0.0 34.73 4.20 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
97 98 0.742281 GTGTGCGCATGAGTGAGGAT 60.742 55.000 15.91 0.0 0.00 3.24
149 150 1.457831 GGGCCAGTCTAGATCCCGT 60.458 63.158 4.39 0.0 0.00 5.28
244 245 1.514678 GATGTTTGCGGACAGGTGCA 61.515 55.000 0.00 0.0 39.81 4.57
286 287 3.621805 TGACCCGTCGTGGCACAT 61.622 61.111 19.09 0.0 44.52 3.21
327 328 2.028112 ACTGGATGCACAGACGTATGTT 60.028 45.455 14.19 0.0 40.97 2.71
421 422 7.069331 CCTGGCTTATTAGGGATGATAGACTAG 59.931 44.444 0.00 0.0 0.00 2.57
468 474 0.693049 AGCCCATTCGGACAGAACTT 59.307 50.000 0.00 0.0 42.39 2.66
488 494 5.428253 ACTTCAAAGTTAAGTGTGCTCAGA 58.572 37.500 0.00 0.0 35.87 3.27
573 579 3.815401 ACAAAGTGCGCAGAAAAGACTAT 59.185 39.130 12.22 0.0 0.00 2.12
585 591 9.249457 CGCAGAAAAGACTATTATTGATCTGTA 57.751 33.333 0.00 0.0 35.42 2.74
696 702 2.713167 ACATGCAGCCTATCCACCTAAT 59.287 45.455 0.00 0.0 0.00 1.73
752 758 0.395173 ATACGGGACCAACCAATGCC 60.395 55.000 0.00 0.0 41.20 4.40
812 820 4.460263 GCCCAATACAATATGTCCTCACA 58.540 43.478 0.00 0.0 36.78 3.58
966 1888 3.939066 ACAAATGTTCCTCCCTAAGACG 58.061 45.455 0.00 0.0 0.00 4.18
989 1912 2.903135 CCTAATCTCTCCCATCCAGTCC 59.097 54.545 0.00 0.0 0.00 3.85
1038 1963 3.386237 GGGTGGCTGCTCGACTCT 61.386 66.667 0.00 0.0 0.00 3.24
1270 2306 2.900337 CGCCCCGGCTAATTCACC 60.900 66.667 3.84 0.0 39.32 4.02
1331 2427 2.938956 GCTGATGCTAAGGTATGGGT 57.061 50.000 0.00 0.0 36.03 4.51
1332 2428 2.498167 GCTGATGCTAAGGTATGGGTG 58.502 52.381 0.00 0.0 36.03 4.61
1349 2445 1.063972 TGTTTGTGAGCAAGCACGC 59.936 52.632 0.00 0.0 40.14 5.34
1383 2479 5.248020 CCCTGTGATTAGAGGCTGATTAGAT 59.752 44.000 0.00 0.0 36.05 1.98
1431 2527 3.281727 AGCTGTTTTTGTGACTCTCCA 57.718 42.857 0.00 0.0 0.00 3.86
1590 2691 1.699634 AGGACTTTGCTGTGAAGCCTA 59.300 47.619 0.00 0.0 32.57 3.93
1687 2817 2.659428 CCTTTCCCATCTTGGTGATCC 58.341 52.381 0.00 0.0 35.17 3.36
1872 3011 6.761714 GCTATAGTGTGCTTGGTTAGTATGTT 59.238 38.462 0.84 0.0 0.00 2.71
1902 3041 2.944349 GTTGTTTGTTCCCTCGGTTGTA 59.056 45.455 0.00 0.0 0.00 2.41
2035 3361 9.985730 AAGCAAGTTATTCTCATTGATTTTCAA 57.014 25.926 0.00 0.0 41.09 2.69
2218 3571 5.312895 AGGACAAATTATACACTGTGTGCA 58.687 37.500 22.97 4.7 36.98 4.57
2253 3607 8.036273 TCATTTTCTTCGGAATAACTGGTAAC 57.964 34.615 0.00 0.0 33.58 2.50
2296 3650 5.610398 TCAAAGTGATGTCTTACTTGCTGA 58.390 37.500 0.00 0.0 37.23 4.26
