Multiple sequence alignment - TraesCS6A01G217800

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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 TraesCS6A01G217800 chr6A 100.000 2788 0 0 1 2788 401364443 401367230 0 5149
1 TraesCS6A01G217800 chr4A 96.166 2791 93 7 2 2788 490340961 490343741 0 4549
2 TraesCS6A01G217800 chr4A 94.972 2824 92 9 2 2788 429488137 429490947 0 4383
3 TraesCS6A01G217800 chr4A 94.968 2007 93 8 787 2788 523832642 523834645 0 3140
4 TraesCS6A01G217800 chr5A 95.541 2736 94 10 2 2733 133817750 133820461 0 4351
5 TraesCS6A01G217800 chr5A 94.121 2041 91 19 753 2788 501869175 501871191 0 3077
6 TraesCS6A01G217800 chr5A 95.568 1647 48 4 2 1644 345672839 345671214 0 2614
7 TraesCS6A01G217800 chr1A 96.024 2641 101 2 151 2788 575419163 575421802 0 4292
8 TraesCS6A01G217800 chr1A 95.083 2400 97 12 390 2788 580783461 580785840 0 3759
9 TraesCS6A01G217800 chr7B 94.872 1989 78 6 802 2788 471054623 471056589 0 3086
10 TraesCS6A01G217800 chr2B 94.356 2002 89 4 789 2788 131501159 131499180 0 3049
11 TraesCS6A01G217800 chr7A 94.498 1872 92 2 918 2788 153039565 153037704 0 2876
12 TraesCS6A01G217800 chr7A 94.336 1642 62 8 2 1638 644066760 644065145 0 2488
13 TraesCS6A01G217800 chr3A 95.687 1646 66 3 2 1644 513294964 513296607 0 2641
14 TraesCS6A01G217800 chr3A 93.121 1570 80 14 1 1563 733887402 733885854 0 2276
15 TraesCS6A01G217800 chr2A 96.555 958 27 3 126 1080 605761987 605762941 0 1581


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 TraesCS6A01G217800 chr6A 401364443 401367230 2787 False 5149 5149 100.000 1 2788 1 chr6A.!!$F1 2787
1 TraesCS6A01G217800 chr4A 490340961 490343741 2780 False 4549 4549 96.166 2 2788 1 chr4A.!!$F2 2786
2 TraesCS6A01G217800 chr4A 429488137 429490947 2810 False 4383 4383 94.972 2 2788 1 chr4A.!!$F1 2786
3 TraesCS6A01G217800 chr4A 523832642 523834645 2003 False 3140 3140 94.968 787 2788 1 chr4A.!!$F3 2001
4 TraesCS6A01G217800 chr5A 133817750 133820461 2711 False 4351 4351 95.541 2 2733 1 chr5A.!!$F1 2731
5 TraesCS6A01G217800 chr5A 501869175 501871191 2016 False 3077 3077 94.121 753 2788 1 chr5A.!!$F2 2035
6 TraesCS6A01G217800 chr5A 345671214 345672839 1625 True 2614 2614 95.568 2 1644 1 chr5A.!!$R1 1642
7 TraesCS6A01G217800 chr1A 575419163 575421802 2639 False 4292 4292 96.024 151 2788 1 chr1A.!!$F1 2637
8 TraesCS6A01G217800 chr1A 580783461 580785840 2379 False 3759 3759 95.083 390 2788 1 chr1A.!!$F2 2398
9 TraesCS6A01G217800 chr7B 471054623 471056589 1966 False 3086 3086 94.872 802 2788 1 chr7B.!!$F1 1986
10 TraesCS6A01G217800 chr2B 131499180 131501159 1979 True 3049 3049 94.356 789 2788 1 chr2B.!!$R1 1999
11 TraesCS6A01G217800 chr7A 153037704 153039565 1861 True 2876 2876 94.498 918 2788 1 chr7A.!!$R1 1870
12 TraesCS6A01G217800 chr7A 644065145 644066760 1615 True 2488 2488 94.336 2 1638 1 chr7A.!!$R2 1636
13 TraesCS6A01G217800 chr3A 513294964 513296607 1643 False 2641 2641 95.687 2 1644 1 chr3A.!!$F1 1642
14 TraesCS6A01G217800 chr3A 733885854 733887402 1548 True 2276 2276 93.121 1 1563 1 chr3A.!!$R1 1562
15 TraesCS6A01G217800 chr2A 605761987 605762941 954 False 1581 1581 96.555 126 1080 1 chr2A.!!$F1 954

