Multiple sequence alignment - TraesCS6B01G291500

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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 TraesCS6B01G291500 chr6B 100.000 2717 0 0 1 2717 524964696 524961980 0.000000e+00 5018
1 TraesCS6B01G291500 chr6D 92.737 2079 78 33 674 2717 353650123 353652163 0.000000e+00 2935
2 TraesCS6B01G291500 chr6D 93.535 495 9 6 184 670 353649587 353650066 0.000000e+00 715
3 TraesCS6B01G291500 chr6D 93.642 173 9 2 13 185 353649383 353649553 9.650000e-65 257
4 TraesCS6B01G291500 chr6A 90.993 1299 49 21 677 1926 488606057 488604778 0.000000e+00 1688
5 TraesCS6B01G291500 chr6A 85.063 790 49 30 1951 2717 488604528 488603785 0.000000e+00 741
6 TraesCS6B01G291500 chr6A 86.278 634 41 25 67 670 488606733 488606116 0.000000e+00 647


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 TraesCS6B01G291500 chr6B 524961980 524964696 2716 True 5018.000000 5018 100.000000 1 2717 1 chr6B.!!$R1 2716
1 TraesCS6B01G291500 chr6D 353649383 353652163 2780 False 1302.333333 2935 93.304667 13 2717 3 chr6D.!!$F1 2704
2 TraesCS6B01G291500 chr6A 488603785 488606733 2948 True 1025.333333 1688 87.444667 67 2717 3 chr6A.!!$R1 2650

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
591 641 0.944311 CCGTCGTGCTTAACTGCTGT 60.944 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2573 3000 0.180406 AGGTTGCACAAGACCGACTT 59.82 50.0 0.0 0.0 40.89 3.01 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
22 23 5.786401 GAACAGCTCAAATACTGGTAGTG 57.214 43.478 0.00 0.00 38.25 2.74
30 31 4.281435 TCAAATACTGGTAGTGGTGACGAA 59.719 41.667 0.00 0.00 0.00 3.85
44 45 1.719246 TGACGAAGCGAGACATTTTCG 59.281 47.619 4.18 4.18 45.62 3.46
53 54 3.059188 GCGAGACATTTTCGTTTCTGGAA 60.059 43.478 0.00 0.00 40.08 3.53
54 55 4.702392 CGAGACATTTTCGTTTCTGGAAG 58.298 43.478 0.00 0.00 33.57 3.46
55 56 4.447724 CGAGACATTTTCGTTTCTGGAAGA 59.552 41.667 0.00 0.00 35.60 2.87
56 57 8.415017 GCGAGACATTTTCGTTTCTGGAAGAA 62.415 42.308 0.00 0.00 44.49 2.52
190 226 2.280797 GCGGTGAACCAGCTCACA 60.281 61.111 6.21 0.00 46.31 3.58
591 641 0.944311 CCGTCGTGCTTAACTGCTGT 60.944 55.000 0.00 0.00 0.00 4.40
599 649 3.058914 GTGCTTAACTGCTGTTCGATGTT 60.059 43.478 12.67 0.00 37.59 2.71
717 826 6.432403 TGGGAGCTTAAAATGTCCAATTTT 57.568 33.333 0.00 2.04 35.62 1.82
