Multiple sequence alignment - TraesCS4A01G384900

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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 TraesCS4A01G384900 chr4A 100.000 3542 0 0 1 3542 662324114 662327655 0.000000e+00 6541
1 TraesCS4A01G384900 chr4A 90.756 238 21 1 1525 1762 661526581 661526345 2.050000e-82 316
2 TraesCS4A01G384900 chr4A 79.130 460 79 13 1 450 216434627 216434175 5.750000e-78 302
3 TraesCS4A01G384900 chr7A 93.956 2068 104 12 499 2560 50113403 50115455 0.000000e+00 3107
4 TraesCS4A01G384900 chr7A 98.265 980 15 2 2565 3542 264326774 264325795 0.000000e+00 1714
5 TraesCS4A01G384900 chr7A 82.632 190 31 2 2281 2469 49910133 49909945 2.190000e-37 167
6 TraesCS4A01G384900 chr7D 92.496 1959 104 22 625 2549 47403869 47401920 0.000000e+00 2763
7 TraesCS4A01G384900 chr7D 90.835 982 74 11 2565 3542 630373393 630374362 0.000000e+00 1301
8 TraesCS4A01G384900 chrUn 100.000 1279 0 0 1 1279 296181973 296183251 0.000000e+00 2362
9 TraesCS4A01G384900 chr5B 98.160 978 17 1 2566 3542 697825950 697826927 0.000000e+00 1705
10 TraesCS4A01G384900 chr5B 79.661 295 58 2 2203 2496 400563105 400562812 9.960000e-51 211
11 TraesCS4A01G384900 chr5B 87.963 108 12 1 2190 2296 328367188 328367295 3.710000e-25 126
12 TraesCS4A01G384900 chr2A 97.868 985 20 1 2559 3542 738352081 738353065 0.000000e+00 1701
13 TraesCS4A01G384900 chr1B 97.757 981 21 1 2563 3542 95401200 95400220 0.000000e+00 1688
14 TraesCS4A01G384900 chr1B 82.072 502 55 12 6 476 376054158 376054655 2.560000e-106 396
15 TraesCS4A01G384900 chr1B 79.174 533 71 21 1 495 470781875 470781345 2.040000e-87 333
16 TraesCS4A01G384900 chr1B 79.856 417 77 7 1049 1460 670187762 670187348 7.430000e-77 298
17 TraesCS4A01G384900 chr2D 93.096 985 63 3 2563 3542 12896680 12895696 0.000000e+00 1437
18 TraesCS4A01G384900 chr2D 90.588 85 8 0 2198 2282 407981758 407981842 2.890000e-21 113
19 TraesCS4A01G384900 chr1A 92.668 982 68 2 2565 3542 547342622 547343603 0.000000e+00 1411
20 TraesCS4A01G384900 chr6D 92.229 978 72 2 2566 3539 39585117 39586094 0.000000e+00 1382
21 TraesCS4A01G384900 chr6D 91.793 926 69 4 2563 3484 354363147 354364069 0.000000e+00 1282
22 TraesCS4A01G384900 chr3A 76.606 1043 229 15 1457 2493 66354047 66355080 8.590000e-156 560
23 TraesCS4A01G384900 chr3A 79.391 427 79 9 1041 1460 66353546 66353970 3.460000e-75 292
24 TraesCS4A01G384900 chr3A 76.899 316 65 8 2183 2494 706923618 706923929 4.700000e-39 172
25 TraesCS4A01G384900 chr1D 81.310 519 67 17 1 494 318549986 318549473 9.220000e-106 394
26 TraesCS4A01G384900 chr1D 86.032 315 35 7 186 494 52738835 52738524 2.640000e-86 329
27 TraesCS4A01G384900 chr6A 80.361 499 80 12 1 493 550621077 550620591 2.600000e-96 363
28 TraesCS4A01G384900 chr3D 79.175 509 79 22 1 494 159784667 159785163 9.480000e-86 327
29 TraesCS4A01G384900 chr3D 79.087 416 82 5 1049 1460 57234056 57234470 7.490000e-72 281
30 TraesCS4A01G384900 chr3D 73.981 319 80 3 2190 2506 572101025 572100708 3.710000e-25 126
31 TraesCS4A01G384900 chr4D 81.340 418 54 15 100 494 348293374 348292958 5.710000e-83 318
32 TraesCS4A01G384900 chr3B 78.220 427 83 9 1041 1460 90165368 90165791 7.540000e-67 265
33 TraesCS4A01G384900 chr5D 79.661 295 58 2 2203 2496 341075595 341075302 9.960000e-51 211
34 TraesCS4A01G384900 chr5D 76.109 293 65 5 2200 2489 1885280 1884990 7.920000e-32 148
35 TraesCS4A01G384900 chr5D 75.758 264 62 2 2190 2452 289074204 289074466 7.980000e-27 132
36 TraesCS4A01G384900 chr5A 79.661 295 58 2 2203 2496 442291115 442290822 9.960000e-51 211
37 TraesCS4A01G384900 chr5A 78.694 291 60 2 2203 2492 442504895 442504606 3.610000e-45 193


