Multiple sequence alignment - TraesCS6A01G094000

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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 TraesCS6A01G094000 chr6A 100.000 4074 0 0 1 4074 61397802 61393729 0.000000e+00 7524
1 TraesCS6A01G094000 chr6A 95.986 4086 126 19 1 4074 607430560 607434619 0.000000e+00 6602
2 TraesCS6A01G094000 chr6A 90.254 236 21 1 784 1017 85544430 85544665 1.420000e-79 307
3 TraesCS6A01G094000 chr5A 95.922 4095 130 17 1 4074 324947694 324951772 0.000000e+00 6602
4 TraesCS6A01G094000 chr5A 88.103 311 26 8 12 321 10035516 10035816 3.870000e-95 359
5 TraesCS6A01G094000 chr5B 95.646 4088 126 20 1 4074 6850904 6846855 0.000000e+00 6516
6 TraesCS6A01G094000 chr3B 95.471 4085 126 22 1 4074 12025701 12029737 0.000000e+00 6464
7 TraesCS6A01G094000 chr3B 86.932 176 20 2 1908 2082 521612424 521612251 1.160000e-45 195
8 TraesCS6A01G094000 chr1B 96.203 3555 111 9 529 4074 608359832 608363371 0.000000e+00 5795
9 TraesCS6A01G094000 chr1B 94.018 652 34 3 3423 4074 117287611 117286965 0.000000e+00 983
10 TraesCS6A01G094000 chr1B 92.381 315 11 2 1 314 608359198 608359500 1.740000e-118 436
11 TraesCS6A01G094000 chr1B 92.333 300 18 3 3516 3815 117287200 117286906 4.870000e-114 422
12 TraesCS6A01G094000 chr1B 92.245 245 13 4 3833 4074 117287520 117287279 3.900000e-90 342
13 TraesCS6A01G094000 chr1B 80.085 236 26 8 784 1017 127294904 127294688 5.450000e-34 156
14 TraesCS6A01G094000 chrUn 97.288 1143 23 6 1702 2840 434647776 434646638 0.000000e+00 1932
15 TraesCS6A01G094000 chr4D 89.754 976 88 8 2115 3081 467219950 467220922 0.000000e+00 1238
16 TraesCS6A01G094000 chr4D 91.743 218 18 0 784 1001 450211890 450212107 1.840000e-78 303
17 TraesCS6A01G094000 chr4D 88.660 97 9 2 1796 1892 278194334 278194240 2.570000e-22 117
18 TraesCS6A01G094000 chr6D 87.593 1072 123 7 319 1381 226684356 226683286 0.000000e+00 1234
19 TraesCS6A01G094000 chr6D 95.343 773 32 4 2459 3229 364857533 364858303 0.000000e+00 1225
20 TraesCS6A01G094000 chr6D 92.173 741 53 4 1420 2159 226683281 226682545 0.000000e+00 1042
21 TraesCS6A01G094000 chr6D 87.470 423 27 21 12 427 346333990 346334393 7.980000e-127 464
22 TraesCS6A01G094000 chr6D 91.290 310 21 5 12 321 226690636 226690333 6.300000e-113 418
23 TraesCS6A01G094000 chr7D 94.696 773 37 4 2459 3229 50399470 50400240 0.000000e+00 1197
24 TraesCS6A01G094000 chr7D 86.118 389 24 17 1410 1797 220289083 220288724 3.820000e-105 392
25 TraesCS6A01G094000 chr7D 86.145 332 30 10 12 342 287702628 287702944 1.080000e-90 344
