Multiple sequence alignment - TraesCS1B01G389600

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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 TraesCS1B01G389600 chr1B 100.000 3524 0 0 1 3524 623546526 623550049 0 6508
1 TraesCS1B01G389600 chr1D 96.006 3530 126 12 1 3524 453112346 453115866 0 5723
2 TraesCS1B01G389600 chr7B 85.131 2744 350 30 686 3399 724956243 724953528 0 2754
3 TraesCS1B01G389600 chr7B 85.585 2539 334 19 879 3405 466668770 466671288 0 2632
4 TraesCS1B01G389600 chr7B 81.702 2421 406 23 1003 3405 723929179 723931580 0 1982
5 TraesCS1B01G389600 chr7D 84.378 2791 375 29 639 3399 625355754 625352995 0 2682
6 TraesCS1B01G389600 chr7D 84.794 2453 340 17 965 3405 448855381 448857812 0 2433
7 TraesCS1B01G389600 chr7D 80.768 2995 479 68 466 3399 625249968 625252926 0 2250
8 TraesCS1B01G389600 chr7A 83.782 2454 366 18 965 3405 547114175 547111741 0 2298
9 TraesCS1B01G389600 chr7A 80.338 3021 488 65 447 3405 720864927 720861951 0 2191
10 TraesCS1B01G389600 chr6A 81.579 2432 407 24 996 3405 608493799 608491387 0 1971


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 TraesCS1B01G389600 chr1B 623546526 623550049 3523 False 6508 6508 100.000 1 3524 1 chr1B.!!$F1 3523
1 TraesCS1B01G389600 chr1D 453112346 453115866 3520 False 5723 5723 96.006 1 3524 1 chr1D.!!$F1 3523
2 TraesCS1B01G389600 chr7B 724953528 724956243 2715 True 2754 2754 85.131 686 3399 1 chr7B.!!$R1 2713
3 TraesCS1B01G389600 chr7B 466668770 466671288 2518 False 2632 2632 85.585 879 3405 1 chr7B.!!$F1 2526
4 TraesCS1B01G389600 chr7B 723929179 723931580 2401 False 1982 1982 81.702 1003 3405 1 chr7B.!!$F2 2402
5 TraesCS1B01G389600 chr7D 625352995 625355754 2759 True 2682 2682 84.378 639 3399 1 chr7D.!!$R1 2760
6 TraesCS1B01G389600 chr7D 448855381 448857812 2431 False 2433 2433 84.794 965 3405 1 chr7D.!!$F1 2440
7 TraesCS1B01G389600 chr7D 625249968 625252926 2958 False 2250 2250 80.768 466 3399 1 chr7D.!!$F2 2933
8 TraesCS1B01G389600 chr7A 547111741 547114175 2434 True 2298 2298 83.782 965 3405 1 chr7A.!!$R1 2440
9 TraesCS1B01G389600 chr7A 720861951 720864927 2976 True 2191 2191 80.338 447 3405 1 chr7A.!!$R2 2958
10 TraesCS1B01G389600 chr6A 608491387 608493799 2412 True 1971 1971 81.579 996 3405 1 chr6A.!!$R1 2409

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
580 585 2.362717 CCCGGCAACTTTTGTAGGAAAA 59.637 45.455 0.0 0.0 33.32 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2523 2630 2.234908 AGTAGCTCTCCGCAACTCATTT 59.765 45.455 0.0 0.0 42.61 2.32 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
