Multiple sequence alignment - TraesCS6A01G384400

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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 TraesCS6A01G384400 chr6A 100.000 3392 0 0 1 3392 602828941 602832332 0.000000e+00 6264.0
1 TraesCS6A01G384400 chr3B 95.789 2446 65 6 1 2445 561699848 561702256 0.000000e+00 3912.0
2 TraesCS6A01G384400 chr3B 86.207 899 60 18 1593 2445 793141591 793142471 0.000000e+00 915.0
3 TraesCS6A01G384400 chr3B 87.891 512 53 6 312 819 70002913 70003419 8.100000e-166 593.0
4 TraesCS6A01G384400 chr3B 87.941 340 30 7 219 557 630160630 630160301 1.140000e-104 390.0
5 TraesCS6A01G384400 chr3B 90.164 122 9 3 1246 1365 774716298 774716418 4.530000e-34 156.0
6 TraesCS6A01G384400 chr5A 97.017 1877 52 2 570 2445 403898475 403900348 0.000000e+00 3153.0
7 TraesCS6A01G384400 chr5A 86.549 736 67 10 1 719 523024210 523024930 0.000000e+00 782.0
8 TraesCS6A01G384400 chr5A 97.573 412 9 1 1 411 403898062 403898473 0.000000e+00 704.0
9 TraesCS6A01G384400 chr2A 96.913 1879 52 3 570 2445 306684342 306682467 0.000000e+00 3144.0
10 TraesCS6A01G384400 chr2A 96.042 1895 53 5 570 2445 69256670 69258561 0.000000e+00 3064.0
11 TraesCS6A01G384400 chr2A 97.573 412 9 1 1 411 306684755 306684344 0.000000e+00 704.0
12 TraesCS6A01G384400 chr2A 97.330 412 10 1 1 411 69256257 69256668 0.000000e+00 699.0
13 TraesCS6A01G384400 chr3A 96.702 1213 31 6 1238 2445 405833217 405832009 0.000000e+00 2010.0
14 TraesCS6A01G384400 chr3A 96.880 673 21 0 570 1242 405842440 405841768 0.000000e+00 1127.0
15 TraesCS6A01G384400 chr3A 97.573 412 9 1 1 411 405842853 405842442 0.000000e+00 704.0
16 TraesCS6A01G384400 chr3A 96.296 108 4 0 2063 2170 42045565 42045458 9.670000e-41 178.0
17 TraesCS6A01G384400 chr7B 93.100 942 47 10 2455 3392 356534350 356535277 0.000000e+00 1363.0
18 TraesCS6A01G384400 chr4B 92.624 949 51 15 2455 3392 172478897 172479837 0.000000e+00 1347.0
19 TraesCS6A01G384400 chr4B 87.320 347 32 8 213 557 241184998 241185334 1.480000e-103 387.0
20 TraesCS6A01G384400 chrUn 96.989 797 24 0 1649 2445 384178460 384179256 0.000000e+00 1339.0
21 TraesCS6A01G384400 chrUn 91.688 397 25 5 3000 3392 259678036 259677644 8.280000e-151 544.0
22 TraesCS6A01G384400 chrUn 91.688 397 25 5 3000 3392 393014094 393013702 8.280000e-151 544.0
23 TraesCS6A01G384400 chrUn 91.688 397 25 5 3000 3392 393015709 393015317 8.280000e-151 544.0
24 TraesCS6A01G384400 chr2D 92.235 953 32 8 2442 3391 25858716 25859629 0.000000e+00 1312.0
