Multiple sequence alignment - TraesCS6D01G238000

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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 TraesCS6D01G238000 chr6D 100.000 3647 0 0 1 3647 338138551 338134905 0.000000e+00 6735.0
1 TraesCS6D01G238000 chr6D 94.998 3159 87 29 3 3125 197263403 197266526 0.000000e+00 4892.0
2 TraesCS6D01G238000 chr6D 95.810 525 17 3 3121 3645 189258306 189258825 0.000000e+00 843.0
3 TraesCS6D01G238000 chr6D 95.619 525 19 2 3120 3644 331068964 331069484 0.000000e+00 839.0
4 TraesCS6D01G238000 chr2D 95.769 2671 70 9 461 3125 161651320 161648687 0.000000e+00 4266.0
5 TraesCS6D01G238000 chr2D 96.320 462 10 1 1 462 161651804 161651350 0.000000e+00 752.0
6 TraesCS6D01G238000 chr2D 88.312 77 9 0 5 81 298539152 298539228 3.880000e-15 93.5
7 TraesCS6D01G238000 chr2B 94.347 2671 117 15 461 3125 430822376 430819734 0.000000e+00 4065.0
8 TraesCS6D01G238000 chr2B 93.506 462 25 4 1 462 430822862 430822406 0.000000e+00 682.0
9 TraesCS6D01G238000 chr2B 89.713 418 17 2 2710 3126 602888718 602888326 9.030000e-141 510.0
10 TraesCS6D01G238000 chr2B 89.021 419 17 10 2710 3125 669355657 669356049 3.270000e-135 492.0
11 TraesCS6D01G238000 chr4A 93.968 2669 125 13 461 3125 418290634 418287998 0.000000e+00 4004.0
12 TraesCS6D01G238000 chr4A 93.506 462 23 1 1 462 418291118 418290664 0.000000e+00 680.0
13 TraesCS6D01G238000 chr3A 95.728 2458 88 6 461 2916 217012440 217014882 0.000000e+00 3941.0
14 TraesCS6D01G238000 chr3A 93.400 2682 124 18 461 3119 216936972 216939623 0.000000e+00 3923.0
15 TraesCS6D01G238000 chr3A 95.238 462 15 1 1 462 217011956 217012410 0.000000e+00 725.0
16 TraesCS6D01G238000 chr3A 93.939 462 20 2 1 462 216936489 216936942 0.000000e+00 691.0
17 TraesCS6D01G238000 chr3A 93.491 169 9 2 2960 3126 217015126 217015294 2.170000e-62 250.0
18 TraesCS6D01G238000 chr3B 96.240 1436 50 3 1365 2800 241261628 241260197 0.000000e+00 2350.0
19 TraesCS6D01G238000 chr6A 91.237 1746 108 16 469 2200 568172634 568174348 0.000000e+00 2335.0
20 TraesCS6D01G238000 chr4B 96.017 1431 54 3 1365 2794 199721268 199722696 0.000000e+00 2324.0
21 TraesCS6D01G238000 chr4B 93.558 1335 66 12 507 1829 527931247 527929921 0.000000e+00 1971.0
22 TraesCS6D01G238000 chr4B 89.516 372 11 3 2757 3125 199722697 199723043 2.580000e-121 446.0
23 TraesCS6D01G238000 chr4B 85.388 438 48 13 11 442 115709328 115708901 1.200000e-119 440.0
24 TraesCS6D01G238000 chr6B 92.759 1381 75 12 461 1822 129871403 129870029 0.000000e+00 1973.0
25 TraesCS6D01G238000 chr6B 89.286 84 7 2 11 92 353096126 353096043 1.790000e-18 104.0
26 TraesCS6D01G238000 chr7A 93.082 1301 61 11 1827 3125 276742033 276743306 0.000000e+00 1877.0
27 TraesCS6D01G238000 chr5B 91.996 912 31 5 1 879 357076115 357075213 0.000000e+00 1242.0
