Multiple sequence alignment - TraesCS2A01G183300

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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 TraesCS2A01G183300 chr2A 100.000 2996 0 0 1 2996 143218373 143215378 0.000000e+00 5533
1 TraesCS2A01G183300 chr2D 95.346 2170 73 13 842 2996 135309945 135307789 0.000000e+00 3422
2 TraesCS2A01G183300 chr2D 92.500 320 18 4 491 809 135310675 135310361 1.270000e-123 453
3 TraesCS2A01G183300 chr2D 88.722 266 12 3 207 456 135316968 135316705 2.900000e-80 309
4 TraesCS2A01G183300 chr2D 85.930 199 22 5 1 198 135317307 135317114 1.090000e-49 207
5 TraesCS2A01G183300 chr2D 81.988 161 18 8 88 247 249890193 249890043 3.140000e-25 126
6 TraesCS2A01G183300 chr2B 95.289 2059 80 7 953 2996 192368143 192366087 0.000000e+00 3249
7 TraesCS2A01G183300 chr2B 87.421 946 57 21 1 906 192369556 192368633 0.000000e+00 1031
8 TraesCS2A01G183300 chr2B 80.982 163 19 10 89 247 152501392 152501238 5.250000e-23 119
9 TraesCS2A01G183300 chr3D 83.125 160 21 4 88 247 431236074 431235921 1.120000e-29 141
10 TraesCS2A01G183300 chr1D 83.117 154 17 6 88 241 137418299 137418443 6.740000e-27 132
11 TraesCS2A01G183300 chr1D 86.441 118 15 1 88 205 468265263 468265379 8.720000e-26 128
12 TraesCS2A01G183300 chr1B 83.221 149 19 5 88 236 646931105 646931247 6.740000e-27 132
13 TraesCS2A01G183300 chr6D 81.875 160 24 4 88 247 386179446 386179292 2.420000e-26 130


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 TraesCS2A01G183300 chr2A 143215378 143218373 2995 True 5533.0 5533 100.000 1 2996 1 chr2A.!!$R1 2995
1 TraesCS2A01G183300 chr2D 135307789 135310675 2886 True 1937.5 3422 93.923 491 2996 2 chr2D.!!$R2 2505
2 TraesCS2A01G183300 chr2D 135316705 135317307 602 True 258.0 309 87.326 1 456 2 chr2D.!!$R3 455
3 TraesCS2A01G183300 chr2B 192366087 192369556 3469 True 2140.0 3249 91.355 1 2996 2 chr2B.!!$R2 2995

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
456 621 0.104671 AGCGGCATTTGCAAGTGTTT 59.895 45.0 21.29 4.28 44.36 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 3395 1.208052 TCAGAGCCATCAGTACCTTGC 59.792 52.381 0.0 0.0 0.0 4.01 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
63 65 5.938125 TGGTTCTTTTTACTATCACAGCTCC 59.062 40.000 0.00 0.00 0.00 4.70
65 67 6.599638 GGTTCTTTTTACTATCACAGCTCCAT 59.400 38.462 0.00 0.00 0.00 3.41
68 70 5.339008 TTTTACTATCACAGCTCCATCGT 57.661 39.130 0.00 0.00 0.00 3.73
69 71 4.569761 TTACTATCACAGCTCCATCGTC 57.430 45.455 0.00 0.00 0.00 4.20
70 72 2.379005 ACTATCACAGCTCCATCGTCA 58.621 47.619 0.00 0.00 0.00 4.35
74 76 1.409064 TCACAGCTCCATCGTCATACC 59.591 52.381 0.00 0.00 0.00 2.73
78 80 3.062763 CAGCTCCATCGTCATACCATTC 58.937 50.000 0.00 0.00 0.00 2.67
84 86 5.436175 TCCATCGTCATACCATTCACATTT 58.564 37.500 0.00 0.00 0.00 2.32
85 87 6.587273 TCCATCGTCATACCATTCACATTTA 58.413 36.000 0.00 0.00 0.00 1.40