30 31 8.425577 TGTAATGCAAGACTAGCTAGAAAATC 57.574 34.615 27.45 13.78 0.00 2.17
31 32 8.040727 TGTAATGCAAGACTAGCTAGAAAATCA 58.959 33.333 27.45 17.32 0.00 2.57
34 35 5.187772 TGCAAGACTAGCTAGAAAATCAGGA 59.812 40.000 27.45 9.18 0.00 3.86
85 86 3.417069 TGCTACATACACAAGGTTGCT 57.583 42.857 0.00 0.00 34.98 3.91
105 106 6.061022 TGCTTTTAGAGGATTCACATGGTA 57.939 37.500 0.00 0.00 0.00 3.25
112 113 3.535561 AGGATTCACATGGTAAAGCTCG 58.464 45.455 0.00 0.00 0.00 5.03
114 115 3.309954 GGATTCACATGGTAAAGCTCGTC 59.690 47.826 0.00 0.00 0.00 4.20
136 138 3.199071 CCTTGCCATGTACTACCAGGTAA 59.801 47.826 0.00 0.00 0.00 2.85
156 158 6.375455 AGGTAAGTAGCATTGTGATTGGAAAG 59.625 38.462 0.00 0.00 0.00 2.62
219 221 9.727627 CTGAAGATAAATTTGCTAAATCTCCAC 57.272 33.333 0.00 0.00 0.00 4.02
230 232 4.441356 GCTAAATCTCCACTCTCCAGTCTG 60.441 50.000 0.00 0.00 0.00 3.51
252 254 5.492895 TGCTGGTAATTATTCGTCTGGAAA 58.507 37.500 0.00 0.00 38.36 3.13
297 299 7.962918 GTGTGTTCAGTTTGAATCATATACCAC 59.037 37.037 0.00 0.00 38.79 4.16
305 307 6.484818 TTGAATCATATACCACGATGCATG 57.515 37.500 2.46 0.00 0.00 4.06
343 345 6.406093 TGTTTTTCTGTTTGCATGTTCAAG 57.594 33.333 0.00 0.00 0.00 3.02
346 348 3.713858 TCTGTTTGCATGTTCAAGGTG 57.286 42.857 0.00 0.00 0.00 4.00
350 352 3.243367 TGTTTGCATGTTCAAGGTGTAGC 60.243 43.478 0.00 0.00 0.00 3.58
358 360 6.449698 CATGTTCAAGGTGTAGCTTTTTCAT 58.550 36.000 0.00 0.00 0.00 2.57
361 363 5.689383 TCAAGGTGTAGCTTTTTCATGTC 57.311 39.130 0.00 0.00 0.00 3.06
390 392 2.733956 ACCAGTTGAAAGCCTGAAACA 58.266 42.857 0.00 0.00 0.00 2.83
392 394 3.131046 ACCAGTTGAAAGCCTGAAACAAG 59.869 43.478 0.00 0.00 0.00 3.16
407 409 5.935945 TGAAACAAGGGACAATTCTACAGA 58.064 37.500 0.00 0.00 0.00 3.41
427 429 2.550180 GAGCTGGACCTTGAAAGACAAC 59.450 50.000 0.00 0.00 34.56 3.32
444 446 5.164233 AGACAACGACATCACAGAATAGTG 58.836 41.667 0.00 0.00 40.85 2.74
580 585 2.362717 CCCGGCAACTTTTGTAGGAAAA 59.637 45.455 0.00 0.00 33.32 2.29
673 686 5.682234 TCTGTTGTGTGATGGATGACTAT 57.318 39.130 0.00 0.00 0.00 2.12
674 687 5.422145 TCTGTTGTGTGATGGATGACTATG 58.578 41.667 0.00 0.00 0.00 2.23
781 824 7.553334 AGAGACAATTCTACCACGCTTAAATA 58.447 34.615 0.00 0.00 29.47 1.40
866 909 5.614324 TCACTCTCAAGAAAAGGACAAGA 57.386 39.130 0.00 0.00 0.00 3.02
1050 1131 8.484641 TTCTACTAACTTTGATTCATCTGCTG 57.515 34.615 0.00 0.00 0.00 4.41
1131 1212 1.077429 GGACAGGCTCCATTCACCC 60.077 63.158 0.00 0.00 39.21 4.61
1478 1562 6.237901 TGCTACCAAATCAGAACATAACTGT 58.762 36.000 0.00 0.00 37.12 3.55