28 TraesCS6D01G238000 chr1D 96.205 527 16 2 3121 3647 143258445 143258967 0.000000e+00 859.0
29 TraesCS6D01G238000 chr5D 96.198 526 16 2 3122 3647 377379579 377380100 0.000000e+00 857.0
30 TraesCS6D01G238000 chr7D 95.833 528 18 2 3121 3647 334683605 334684129 0.000000e+00 850.0
31 TraesCS6D01G238000 chr7D 95.644 528 20 1 3120 3647 355379887 355379363 0.000000e+00 845.0
32 TraesCS6D01G238000 chr7D 95.627 526 20 1 3122 3647 245341410 245340888 0.000000e+00 841.0
33 TraesCS6D01G238000 chr4D 95.636 527 20 1 3121 3647 370833648 370833125 0.000000e+00 843.0
34 TraesCS6D01G238000 chr3D 95.636 527 19 2 3122 3647 123597814 123598337 0.000000e+00 843.0
35 TraesCS6D01G238000 chr1A 86.143 433 47 11 11 439 371317266 371317689 4.290000e-124 455.0


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 TraesCS6D01G238000 chr6D 338134905 338138551 3646 True 6735.000000 6735 100.0000 1 3647 1 chr6D.!!$R1 3646
1 TraesCS6D01G238000 chr6D 197263403 197266526 3123 False 4892.000000 4892 94.9980 3 3125 1 chr6D.!!$F2 3122
2 TraesCS6D01G238000 chr6D 189258306 189258825 519 False 843.000000 843 95.8100 3121 3645 1 chr6D.!!$F1 524
3 TraesCS6D01G238000 chr6D 331068964 331069484 520 False 839.000000 839 95.6190 3120 3644 1 chr6D.!!$F3 524
4 TraesCS6D01G238000 chr2D 161648687 161651804 3117 True 2509.000000 4266 96.0445 1 3125 2 chr2D.!!$R1 3124
5 TraesCS6D01G238000 chr2B 430819734 430822862 3128 True 2373.500000 4065 93.9265 1 3125 2 chr2B.!!$R2 3124
6 TraesCS6D01G238000 chr4A 418287998 418291118 3120 True 2342.000000 4004 93.7370 1 3125 2 chr4A.!!$R1 3124
7 TraesCS6D01G238000 chr3A 216936489 216939623 3134 False 2307.000000 3923 93.6695 1 3119 2 chr3A.!!$F1 3118
8 TraesCS6D01G238000 chr3A 217011956 217015294 3338 False 1638.666667 3941 94.8190 1 3126 3 chr3A.!!$F2 3125
9 TraesCS6D01G238000 chr3B 241260197 241261628 1431 True 2350.000000 2350 96.2400 1365 2800 1 chr3B.!!$R1 1435
10 TraesCS6D01G238000 chr6A 568172634 568174348 1714 False 2335.000000 2335 91.2370 469 2200 1 chr6A.!!$F1 1731
11 TraesCS6D01G238000 chr4B 527929921 527931247 1326 True 1971.000000 1971 93.5580 507 1829 1 chr4B.!!$R2 1322
12 TraesCS6D01G238000 chr4B 199721268 199723043 1775 False 1385.000000 2324 92.7665 1365 3125 2 chr4B.!!$F1 1760
13 TraesCS6D01G238000 chr6B 129870029 129871403 1374 True 1973.000000 1973 92.7590 461 1822 1 chr6B.!!$R1 1361
14 TraesCS6D01G238000 chr7A 276742033 276743306 1273 False 1877.000000 1877 93.0820 1827 3125 1 chr7A.!!$F1 1298
15 TraesCS6D01G238000 chr5B 357075213 357076115 902 True 1242.000000 1242 91.9960 1 879 1 chr5B.!!$R1 878
16 TraesCS6D01G238000 chr1D 143258445 143258967 522 False 859.000000 859 96.2050 3121 3647 1 chr1D.!!$F1 526
17 TraesCS6D01G238000 chr5D 377379579 377380100 521 False 857.000000 857 96.1980 3122 3647 1 chr5D.!!$F1 525