26 TraesCS6A01G094000 chr7D 96.053 76 3 0 1304 1379 220289157 220289082 1.540000e-24 124
27 TraesCS6A01G094000 chr7D 77.604 192 29 6 3355 3533 15896899 15897089 2.000000e-18 104
28 TraesCS6A01G094000 chr2D 94.696 773 37 4 2459 3229 174944602 174945372 0.000000e+00 1197
29 TraesCS6A01G094000 chr2D 94.696 773 34 5 2459 3229 476468198 476468965 0.000000e+00 1194
30 TraesCS6A01G094000 chr2D 93.697 238 9 3 12 249 107744814 107745045 6.480000e-93 351
31 TraesCS6A01G094000 chr2D 81.818 132 23 1 655 785 72151361 72151230 4.310000e-20 110
32 TraesCS6A01G094000 chr4B 88.450 987 96 9 2096 3081 585017989 585018958 0.000000e+00 1175
33 TraesCS6A01G094000 chr5D 93.064 692 43 4 3244 3933 358665217 358664529 0.000000e+00 1007
34 TraesCS6A01G094000 chr5D 92.469 239 13 3 3839 4074 358664941 358664705 1.810000e-88 337
35 TraesCS6A01G094000 chr2A 91.806 537 44 0 3280 3816 207136931 207137467 0.000000e+00 749
36 TraesCS6A01G094000 chr2A 91.020 245 15 5 3835 4074 207137166 207137408 1.410000e-84 324
37 TraesCS6A01G094000 chr3D 86.095 525 44 22 784 1283 592965798 592966318 4.630000e-149 538
38 TraesCS6A01G094000 chr3D 87.500 176 20 1 1902 2077 395839786 395839613 6.900000e-48 202
39 TraesCS6A01G094000 chr3D 87.629 97 10 2 1796 1892 395850398 395850304 1.200000e-20 111
40 TraesCS6A01G094000 chr7B 90.691 376 24 9 1421 1791 179247977 179248346 1.320000e-134 490
41 TraesCS6A01G094000 chr3A 92.086 278 17 2 1011 1283 120239405 120239682 1.780000e-103 387
42 TraesCS6A01G094000 chr2B 91.549 284 19 2 1011 1289 190041311 190041028 1.780000e-103 387
43 TraesCS6A01G094000 chr4A 81.310 519 53 27 12 500 216819246 216818742 8.260000e-102 381
44 TraesCS6A01G094000 chr1D 90.909 209 17 2 2321 2528 455904812 455905019 3.100000e-71 279
45 TraesCS6A01G094000 chr7A 79.135 393 43 24 1410 1797 232596535 232596177 6.810000e-58 235
46 TraesCS6A01G094000 chr7A 77.487 191 29 6 3356 3533 241732933 241733122 7.200000e-18 102


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 TraesCS6A01G094000 chr6A 61393729 61397802 4073 True 7524.000000 7524 100.000000 1 4074 1 chr6A.!!$R1 4073
1 TraesCS6A01G094000 chr6A 607430560 607434619 4059 False 6602.000000 6602 95.986000 1 4074 1 chr6A.!!$F2 4073
2 TraesCS6A01G094000 chr5A 324947694 324951772 4078 False 6602.000000 6602 95.922000 1 4074 1 chr5A.!!$F2 4073
3 TraesCS6A01G094000 chr5B 6846855 6850904 4049 True 6516.000000 6516 95.646000 1 4074 1 chr5B.!!$R1 4073