86 88 7.223584 TCCATCGTCATACCATTCACATTTAT 58.776 34.615 0.00 0.00 0.00 1.40
102 104 5.049405 CACATTTATTACTCCCTCCATTCGC 60.049 44.000 0.00 0.00 0.00 4.70
111 113 5.690865 ACTCCCTCCATTCGCAAATATAAA 58.309 37.500 0.00 0.00 0.00 1.40
112 114 5.765182 ACTCCCTCCATTCGCAAATATAAAG 59.235 40.000 0.00 0.00 0.00 1.85
113 115 5.935945 TCCCTCCATTCGCAAATATAAAGA 58.064 37.500 0.00 0.00 0.00 2.52
114 116 6.542821 TCCCTCCATTCGCAAATATAAAGAT 58.457 36.000 0.00 0.00 0.00 2.40
115 117 6.430925 TCCCTCCATTCGCAAATATAAAGATG 59.569 38.462 0.00 0.00 0.00 2.90
170 172 7.970061 CGGATTGAAATGAGTGAATAAACACAT 59.030 33.333 0.00 0.00 42.45 3.21
264 403 9.343103 GAGAGAATAAAAGTTATATCGATCGCA 57.657 33.333 11.09 0.27 0.00 5.10
456 621 0.104671 AGCGGCATTTGCAAGTGTTT 59.895 45.000 21.29 4.28 44.36 2.83
458 623 1.070643 GCGGCATTTGCAAGTGTTTTC 60.071 47.619 21.29 6.32 44.36 2.29
470 635 3.127425 AGTGTTTTCTAGACCAGTGGC 57.873 47.619 9.78 1.85 0.00 5.01
476 641 1.227380 CTAGACCAGTGGCCATCGC 60.227 63.158 9.72 0.00 0.00 4.58
495 665 3.248363 TCGCTGTTCATGAGTGTCAAAAG 59.752 43.478 0.00 0.00 0.00 2.27
501 671 1.815003 CATGAGTGTCAAAAGGGAGGC 59.185 52.381 0.00 0.00 0.00 4.70
513 683 3.905249 GGAGGCGACCCAAATGAC 58.095 61.111 0.00 0.00 0.00 3.06
528 698 0.842635 ATGACTTCTCCATGGCCTCC 59.157 55.000 6.96 0.00 0.00 4.30
568 738 2.904866 TGCACAGCACGGAAACCC 60.905 61.111 0.00 0.00 31.71 4.11
577 747 2.264794 CGGAAACCCAGGGACGAG 59.735 66.667 14.54 0.00 0.00 4.18
587 757 4.716977 GGGACGAGACCCCACCCT 62.717 72.222 0.00 0.00 43.81 4.34
588 758 3.075641 GGACGAGACCCCACCCTC 61.076 72.222 0.00 0.00 0.00 4.30
975 1972 4.554036 GATCTGACCCGGCCAGGC 62.554 72.222 18.22 1.26 39.21 4.85
1647 2644 2.373938 CGGAGTCATTGCCGTTCTC 58.626 57.895 0.00 0.00 42.49 2.87
1656 2653 1.236616 TTGCCGTTCTCGAGGACGTA 61.237 55.000 36.89 25.69 40.69 3.57
1716 2713 2.282887 GGCCAAACCCATGTCGGT 60.283 61.111 0.00 0.00 37.93 4.69
1734 2731 2.414481 CGGTCTGCTCATCTTTCTTGTG 59.586 50.000 0.00 0.00 0.00 3.33
2157 3154 4.450080 CGATCGATTCATGTTCATGGTGAT 59.550 41.667 10.26 9.93 0.00 3.06
2227 3224 1.394917 CGGATGCAAAAGAGAAGACCG 59.605 52.381 0.00 0.00 0.00 4.79
2268 3265 4.502282 GTGTATTCTTGATCTGTCTCAGCG 59.498 45.833 0.00 0.00 0.00 5.18
2274 3271 1.827344 TGATCTGTCTCAGCGGTGATT 59.173 47.619 18.98 0.00 30.18 2.57
2316 3313 6.086765 GTGTAGCATTCTTTTGAAACGATGTG 59.913 38.462 0.00 0.00 42.31 3.21
2354 3351 6.900568 TCAATTGTTGTGGATTTTTGTCAC 57.099 33.333 5.13 0.00 0.00 3.67
2371 3368 3.123050 GTCACCTCAACACATTTTTGGC 58.877 45.455 0.00 0.00 0.00 4.52
2381 3378 5.560966 ACACATTTTTGGCTATACGGAAG 57.439 39.130 0.00 0.00 0.00 3.46
2399 3396 5.995897 ACGGAAGGGAACATATTGTAATAGC 59.004 40.000 0.00 0.00 0.00 2.97
2412 3409 8.939929 CATATTGTAATAGCAAGGTACTGATGG 58.060 37.037 0.00 0.00 40.86 3.51
