Multiple sequence alignment - TraesCS5D01G162100

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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 TraesCS5D01G162100 chr5D 100.000 4203 0 0 1 4203 253179528 253183730 0.000000e+00 7762
1 TraesCS5D01G162100 chr5B 95.352 4217 152 22 1 4203 285500706 285504892 0.000000e+00 6661
2 TraesCS5D01G162100 chr5A 96.945 2226 60 6 1 2222 335673777 335675998 0.000000e+00 3727
3 TraesCS5D01G162100 chr5A 93.648 2015 65 18 2219 4203 335676120 335678101 0.000000e+00 2953
4 TraesCS5D01G162100 chrUn 84.488 361 47 6 2198 2552 224667104 224666747 8.650000e-92 348
5 TraesCS5D01G162100 chrUn 80.851 235 17 12 2443 2675 67091782 67091990 4.350000e-35 159


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 TraesCS5D01G162100 chr5D 253179528 253183730 4202 False 7762 7762 100.0000 1 4203 1 chr5D.!!$F1 4202
1 TraesCS5D01G162100 chr5B 285500706 285504892 4186 False 6661 6661 95.3520 1 4203 1 chr5B.!!$F1 4202
2 TraesCS5D01G162100 chr5A 335673777 335678101 4324 False 3340 3727 95.2965 1 4203 2 chr5A.!!$F1 4202

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
45 46 1.330521 ACAAACACTGTGATGTCGCAC 59.669 47.619 15.86 0.00 36.69 5.34 F
1107 1111 0.249911 ACTTCACTGCGACTGGTTCC 60.250 55.000 0.00 0.00 0.00 3.62 F
1906 1910 0.539051 GCAGAAAGCCAGCTAGGAGA 59.461 55.000 6.40 0.00 41.22 3.71 F
2726 2859 0.740737 AAGTATCGCAAATGGCCTGC 59.259 50.000 3.32 4.54 40.31 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 1910 0.179045 AACAAGAGCGAGGTTGCACT 60.179 50.0 0.0 0.0 37.39 4.40 R
2728 2861 0.322975 GAGCAGCCTCACCAGAAGAA 59.677 55.0 0.0 0.0 38.03 2.52 R
2729 2862 1.548357 GGAGCAGCCTCACCAGAAGA 61.548 60.0 0.0 0.0 39.96 2.87 R
3821 3975 2.260844 ACAACTGGGGATATGATGCG 57.739 50.0 0.0 0.0 0.00 4.73 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
45 46 1.330521 ACAAACACTGTGATGTCGCAC 59.669 47.619 15.86 0.00 36.69 5.34
88 89 8.252417 TGTTTGATTGGTATTTGAATGATGAGG 58.748 33.333 0.00 0.00 0.00 3.86
398 399 2.139323 TGCATCTACCAGTCTACGGT 57.861 50.000 0.00 0.00 40.73 4.83
409 410 2.293677 CAGTCTACGGTTGTGACTGAGT 59.706 50.000 22.49 0.00 46.11 3.41
439 440 1.611261 ACAAGGGCCTAGGTACGCA 60.611 57.895 6.41 0.00 0.00 5.24
527 528 5.470437 TGTTCATACGTGCATAACAGGAAAA 59.530 36.000 0.00 0.00 37.59 2.29
528 529 6.150307 TGTTCATACGTGCATAACAGGAAAAT 59.850 34.615 0.00 0.00 37.59 1.82