800 909 3.059386 GGAAATGACGCCGCCCAA 61.059 61.111 0.00 0.00 0.00 4.12
961 1076 4.633565 CCTCCTAAAAGCAACAGACAGATC 59.366 45.833 0.00 0.00 0.00 2.75
1038 1154 2.435938 TGCCCGAACGCCTTCATC 60.436 61.111 0.00 0.00 0.00 2.92
1389 1517 4.554036 GAGGATGGGGAGGCGCAC 62.554 72.222 10.83 1.82 0.00 5.34
1895 2055 4.684265 CGTGTAGAGCGCGTACAT 57.316 55.556 23.04 0.00 45.13 2.29
1927 2087 6.385649 AGAAACAGCTTCCGATTTGTTTTA 57.614 33.333 3.35 0.00 42.09 1.52
1936 2096 6.237201 GCTTCCGATTTGTTTTATTTGTAGCG 60.237 38.462 0.00 0.00 0.00 4.26
1953 2338 0.455633 GCGCAAATCTGGCTTGACAG 60.456 55.000 0.30 0.00 39.84 3.51
1967 2352 1.464734 TGACAGATCTCCAGTCCGAC 58.535 55.000 8.71 0.00 0.00 4.79
1978 2363 0.315251 CAGTCCGACTCTGAGCAACA 59.685 55.000 4.19 0.00 35.20 3.33
2236 2636 2.956964 CTCGCGGATCTGGTTCGC 60.957 66.667 6.13 2.82 45.15 4.70
2305 2708 1.730772 GCGCTACTGACTGACTGACTG 60.731 57.143 0.00 0.00 0.00 3.51
2306 2709 1.807142 CGCTACTGACTGACTGACTGA 59.193 52.381 0.00 0.00 0.00 3.41
2307 2710 2.413502 CGCTACTGACTGACTGACTGAC 60.414 54.545 0.00 0.00 0.00 3.51
2308 2711 2.094957 GCTACTGACTGACTGACTGACC 60.095 54.545 0.00 0.00 0.00 4.02
2312 2715 0.894184 GACTGACTGACTGACCCGGA 60.894 60.000 0.73 0.00 0.00 5.14
2484 2898 4.415881 TTGAGTTCTGTTACCAGCTTCA 57.584 40.909 0.00 0.00 38.66 3.02
2556 2983 2.688958 AGATTAGTACGAGGAGTGCACC 59.311 50.000 14.63 4.90 37.96 5.01
2568 2995 1.002868 GTGCACCTCACCTGCATCT 60.003 57.895 5.22 0.00 46.08 2.90
2573 3000 1.277273 CACCTCACCTGCATCTCTTGA 59.723 52.381 0.00 0.00 0.00 3.02
2590 3023 1.295792 TGAAGTCGGTCTTGTGCAAC 58.704 50.000 0.00 0.00 36.40 4.17
2591 3024 0.586802 GAAGTCGGTCTTGTGCAACC 59.413 55.000 0.00 0.00 36.40 3.77
2592 3025 0.180406 AAGTCGGTCTTGTGCAACCT 59.820 50.000 3.88 0.00 34.77 3.50
2593 3026 0.180406 AGTCGGTCTTGTGCAACCTT 59.820 50.000 3.88 0.00 34.36 3.50
2595 3028 1.002792 GTCGGTCTTGTGCAACCTTTC 60.003 52.381 3.88 0.00 34.36 2.62
2596 3029 1.021202 CGGTCTTGTGCAACCTTTCA 58.979 50.000 3.88 0.00 34.36 2.69
2597 3030 1.002468 CGGTCTTGTGCAACCTTTCAG 60.002 52.381 3.88 0.00 34.36 3.02
2602 3035 5.167845 GTCTTGTGCAACCTTTCAGAAAAA 58.832 37.500 0.00 0.00 34.36 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.631813 CCACTACCAGTATTTGAGCTGTTC 59.368 45.833 0.00 0.00 0.00 3.18
1 2 4.041691 ACCACTACCAGTATTTGAGCTGTT 59.958 41.667 0.00 0.00 0.00 3.16