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 TraesCS4A01G384900 chr4A 662324114 662327655 3541 False 6541 6541 100.0000 1 3542 1 chr4A.!!$F1 3541
1 TraesCS4A01G384900 chr7A 50113403 50115455 2052 False 3107 3107 93.9560 499 2560 1 chr7A.!!$F1 2061
2 TraesCS4A01G384900 chr7A 264325795 264326774 979 True 1714 1714 98.2650 2565 3542 1 chr7A.!!$R2 977
3 TraesCS4A01G384900 chr7D 47401920 47403869 1949 True 2763 2763 92.4960 625 2549 1 chr7D.!!$R1 1924
4 TraesCS4A01G384900 chr7D 630373393 630374362 969 False 1301 1301 90.8350 2565 3542 1 chr7D.!!$F1 977
5 TraesCS4A01G384900 chrUn 296181973 296183251 1278 False 2362 2362 100.0000 1 1279 1 chrUn.!!$F1 1278
6 TraesCS4A01G384900 chr5B 697825950 697826927 977 False 1705 1705 98.1600 2566 3542 1 chr5B.!!$F2 976
7 TraesCS4A01G384900 chr2A 738352081 738353065 984 False 1701 1701 97.8680 2559 3542 1 chr2A.!!$F1 983
8 TraesCS4A01G384900 chr1B 95400220 95401200 980 True 1688 1688 97.7570 2563 3542 1 chr1B.!!$R1 979
9 TraesCS4A01G384900 chr1B 470781345 470781875 530 True 333 333 79.1740 1 495 1 chr1B.!!$R2 494
10 TraesCS4A01G384900 chr2D 12895696 12896680 984 True 1437 1437 93.0960 2563 3542 1 chr2D.!!$R1 979
11 TraesCS4A01G384900 chr1A 547342622 547343603 981 False 1411 1411 92.6680 2565 3542 1 chr1A.!!$F1 977
12 TraesCS4A01G384900 chr6D 39585117 39586094 977 False 1382 1382 92.2290 2566 3539 1 chr6D.!!$F1 973
13 TraesCS4A01G384900 chr6D 354363147 354364069 922 False 1282 1282 91.7930 2563 3484 1 chr6D.!!$F2 921
14 TraesCS4A01G384900 chr3A 66353546 66355080 1534 False 426 560 77.9985 1041 2493 2 chr3A.!!$F2 1452
15 TraesCS4A01G384900 chr1D 318549473 318549986 513 True 394 394 81.3100 1 494 1 chr1D.!!$R2 493