4 TraesCS6A01G094000 chr3B 12025701 12029737 4036 False 6464.000000 6464 95.471000 1 4074 1 chr3B.!!$F1 4073
5 TraesCS6A01G094000 chr1B 608359198 608363371 4173 False 3115.500000 5795 94.292000 1 4074 2 chr1B.!!$F1 4073
6 TraesCS6A01G094000 chr1B 117286906 117287611 705 True 582.333333 983 92.865333 3423 4074 3 chr1B.!!$R2 651
7 TraesCS6A01G094000 chrUn 434646638 434647776 1138 True 1932.000000 1932 97.288000 1702 2840 1 chrUn.!!$R1 1138
8 TraesCS6A01G094000 chr4D 467219950 467220922 972 False 1238.000000 1238 89.754000 2115 3081 1 chr4D.!!$F2 966
9 TraesCS6A01G094000 chr6D 364857533 364858303 770 False 1225.000000 1225 95.343000 2459 3229 1 chr6D.!!$F2 770
10 TraesCS6A01G094000 chr6D 226682545 226684356 1811 True 1138.000000 1234 89.883000 319 2159 2 chr6D.!!$R2 1840
11 TraesCS6A01G094000 chr7D 50399470 50400240 770 False 1197.000000 1197 94.696000 2459 3229 1 chr7D.!!$F2 770
12 TraesCS6A01G094000 chr2D 174944602 174945372 770 False 1197.000000 1197 94.696000 2459 3229 1 chr2D.!!$F2 770
13 TraesCS6A01G094000 chr2D 476468198 476468965 767 False 1194.000000 1194 94.696000 2459 3229 1 chr2D.!!$F3 770
14 TraesCS6A01G094000 chr4B 585017989 585018958 969 False 1175.000000 1175 88.450000 2096 3081 1 chr4B.!!$F1 985
15 TraesCS6A01G094000 chr5D 358664529 358665217 688 True 672.000000 1007 92.766500 3244 4074 2 chr5D.!!$R1 830
16 TraesCS6A01G094000 chr2A 207136931 207137467 536 False 536.500000 749 91.413000 3280 4074 2 chr2A.!!$F1 794
17 TraesCS6A01G094000 chr3D 592965798 592966318 520 False 538.000000 538 86.095000 784 1283 1 chr3D.!!$F1 499
18 TraesCS6A01G094000 chr4A 216818742 216819246 504 True 381.000000 381 81.310000 12 500 1 chr4A.!!$R1 488

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
535 676 2.582978 GGGCTTGGGACTACGACC 59.417 66.667 0.0 0.0 0.0 4.79 F
1319 1502 0.617413 CTGGGATGTGCTTGAGTCCT 59.383 55.000 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1524 0.892358 CTGCTCAAGAAGGGCAGCAA 60.892 55.0 3.80 0.00 45.04 3.91 R
3307 3587 0.880278 TCACCAAGAACGCAGACTGC 60.880 55.0 17.84 17.84 40.69 4.40 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
299 323 4.475919 AAGGCCCAAATTAGCTATCCAT 57.524 40.909 0.00 0.00 0.00 3.41
527 556 3.955543 GAATTGGCGGGGCTTGGGA 62.956 63.158 0.00 0.00 0.00 4.37
535 676 2.582978 GGGCTTGGGACTACGACC 59.417 66.667 0.00 0.00 0.00 4.79
571 712 4.498520 CGACGGAGGCAGACGCAT 62.499 66.667 0.00 0.00 41.24 4.73
610 751 4.194720 GCGTGCTCGATCCGGTCT 62.195 66.667 13.13 0.00 39.71 3.85
