Multiple sequence alignment - TraesCS1A01G121900

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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 TraesCS1A01G121900 chr1A 100.000 3437 0 0 1 3437 135966056 135969492 0.000000e+00 6348
1 TraesCS1A01G121900 chr1D 96.080 3087 84 10 376 3437 123698282 123701356 0.000000e+00 4996
2 TraesCS1A01G121900 chr1D 84.673 398 35 15 2 390 123697883 123698263 1.160000e-99 374
3 TraesCS1A01G121900 chr1B 95.603 3070 92 11 395 3437 188260105 188263158 0.000000e+00 4881
4 TraesCS1A01G121900 chr2D 83.877 1011 141 8 1336 2337 43284097 43285094 0.000000e+00 944
5 TraesCS1A01G121900 chr2B 79.797 985 160 25 1374 2346 68149781 68150738 0.000000e+00 680
6 TraesCS1A01G121900 chr3A 74.276 898 194 28 1403 2277 77411061 77410178 9.130000e-91 344
7 TraesCS1A01G121900 chr2A 81.419 296 45 6 1560 1846 44849736 44850030 2.060000e-57 233
8 TraesCS1A01G121900 chr3D 75.256 489 105 11 1460 1934 66310396 66310882 5.780000e-53 219
9 TraesCS1A01G121900 chr3B 86.301 146 15 2 1 141 134615665 134615520 1.650000e-33 154
10 TraesCS1A01G121900 chr3B 86.301 146 15 2 1 141 135357422 135357567 1.650000e-33 154
11 TraesCS1A01G121900 chr6B 85.616 146 15 4 1 142 94126395 94126252 7.690000e-32 148


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 TraesCS1A01G121900 chr1A 135966056 135969492 3436 False 6348 6348 100.0000 1 3437 1 chr1A.!!$F1 3436
1 TraesCS1A01G121900 chr1D 123697883 123701356 3473 False 2685 4996 90.3765 2 3437 2 chr1D.!!$F1 3435
2 TraesCS1A01G121900 chr1B 188260105 188263158 3053 False 4881 4881 95.6030 395 3437 1 chr1B.!!$F1 3042
3 TraesCS1A01G121900 chr2D 43284097 43285094 997 False 944 944 83.8770 1336 2337 1 chr2D.!!$F1 1001
4 TraesCS1A01G121900 chr2B 68149781 68150738 957 False 680 680 79.7970 1374 2346 1 chr2B.!!$F1 972
5 TraesCS1A01G121900 chr3A 77410178 77411061 883 True 344 344 74.2760 1403 2277 1 chr3A.!!$R1 874

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
487 523 0.037232 AGAAACCCGCGGAAAGAGAG 60.037 55.0 30.73 10.69 0.0 3.20 F
605 652 1.040893 CCATTTTCCCCTAACCCCGC 61.041 60.0 0.00 0.00 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2463 0.247736 GGTCGTGAGCAATCCTGTCT 59.752 55.000 0.00 0.00 0.00 3.41 R
2601 2685 3.796717 TGCGCTACGTTTTCTGATATCAG 59.203 43.478 24.32 24.32 45.08 2.90 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
34 35 5.079643 ACACTAGGTGCAAAATTGATTCCT 58.920 37.500 0.00 3.91 36.98 3.36
81 82 4.578516 TGTGTGACACCCTGTTTTTAGATG 59.421 41.667 13.85 0.00 32.73 2.90
127 128 3.604582 GGACAGTCATTTTCTCTCTGGG 58.395 50.000 2.17 0.00 0.00 4.45
130 131 3.008485 ACAGTCATTTTCTCTCTGGGTCC 59.992 47.826 0.00 0.00 0.00 4.46
131 132 2.234908 AGTCATTTTCTCTCTGGGTCCG 59.765 50.000 0.00 0.00 0.00 4.79
164 165 0.807667 GCGAGCATCCGTCAACTCAT 60.808 55.000 0.00 0.00 0.00 2.90
174 175 2.611518 CGTCAACTCATCAGGACCTTC 58.388 52.381 0.00 0.00 0.00 3.46
