Multiple sequence alignment - TraesCS3D01G121300

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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 TraesCS3D01G121300 chr3D 100.000 2975 0 0 1 2975 77998385 78001359 0.000000e+00 5494
1 TraesCS3D01G121300 chr3D 95.299 2978 136 4 1 2975 78096078 78099054 0.000000e+00 4721
2 TraesCS3D01G121300 chr3B 88.509 2985 290 25 1 2975 124121271 124118330 0.000000e+00 3563
3 TraesCS3D01G121300 chr3A 93.548 2077 108 9 900 2974 91285685 91283633 0.000000e+00 3070
4 TraesCS3D01G121300 chr3A 88.508 905 87 6 1 904 91289037 91288149 0.000000e+00 1079
5 TraesCS3D01G121300 chr7A 90.247 2225 200 12 1 2210 181014043 181016265 0.000000e+00 2891
6 TraesCS3D01G121300 chr7A 90.153 2224 194 16 1 2210 180842992 180845204 0.000000e+00 2870
7 TraesCS3D01G121300 chr7A 89.964 2232 199 17 1 2210 181168116 181170344 0.000000e+00 2857
8 TraesCS3D01G121300 chr7A 89.658 2224 210 14 3 2210 180984023 180986242 0.000000e+00 2815
9 TraesCS3D01G121300 chr7A 88.964 2229 222 18 1 2210 181049605 181051828 0.000000e+00 2732
10 TraesCS3D01G121300 chr7A 97.403 231 6 0 2745 2975 180845197 180845427 7.730000e-106 394
11 TraesCS3D01G121300 chr7A 97.403 231 6 0 2745 2975 180986235 180986465 7.730000e-106 394
12 TraesCS3D01G121300 chr7A 96.970 231 7 0 2745 2975 181016258 181016488 3.600000e-104 388
13 TraesCS3D01G121300 chr7A 95.671 231 10 0 2745 2975 181170337 181170567 3.620000e-99 372
14 TraesCS3D01G121300 chr7A 95.028 181 9 0 2745 2925 181051821 181052001 4.850000e-73 285
15 TraesCS3D01G121300 chr4B 89.123 1802 168 12 891 2677 476571577 476569789 0.000000e+00 2217
16 TraesCS3D01G121300 chr4B 79.820 887 139 26 1 862 476572976 476572105 7.050000e-171 610
17 TraesCS3D01G121300 chr7D 93.580 1433 91 1 779 2210 177169041 177170473 0.000000e+00 2135
18 TraesCS3D01G121300 chr7D 93.939 231 4 1 2745 2975 177170466 177170686 1.020000e-89 340
19 TraesCS3D01G121300 chr4D 89.249 1572 141 10 891 2446 388250875 388249316 0.000000e+00 1941
20 TraesCS3D01G121300 chr4D 74.826 576 109 26 315 861 122009000 122008432 8.300000e-56 228
21 TraesCS3D01G121300 chr4A 78.082 876 163 18 1 856 69512586 69511720 7.300000e-146 527


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 TraesCS3D01G121300 chr3D 77998385 78001359 2974 False 5494.0 5494 100.0000 1 2975 1 chr3D.!!$F1 2974
1 TraesCS3D01G121300 chr3D 78096078 78099054 2976 False 4721.0 4721 95.2990 1 2975 1 chr3D.!!$F2 2974
2 TraesCS3D01G121300 chr3B 124118330 124121271 2941 True 3563.0 3563 88.5090 1 2975 1 chr3B.!!$R1 2974
3 TraesCS3D01G121300 chr3A 91283633 91289037 5404 True 2074.5 3070 91.0280 1 2974 2 chr3A.!!$R1 2973
4 TraesCS3D01G121300 chr7A 181014043 181016488 2445 False 1639.5 2891 93.6085 1 2975 2 chr7A.!!$F3 2974
5 TraesCS3D01G121300 chr7A 180842992 180845427 2435 False 1632.0 2870 93.7780 1 2975 2 chr7A.!!$F1 2974
6 TraesCS3D01G121300 chr7A 181168116 181170567 2451 False 1614.5 2857 92.8175 1 2975 2 chr7A.!!$F5 2974
7 TraesCS3D01G121300 chr7A 180984023 180986465 2442 False 1604.5 2815 93.5305 3 2975 2 chr7A.!!$F2 2972