756 899 4.959210 CCTCTCCTCTTCTTCTTCCACATA 59.041 45.833 0.00 0.00 0.00 2.29
1162 1340 2.838693 TTGGCCTGCTTGCTTGCA 60.839 55.556 3.32 4.34 41.05 4.08
1202 1384 3.194861 GTTGGTTGGTTGCTTTCTTTCC 58.805 45.455 0.00 0.00 0.00 3.13
1319 1502 0.617413 CTGGGATGTGCTTGAGTCCT 59.383 55.000 0.00 0.00 0.00 3.85
1341 1524 2.114616 CATAGCTGTGGAGGAGGAAGT 58.885 52.381 1.86 0.00 0.00 3.01
1381 1564 6.212955 GCAGTTTGCAAAGGTAAATCAGTTA 58.787 36.000 13.26 0.00 44.26 2.24
1592 1776 6.518493 TCCCATAATTGTTGTACGGATACTC 58.482 40.000 0.00 0.00 32.00 2.59
1968 2154 6.687081 TTCGAGAAAGAAAAAGCCTTGTTA 57.313 33.333 0.00 0.00 0.00 2.41
2000 2186 2.974489 GCACTGCAGCACGCTGAAT 61.974 57.895 22.81 3.88 46.30 2.57
2098 2285 6.825284 TGTGTTGCTCAAATAACATGTTTG 57.175 33.333 17.78 9.42 38.84 2.93
2386 2577 8.867097 TGGAAACTTGTTTAGTAGTAGATGACT 58.133 33.333 0.00 0.00 42.69 3.41
2431 2622 2.226437 CACCCAAGCATGTTGAGTGTAC 59.774 50.000 11.69 0.00 0.00 2.90
2441 2632 8.165239 AGCATGTTGAGTGTACTTATGAAAAA 57.835 30.769 0.00 0.00 0.00 1.94
2568 2768 8.947055 AAGTGTTTGCTGTTTTAATCTTGAAT 57.053 26.923 0.00 0.00 0.00 2.57
2790 2990 3.791245 CTTACACAGATCCTGAGAAGCC 58.209 50.000 0.45 0.00 35.18 4.35
3289 3569 2.158900 AGGCATAGACCCACAAAGATCG 60.159 50.000 0.00 0.00 0.00 3.69
3307 3587 9.627657 CAAAGATCGCAAAAATAATTAAGCATG 57.372 29.630 0.00 0.00 0.00 4.06
3352 3632 4.074259 GCCATGCATCTGGACATATTGTA 58.926 43.478 10.63 0.00 38.69 2.41
3354 3634 5.882000 GCCATGCATCTGGACATATTGTATA 59.118 40.000 10.63 0.00 38.69 1.47
3405 3685 1.068588 GTCATCCGAATCCGATCACCA 59.931 52.381 0.00 0.00 38.22 4.17
3406 3686 1.970640 TCATCCGAATCCGATCACCAT 59.029 47.619 0.00 0.00 38.22 3.55
3429 3709 3.869246 CGTTGGACCTCGCAACTAATAAT 59.131 43.478 0.00 0.00 0.00 1.28
3554 3834 1.627297 GGGACCTCCACCCATGAGAC 61.627 65.000 0.00 0.00 46.05 3.36
3626 3906 3.381136 GCTTTGGGGCCGCATCAA 61.381 61.111 24.75 14.79 0.00 2.57
3741 4021 6.971184 ACAAATCCGAGTTTAGATGTAGTACG 59.029 38.462 0.00 0.00 0.00 3.67
3751 4031 9.302345 AGTTTAGATGTAGTACGTGAATGATTG 57.698 33.333 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
196 200 9.862371 TCACAAAAACAATAAAAGTGTGTGTAT 57.138 25.926 0.00 0.00 36.96 2.29
197 201 9.347934 CTCACAAAAACAATAAAAGTGTGTGTA 57.652 29.630 0.00 0.00 36.96 2.90
198 202 7.330700 CCTCACAAAAACAATAAAAGTGTGTGT 59.669 33.333 0.00 0.00 36.96 3.72
199 203 7.330700 ACCTCACAAAAACAATAAAAGTGTGTG 59.669 33.333 0.00 0.00 36.96 3.82
200 204 7.382898 ACCTCACAAAAACAATAAAAGTGTGT 58.617 30.769 0.00 0.00 36.96 3.72