2 3 3.583086 ACCACTACCAGTATTTGAGCTGT 59.417 43.478 0.00 0.00 0.00 4.40
3 4 3.935203 CACCACTACCAGTATTTGAGCTG 59.065 47.826 0.00 0.00 0.00 4.24
4 5 3.838317 TCACCACTACCAGTATTTGAGCT 59.162 43.478 0.00 0.00 0.00 4.09
5 6 3.933332 GTCACCACTACCAGTATTTGAGC 59.067 47.826 0.00 0.00 0.00 4.26
6 7 4.082408 TCGTCACCACTACCAGTATTTGAG 60.082 45.833 0.00 0.00 0.00 3.02
7 8 3.827876 TCGTCACCACTACCAGTATTTGA 59.172 43.478 0.00 0.00 0.00 2.69
8 9 4.182693 TCGTCACCACTACCAGTATTTG 57.817 45.455 0.00 0.00 0.00 2.32
9 10 4.817517 CTTCGTCACCACTACCAGTATTT 58.182 43.478 0.00 0.00 0.00 1.40
10 11 3.368116 GCTTCGTCACCACTACCAGTATT 60.368 47.826 0.00 0.00 0.00 1.89
11 12 2.165845 GCTTCGTCACCACTACCAGTAT 59.834 50.000 0.00 0.00 0.00 2.12
16 17 0.456312 CTCGCTTCGTCACCACTACC 60.456 60.000 0.00 0.00 0.00 3.18
22 23 1.429463 AAATGTCTCGCTTCGTCACC 58.571 50.000 0.00 0.00 0.00 4.02
30 31 2.480419 CCAGAAACGAAAATGTCTCGCT 59.520 45.455 0.00 0.00 39.97 4.93
44 45 5.444663 AAGATTGCACTTCTTCCAGAAAC 57.555 39.130 5.46 0.00 33.19 2.78
54 55 3.997021 TCTTTCGGAGAAGATTGCACTTC 59.003 43.478 8.63 8.63 45.90 3.01
55 56 4.008074 TCTTTCGGAGAAGATTGCACTT 57.992 40.909 0.00 0.00 45.90 3.16
56 57 3.685139 TCTTTCGGAGAAGATTGCACT 57.315 42.857 0.00 0.00 45.90 4.40
57 58 4.201861 GGAATCTTTCGGAGAAGATTGCAC 60.202 45.833 24.46 15.22 43.80 4.57
58 59 3.941483 GGAATCTTTCGGAGAAGATTGCA 59.059 43.478 24.46 0.00 43.80 4.08
551 598 3.491964 GGCACCACTATCATTAGCGTGTA 60.492 47.826 0.00 0.00 34.10 2.90
591 641 1.070914 TGGTACCAGCACAACATCGAA 59.929 47.619 11.60 0.00 0.00 3.71
599 649 0.394938 AACACGATGGTACCAGCACA 59.605 50.000 28.50 0.53 31.91 4.57
670 723 2.233676 TGATCTGCGCTACTTCCTTGAA 59.766 45.455 9.73 0.00 0.00 2.69
671 724 1.824852 TGATCTGCGCTACTTCCTTGA 59.175 47.619 9.73 0.00 0.00 3.02
672 725 2.299993 TGATCTGCGCTACTTCCTTG 57.700 50.000 9.73 0.00 0.00 3.61
676 783 2.289002 CCCATTTGATCTGCGCTACTTC 59.711 50.000 9.73 0.84 0.00 3.01
717 826 2.097036 CTCCACCGTGTAGTACCATCA 58.903 52.381 0.00 0.00 0.00 3.07
756 865 2.093711 GCTTTTGTTGTCCCTTGGTGTT 60.094 45.455 0.00 0.00 0.00 3.32
800 909 1.134946 GCAATGCGCTCAATTACCCTT 59.865 47.619 9.73 0.00 37.77 3.95
975 1091 2.367202 GCGGGGGTGAGATTCCTCA 61.367 63.158 0.00 0.00 46.48 3.86
1025 1141 3.564027 GCCCGATGAAGGCGTTCG 61.564 66.667 13.98 3.49 41.41 3.95