18 TraesCS6D01G238000 chr7D 334683605 334684129 524 False 850.000000 850 95.8330 3121 3647 1 chr7D.!!$F1 526
19 TraesCS6D01G238000 chr7D 355379363 355379887 524 True 845.000000 845 95.6440 3120 3647 1 chr7D.!!$R2 527
20 TraesCS6D01G238000 chr7D 245340888 245341410 522 True 841.000000 841 95.6270 3122 3647 1 chr7D.!!$R1 525
21 TraesCS6D01G238000 chr4D 370833125 370833648 523 True 843.000000 843 95.6360 3121 3647 1 chr4D.!!$R1 526
22 TraesCS6D01G238000 chr3D 123597814 123598337 523 False 843.000000 843 95.6360 3122 3647 1 chr3D.!!$F1 525


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
24 25 1.000607 TCGAGTAGCAAAGTTGTCGCT 60.001 47.619 0.0 0.00 39.8 4.93 F
1092 1176 0.393077 GTCACCTAGGTATGCGCCAT 59.607 55.000 15.8 0.63 0.0 4.40 F
1830 1922 1.001974 TCTCCATGACAACAAGGACGG 59.998 52.381 0.0 0.00 38.7 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1264 1.203287 GTTTCTAGGTACGGCGGACTT 59.797 52.381 23.25 18.13 0.0 3.01 R
1985 2078 2.363925 GGTCGAGGGCAGTAGGGT 60.364 66.667 0.00 0.00 0.0 4.34 R
3109 3491 2.550606 GGGCGTGACATGAACTTTTACA 59.449 45.455 0.00 0.00 0.0 2.41 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
24 25 1.000607 TCGAGTAGCAAAGTTGTCGCT 60.001 47.619 0.00 0.00 39.80 4.93
202 203 6.166279 TGAGAGACACATTTGTTCTGTATCC 58.834 40.000 2.69 0.00 35.47 2.59
247 248 3.321039 TCCCATCCATGCTTAGATGAGT 58.679 45.455 9.16 0.00 42.04 3.41
251 252 5.009410 CCCATCCATGCTTAGATGAGTTTTC 59.991 44.000 9.16 0.00 42.04 2.29
255 256 7.423844 TCCATGCTTAGATGAGTTTTCTCTA 57.576 36.000 0.00 0.00 46.30 2.43
381 382 2.876368 ATAAGGGAGCCGCTGTGCAC 62.876 60.000 10.75 10.75 0.00 4.57
413 414 4.470334 ACACAAGGTTGTTGCATTTCTT 57.530 36.364 0.00 0.00 39.91 2.52
453 456 2.360852 CCAAGGGAGCTGCTGTGG 60.361 66.667 7.01 9.20 0.00 4.17
835 875 4.558538 AATGTGAACTGAAGCTGTTGTC 57.441 40.909 0.00 0.00 0.00 3.18
864 904 7.041712 GCAAATTAGGAATAGTTGCCTACTCTC 60.042 40.741 0.00 0.00 38.88 3.20
947 1019 2.357637 CGTGTTCTGGACAATTTGTGGT 59.642 45.455 6.80 0.00 40.65 4.16
1092 1176 0.393077 GTCACCTAGGTATGCGCCAT 59.607 55.000 15.80 0.63 0.00 4.40
1099 1183 2.203015 GTATGCGCCATCACCCGT 60.203 61.111 4.18 0.00 0.00 5.28
1106 1190 4.201679 CCATCACCCGTCGCGCTA 62.202 66.667 5.56 0.00 0.00 4.26
1178 1263 4.692129 CGAGTTAGTCGCGAGCAT 57.308 55.556 10.24 0.37 43.03 3.79
1179 1264 3.819919 CGAGTTAGTCGCGAGCATA 57.180 52.632 10.24 0.00 43.03 3.14
1490 1576 8.031277 GGCAACAAAGAGAAAAATGAGTATGAT 58.969 33.333 0.00 0.00 0.00 2.45
1668 1760 6.506147 TCAGTTCAATGACAGAAAAACATGG 58.494 36.000 0.00 0.00 0.00 3.66
1724 1816 8.392372 AGCTGAAAGATACGATATGTGTACTA 57.608 34.615 0.00 0.00 34.07 1.82
1758 1850 8.609176 TCTCAAACATGTGTTACTCAACTTTAC 58.391 33.333 0.00 0.00 37.25 2.01