25 TraesCS6A01G384400 chr2D 87.415 294 34 2 137 428 117801407 117801699 5.420000e-88 335.0
26 TraesCS6A01G384400 chr6B 92.928 905 51 8 2490 3392 345159649 345160542 0.000000e+00 1304.0
27 TraesCS6A01G384400 chr6B 87.619 420 44 6 404 819 599819311 599819726 6.580000e-132 481.0
28 TraesCS6A01G384400 chr5D 90.777 618 27 7 2777 3392 553280511 553281100 0.000000e+00 798.0
29 TraesCS6A01G384400 chr5D 95.105 286 13 1 2442 2726 553280226 553280511 1.860000e-122 449.0
30 TraesCS6A01G384400 chr4D 92.273 440 25 4 2955 3392 381739467 381739899 1.730000e-172 616.0
31 TraesCS6A01G384400 chr5B 89.749 439 41 2 2954 3392 700066185 700065751 2.960000e-155 558.0
32 TraesCS6A01G384400 chr5B 87.560 418 42 8 407 819 672541311 672540899 3.060000e-130 475.0
33 TraesCS6A01G384400 chr5B 80.286 350 43 11 1715 2042 347127649 347127994 1.220000e-59 241.0
34 TraesCS6A01G384400 chr5B 85.022 227 29 4 1144 1365 533416995 533417221 3.410000e-55 226.0
35 TraesCS6A01G384400 chr7A 96.407 334 11 1 2442 2774 632038489 632038156 1.780000e-152 549.0
36 TraesCS6A01G384400 chr7A 90.164 122 10 2 1246 1365 121783571 121783692 1.260000e-34 158.0
37 TraesCS6A01G384400 chr2B 88.010 417 42 6 407 819 183534587 183534175 1.410000e-133 486.0
38 TraesCS6A01G384400 chr4A 89.521 334 33 1 2052 2385 222106839 222107170 4.050000e-114 422.0
39 TraesCS6A01G384400 chr1B 96.500 200 5 2 2442 2639 159411103 159410904 2.520000e-86 329.0
40 TraesCS6A01G384400 chr1B 89.431 123 10 3 1246 1365 562727811 562727689 5.860000e-33 152.0
41 TraesCS6A01G384400 chr6D 90.769 65 4 1 1707 1771 226910923 226910861 6.030000e-13 86.1
42 TraesCS6A01G384400 chr7D 89.286 56 3 3 2867 2920 581295056 581295110 2.180000e-07 67.6


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 TraesCS6A01G384400 chr6A 602828941 602832332 3391 False 6264.0 6264 100.0000 1 3392 1 chr6A.!!$F1 3391
1 TraesCS6A01G384400 chr3B 561699848 561702256 2408 False 3912.0 3912 95.7890 1 2445 1 chr3B.!!$F2 2444
2 TraesCS6A01G384400 chr3B 793141591 793142471 880 False 915.0 915 86.2070 1593 2445 1 chr3B.!!$F4 852
3 TraesCS6A01G384400 chr3B 70002913 70003419 506 False 593.0 593 87.8910 312 819 1 chr3B.!!$F1 507
4 TraesCS6A01G384400 chr5A 403898062 403900348 2286 False 1928.5 3153 97.2950 1 2445 2 chr5A.!!$F2 2444
5 TraesCS6A01G384400 chr5A 523024210 523024930 720 False 782.0 782 86.5490 1 719 1 chr5A.!!$F1 718
6 TraesCS6A01G384400 chr2A 306682467 306684755 2288 True 1924.0 3144 97.2430 1 2445 2 chr2A.!!$R1 2444