1625 1709 7.470563 GCCAAACCCTTTCATTAATATCTGGAG 60.471 40.741 0.00 0.00 0.00 3.86
1788 1872 7.195374 TGGCAACCTTAGATTATACAGTCTT 57.805 36.000 0.00 0.00 0.00 3.01
1789 1873 7.047891 TGGCAACCTTAGATTATACAGTCTTG 58.952 38.462 0.00 0.00 0.00 3.02
2133 2221 4.565652 GGTTTCTCATACTGGCAAGGAGAA 60.566 45.833 11.14 11.14 41.41 2.87
2160 2249 3.879892 GCTGTTATCCAAAGTCATCCCTC 59.120 47.826 0.00 0.00 0.00 4.30
2396 2503 6.798959 GGATTCTTATCAGCGATATTTTGTGC 59.201 38.462 0.00 0.00 32.09 4.57
2409 2516 4.637483 ATTTTGTGCCGAGGTGATATTG 57.363 40.909 0.00 0.00 0.00 1.90
2481 2588 1.075525 AGTATGGCCGGCTGAGGTA 60.076 57.895 28.56 9.40 0.00 3.08
2523 2630 4.839121 ACCATTTCCGCAGATACACTTAA 58.161 39.130 0.00 0.00 0.00 1.85
2936 3046 1.345741 TGACCTGAAGCCAGAGAACAG 59.654 52.381 0.00 0.00 43.02 3.16
3073 3183 1.912043 CTCCTGAGTGGGTTTCTGGAT 59.088 52.381 2.04 0.00 40.49 3.41
3267 3386 4.210746 CAGTTATGGATCGCTGACTTCATG 59.789 45.833 0.00 0.00 0.00 3.07
3410 3529 4.566004 CTTGTTTCGGTAGATGAGGACAA 58.434 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.775594 TTCTAGCTAGTCTTGCATTACAGA 57.224 37.500 20.10 0.00 0.00 3.41
6 7 8.425577 TGATTTTCTAGCTAGTCTTGCATTAC 57.574 34.615 20.10 4.42 0.00 1.89
17 18 5.127845 TGTCAGGTCCTGATTTTCTAGCTAG 59.872 44.000 24.46 15.01 42.73 3.42
30 31 2.288825 ACGTGTAACATGTCAGGTCCTG 60.289 50.000 13.21 13.21 35.74 3.86
31 32 1.968493 ACGTGTAACATGTCAGGTCCT 59.032 47.619 0.00 0.00 35.74 3.85
85 86 7.175104 AGCTTTACCATGTGAATCCTCTAAAA 58.825 34.615 0.00 0.00 0.00 1.52
105 106 0.250901 ACATGGCAAGGACGAGCTTT 60.251 50.000 0.00 0.00 0.00 3.51
112 113 2.420129 CCTGGTAGTACATGGCAAGGAC 60.420 54.545 0.00 0.00 0.00 3.85
114 115 1.559682 ACCTGGTAGTACATGGCAAGG 59.440 52.381 0.00 0.00 0.00 3.61
136 138 4.338879 AGCTTTCCAATCACAATGCTACT 58.661 39.130 0.00 0.00 32.73 2.57
156 158 3.971032 ACTGAAACTACTGCAACAAGC 57.029 42.857 0.00 0.00 45.96 4.01
230 232 5.220796 GGTTTCCAGACGAATAATTACCAGC 60.221 44.000 0.00 0.00 29.94 4.85
234 236 7.700656 CCATTTGGTTTCCAGACGAATAATTAC 59.299 37.037 0.00 0.00 33.81 1.89
242 244 2.940994 TCCATTTGGTTTCCAGACGA 57.059 45.000 0.00 0.00 33.81 4.20
244 246 5.253330 TGTCTATCCATTTGGTTTCCAGAC 58.747 41.667 0.00 4.73 33.81 3.51
252 254 4.761739 CACACAACTGTCTATCCATTTGGT 59.238 41.667 0.00 0.00 36.34 3.67
297 299 2.664568 CAGTTTTTGGCTTCATGCATCG 59.335 45.455 0.00 0.00 45.15 3.84
331 333 2.862541 AGCTACACCTTGAACATGCAA 58.137 42.857 0.00 0.00 0.00 4.08
343 345 3.821033 ACAGGACATGAAAAAGCTACACC 59.179 43.478 0.00 0.00 0.00 4.16
346 348 7.381408 GGTTAAAACAGGACATGAAAAAGCTAC 59.619 37.037 0.00 0.00 0.00 3.58