175 176 2.029020 CGTCAACTCATCAGGACCTTCA 60.029 50.000 0.00 0.00 0.00 3.02
190 191 0.241749 CTTCATTGCGCCTTTGCTGA 59.758 50.000 4.18 0.00 35.36 4.26
198 199 1.403249 GCGCCTTTGCTGATTCATTGT 60.403 47.619 0.00 0.00 34.43 2.71
199 200 2.256174 CGCCTTTGCTGATTCATTGTG 58.744 47.619 0.00 0.00 34.43 3.33
200 201 2.613691 GCCTTTGCTGATTCATTGTGG 58.386 47.619 0.00 0.00 33.53 4.17
201 202 2.231964 GCCTTTGCTGATTCATTGTGGA 59.768 45.455 0.00 0.00 33.53 4.02
203 204 4.430007 CCTTTGCTGATTCATTGTGGATG 58.570 43.478 0.00 0.00 37.08 3.51
204 205 4.081862 CCTTTGCTGATTCATTGTGGATGT 60.082 41.667 0.00 0.00 37.06 3.06
205 206 4.707030 TTGCTGATTCATTGTGGATGTC 57.293 40.909 0.00 0.00 37.06 3.06
206 207 3.959293 TGCTGATTCATTGTGGATGTCT 58.041 40.909 0.00 0.00 37.06 3.41
207 208 3.943381 TGCTGATTCATTGTGGATGTCTC 59.057 43.478 0.00 0.00 37.06 3.36
225 226 4.876107 TGTCTCTTGAGGTGAAGTTTGTTC 59.124 41.667 0.00 0.00 0.00 3.18
263 264 4.585879 ACGCAGGGATATTTGTGTTAGTT 58.414 39.130 0.00 0.00 34.61 2.24
268 277 8.024285 CGCAGGGATATTTGTGTTAGTTAAAAA 58.976 33.333 0.00 0.00 0.00 1.94
290 299 0.040425 GAGCGTGCCGTCACAAAAAT 60.040 50.000 0.00 0.00 43.28 1.82
305 314 6.019479 GTCACAAAAATTTGACCGCAACATTA 60.019 34.615 12.54 0.00 40.55 1.90
307 316 6.791299 CACAAAAATTTGACCGCAACATTATG 59.209 34.615 12.54 0.00 40.55 1.90
308 317 6.073331 ACAAAAATTTGACCGCAACATTATGG 60.073 34.615 12.54 0.00 40.55 2.74
309 318 4.799564 AATTTGACCGCAACATTATGGT 57.200 36.364 0.00 0.00 37.44 3.55
311 320 5.906113 ATTTGACCGCAACATTATGGTAA 57.094 34.783 0.00 0.00 34.12 2.85
312 321 5.906113 TTTGACCGCAACATTATGGTAAT 57.094 34.783 0.00 0.00 34.12 1.89
314 323 3.880490 TGACCGCAACATTATGGTAATCC 59.120 43.478 0.00 0.00 34.12 3.01
315 324 3.219281 ACCGCAACATTATGGTAATCCC 58.781 45.455 0.00 0.00 31.60 3.85
316 325 2.225491 CCGCAACATTATGGTAATCCCG 59.775 50.000 0.00 0.00 35.15 5.14
317 326 2.350388 CGCAACATTATGGTAATCCCGC 60.350 50.000 0.00 0.00 35.15 6.13
320 329 4.440802 GCAACATTATGGTAATCCCGCAAA 60.441 41.667 0.00 0.00 35.15 3.68
360 369 7.554959 TGGTAATCCACTTCTTTCTAGAACT 57.445 36.000 4.18 0.00 39.03 3.01
367 376 6.070767 TCCACTTCTTTCTAGAACTACATGGG 60.071 42.308 17.83 10.34 35.49 4.00
369 378 4.755266 TCTTTCTAGAACTACATGGGGC 57.245 45.455 4.18 0.00 0.00 5.80
370 379 3.454812 TCTTTCTAGAACTACATGGGGCC 59.545 47.826 4.18 0.00 0.00 5.80
371 380 1.410004 TCTAGAACTACATGGGGCCG 58.590 55.000 0.00 0.00 0.00 6.13
372 381 1.120530 CTAGAACTACATGGGGCCGT 58.879 55.000 0.00 0.00 0.00 5.68
373 382 2.091720 TCTAGAACTACATGGGGCCGTA 60.092 50.000 0.00 0.00 0.00 4.02
487 523 0.037232 AGAAACCCGCGGAAAGAGAG 60.037 55.000 30.73 10.69 0.00 3.20
527 563 2.445085 TCCACCACTCCACACGGT 60.445 61.111 0.00 0.00 0.00 4.83
605 652 1.040893 CCATTTTCCCCTAACCCCGC 61.041 60.000 0.00 0.00 0.00 6.13
666 713 2.762234 AACTCTACTCGGCTCGGCG 61.762 63.158 0.00 0.00 0.00 6.46
669 716 4.253257 CTACTCGGCTCGGCGACC 62.253 72.222 4.99 11.95 0.00 4.79