7 TraesCS6A01G384400 chr2A 69256257 69258561 2304 False 1881.5 3064 96.6860 1 2445 2 chr2A.!!$F1 2444
8 TraesCS6A01G384400 chr3A 405832009 405833217 1208 True 2010.0 2010 96.7020 1238 2445 1 chr3A.!!$R2 1207
9 TraesCS6A01G384400 chr3A 405841768 405842853 1085 True 915.5 1127 97.2265 1 1242 2 chr3A.!!$R3 1241
10 TraesCS6A01G384400 chr7B 356534350 356535277 927 False 1363.0 1363 93.1000 2455 3392 1 chr7B.!!$F1 937
11 TraesCS6A01G384400 chr4B 172478897 172479837 940 False 1347.0 1347 92.6240 2455 3392 1 chr4B.!!$F1 937
12 TraesCS6A01G384400 chrUn 384178460 384179256 796 False 1339.0 1339 96.9890 1649 2445 1 chrUn.!!$F1 796
13 TraesCS6A01G384400 chrUn 393013702 393015709 2007 True 544.0 544 91.6880 3000 3392 2 chrUn.!!$R2 392
14 TraesCS6A01G384400 chr2D 25858716 25859629 913 False 1312.0 1312 92.2350 2442 3391 1 chr2D.!!$F1 949
15 TraesCS6A01G384400 chr6B 345159649 345160542 893 False 1304.0 1304 92.9280 2490 3392 1 chr6B.!!$F1 902
16 TraesCS6A01G384400 chr5D 553280226 553281100 874 False 623.5 798 92.9410 2442 3392 2 chr5D.!!$F1 950

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
74 75 0.547712 ATGCCCTGTAGTGGACTGGT 60.548 55.000 0.00 0.0 43.90 4.00 F
930 950 2.896685 TGTTCATTTCCCTTTCCGCAAT 59.103 40.909 0.00 0.0 0.00 3.56 F
1534 1574 1.271871 CCAGCCAACATGGTGACCTAA 60.272 52.381 13.74 0.0 40.46 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1181 1201 0.037447 GCAAGGAGACCCAGCTCTTT 59.963 55.0 0.00 0.0 34.94 2.52 R
2052 2127 0.800631 CGCAATGCTTCAGCTCAAGA 59.199 50.0 0.00 0.0 42.66 3.02 R
3156 4880 0.809241 GAAGAGGCAGCGATGGTGAG 60.809 60.0 1.46 0.0 32.22 3.51 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
74 75 0.547712 ATGCCCTGTAGTGGACTGGT 60.548 55.000 0.00 0.00 43.90 4.00
251 252 3.843422 AGTTTGTCAACCAATGGGATGA 58.157 40.909 3.55 5.02 43.02 2.92
592 601 7.728895 CAATTGTTTGGGACATTTATTTCGAC 58.271 34.615 0.00 0.00 39.30 4.20
605 614 7.169308 ACATTTATTTCGACGCTTCCTATACTG 59.831 37.037 0.00 0.00 0.00 2.74
767 786 4.326826 ACAGGTAATTCCACACATCACTG 58.673 43.478 0.00 0.00 39.02 3.66
930 950 2.896685 TGTTCATTTCCCTTTCCGCAAT 59.103 40.909 0.00 0.00 0.00 3.56
1029 1049 6.556116 TGTTGGTAGGTAAGTCTAAACTCCTT 59.444 38.462 0.00 0.00 33.13 3.36
1181 1201 2.283529 GGGAGCCAGTGTCTTCGGA 61.284 63.158 0.00 0.00 0.00 4.55
1299 1320 9.883142 CCTCTCTTCTTTGATAGTGATTACTTT 57.117 33.333 0.00 0.00 38.36 2.66
1310 1331 7.860373 TGATAGTGATTACTTTGTTGTTGTTGC 59.140 33.333 0.00 0.00 38.36 4.17
1311 1332 6.207691 AGTGATTACTTTGTTGTTGTTGCT 57.792 33.333 0.00 0.00 31.66 3.91