1807 1899 1.735386 CAATGTCTCCAGCAGTCCTG 58.265 55.000 0.00 0.00 41.41 3.86
1830 1922 1.001974 TCTCCATGACAACAAGGACGG 59.998 52.381 0.00 0.00 38.70 4.79
1985 2078 3.555324 TCCTTCGCCCACTGTGCA 61.555 61.111 1.29 0.00 0.00 4.57
2014 2107 1.658686 CCTCGACCTCCTTCCTCACG 61.659 65.000 0.00 0.00 0.00 4.35
2136 2230 2.880963 TTTTAGTTTGCTTTGCCGCT 57.119 40.000 0.00 0.00 0.00 5.52
2454 2551 7.931046 AGAGGTACTAGTAGAAGAGGAAGAAA 58.069 38.462 1.87 0.00 41.55 2.52
2573 2671 3.181479 GGTCTGTAGATGCACCGTAATGA 60.181 47.826 0.00 0.00 0.00 2.57
2595 2694 9.566432 AATGAATCTAGGAAGTATGAATGGTTC 57.434 33.333 0.00 0.00 0.00 3.62
2672 2771 4.244862 GTTGTGGAGCAATTTAATGGTGG 58.755 43.478 0.00 0.00 39.55 4.61
2760 2859 0.392193 AAATCTGGAGCAGTCTGGCG 60.392 55.000 1.14 0.00 39.27 5.69
2944 3326 9.535878 AAGTTCACAGAAAACAAAAGTTGTAAA 57.464 25.926 0.00 0.00 44.59 2.01
3415 3799 4.388469 CGAAGAAGAAGCAGAAGAAGAAGG 59.612 45.833 0.00 0.00 0.00 3.46
3416 3800 5.546526 GAAGAAGAAGCAGAAGAAGAAGGA 58.453 41.667 0.00 0.00 0.00 3.36
3418 3802 4.592778 AGAAGAAGCAGAAGAAGAAGGACT 59.407 41.667 0.00 0.00 0.00 3.85
3419 3803 4.972751 AGAAGCAGAAGAAGAAGGACTT 57.027 40.909 0.00 0.00 42.03 3.01
3420 3804 4.640364 AGAAGCAGAAGAAGAAGGACTTG 58.360 43.478 0.00 0.00 39.13 3.16
3421 3805 4.346418 AGAAGCAGAAGAAGAAGGACTTGA 59.654 41.667 0.00 0.00 39.13 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.248280 TTGGAGCGACAACTTTGCTA 57.752 45.000 0.00 0.00 46.01 3.49
24 25 1.536766 CAGCAGCAAGTTCGATTTGGA 59.463 47.619 10.91 0.00 0.00 3.53
247 248 5.649395 CCCAAGTCTGATTGCATAGAGAAAA 59.351 40.000 0.00 0.00 0.00 2.29
251 252 2.877168 GCCCAAGTCTGATTGCATAGAG 59.123 50.000 0.00 0.00 0.00 2.43
255 256 2.422519 CCTAGCCCAAGTCTGATTGCAT 60.423 50.000 0.00 0.00 0.00 3.96
381 382 6.636850 GCAACAACCTTGTGTTTCAATAGTAG 59.363 38.462 0.00 0.00 41.31 2.57
421 422 8.429641 CAGCTCCCTTGGTTTAGACTATTATTA 58.570 37.037 0.00 0.00 0.00 0.98
422 423 7.283329 CAGCTCCCTTGGTTTAGACTATTATT 58.717 38.462 0.00 0.00 0.00 1.40
423 424 6.689177 GCAGCTCCCTTGGTTTAGACTATTAT 60.689 42.308 0.00 0.00 0.00 1.28
424 425 5.396436 GCAGCTCCCTTGGTTTAGACTATTA 60.396 44.000 0.00 0.00 0.00 0.98
425 426 4.626529 GCAGCTCCCTTGGTTTAGACTATT 60.627 45.833 0.00 0.00 0.00 1.73
426 427 3.118223 GCAGCTCCCTTGGTTTAGACTAT 60.118 47.826 0.00 0.00 0.00 2.12
427 428 2.236395 GCAGCTCCCTTGGTTTAGACTA 59.764 50.000 0.00 0.00 0.00 2.59
453 456 1.223763 GGGAACTCGGGGATTGGTC 59.776 63.158 0.00 0.00 0.00 4.02
642 676 7.444792 ACACCGTACTGTTTTATATGTTTTCCA 59.555 33.333 0.00 0.00 0.00 3.53
835 875 4.848757 GGCAACTATTCCTAATTTGCTCG 58.151 43.478 4.75 0.00 41.84 5.03
864 904 3.044059 GCAAGGTAGCAGCGGCAAG 62.044 63.158 12.44 0.00 44.61 4.01
947 1019 0.107831 AACTTGCGCCTCCACACTTA 59.892 50.000 4.18 0.00 0.00 2.24