2299 3653 3.834813 AGTGATGTCTTACTTGCTGAGGA 59.165 43.478 0.00 0.0 0.00 3.71
2517 3882 8.739972 GTGTTCCATGTAGATGTTAGGAAAAAT 58.260 33.333 0.00 0.0 36.95 1.82
2639 4004 5.784578 AGTTTTGTGGGAACAGGAATTAC 57.215 39.130 0.00 0.0 44.46 1.89
2745 4121 9.578439 AAAGATACCAGTGTAACGACTATTTAC 57.422 33.333 0.00 0.0 45.86 2.01
2849 4230 5.237344 GCGCAAAATCCTAGATGTTATCAGT 59.763 40.000 0.30 0.0 0.00 3.41
2853 4234 7.306866 GCAAAATCCTAGATGTTATCAGTCGTC 60.307 40.741 0.00 0.0 0.00 4.20
2870 4251 1.207089 CGTCTTACTGAGCCATTGGGA 59.793 52.381 4.53 0.0 35.59 4.37
2873 4254 4.079253 GTCTTACTGAGCCATTGGGAAAA 58.921 43.478 4.53 0.0 35.59 2.29
2878 4259 1.344114 TGAGCCATTGGGAAAAGCAAC 59.656 47.619 4.53 0.0 35.59 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 0.823460 TATCCTCACTCATGCGCACA 59.177 50.000 14.90 0.11 0.00 4.57
87 88 1.275010 TGCGCACTTTATCCTCACTCA 59.725 47.619 5.66 0.00 0.00 3.41
97 98 4.628074 ACTAGTCTTTTCTGCGCACTTTA 58.372 39.130 5.66 0.00 0.00 1.85
327 328 1.697432 ACATGAACGTTCCCTCTTGGA 59.303 47.619 24.78 4.49 43.18 3.53
421 422 7.119846 CCGGAAAAGAAGGGATATTGATATGAC 59.880 40.741 0.00 0.00 0.00 3.06
434 440 0.965866 GGGCTTCCGGAAAAGAAGGG 60.966 60.000 19.39 5.64 40.91 3.95
468 474 5.239306 CCAATCTGAGCACACTTAACTTTGA 59.761 40.000 0.00 0.00 0.00 2.69
479 485 4.040339 TGAAACTACTCCAATCTGAGCACA 59.960 41.667 0.00 0.00 35.72 4.57
488 494 3.852578 ACCCATCCTGAAACTACTCCAAT 59.147 43.478 0.00 0.00 0.00 3.16
520 526 2.742372 CACCCGGGAGCAACTTCG 60.742 66.667 32.02 0.00 0.00 3.79
573 579 4.298626 AGACTGGCCCTACAGATCAATAA 58.701 43.478 0.00 0.00 40.97 1.40
585 591 1.152440 CGGGATCTAGACTGGCCCT 60.152 63.158 15.76 0.00 36.62 5.19
627 633 2.841881 ACTTGTAACACCCCGGACATAT 59.158 45.455 0.73 0.00 0.00 1.78
696 702 1.229975 CGCTGATGTGGCAAGTGTGA 61.230 55.000 0.00 0.00 0.00 3.58
812 820 3.181440 TGAATCAGAGTGAAAGGGTGCTT 60.181 43.478 0.00 0.00 0.00 3.91
951 1000 1.849977 AGGACGTCTTAGGGAGGAAC 58.150 55.000 16.46 0.00 34.32 3.62
966 1888 3.576550 GACTGGATGGGAGAGATTAGGAC 59.423 52.174 0.00 0.00 0.00 3.85
989 1912 1.966901 TAGGTACATGTGCTGGCGGG 61.967 60.000 13.86 0.00 0.00 6.13
994 1918 1.134128 TGGGCATAGGTACATGTGCTG 60.134 52.381 24.97 5.66 37.70 4.41
1038 1963 0.391130 CTTCGATCGGCAGGTGGAAA 60.391 55.000 16.41 0.00 0.00 3.13
1270 2306 4.322080 TTCCTGCAGTATAATCTGGTCG 57.678 45.455 13.81 0.00 36.12 4.79