2422 3419 2.237392 AGGTACTGATGGCTCTGAAACC 59.763 50.000 0.00 0.00 37.18 3.27
2435 3432 5.126707 GGCTCTGAAACCTGATTCATGAATT 59.873 40.000 21.57 5.92 38.55 2.17
2443 3440 5.014858 ACCTGATTCATGAATTTGCACTCT 58.985 37.500 21.57 0.00 0.00 3.24
2448 3445 6.829811 TGATTCATGAATTTGCACTCTATCCA 59.170 34.615 21.57 7.78 0.00 3.41
2487 3484 7.492994 AGTGAACTTCAAGTCTGTCTTCTAAAC 59.507 37.037 0.00 0.00 33.63 2.01
2495 3492 4.926238 AGTCTGTCTTCTAAACGATGCTTG 59.074 41.667 0.00 0.00 0.00 4.01
2499 3511 4.814234 TGTCTTCTAAACGATGCTTGTTGT 59.186 37.500 0.00 0.00 0.00 3.32
2513 3525 6.892658 TGCTTGTTGTTAACCACATAAGAT 57.107 33.333 12.80 0.00 34.27 2.40
2517 3529 7.915397 GCTTGTTGTTAACCACATAAGATATGG 59.085 37.037 12.80 0.00 39.57 2.74
2549 3561 8.415950 TTCTTATTTTGTTGGCCTATTCTTCA 57.584 30.769 3.32 0.00 0.00 3.02
2826 3838 0.179108 ATGCTTTCTCGAGGCGGTAC 60.179 55.000 13.56 0.00 0.00 3.34
2886 3898 6.394345 ACTCCTTTTCCAACCTTAGATCAT 57.606 37.500 0.00 0.00 0.00 2.45
2918 3930 9.193133 CGGTATATTGACTTCCATTTAGTACTG 57.807 37.037 5.39 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.133221 AGAACCAAGTCTAGCAACACAAAT 58.867 37.500 0.00 0.00 0.00 2.32
63 65 9.811655 GTAATAAATGTGAATGGTATGACGATG 57.188 33.333 0.00 0.00 0.00 3.84
65 67 9.256477 GAGTAATAAATGTGAATGGTATGACGA 57.744 33.333 0.00 0.00 0.00 4.20
68 70 8.723365 AGGGAGTAATAAATGTGAATGGTATGA 58.277 33.333 0.00 0.00 0.00 2.15
69 71 8.924511 AGGGAGTAATAAATGTGAATGGTATG 57.075 34.615 0.00 0.00 0.00 2.39
70 72 8.164070 GGAGGGAGTAATAAATGTGAATGGTAT 58.836 37.037 0.00 0.00 0.00 2.73
74 76 8.469309 AATGGAGGGAGTAATAAATGTGAATG 57.531 34.615 0.00 0.00 0.00 2.67
78 80 5.049405 GCGAATGGAGGGAGTAATAAATGTG 60.049 44.000 0.00 0.00 0.00 3.21
84 86 4.764050 TTTGCGAATGGAGGGAGTAATA 57.236 40.909 0.00 0.00 0.00 0.98
85 87 3.644966 TTTGCGAATGGAGGGAGTAAT 57.355 42.857 0.00 0.00 0.00 1.89
86 88 3.644966 ATTTGCGAATGGAGGGAGTAA 57.355 42.857 0.00 0.00 0.00 2.24
128 130 6.822073 TCAATCCGTATTTCGTTCATACTG 57.178 37.500 0.00 0.00 37.94 2.74
130 132 8.332464 TCATTTCAATCCGTATTTCGTTCATAC 58.668 33.333 0.00 0.00 37.94 2.39
144 146 7.304735 TGTGTTTATTCACTCATTTCAATCCG 58.695 34.615 0.00 0.00 38.90 4.18
236 375 9.841880 CGATCGATATAACTTTTATTCTCTCCA 57.158 33.333 10.26 0.00 0.00 3.86
273 414 9.764363 AATAGTTTCTTGCGTGATCAATATCTA 57.236 29.630 0.00 0.00 32.93 1.98
307 448 8.335532 TGCAATTTTAATAGCTACTCAAGTGT 57.664 30.769 0.00 0.00 0.00 3.55
456 621 0.824109 CGATGGCCACTGGTCTAGAA 59.176 55.000 8.16 0.00 0.00 2.10
458 623 1.227380 GCGATGGCCACTGGTCTAG 60.227 63.158 8.16 0.00 0.00 2.43
470 635 1.662629 GACACTCATGAACAGCGATGG 59.337 52.381 5.32 0.00 0.00 3.51
476 641 4.136796 TCCCTTTTGACACTCATGAACAG 58.863 43.478 0.00 0.00 0.00 3.16
501 671 2.472695 TGGAGAAGTCATTTGGGTCG 57.527 50.000 0.00 0.00 0.00 4.79
508 678 1.213926 GGAGGCCATGGAGAAGTCATT 59.786 52.381 18.40 0.00 0.00 2.57