8 TraesCS3D01G121300 chr7A 181049605 181052001 2396 False 1508.5 2732 91.9960 1 2925 2 chr7A.!!$F4 2924
9 TraesCS3D01G121300 chr4B 476569789 476572976 3187 True 1413.5 2217 84.4715 1 2677 2 chr4B.!!$R1 2676
10 TraesCS3D01G121300 chr7D 177169041 177170686 1645 False 1237.5 2135 93.7595 779 2975 2 chr7D.!!$F1 2196
11 TraesCS3D01G121300 chr4D 388249316 388250875 1559 True 1941.0 1941 89.2490 891 2446 1 chr4D.!!$R2 1555
12 TraesCS3D01G121300 chr4D 122008432 122009000 568 True 228.0 228 74.8260 315 861 1 chr4D.!!$R1 546
13 TraesCS3D01G121300 chr4A 69511720 69512586 866 True 527.0 527 78.0820 1 856 1 chr4A.!!$R1 855

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
845 930 0.563173 TGGTGGGGAATTTTGGGTCA 59.437 50.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 5140 0.034059 CCGAAAGCCGCTCATCCTAT 59.966 55.0 0.0 0.0 36.84 2.57 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
93 101 3.568853 TCGAGAGTAGGGATCCGAATTTC 59.431 47.826 5.45 0.00 0.00 2.17
163 187 2.445274 GCGAACCCTAGCCCCCTA 60.445 66.667 0.00 0.00 0.00 3.53
772 856 1.404986 CGAGGTTGATTCAAGGCCGTA 60.405 52.381 0.00 0.00 0.00 4.02
820 904 2.176045 TGGTGGAGAACTCGCATTCTA 58.824 47.619 1.49 0.00 39.08 2.10
835 920 2.608368 CTACGGGGTGGTGGGGAA 60.608 66.667 0.00 0.00 0.00 3.97
845 930 0.563173 TGGTGGGGAATTTTGGGTCA 59.437 50.000 0.00 0.00 0.00 4.02
996 4037 2.358582 TGTGCACAATGAGTTTGACCTG 59.641 45.455 19.28 0.00 38.76 4.00
1004 4045 5.240183 ACAATGAGTTTGACCTGTTCATGAG 59.760 40.000 0.00 0.00 38.76 2.90
1201 4242 1.202568 CGTCTGCGCAGTGAACAAG 59.797 57.895 34.70 15.27 0.00 3.16
1233 4274 6.040878 ACTTGAAGCGTACAATACATACTCC 58.959 40.000 0.00 0.00 0.00 3.85
1257 4298 6.260936 CCATCAATGTTTCTTACCTAGCGAAT 59.739 38.462 0.00 0.00 0.00 3.34
1444 4485 8.980143 ACCATTCTTTTCCACAATTAATTACG 57.020 30.769 0.00 0.00 0.00 3.18
1618 4661 9.221775 CTAATTAAAATGACGCATACCTGAAAC 57.778 33.333 0.00 0.00 0.00 2.78
1649 4692 2.482374 GCAAGATGCAGCGGTGTC 59.518 61.111 17.07 6.80 44.26 3.67
1651 4694 1.651240 GCAAGATGCAGCGGTGTCAT 61.651 55.000 19.50 19.50 44.26 3.06
1694 4737 4.840716 AATGAGAGGCTGAAGACTGAAT 57.159 40.909 0.00 0.00 30.09 2.57
1726 4769 5.149973 TCATGTTGGCTATGCAAAACAAT 57.850 34.783 11.87 2.50 39.06 2.71
1915 4959 4.649218 TGACCATACCATCTTCGATCTTCA 59.351 41.667 0.00 0.00 0.00 3.02
2096 5140 0.407528 TGGAAGCAATGTAGGGGCAA 59.592 50.000 0.00 0.00 0.00 4.52
2113 5157 1.265365 GCAATAGGATGAGCGGCTTTC 59.735 52.381 2.97 4.60 0.00 2.62
2145 5189 0.684535 TGTGAAGCTCGGTCCAATGA 59.315 50.000 0.00 0.00 0.00 2.57
2222 5266 8.593492 AAATAGAGAAAAACAAACATGGAAGC 57.407 30.769 0.00 0.00 0.00 3.86
2236 5280 2.585330 TGGAAGCTGCAAGTTGAATGA 58.415 42.857 7.16 0.00 35.30 2.57
2332 5390 4.452795 TCGATGTTTTTCGGCAACATAAGA 59.547 37.500 7.48 7.71 43.47 2.10
2336 5394 7.148820 CGATGTTTTTCGGCAACATAAGAATTT 60.149 33.333 7.48 0.00 43.47 1.82
2357 5415 6.768641 TTTATCATCTTCTGGATCCATGGA 57.231 37.500 18.88 18.88 31.27 3.41
2379 5437 0.165944 GAAGTGAACCACAATCGCCG 59.834 55.000 0.00 0.00 36.74 6.46
2593 5652 0.454600 GCATGTCCATGGAGCACAAG 59.545 55.000 16.81 8.80 39.16 3.16
2601 5660 1.546923 CATGGAGCACAAGCCAATCAA 59.453 47.619 0.00 0.00 43.56 2.57