1331 2427 1.063972 GCGTGCTTGCTCACAAACA 59.936 52.632 5.47 0.00 36.80 2.83
1332 2428 1.658409 GGCGTGCTTGCTCACAAAC 60.658 57.895 0.92 0.00 36.80 2.93
1349 2445 5.454471 CCTCTAATCACAGGGAGAAAGATGG 60.454 48.000 0.00 0.00 0.00 3.51
1383 2479 5.637810 CGCTATCAAAAACACCAAGAGTCTA 59.362 40.000 0.00 0.00 0.00 2.59
1431 2527 7.343357 TCGTCCTTCTATACCATCCAAAATTT 58.657 34.615 0.00 0.00 0.00 1.82
1590 2691 6.186234 ACCTAGTATCGTACCTGAAAGAAGT 58.814 40.000 0.00 0.00 34.07 3.01
1687 2817 5.851177 ACTTTCAAGCAAACATATTCGTTCG 59.149 36.000 0.00 0.00 0.00 3.95
1734 2864 7.432148 TGTGCAGAGGTTATAGAATTCCTAA 57.568 36.000 0.65 0.00 0.00 2.69
1751 2881 5.664294 AAATAGCCATGAAAATGTGCAGA 57.336 34.783 0.00 0.00 0.00 4.26
1872 3011 5.008217 CGAGGGAACAAACAACAACTAATGA 59.992 40.000 0.00 0.00 0.00 2.57
1902 3041 4.201657 ACCTTAAAACCTTACAACGCTGT 58.798 39.130 0.00 0.00 39.75 4.40
1984 3309 6.713450 TCTTGTTAACTTAAGACATGGAACCC 59.287 38.462 10.09 0.00 0.00 4.11
1985 3310 7.739498 TCTTGTTAACTTAAGACATGGAACC 57.261 36.000 10.09 0.00 0.00 3.62
2022 3347 5.106317 GCCCGTAGAAGTTGAAAATCAATGA 60.106 40.000 0.00 0.00 38.79 2.57
2035 3361 1.686110 CTGGAGGGCCCGTAGAAGT 60.686 63.158 18.44 0.00 37.93 3.01
2218 3571 5.253330 TCCGAAGAAAATGATTACCAGCTT 58.747 37.500 0.00 0.00 0.00 3.74
2253 3607 8.829612 ACTTTGAAATTGCTTCAGTTATTTTGG 58.170 29.630 0.00 0.00 44.84 3.28
2420 3783 4.139786 GGAAGCAAGCCATAATGATCTGA 58.860 43.478 0.00 0.00 0.00 3.27
2549 3914 9.308000 TCACCCATGTTAAAGAAGAAATTGTAT 57.692 29.630 0.00 0.00 0.00 2.29
2559 3924 5.875224 TCTGTGATCACCCATGTTAAAGAA 58.125 37.500 22.85 0.00 0.00 2.52
2639 4004 7.943952 TGTTGAACAAAGTTTAACAATGTTCG 58.056 30.769 25.71 0.00 43.09 3.95
2660 4028 5.865013 TGAGCAAATGTAATGCAGAATGTTG 59.135 36.000 0.00 0.00 46.22 3.33
2801 4180 6.431234 GCAAATCGACTATCAGGGGAAATTAT 59.569 38.462 0.00 0.00 0.00 1.28
2849 4230 1.207089 CCCAATGGCTCAGTAAGACGA 59.793 52.381 0.00 0.00 34.73 4.20
2853 4234 3.119352 GCTTTTCCCAATGGCTCAGTAAG 60.119 47.826 0.00 0.00 0.00 2.34
2870 4251 4.393062 CGAGTGGATGATAGTGTTGCTTTT 59.607 41.667 0.00 0.00 0.00 2.27
2873 4254 2.739932 GCGAGTGGATGATAGTGTTGCT 60.740 50.000 0.00 0.00 0.00 3.91
2878 4259 3.119291 GAGTTGCGAGTGGATGATAGTG 58.881 50.000 0.00 0.00 0.00 2.74
2949 4330 7.791029 TCACCAGACATCTTTAGCAATATACA 58.209 34.615 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.