579 583 5.698832 TCATTAGTATGTTGCTGTTGTTGC 58.301 37.500 0.00 0.00 33.34 4.17
597 601 1.881973 TGCTGCTTGATCAACCTTCAC 59.118 47.619 3.38 0.00 0.00 3.18
611 615 7.106439 TCAACCTTCACAATTCAGCTAAAAA 57.894 32.000 0.00 0.00 0.00 1.94
750 754 5.481105 TCAAATTCTCAATGGTTTCATGCC 58.519 37.500 0.00 0.00 33.18 4.40
951 955 3.863424 ACGTAACCTAGCGTGATTGATTG 59.137 43.478 0.00 0.00 40.03 2.67
1107 1111 0.249911 ACTTCACTGCGACTGGTTCC 60.250 55.000 0.00 0.00 0.00 3.62
1256 1260 7.377766 TCAGTTTATCCTTCTTCGGAATTTG 57.622 36.000 0.00 0.00 36.49 2.32
1270 1274 8.716909 TCTTCGGAATTTGGAAATAAAATTTGC 58.283 29.630 0.00 0.00 37.35 3.68
1327 1331 8.156820 TCACTCCGATCCATAATAATTGTCATT 58.843 33.333 0.00 0.00 0.00 2.57
1906 1910 0.539051 GCAGAAAGCCAGCTAGGAGA 59.461 55.000 6.40 0.00 41.22 3.71
1989 1993 4.151070 CGTCGATGAATTTGGAAACACTG 58.849 43.478 0.00 0.00 42.67 3.66
2028 2032 5.707764 TGCAACACAAGGTATGCTAATGTTA 59.292 36.000 0.00 0.00 35.73 2.41
2092 2096 2.092323 GGAGGTTGTGGGTTAGAATGC 58.908 52.381 0.00 0.00 0.00 3.56
2142 2147 4.829064 AACGGTCACTTACAGTTACGTA 57.171 40.909 0.00 0.00 43.51 3.57
2143 2148 5.376854 AACGGTCACTTACAGTTACGTAT 57.623 39.130 0.00 0.00 43.51 3.06
2157 2162 8.361592 ACAGTTACGTATTTATGGTATTCTGC 57.638 34.615 0.00 0.00 0.00 4.26
2252 2379 2.292828 ACTGCATTGTGCTACCCTTT 57.707 45.000 3.41 0.00 45.31 3.11
2263 2390 1.266989 GCTACCCTTTGCAACACTGAC 59.733 52.381 0.00 0.00 0.00 3.51
2355 2484 4.617253 AACAATGCAGTGTGTCTACCTA 57.383 40.909 21.94 0.00 0.00 3.08
2407 2536 9.747293 GGAGTGGAATACTAACTCTTAATGTAC 57.253 37.037 0.00 0.00 40.53 2.90
2420 2549 8.743085 ACTCTTAATGTACGAGAACTATGGTA 57.257 34.615 0.00 0.00 0.00 3.25
2475 2604 6.182507 ACTACAGTATGGTCAGGAAAACAA 57.817 37.500 0.00 0.00 43.62 2.83
2476 2605 6.779860 ACTACAGTATGGTCAGGAAAACAAT 58.220 36.000 0.00 0.00 43.62 2.71
2544 2673 3.515562 AGGAGGAATGTCTGTCAGACTT 58.484 45.455 28.67 21.60 45.27 3.01
2569 2702 8.499514 TGTTGCTTGATTTTTGTTTTGTTTTC 57.500 26.923 0.00 0.00 0.00 2.29
2591 2724 8.689251 TTTCGAAATGAGTATGTCTAGTCAAG 57.311 34.615 6.47 0.00 39.99 3.02
2691 2824 5.122519 TGTTTGAAATTTCCTTTTCAGCCC 58.877 37.500 15.48 0.00 44.12 5.19
2710 2843 3.160269 CCCAAAGGAGAAGCAATCAAGT 58.840 45.455 0.00 0.00 33.47 3.16
2726 2859 0.740737 AAGTATCGCAAATGGCCTGC 59.259 50.000 3.32 4.54 40.31 4.85
2727 2860 1.103398 AGTATCGCAAATGGCCTGCC 61.103 55.000 3.32 0.00 40.31 4.85