1312 1333 6.035843 AGTGATTACTTTGTTGTTGTTGCTG 58.964 36.000 0.00 0.00 31.66 4.41
1344 1365 7.775397 AACCAAAACATGTTTGAGATTTCAG 57.225 32.000 23.93 8.76 34.15 3.02
1413 1453 5.072193 AGAGAGAGAGAGAGAGATGTATGCA 59.928 44.000 0.00 0.00 0.00 3.96
1453 1493 7.177878 AGGAGGACATGTACATTTTTCTTGAT 58.822 34.615 11.55 0.00 0.00 2.57
1534 1574 1.271871 CCAGCCAACATGGTGACCTAA 60.272 52.381 13.74 0.00 40.46 2.69
1603 1643 6.545508 TCGATTGCAACTGAACTTATTCATG 58.454 36.000 0.00 0.00 43.92 3.07
1688 1728 8.034215 ACATTACCATTGATACCATGTTTTGTG 58.966 33.333 0.00 0.00 0.00 3.33
1831 1906 7.331934 TCAACTTATTCATGACTGCACTTACTC 59.668 37.037 0.00 0.00 0.00 2.59
1950 2025 4.273480 GGCGATATAATGTGCTTGACAAGT 59.727 41.667 16.39 0.00 38.36 3.16
2052 2127 9.426837 TCACGCAGTATAACTTTATTGTAGTTT 57.573 29.630 0.00 0.00 41.61 2.66
2082 2168 0.168788 AGCATTGCGATGGTGAAACG 59.831 50.000 17.82 0.00 42.13 3.60
2133 2219 7.148000 GGAAATGCTATAAAAGAGAAGCTGGTT 60.148 37.037 0.00 0.00 35.95 3.67
2153 2239 5.072058 TGGTTAGTTAGGTTCCTTAGTTGCA 59.928 40.000 0.00 0.00 0.00 4.08
2301 2387 0.540365 CTTGGTTGGGCACACAGGAT 60.540 55.000 0.00 0.00 0.00 3.24
2419 2505 4.359434 TGGCTGAACCATGTTAGTACAA 57.641 40.909 0.00 0.00 46.36 2.41
2483 2570 5.356751 AGATTAAGTGATTATTTGTGCCGCA 59.643 36.000 0.00 0.00 0.00 5.69
2577 2665 7.611770 AGATAATATACGCCTGCTTCATACAA 58.388 34.615 0.00 0.00 0.00 2.41
2900 2991 0.627451 TTGGATGGCTGGAGATGCTT 59.373 50.000 0.00 0.00 0.00 3.91
2984 3089 1.875514 CGATCTGCAGGAGAGAGAGAG 59.124 57.143 15.13 0.00 32.80 3.20
2985 3090 2.485302 CGATCTGCAGGAGAGAGAGAGA 60.485 54.545 15.13 0.00 32.80 3.10
2986 3091 2.715749 TCTGCAGGAGAGAGAGAGAG 57.284 55.000 15.13 0.00 0.00 3.20
2987 3092 2.195727 TCTGCAGGAGAGAGAGAGAGA 58.804 52.381 15.13 0.00 0.00 3.10
2994 3099 6.006449 GCAGGAGAGAGAGAGAGAAGATAAT 58.994 44.000 0.00 0.00 0.00 1.28
3123 4847 1.200760 TAGCCACCATGCTCCTGTGT 61.201 55.000 0.00 0.00 41.68 3.72
3145 4869 2.769621 TGCATCCCCGCATCTCCT 60.770 61.111 0.00 0.00 36.86 3.69
3153 4877 1.303309 CCCGCATCTCCTGTTTCATC 58.697 55.000 0.00 0.00 0.00 2.92
3156 4880 2.547211 CCGCATCTCCTGTTTCATCATC 59.453 50.000 0.00 0.00 0.00 2.92
3184 4908 0.901124 GCTGCCTCTTCTCCTCTTCA 59.099 55.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.203287 CCTGATGCTCGACAGTCTCAA 59.797 52.381 0.00 0.00 32.93 3.02
251 252 8.483758 ACCATAACGAGAAGGTCAAGTTTATAT 58.516 33.333 0.00 0.00 0.00 0.86
592 601 3.119291 CAAGAGTGCAGTATAGGAAGCG 58.881 50.000 0.00 0.00 0.00 4.68
605 614 5.679734 TGAACAGAAAGAATCAAGAGTGC 57.320 39.130 0.00 0.00 0.00 4.40