1092 1176 2.827190 ATCTAGCGCGACGGGTGA 60.827 61.111 12.10 9.74 0.00 4.02
1106 1190 2.903135 GCTATGGGAGTAGGAAGCATCT 59.097 50.000 0.00 0.00 0.00 2.90
1178 1263 2.418368 TTCTAGGTACGGCGGACTTA 57.582 50.000 23.25 18.31 0.00 2.24
1179 1264 1.203287 GTTTCTAGGTACGGCGGACTT 59.797 52.381 23.25 18.13 0.00 3.01
1429 1515 4.142403 GCTTACAGCCACATGAGCAAAATA 60.142 41.667 13.56 0.20 34.48 1.40
1496 1582 8.161699 ACTGAACTTAACAATACGGAAACAAT 57.838 30.769 0.00 0.00 0.00 2.71
1668 1760 6.319399 TCAAGAGTCAAAAACTTTTCGAACC 58.681 36.000 0.00 0.00 38.74 3.62
1758 1850 6.411492 GCAGCACAACAATTTTACATGTTTTG 59.589 34.615 2.30 6.34 39.20 2.44
1807 1899 2.485814 GTCCTTGTTGTCATGGAGAAGC 59.514 50.000 0.00 0.00 44.73 3.86
1985 2078 2.363925 GGTCGAGGGCAGTAGGGT 60.364 66.667 0.00 0.00 0.00 4.34
2136 2230 2.819608 GTGAAGTTTCAGCAATGCCCTA 59.180 45.455 0.00 0.00 37.98 3.53
2380 2476 4.446745 CCCTGATGATGATTGGGCTTCTTA 60.447 45.833 0.00 0.00 0.00 2.10
2672 2771 8.888579 AACAATGTATACTTCAGTACATAGCC 57.111 34.615 4.17 0.00 39.83 3.93
2700 2799 3.261580 TGAGCCGATGTACAAGAACATG 58.738 45.455 0.00 0.00 40.17 3.21
2760 2859 9.326339 GAGTTTGAACGGATGTAAATACTTTTC 57.674 33.333 0.00 0.00 0.00 2.29
2979 3361 8.733458 ACTCCGAACTTTACTTTACTTTTTGTT 58.267 29.630 0.00 0.00 0.00 2.83
2980 3362 8.179615 CACTCCGAACTTTACTTTACTTTTTGT 58.820 33.333 0.00 0.00 0.00 2.83
2981 3363 8.179615 ACACTCCGAACTTTACTTTACTTTTTG 58.820 33.333 0.00 0.00 0.00 2.44
2982 3364 8.179615 CACACTCCGAACTTTACTTTACTTTTT 58.820 33.333 0.00 0.00 0.00 1.94
2983 3365 7.550196 TCACACTCCGAACTTTACTTTACTTTT 59.450 33.333 0.00 0.00 0.00 2.27
2984 3366 7.043565 TCACACTCCGAACTTTACTTTACTTT 58.956 34.615 0.00 0.00 0.00 2.66
2985 3367 6.576185 TCACACTCCGAACTTTACTTTACTT 58.424 36.000 0.00 0.00 0.00 2.24
2986 3368 6.152932 TCACACTCCGAACTTTACTTTACT 57.847 37.500 0.00 0.00 0.00 2.24
2987 3369 6.833342 TTCACACTCCGAACTTTACTTTAC 57.167 37.500 0.00 0.00 0.00 2.01
2988 3370 7.846644 TTTTCACACTCCGAACTTTACTTTA 57.153 32.000 0.00 0.00 0.00 1.85
2989 3371 6.746745 TTTTCACACTCCGAACTTTACTTT 57.253 33.333 0.00 0.00 0.00 2.66
2990 3372 6.937436 ATTTTCACACTCCGAACTTTACTT 57.063 33.333 0.00 0.00 0.00 2.24
2991 3373 6.987992 TGTATTTTCACACTCCGAACTTTACT 59.012 34.615 0.00 0.00 0.00 2.24
3109 3491 2.550606 GGGCGTGACATGAACTTTTACA 59.449 45.455 0.00 0.00 0.00 2.41
3318 3701 4.349663 TTGAGTTTCTGTTGGTGTTTCG 57.650 40.909 0.00 0.00 0.00 3.46
3418 3802 5.333035 CGAGAGCGATGTTACTTGTTTTCAA 60.333 40.000 0.00 0.00 40.82 2.69
3419 3803 4.149922 CGAGAGCGATGTTACTTGTTTTCA 59.850 41.667 0.00 0.00 40.82 2.69
3420 3804 4.629065 CGAGAGCGATGTTACTTGTTTTC 58.371 43.478 0.00 0.00 40.82 2.29
3421 3805 4.647291 CGAGAGCGATGTTACTTGTTTT 57.353 40.909 0.00 0.00 40.82 2.43



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

AutoCloner maintained by Alex Coulton.