2728 2861 1.103398 GTATCGCAAATGGCCTGCCT 61.103 55.000 9.97 0.00 40.31 4.75
2729 2862 0.395586 TATCGCAAATGGCCTGCCTT 60.396 50.000 9.97 0.00 40.31 4.35
2891 3024 3.202818 ACAGCCACCTCCATGAATTCATA 59.797 43.478 20.32 5.71 34.26 2.15
3007 3140 5.960113 ACTGCATTCAACAAACACAAGTAA 58.040 33.333 0.00 0.00 0.00 2.24
3681 3825 9.972106 AAATAAATTATCATCCCAAAGGCAAAA 57.028 25.926 0.00 0.00 0.00 2.44
3682 3826 9.972106 AATAAATTATCATCCCAAAGGCAAAAA 57.028 25.926 0.00 0.00 0.00 1.94
3812 3966 2.492881 TGTACGCAATACTTCCTCCGAA 59.507 45.455 0.00 0.00 34.56 4.30
3821 3975 3.828875 ACTTCCTCCGAAAGATCATCC 57.171 47.619 0.00 0.00 0.00 3.51
3905 4059 4.155826 CGGTCTGAATGTCCAAAGCATTTA 59.844 41.667 0.00 0.00 35.03 1.40
3910 4064 8.650714 GTCTGAATGTCCAAAGCATTTATTTTC 58.349 33.333 0.00 0.00 35.03 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 5.523369 AGAGAATACTTTGCAGCAAACAAC 58.477 37.500 16.93 7.00 0.00 3.32
137 138 6.767902 ACAGTAGCCCATTGTATTCATTGTAG 59.232 38.462 0.00 0.00 0.00 2.74
398 399 1.756538 TCTGTGCTCACTCAGTCACAA 59.243 47.619 0.00 0.00 38.14 3.33
409 410 1.071987 CCCTTGTGCTCTGTGCTCA 59.928 57.895 3.20 2.94 42.51 4.26
527 528 6.142817 CGCAACTTCAAAGTGCTAACTTAAT 58.857 36.000 12.29 0.00 46.15 1.40
528 529 5.065474 ACGCAACTTCAAAGTGCTAACTTAA 59.935 36.000 12.29 0.00 46.15 1.85
579 583 4.778534 ATTGTGAAGGTTGATCAAGCAG 57.221 40.909 32.68 0.00 40.96 4.24
705 709 6.820335 TGAGATGACAACAGAGAAAAGAGAA 58.180 36.000 0.00 0.00 0.00 2.87
706 710 6.410942 TGAGATGACAACAGAGAAAAGAGA 57.589 37.500 0.00 0.00 0.00 3.10
750 754 8.352942 GCTTTTTAATGGAGATTACAGGTATGG 58.647 37.037 0.00 0.00 0.00 2.74
789 793 8.737168 TTAACTTATGAGCAGAGCACAATAAT 57.263 30.769 0.00 0.00 32.39 1.28
951 955 8.459635 GGAGAAAATTCATGAACTACTAAACCC 58.540 37.037 11.07 1.03 0.00 4.11
1107 1111 0.248825 CTGGAGAGGTGATCTTCGCG 60.249 60.000 0.00 0.00 38.84 5.87
1157 1161 2.720750 GCGGTGCGAAACGTGTTG 60.721 61.111 1.11 0.00 0.00 3.33
1249 1253 8.286097 TGAACGCAAATTTTATTTCCAAATTCC 58.714 29.630 0.00 0.00 33.56 3.01
1256 1260 7.810766 TCAGATGAACGCAAATTTTATTTCC 57.189 32.000 0.00 0.00 0.00 3.13
1351 1355 4.464951 AGATCCATAACAAGTGTCGTGGTA 59.535 41.667 12.25 0.00 35.36 3.25
1828 1832 2.299013 ACTTCTGTACTTGCCGATGACA 59.701 45.455 0.00 0.00 0.00 3.58
1906 1910 0.179045 AACAAGAGCGAGGTTGCACT 60.179 50.000 0.00 0.00 37.39 4.40