201 205 7.826260 ACCTCACAAAAACAATAAAAGTGTG 57.174 32.000 0.00 0.00 36.96 3.82
299 323 4.947147 GTGCTGGTTGGGCCGTGA 62.947 66.667 0.00 0.00 41.21 4.35
527 556 1.006102 GCACACAGCTGGTCGTAGT 60.006 57.895 19.93 3.62 41.15 2.73
564 705 1.140589 CAGGAAGCTCGATGCGTCT 59.859 57.895 17.06 7.71 46.78 4.18
571 712 3.068691 CCGGGTCAGGAAGCTCGA 61.069 66.667 0.00 0.00 0.00 4.04
718 859 4.133373 AGGGGGCGCATCAAGCAT 62.133 61.111 10.83 0.00 46.13 3.79
756 899 3.564352 GGAAACCACATCAGGGAAGGAAT 60.564 47.826 0.00 0.00 0.00 3.01
1025 1203 2.951458 GTTCCGGTTTCTTGGCCG 59.049 61.111 0.00 0.00 46.80 6.13
1059 1237 1.043116 TCGATGGAGATGCCGAGGTT 61.043 55.000 0.00 0.00 40.66 3.50
1162 1340 3.463048 ACAAATTCAGATGAGGGGCTT 57.537 42.857 0.00 0.00 0.00 4.35
1202 1384 1.268899 CCTGTTTCTTGGCTTGCTGAG 59.731 52.381 0.00 0.00 0.00 3.35
1319 1502 0.325577 TCCTCCTCCACAGCTATGCA 60.326 55.000 0.00 0.00 0.00 3.96
1341 1524 0.892358 CTGCTCAAGAAGGGCAGCAA 60.892 55.000 3.80 0.00 45.04 3.91
1394 1577 4.260170 CAGCAGCTTCCTCAAAGAAGTAT 58.740 43.478 0.00 0.00 44.27 2.12
2000 2186 3.452990 ACATGGGTGGATGTTATACACGA 59.547 43.478 0.00 0.00 45.29 4.35
2098 2285 6.628919 ACACAACATTAGGGTAAGACAAAC 57.371 37.500 0.00 0.00 0.00 2.93
2396 2587 2.187946 GGTGACAGATGCCCTCGG 59.812 66.667 0.00 0.00 0.00 4.63
2441 2632 4.756642 TCAGATGCAAACACTCGAGAAATT 59.243 37.500 21.68 7.09 0.00 1.82
2442 2633 4.318332 TCAGATGCAAACACTCGAGAAAT 58.682 39.130 21.68 0.11 0.00 2.17
2444 2635 3.385193 TCAGATGCAAACACTCGAGAA 57.615 42.857 21.68 0.00 0.00 2.87
2790 2990 7.477144 TCAACTTACACATTTATAGCATCCG 57.523 36.000 0.00 0.00 0.00 4.18
3289 3569 7.396419 CAGACTGCATGCTTAATTATTTTTGC 58.604 34.615 20.33 0.00 0.00 3.68
3307 3587 0.880278 TCACCAAGAACGCAGACTGC 60.880 55.000 17.84 17.84 40.69 4.40
3352 3632 7.928307 AGCTGTGAAAATTCATGTGTACTAT 57.072 32.000 0.00 0.00 39.73 2.12
3354 3634 6.639632 AAGCTGTGAAAATTCATGTGTACT 57.360 33.333 0.00 0.00 39.73 2.73
3405 3685 0.892755 TAGTTGCGAGGTCCAACGAT 59.107 50.000 11.68 0.00 45.38 3.73
3406 3686 0.675083 TTAGTTGCGAGGTCCAACGA 59.325 50.000 11.68 0.00 45.38 3.85
3573 3853 4.321675 GGACCACCACACAATATGAAAACC 60.322 45.833 0.00 0.00 35.97 3.27
3741 4021 7.462731 TCTTTTGTTGTTTTGCAATCATTCAC 58.537 30.769 0.00 0.00 39.55 3.18
3837 4117 6.434965 GGAGGTCCCTGTATAGTCTCTTATTC 59.565 46.154 0.00 0.00 0.00 1.75
4027 4307 7.227910 ACATCTAAACTCGGCTTTGTTTTTCTA 59.772 33.333 6.76 0.00 37.53 2.10


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

AutoCloner maintained by Alex Coulton.