767 786 1.676006 ACAGTAGCAGGCACACAAAAC 59.324 47.619 0.00 0.00 0.00 2.43
1170 1190 1.001406 CCAGCTCTTTCCGAAGACACT 59.999 52.381 0.00 0.00 36.99 3.55
1181 1201 0.037447 GCAAGGAGACCCAGCTCTTT 59.963 55.000 0.00 0.00 34.94 2.52
1299 1320 3.523606 ATTTCTGCAGCAACAACAACA 57.476 38.095 9.47 0.00 0.00 3.33
1310 1331 7.224362 TCAAACATGTTTTGGTTATTTCTGCAG 59.776 33.333 21.10 7.63 31.92 4.41
1311 1332 7.044181 TCAAACATGTTTTGGTTATTTCTGCA 58.956 30.769 21.10 0.00 31.92 4.41
1312 1333 7.437862 TCTCAAACATGTTTTGGTTATTTCTGC 59.562 33.333 21.10 0.00 31.92 4.26
1365 1387 4.584638 TTCTCTCTCTCTAGAACTGGCT 57.415 45.455 0.00 0.00 0.00 4.75
1413 1453 5.269189 TGTCCTCCTCTTTTTCTTGGTTTT 58.731 37.500 0.00 0.00 0.00 2.43
1492 1532 4.380444 GGTCAATTATGCACACACGGAAAT 60.380 41.667 0.00 0.00 0.00 2.17
1534 1574 5.081728 GGGTAAAGTTAATTCAGTTGGGGT 58.918 41.667 0.00 0.00 0.00 4.95
1688 1728 9.600646 GTGCAGTTCTTAATAGAAGAAGAAAAC 57.399 33.333 0.06 0.00 41.93 2.43
1831 1906 2.703416 TGAGCACATAGGCTGACAAAG 58.297 47.619 0.00 0.00 45.99 2.77
1950 2025 4.910195 AGGCATATGAATTATCTCGGCAA 58.090 39.130 6.97 0.00 0.00 4.52
2052 2127 0.800631 CGCAATGCTTCAGCTCAAGA 59.199 50.000 0.00 0.00 42.66 3.02
2153 2239 6.435292 AACTGGTAATTCTACAGGAACAGT 57.565 37.500 8.30 0.00 38.40 3.55
2419 2505 9.359653 AGCATGTTTTCTATGGATATTTAGCTT 57.640 29.630 0.00 0.00 0.00 3.74
2483 2570 7.667043 TTTTAGATGATTTGTTGTAGCGACT 57.333 32.000 0.00 0.00 0.00 4.18
2577 2665 5.456921 TGCCCCTCTCAGAAAGAATAATT 57.543 39.130 0.00 0.00 32.23 1.40
2839 2930 4.929808 ACTTCAACAGCTACGTGAAATAGG 59.070 41.667 0.00 0.38 0.00 2.57
2853 2944 4.082571 CCTTTCAAGGCCATACTTCAACAG 60.083 45.833 5.01 0.00 39.76 3.16
2984 3089 6.147437 TCTCTCTCCCCCTATTATCTTCTC 57.853 45.833 0.00 0.00 0.00 2.87
2985 3090 6.470124 CCTTCTCTCTCCCCCTATTATCTTCT 60.470 46.154 0.00 0.00 0.00 2.85
2986 3091 5.719563 CCTTCTCTCTCCCCCTATTATCTTC 59.280 48.000 0.00 0.00 0.00 2.87
2987 3092 5.380206 TCCTTCTCTCTCCCCCTATTATCTT 59.620 44.000 0.00 0.00 0.00 2.40
2994 3099 1.576272 CCTTCCTTCTCTCTCCCCCTA 59.424 57.143 0.00 0.00 0.00 3.53
3145 4869 2.938451 GCGATGGTGAGATGATGAAACA 59.062 45.455 0.00 0.00 0.00 2.83
3153 4877 0.879400 GAGGCAGCGATGGTGAGATG 60.879 60.000 1.46 0.00 32.22 2.90
3156 4880 0.809241 GAAGAGGCAGCGATGGTGAG 60.809 60.000 1.46 0.00 32.22 3.51
3184 4908 0.998145 AGGGGAAGAAGCAGAGCAAT 59.002 50.000 0.00 0.00 0.00 3.56
3293 5023 2.660552 CGTTGACCACCGCTTCGT 60.661 61.111 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.