1989 1993 0.535335 TTGCAGTGATAGACCGGACC 59.465 55.000 9.46 0.00 0.00 4.46
2053 2057 5.070001 CCTCCACATGTTCTGGAAACTAAA 58.930 41.667 0.00 0.00 37.36 1.85
2142 2147 8.571336 GCTTGTTCATAGCAGAATACCATAAAT 58.429 33.333 0.00 0.00 38.51 1.40
2143 2148 7.555914 TGCTTGTTCATAGCAGAATACCATAAA 59.444 33.333 0.00 0.00 43.30 1.40
2157 2162 3.002791 ACGACATGGTGCTTGTTCATAG 58.997 45.455 0.00 0.00 0.00 2.23
2252 2379 0.815213 GCAGTCCAGTCAGTGTTGCA 60.815 55.000 0.00 0.00 0.00 4.08
2285 2412 7.510675 AGGACACCTAGGATTTATTTCTTCA 57.489 36.000 17.98 0.00 28.47 3.02
2286 2413 7.283354 CCAAGGACACCTAGGATTTATTTCTTC 59.717 40.741 17.98 0.00 31.13 2.87
2355 2484 4.335735 TGGAAACCCCATGAATCTCAAT 57.664 40.909 0.00 0.00 40.82 2.57
2407 2536 5.632347 ACGAAACTTTGTACCATAGTTCTCG 59.368 40.000 19.57 19.57 39.05 4.04
2453 2582 8.041323 ACTATTGTTTTCCTGACCATACTGTAG 58.959 37.037 0.00 0.00 0.00 2.74
2475 2604 4.941713 AGACCTGAACCTTGAGAGACTAT 58.058 43.478 0.00 0.00 0.00 2.12
2476 2605 4.390129 AGACCTGAACCTTGAGAGACTA 57.610 45.455 0.00 0.00 0.00 2.59
2544 2673 7.322222 CGAAAACAAAACAAAAATCAAGCAACA 59.678 29.630 0.00 0.00 0.00 3.33
2569 2702 8.864069 AATCTTGACTAGACATACTCATTTCG 57.136 34.615 0.00 0.00 35.19 3.46
2615 2748 6.651643 AGCAAAAACAATGACATGCATTACAT 59.348 30.769 12.87 2.80 45.23 2.29
2616 2749 5.990386 AGCAAAAACAATGACATGCATTACA 59.010 32.000 12.87 0.02 45.23 2.41
2691 2824 5.728898 GCGATACTTGATTGCTTCTCCTTTG 60.729 44.000 0.00 0.00 41.29 2.77
2710 2843 0.395586 AAGGCAGGCCATTTGCGATA 60.396 50.000 13.63 0.00 42.42 2.92
2726 2859 0.676151 GCAGCCTCACCAGAAGAAGG 60.676 60.000 0.00 0.00 0.00 3.46
2727 2860 0.324285 AGCAGCCTCACCAGAAGAAG 59.676 55.000 0.00 0.00 0.00 2.85
2728 2861 0.322975 GAGCAGCCTCACCAGAAGAA 59.677 55.000 0.00 0.00 38.03 2.52
2729 2862 1.548357 GGAGCAGCCTCACCAGAAGA 61.548 60.000 0.00 0.00 39.96 2.87
2891 3024 3.450817 CCTGAAAGAAAAACACAAGGGGT 59.549 43.478 0.00 0.00 34.07 4.95
2947 3080 8.780249 ACACCTTAAACACAAACACTACATATC 58.220 33.333 0.00 0.00 0.00 1.63
3354 3488 2.038814 TTGTCCACGGCTGCTCAAGA 62.039 55.000 0.00 0.00 0.00 3.02
3656 3800 9.972106 TTTTTGCCTTTGGGATGATAATTTATT 57.028 25.926 0.00 0.00 33.58 1.40
3812 3966 3.118112 GGGGATATGATGCGGATGATCTT 60.118 47.826 0.00 0.00 0.00 2.40
3821 3975 2.260844 ACAACTGGGGATATGATGCG 57.739 50.000 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.