683 730 3.327404 GACCCGCTTTCCTCCCCA 61.327 66.667 0.00 0.00 0.00 4.96
969 1041 1.961791 CCGATCGAGCTAGCTCCGA 60.962 63.158 33.57 30.81 39.77 4.55
1308 1380 2.208349 AGGAGGAAGGTGCAGGGT 59.792 61.111 0.00 0.00 0.00 4.34
2238 2322 2.108514 CCACAACATGATCGGCGCT 61.109 57.895 7.64 0.00 0.00 5.92
2488 2572 6.256757 GGCTTCTGTAATGTGATGAACTACTC 59.743 42.308 0.00 0.00 0.00 2.59
2547 2631 2.238646 ACATACAGCTTTCGGATGGGAA 59.761 45.455 0.25 0.00 35.35 3.97
2560 2644 6.509523 TCGGATGGGAATAGGACTATTTTT 57.490 37.500 6.08 0.00 36.02 1.94
2601 2685 6.578023 AGAGATATTTAGAAGGCACTGACAC 58.422 40.000 0.00 0.00 40.86 3.67
2629 2713 3.120683 TCAGAAAACGTAGCGCATTCAAG 60.121 43.478 11.47 0.00 30.74 3.02
2636 2720 3.181490 ACGTAGCGCATTCAAGTCTGATA 60.181 43.478 11.47 0.00 0.00 2.15
2694 2778 5.360429 TCATTTGTCCATACCCATGTCATTG 59.640 40.000 0.00 0.00 0.00 2.82
2742 2826 6.873605 AGACCAAATTGGCTAACATTTTAAGC 59.126 34.615 12.67 0.00 42.67 3.09
2753 2837 4.882671 ACATTTTAAGCGCCAGTCTATG 57.117 40.909 2.29 4.07 0.00 2.23
2865 2949 2.344535 CCTGCAACAAGGTCTTGGG 58.655 57.895 14.29 7.69 44.45 4.12
2981 3065 0.673644 CCGGGTCTCGTGCAAAGATT 60.674 55.000 0.00 0.00 37.11 2.40
3031 3115 1.012086 CTGATTCCTGCATCACGGTG 58.988 55.000 0.56 0.56 0.00 4.94
3037 3121 1.672030 CTGCATCACGGTGAAGGCA 60.672 57.895 27.80 27.80 38.06 4.75
3068 3152 2.559698 TGTGTTGTCGGACAATGGAT 57.440 45.000 24.81 0.00 40.59 3.41
3082 3166 7.227314 TCGGACAATGGATGATAGAGAAATTTG 59.773 37.037 0.00 0.00 0.00 2.32
3107 3191 5.767168 GTGAGGCTAATTAGAATCCAGCATT 59.233 40.000 16.85 0.00 33.86 3.56
3173 3258 6.624352 GTCATAGTAGGTGACGTGGTAATA 57.376 41.667 0.00 0.00 36.92 0.98
3261 3346 1.212935 AGATGGGAATGTGGGTGCTAC 59.787 52.381 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.396811 ACCTAGTGTCTTGTGCACCC 59.603 55.000 15.69 0.00 37.56 4.61
15 16 4.837860 ACCAAGGAATCAATTTTGCACCTA 59.162 37.500 0.00 0.00 0.00 3.08
17 18 4.006780 ACCAAGGAATCAATTTTGCACC 57.993 40.909 0.00 0.00 0.00 5.01
110 111 2.234908 CGGACCCAGAGAGAAAATGACT 59.765 50.000 0.00 0.00 0.00 3.41
111 112 2.622436 CGGACCCAGAGAGAAAATGAC 58.378 52.381 0.00 0.00 0.00 3.06
147 148 2.200067 CTGATGAGTTGACGGATGCTC 58.800 52.381 0.00 0.00 0.00 4.26
164 165 1.377202 GGCGCAATGAAGGTCCTGA 60.377 57.895 10.83 0.00 0.00 3.86
190 191 5.191426 CCTCAAGAGACATCCACAATGAAT 58.809 41.667 0.00 0.00 38.83 2.57
198 199 3.242867 ACTTCACCTCAAGAGACATCCA 58.757 45.455 0.00 0.00 0.00 3.41
199 200 3.971245 ACTTCACCTCAAGAGACATCC 57.029 47.619 0.00 0.00 0.00 3.51
200 201 5.059833 ACAAACTTCACCTCAAGAGACATC 58.940 41.667 0.00 0.00 0.00 3.06
201 202 5.041191 ACAAACTTCACCTCAAGAGACAT 57.959 39.130 0.00 0.00 0.00 3.06
203 204 5.119694 AGAACAAACTTCACCTCAAGAGAC 58.880 41.667 0.00 0.00 0.00 3.36
204 205 5.359194 AGAACAAACTTCACCTCAAGAGA 57.641 39.130 0.00 0.00 0.00 3.10
205 206 6.442513 AAAGAACAAACTTCACCTCAAGAG 57.557 37.500 0.00 0.00 0.00 2.85