350 352 7.264947 ACTGGTTAAAACAGGACATGAAAAAG 58.735 34.615 0.00 0.00 40.23 2.27
358 360 5.393678 GCTTTCAACTGGTTAAAACAGGACA 60.394 40.000 11.73 0.00 40.23 4.02
361 363 4.099419 AGGCTTTCAACTGGTTAAAACAGG 59.901 41.667 11.73 0.00 40.23 4.00
390 392 3.054802 CCAGCTCTGTAGAATTGTCCCTT 60.055 47.826 0.00 0.00 0.00 3.95
392 394 2.501723 TCCAGCTCTGTAGAATTGTCCC 59.498 50.000 0.00 0.00 0.00 4.46
407 409 2.576615 GTTGTCTTTCAAGGTCCAGCT 58.423 47.619 0.00 0.00 36.66 4.24
444 446 5.310451 TGGGTGGTAACTTGTTCTATTCAC 58.690 41.667 0.00 0.00 37.61 3.18
544 549 1.818131 GCCGGGTCCAAACTTTTCTCT 60.818 52.381 2.18 0.00 0.00 3.10
612 623 5.473504 ACTTGACTATTCCAATTGTGTGGTC 59.526 40.000 4.43 7.86 39.88 4.02
655 668 4.818005 GCATCATAGTCATCCATCACACAA 59.182 41.667 0.00 0.00 0.00 3.33
673 686 0.599991 GACCACTCGTGTGTGCATCA 60.600 55.000 15.79 0.00 42.34 3.07
674 687 0.599991 TGACCACTCGTGTGTGCATC 60.600 55.000 15.79 8.61 42.34 3.91
754 770 4.273148 AGCGTGGTAGAATTGTCTCTTT 57.727 40.909 0.00 0.00 35.12 2.52
789 832 7.624549 TCAATAATTAGCTGTGAAGTCTCCTT 58.375 34.615 0.00 0.00 0.00 3.36
791 834 8.341173 CAATCAATAATTAGCTGTGAAGTCTCC 58.659 37.037 0.00 0.00 0.00 3.71
792 835 9.102757 TCAATCAATAATTAGCTGTGAAGTCTC 57.897 33.333 0.00 0.00 0.00 3.36
1131 1212 2.002586 CCACAGCTGAAAGTACCATCG 58.997 52.381 23.35 0.00 35.30 3.84
1625 1709 8.296713 TGGTATTAAATGAGTGTCTTTGCTTTC 58.703 33.333 0.00 0.00 0.00 2.62
1788 1872 4.870636 ACCATCTTCCATTTGGCTTATCA 58.129 39.130 0.00 0.00 33.66 2.15
1789 1873 4.023707 CGACCATCTTCCATTTGGCTTATC 60.024 45.833 0.00 0.00 33.66 1.75
1911 1996 3.118112 GGTCAATGATCTCATGTCCAGGT 60.118 47.826 0.00 0.00 36.56 4.00
1958 2043 2.435372 ACTGAGGTTGAACTTTGGCA 57.565 45.000 0.00 0.00 0.00 4.92
2133 2221 4.640771 TGACTTTGGATAACAGCTTCCT 57.359 40.909 3.88 0.00 32.95 3.36
2396 2503 3.685139 ATGCTACCAATATCACCTCGG 57.315 47.619 0.00 0.00 0.00 4.63
2481 2588 9.646522 AAATGGTTAGTTATCATTTCATAGCCT 57.353 29.630 0.00 0.00 36.68 4.58
2523 2630 2.234908 AGTAGCTCTCCGCAACTCATTT 59.765 45.455 0.00 0.00 42.61 2.32
2936 3046 4.867608 GCTCTAAGTTCTCATCCAACAGTC 59.132 45.833 0.00 0.00 0.00 3.51
2985 3095 2.484264 CCCGCCTCTGTTTAGAAGTTTG 59.516 50.000 0.00 0.00 31.21 2.93
3073 3183 4.219115 TCAACCTTTGCTGTTATTGGGAA 58.781 39.130 0.00 0.00 0.00 3.97
3267 3386 1.003580 TGCCTGTTCAATCTGGAGTCC 59.996 52.381 0.73 0.73 0.00 3.85
3410 3529 6.127451 GGTGCTGGTTTATTTAGCTGGTTTAT 60.127 38.462 0.00 0.00 38.25 1.40


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

AutoCloner maintained by Alex Coulton.