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
1602 1765 2.003548 GATCAAGGGAGGCTGGGGT 61.004 63.158 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2703 2870 0.181587 TTTGTGTCCCATGTCGGTGT 59.818 50.0 0.0 0.0 0.0 4.16 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
1602 1765 2.003548 GATCAAGGGAGGCTGGGGT 61.004 63.158 0.00 0.00 0.00 4.95
1750 1913 2.022129 CGTAAGATCCGCGGCATCC 61.022 63.158 23.51 9.08 43.02 3.51
1752 1915 0.320771 GTAAGATCCGCGGCATCCAT 60.321 55.000 23.51 16.89 0.00 3.41
1842 2008 2.989639 CGGATGCTCCTCACCCAA 59.010 61.111 1.51 0.00 33.30 4.12
1845 2011 1.450312 GATGCTCCTCACCCAACGG 60.450 63.158 0.00 0.00 0.00 4.44
1846 2012 1.899437 GATGCTCCTCACCCAACGGA 61.899 60.000 0.00 0.00 0.00 4.69
1872 2038 3.576356 CCGCAGCTGGTTATGGCG 61.576 66.667 17.12 10.71 46.61 5.69
1902 2068 1.202806 CCTTTCTTCCAGCAGGTGACA 60.203 52.381 0.00 0.00 35.89 3.58
2100 2266 4.521062 ATGCTCGGGTCGCAGCTC 62.521 66.667 10.89 0.00 41.22 4.09
2163 2329 2.356278 GTGAGCAAGGGATGGGCA 59.644 61.111 0.00 0.00 0.00 5.36
2167 2333 4.802051 GCAAGGGATGGGCAGCGA 62.802 66.667 0.00 0.00 0.00 4.93
2169 2335 3.011517 AAGGGATGGGCAGCGACT 61.012 61.111 0.00 0.00 0.00 4.18
2560 2726 4.016666 TCTGAAGGAGAGGAGGAGAGAAAT 60.017 45.833 0.00 0.00 0.00 2.17
2561 2727 5.194740 TCTGAAGGAGAGGAGGAGAGAAATA 59.805 44.000 0.00 0.00 0.00 1.40
2703 2870 2.446994 ACCACCGACCAACCTGGA 60.447 61.111 0.00 0.00 40.96 3.86
2929 3096 0.318699 CTTTGACGACGAGCCTCACA 60.319 55.000 0.00 0.00 0.00 3.58
3276 3447 0.400213 AAGAAAGATCACGGCACCCA 59.600 50.000 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1386 1469 0.165295 TGTAGACGTTCAGCGACGAG 59.835 55.000 15.33 0.00 45.47 4.18
1387 1470 0.800631 ATGTAGACGTTCAGCGACGA 59.199 50.000 15.33 0.00 45.47 4.20
1866 2032 3.936203 GGGATCGCCACCGCCATA 61.936 66.667 0.00 0.00 35.15 2.74
1872 2038 0.748367 GGAAGAAAGGGATCGCCACC 60.748 60.000 6.09 0.00 35.15 4.61
1884 2050 1.202806 CCTGTCACCTGCTGGAAGAAA 60.203 52.381 17.64 7.94 34.07 2.52
2090 2256 2.279120 CGATCAGGAGCTGCGACC 60.279 66.667 0.00 10.08 0.00 4.79
2100 2266 2.031616 ATGATGGCGCCGATCAGG 59.968 61.111 31.12 0.00 44.97 3.86
2155 2321 2.037620 ATGAGAGTCGCTGCCCATCC 62.038 60.000 0.00 0.00 0.00 3.51
2156 2322 0.599728 GATGAGAGTCGCTGCCCATC 60.600 60.000 0.00 0.00 0.00 3.51
2163 2329 2.136298 TCAGGAAGATGAGAGTCGCT 57.864 50.000 0.00 0.00 0.00 4.93
2167 2333 1.336440 CGCGATCAGGAAGATGAGAGT 59.664 52.381 0.00 0.00 37.00 3.24
2169 2335 0.670706 CCGCGATCAGGAAGATGAGA 59.329 55.000 8.23 0.00 37.00 3.27
2439 2605 4.457496 ACCTGCTCGATGGGCACG 62.457 66.667 0.00 0.00 35.71 5.34
2499 2665 1.484444 CCTCCTCGGATCCCATTCCC 61.484 65.000 6.06 0.00 31.61 3.97
2693 2860 1.415672 ATGTCGGTGTCCAGGTTGGT 61.416 55.000 0.00 0.00 39.03 3.67
2703 2870 0.181587 TTTGTGTCCCATGTCGGTGT 59.818 50.000 0.00 0.00 0.00 4.16
3288 3459 3.432051 CTTCTTCGGAGCCGGCGAT 62.432 63.158 23.20 3.63 40.25 4.58


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

AutoCloner maintained by Alex Coulton.