513 683 2.002977 TGGGGAGGCCATGGAGAAG 61.003 63.158 18.40 0.00 0.00 2.85
528 698 1.754380 TTCTCGTGTGGGTCAGTGGG 61.754 60.000 0.00 0.00 0.00 4.61
539 709 0.657840 GCTGTGCAGTTTTCTCGTGT 59.342 50.000 0.00 0.00 0.00 4.49
568 738 3.391382 GGTGGGGTCTCGTCCCTG 61.391 72.222 11.40 0.00 46.27 4.45
577 747 3.391382 CTCGTGGAGGGTGGGGTC 61.391 72.222 0.00 0.00 0.00 4.46
643 813 2.027625 GCCTGCGGTATCGGTATGC 61.028 63.158 0.00 0.00 36.79 3.14
942 1496 2.485188 GATCCGAGGCGAGATCAGGC 62.485 65.000 6.65 6.65 39.00 4.85
1293 2290 4.144703 GGGAAGGAGACGACGGCC 62.145 72.222 0.00 0.00 0.00 6.13
1398 2395 2.835895 GCGAGGAGGGAGAGGTCC 60.836 72.222 0.00 0.00 43.05 4.46
1486 2483 3.855853 GAGGAGGGCGAGGAAGGC 61.856 72.222 0.00 0.00 0.00 4.35
1716 2713 3.071457 TGGACACAAGAAAGATGAGCAGA 59.929 43.478 0.00 0.00 0.00 4.26
2157 3154 5.185635 CCCAAATGACTGCAAAAGGATTCTA 59.814 40.000 0.00 0.00 0.00 2.10
2227 3224 7.396339 AGAATACACCAAATCTAAGTTTTCCCC 59.604 37.037 0.00 0.00 0.00 4.81
2268 3265 2.514824 GCCAGCCCTCGAATCACC 60.515 66.667 0.00 0.00 0.00 4.02
2274 3271 2.046023 CACATTGCCAGCCCTCGA 60.046 61.111 0.00 0.00 0.00 4.04
2338 3335 4.464244 TGTTGAGGTGACAAAAATCCACAA 59.536 37.500 0.00 0.00 32.79 3.33
2339 3336 4.019858 TGTTGAGGTGACAAAAATCCACA 58.980 39.130 0.00 0.00 32.79 4.17
2345 3342 6.148480 CCAAAAATGTGTTGAGGTGACAAAAA 59.852 34.615 0.00 0.00 0.00 1.94
2354 3351 5.331902 CGTATAGCCAAAAATGTGTTGAGG 58.668 41.667 0.00 0.00 0.00 3.86
2381 3378 7.937394 AGTACCTTGCTATTACAATATGTTCCC 59.063 37.037 0.00 0.00 0.00 3.97
2398 3395 1.208052 TCAGAGCCATCAGTACCTTGC 59.792 52.381 0.00 0.00 0.00 4.01
2399 3396 3.616956 TTCAGAGCCATCAGTACCTTG 57.383 47.619 0.00 0.00 0.00 3.61
2407 3404 3.009363 TGAATCAGGTTTCAGAGCCATCA 59.991 43.478 0.00 0.00 32.07 3.07
2412 3409 5.831702 ATTCATGAATCAGGTTTCAGAGC 57.168 39.130 15.36 0.00 38.90 4.09
2422 3419 7.012989 TGGATAGAGTGCAAATTCATGAATCAG 59.987 37.037 20.95 16.42 0.00 2.90
2465 3462 6.570692 TCGTTTAGAAGACAGACTTGAAGTT 58.429 36.000 0.00 0.00 39.13 2.66
2487 3484 3.617540 TGTGGTTAACAACAAGCATCG 57.382 42.857 13.59 0.00 38.12 3.84
2513 3525 9.598517 GCCAACAAAATAAGAATGAAATCCATA 57.401 29.630 0.00 0.00 34.45 2.74
2517 3529 9.822185 ATAGGCCAACAAAATAAGAATGAAATC 57.178 29.630 5.01 0.00 0.00 2.17
2525 3537 8.303876 GTTGAAGAATAGGCCAACAAAATAAGA 58.696 33.333 5.01 0.00 38.84 2.10
2538 3550 4.006319 ACTTCTGCAGTTGAAGAATAGGC 58.994 43.478 18.16 0.00 42.37 3.93
2549 3561 2.149578 GCACATCAGACTTCTGCAGTT 58.850 47.619 14.67 0.00 43.46 3.16
2826 3838 4.749245 AAACAGCGGTTATCAGTTCAAG 57.251 40.909 1.70 0.00 35.82 3.02
2886 3898 5.408880 TGGAAGTCAATATACCGTGTTCA 57.591 39.130 0.00 0.00 0.00 3.18
2918 3930 3.638160 TCTTGGGAATAATGCAATCCAGC 59.362 43.478 11.73 0.00 34.82 4.85


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

AutoCloner maintained by Alex Coulton.