206 207 6.432783 TGAAAAGAACAAACTTCACCTCAAGA 59.567 34.615 0.00 0.00 0.00 3.02
207 208 6.528072 GTGAAAAGAACAAACTTCACCTCAAG 59.472 38.462 3.02 0.00 41.06 3.02
275 284 2.538037 GGTCAAATTTTTGTGACGGCAC 59.462 45.455 16.50 16.50 44.19 5.01
290 299 5.163602 GGATTACCATAATGTTGCGGTCAAA 60.164 40.000 0.00 0.00 33.23 2.69
332 341 8.483758 TTCTAGAAAGAAGTGGATTACCATACC 58.516 37.037 1.68 0.00 41.41 2.73
333 342 9.315525 GTTCTAGAAAGAAGTGGATTACCATAC 57.684 37.037 6.78 0.00 42.40 2.39
336 345 7.554959 AGTTCTAGAAAGAAGTGGATTACCA 57.445 36.000 6.78 0.00 42.61 3.25
345 354 5.338463 GCCCCATGTAGTTCTAGAAAGAAGT 60.338 44.000 6.78 1.47 45.44 3.01
360 369 3.530928 ACTACTATACGGCCCCATGTA 57.469 47.619 0.00 0.00 0.00 2.29
364 373 2.839425 ACAAAACTACTATACGGCCCCA 59.161 45.455 0.00 0.00 0.00 4.96
367 376 4.505556 GCACTACAAAACTACTATACGGCC 59.494 45.833 0.00 0.00 0.00 6.13
369 378 5.228635 CGTGCACTACAAAACTACTATACGG 59.771 44.000 16.19 0.00 0.00 4.02
370 379 5.228635 CCGTGCACTACAAAACTACTATACG 59.771 44.000 16.19 0.00 0.00 3.06
371 380 6.034256 CACCGTGCACTACAAAACTACTATAC 59.966 42.308 16.19 0.00 0.00 1.47
372 381 6.094719 CACCGTGCACTACAAAACTACTATA 58.905 40.000 16.19 0.00 0.00 1.31
373 382 4.927425 CACCGTGCACTACAAAACTACTAT 59.073 41.667 16.19 0.00 0.00 2.12
414 450 3.690460 AGTCTTTTTCTATGGGTGCCTG 58.310 45.455 0.00 0.00 0.00 4.85
527 563 3.467226 GGCTGCCTGGCCGTACTA 61.467 66.667 17.53 0.00 42.82 1.82
666 713 3.327404 TGGGGAGGAAAGCGGGTC 61.327 66.667 0.00 0.00 0.00 4.46
669 716 2.269241 GAGTGGGGAGGAAAGCGG 59.731 66.667 0.00 0.00 0.00 5.52
969 1041 0.889638 TCTCGTCGAGTCTTGGCTGT 60.890 55.000 21.15 0.00 0.00 4.40
1539 1611 4.027173 TGCACGGGTATGGCAGCA 62.027 61.111 0.00 0.00 32.95 4.41
1650 1722 2.100197 CAGACCTGGAGGACGATGTTA 58.900 52.381 0.00 0.00 38.94 2.41
1816 1900 0.523072 TTGTAGTACTCGGCCACGTC 59.477 55.000 2.24 0.00 41.85 4.34
2379 2463 0.247736 GGTCGTGAGCAATCCTGTCT 59.752 55.000 0.00 0.00 0.00 3.41
2488 2572 6.060136 TCTTCCTATGCTTTCATGGAAGATG 58.940 40.000 18.45 3.69 46.82 2.90
2601 2685 3.796717 TGCGCTACGTTTTCTGATATCAG 59.203 43.478 24.32 24.32 45.08 2.90
2742 2826 3.375782 TCACATGATCATAGACTGGCG 57.624 47.619 8.15 0.00 0.00 5.69
2753 2837 9.887629 AAATGGAGATGTATCTATCACATGATC 57.112 33.333 0.00 0.00 36.76 2.92
2775 2859 6.403636 GCCTTGTACATACCAGTCAAGAAATG 60.404 42.308 0.00 0.00 38.06 2.32
2865 2949 7.549488 AGAATGGTGCTTGTAAGATTACTGTAC 59.451 37.037 4.50 6.63 34.77 2.90
3031 3115 4.265073 ACACAATGACCTTCTATGCCTTC 58.735 43.478 0.00 0.00 0.00 3.46
3037 3121 4.020573 TCCGACAACACAATGACCTTCTAT 60.021 41.667 0.00 0.00 0.00 1.98
3068 3152 5.441718 AGCCTCACCAAATTTCTCTATCA 57.558 39.130 0.00 0.00 0.00 2.15
3082 3166 4.068599 GCTGGATTCTAATTAGCCTCACC 58.931 47.826 7.67 7.19 0.00 4.02
3261 3346 4.371786 AGCATATTACGTCCACATGACTG 58.628 43.478 0.00 0.00 42.13 3.51


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

AutoCloner maintained by Alex Coulton.