1579 1713 2.515991 AGAGAGAGAGAGCGGGCG 60.516 66.667 0.00 0.00 0.00 6.13
1580 1714 1.152963 AGAGAGAGAGAGAGCGGGC 60.153 63.158 0.00 0.00 0.00 6.13
1581 1715 0.469917 AGAGAGAGAGAGAGAGCGGG 59.530 60.000 0.00 0.00 0.00 6.13
1582 1716 1.586422 CAGAGAGAGAGAGAGAGCGG 58.414 60.000 0.00 0.00 0.00 5.52
1583 1717 0.940126 GCAGAGAGAGAGAGAGAGCG 59.060 60.000 0.00 0.00 0.00 5.03
1584 1718 1.133976 AGGCAGAGAGAGAGAGAGAGC 60.134 57.143 0.00 0.00 0.00 4.09
1642 1795 1.614385 CGACGCTGTGAGTTCGTATT 58.386 50.000 0.00 0.00 36.50 1.89
1719 1876 1.749638 TGCCCGAAAAACCACACGT 60.750 52.632 0.00 0.00 0.00 4.49
1875 2033 1.926886 GTACGCGCTCTACACGTCG 60.927 63.158 5.73 0.00 40.99 5.12
1890 2048 4.453819 AGCTGTTTCTTTGCTCAGATGTAC 59.546 41.667 0.00 0.00 30.41 2.90
1895 2055 2.880890 GGAAGCTGTTTCTTTGCTCAGA 59.119 45.455 4.26 0.00 35.85 3.27
1953 2338 1.946768 CTCAGAGTCGGACTGGAGATC 59.053 57.143 22.61 7.43 36.22 2.75
1967 2352 0.458197 CTCCTCGCTGTTGCTCAGAG 60.458 60.000 12.29 9.48 46.27 3.35
1978 2363 1.304547 ACAGTAGGTGCTCCTCGCT 60.305 57.895 11.38 8.22 43.94 4.93
2217 2617 1.586564 CGAACCAGATCCGCGAGAC 60.587 63.158 8.23 0.00 0.00 3.36
2224 2624 3.567797 GCGCTGCGAACCAGATCC 61.568 66.667 28.07 0.00 44.64 3.36
2236 2636 1.328439 GATACCTACGATTCGCGCTG 58.672 55.000 5.56 0.00 46.04 5.18
2472 2876 5.959618 ATTAACACCTTGAAGCTGGTAAC 57.040 39.130 0.42 0.00 34.79 2.50
2556 2983 3.260740 GACTTCAAGAGATGCAGGTGAG 58.739 50.000 0.00 0.00 0.00 3.51
2568 2995 1.138069 TGCACAAGACCGACTTCAAGA 59.862 47.619 0.00 0.00 36.61 3.02
2573 3000 0.180406 AGGTTGCACAAGACCGACTT 59.820 50.000 0.00 0.00 40.89 3.01
2631 3064 8.099537 TGCATCTTGTCTATTTCTTCTTCTTCT 58.900 33.333 0.00 0.00 0.00 2.85
2632 3065 8.174422 GTGCATCTTGTCTATTTCTTCTTCTTC 58.826 37.037 0.00 0.00 0.00 2.87
2633 3066 7.663081 TGTGCATCTTGTCTATTTCTTCTTCTT 59.337 33.333 0.00 0.00 0.00 2.52
2634 3067 7.118971 GTGTGCATCTTGTCTATTTCTTCTTCT 59.881 37.037 0.00 0.00 0.00 2.85
2635 3068 7.118971 AGTGTGCATCTTGTCTATTTCTTCTTC 59.881 37.037 0.00 0.00 0.00 2.87
2636 3069 6.939163 AGTGTGCATCTTGTCTATTTCTTCTT 59.061 34.615 0.00 0.00 0.00 2.52
2647 3080 1.125021 CGAACGAGTGTGCATCTTGTC 59.875 52.381 12.88 7.76 0.00 3.18


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

AutoCloner maintained by Alex Coulton.