2602 5661 1.250328 TGGAGCACAAGCCAATCAAG 58.750 50.000 0.00 0.00 43.56 3.02
2649 5708 1.072331 GGTGAACCTCTGGTGTGTGAT 59.928 52.381 0.00 0.00 35.34 3.06
2707 5766 6.072838 ACAATGTCAAGATTGTGTGAGATGAC 60.073 38.462 4.86 0.00 43.45 3.06
2709 5768 3.990469 GTCAAGATTGTGTGAGATGACGT 59.010 43.478 0.00 0.00 0.00 4.34
2782 5841 3.196469 AGCAAAGAGTTCGAGATCATGGA 59.804 43.478 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 101 0.735978 GGGGCGGCTTTGAAATTTCG 60.736 55.000 13.34 2.25 0.00 3.46
163 187 0.563672 GGTAGGAGAGGAGGATGGGT 59.436 60.000 0.00 0.00 0.00 4.51
268 315 2.281761 ACACTGCCGCAAGAAGGG 60.282 61.111 0.00 0.00 43.02 3.95
399 447 4.175337 GCCTAGCGGGTGCCATCA 62.175 66.667 1.06 0.00 44.31 3.07
418 466 1.699752 CCCAAAGGGCCCAGATCTT 59.300 57.895 27.56 5.84 35.35 2.40
668 746 0.106519 ACCAACAACTCAGCCAAGCT 60.107 50.000 0.00 0.00 40.77 3.74
820 904 2.026208 AAAATTCCCCACCACCCCGT 62.026 55.000 0.00 0.00 0.00 5.28
835 920 3.337909 AGGGATTTCTCCTGACCCAAAAT 59.662 43.478 0.00 0.00 42.62 1.82
845 930 1.555533 GAACCGACAGGGATTTCTCCT 59.444 52.381 0.00 0.00 43.47 3.69
996 4037 4.044426 GGTTGTGTTTGCTTCTCATGAAC 58.956 43.478 0.00 0.00 0.00 3.18
1004 4045 4.546570 GAATAGGTGGTTGTGTTTGCTTC 58.453 43.478 0.00 0.00 0.00 3.86
1201 4242 2.610374 TGTACGCTTCAAGTTGTTGGAC 59.390 45.455 2.11 0.00 34.09 4.02
1233 4274 6.662414 TTCGCTAGGTAAGAAACATTGATG 57.338 37.500 0.00 0.00 0.00 3.07
1415 4456 8.947055 ATTAATTGTGGAAAAGAATGGTATGC 57.053 30.769 0.00 0.00 0.00 3.14
1444 4485 4.022242 ACTGCATATCGTAGTGACCCATAC 60.022 45.833 0.00 0.00 39.36 2.39
1557 4599 0.672342 GATGCCATGTTCATGAGGGC 59.328 55.000 17.74 17.74 44.82 5.19
1618 4661 4.038282 TGCATCTTGCCCTGCATTTATTAG 59.962 41.667 0.00 0.00 44.23 1.73
1726 4769 2.715046 CCTCTGCATTTGAGGCAAGTA 58.285 47.619 7.49 0.00 43.67 2.24
1886 4929 3.068165 CGAAGATGGTATGGTCAGTAGCA 59.932 47.826 0.00 0.00 37.55 3.49
1915 4959 4.704540 TCATGCGGAAGAATTAACATTGGT 59.295 37.500 0.00 0.00 0.00 3.67
2096 5140 0.034059 CCGAAAGCCGCTCATCCTAT 59.966 55.000 0.00 0.00 36.84 2.57
2113 5157 0.099968 CTTCACAGCAATGCCATCCG 59.900 55.000 0.00 0.00 0.00 4.18
2145 5189 5.817816 ACAAACTCAAAGAGACAAAGACGAT 59.182 36.000 0.31 0.00 33.32 3.73
2222 5266 3.291809 TGTGCATCATTCAACTTGCAG 57.708 42.857 0.00 0.00 44.99 4.41
2236 5280 3.501828 ACACACACGATGTTATTGTGCAT 59.498 39.130 8.69 0.00 46.43 3.96
2332 5390 7.762610 TCCATGGATCCAGAAGATGATAAATT 58.237 34.615 21.33 0.00 34.42 1.82
2336 5394 6.309389 CATCCATGGATCCAGAAGATGATA 57.691 41.667 30.10 14.12 34.42 2.15
2357 5415 1.812571 GCGATTGTGGTTCACTTCCAT 59.187 47.619 0.00 0.00 37.30 3.41
2427 5485 1.661463 GGATCCCCCTCATCATGCTA 58.339 55.000 0.00 0.00 0.00 3.49
2593 5652 2.163211 GTCTTTCTGCTCCTTGATTGGC 59.837 50.000 0.00 0.00 0.00 4.52
2601 5660 0.612744 GCTCCTGTCTTTCTGCTCCT 59.387 55.000 0.00 0.00 0.00 3.69
2602 5661 0.739112 CGCTCCTGTCTTTCTGCTCC 60.739 60.000 0.00 0.00 0.00 4.70
2649 5708 4.039609 CCACTATGCACATCATCTCTGGTA 59.960 45.833 0.00 0.00 36.63 3.25
2782 5841 2.158667 ACAAACTCACCGTCCTTGGATT 60.159 45.455 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.