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
944 961 2.289882 TGCTGTCTAGTGCTTGATTGCT 60.29 45.455 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 2476 1.247567 CCCGCAGTTCAAATTCCAGT 58.752 50.0 0.0 0.0 0.0 4.0 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
40 41 4.101741 CCTTGCTAGGTATGCTAGTTTCCT 59.898 45.833 5.98 0.00 36.74 3.36
81 82 9.087424 CAGTGACGTAGAATTCATCAGAAATAA 57.913 33.333 8.44 0.00 37.29 1.40
220 224 4.254709 AGCGGCACACTGGAGCAA 62.255 61.111 1.45 0.00 31.64 3.91
221 225 4.030452 GCGGCACACTGGAGCAAC 62.030 66.667 0.00 0.00 31.64 4.17
453 457 9.362151 TGTGTTTAAATTGAGAATCTAGGGTTT 57.638 29.630 0.00 0.00 34.92 3.27
599 611 4.455877 GCCATTTATAGTAGACATGGGCAC 59.544 45.833 11.07 0.00 35.79 5.01
600 612 5.620206 CCATTTATAGTAGACATGGGCACA 58.380 41.667 0.00 0.00 32.18 4.57
601 613 6.240894 CCATTTATAGTAGACATGGGCACAT 58.759 40.000 0.00 0.00 37.99 3.21
877 894 7.480810 TCGAGATCGTAATTGAGAAATCTTGA 58.519 34.615 1.70 0.00 40.80 3.02
944 961 2.289882 TGCTGTCTAGTGCTTGATTGCT 60.290 45.455 0.00 0.00 0.00 3.91
976 993 2.435586 CTTGACCCTCGCTGCAGG 60.436 66.667 17.12 5.82 0.00 4.85
1116 1133 1.345715 GCCACATGTACCTAGGGCCT 61.346 60.000 12.58 12.58 35.42 5.19
1229 1246 0.464554 TTCGACAACACCATGTGCCA 60.465 50.000 0.00 0.00 36.98 4.92
1304 1321 3.054065 CCTGTCCTTTTGGCTTCCTCTAT 60.054 47.826 0.00 0.00 40.12 1.98
1352 1369 1.070445 CTTTGTTGCATTTGGCCAGGA 59.930 47.619 5.11 0.00 43.89 3.86
1425 1544 3.532155 AGAGCGGGGATGACGAGC 61.532 66.667 0.00 0.00 0.00 5.03
1426 1545 3.838271 GAGCGGGGATGACGAGCA 61.838 66.667 0.00 0.00 0.00 4.26
1427 1546 3.781770 GAGCGGGGATGACGAGCAG 62.782 68.421 0.00 0.00 0.00 4.24
1428 1547 3.838271 GCGGGGATGACGAGCAGA 61.838 66.667 0.00 0.00 0.00 4.26
1429 1548 3.133014 CGGGGATGACGAGCAGAT 58.867 61.111 0.00 0.00 0.00 2.90
1430 1549 1.006805 CGGGGATGACGAGCAGATC 60.007 63.158 0.00 0.00 0.00 2.75
1440 1559 1.006805 GAGCAGATCGGGGATGACG 60.007 63.158 0.00 0.00 0.00 4.35
1441 1560 1.455773 AGCAGATCGGGGATGACGA 60.456 57.895 0.00 0.00 45.19 4.20
1442 1561 1.006805 GCAGATCGGGGATGACGAG 60.007 63.158 0.00 0.00 44.24 4.18
1509 1628 1.212375 ACATGCTATGGTGGTGGCTA 58.788 50.000 0.00 0.00 33.60 3.93
1521 1640 0.609662 GGTGGCTAACGACAACCCTA 59.390 55.000 0.00 0.00 25.61 3.53
1649 1768 2.028125 CTATGGTGGTGGCGGACGAT 62.028 60.000 0.00 0.00 0.00 3.73
1688 1807 1.588082 GCCTGCAATCCCACAACTG 59.412 57.895 0.00 0.00 0.00 3.16
1749 1868 0.174845 CGTTGGGATTCGCCACTCTA 59.825 55.000 3.91 0.00 38.95 2.43
1814 1933 5.616270 TGTTAAGAAGGTGTTCAGCATGTA 58.384 37.500 4.86 0.00 37.40 2.29
1827 1946 6.712998 TGTTCAGCATGTAAGGTTTAAGCTTA 59.287 34.615 11.93 11.93 33.47 3.09
1903 2022 3.208594 GCTCATGGATGCTGTATGACAA 58.791 45.455 0.00 0.00 0.00 3.18
2081 2213 5.009610 TGCTAAAAACATGACTCAAACCCTC 59.990 40.000 0.00 0.00 0.00 4.30
2296 2429 0.529992 GCATTTCCGACCCTCGTAGG 60.530 60.000 0.00 0.00 38.40 3.18
2343 2476 1.218047 CCGATTCAGCTGGAACCGA 59.782 57.895 15.13 0.00 45.80 4.69
2381 2514 1.382557 TCCTCCATAGCTTGCCCGA 60.383 57.895 0.00 0.00 0.00 5.14
2610 2744 7.930865 AGCAAAAATTCTAAACTTGCAATACCA 59.069 29.630 0.00 0.00 43.77 3.25
2689 2823 5.507985 GGCTTTCAAGTCAAACTAGCAATGT 60.508 40.000 0.00 0.00 29.91 2.71
2699 2833 0.235665 CTAGCAATGTTATGGCCGCG 59.764 55.000 0.00 0.00 0.00 6.46
2715 2849 2.261345 CCGCGTCCGTTGAATAGTTTA 58.739 47.619 4.92 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.531538 GTCACTGTGAAGAGAACCACAA 58.468 45.455 12.81 0.00 42.00 3.33
81 82 1.328279 CCCTTTCGGTCTGCCTTTTT 58.672 50.000 0.00 0.00 0.00 1.94
181 185 7.800380 CCGCTGCATCTTTTTAGACAAATATAG 59.200 37.037 0.00 0.00 0.00 1.31
220 224 4.654724 GGCTAGATCCCCTACAAGTTTAGT 59.345 45.833 0.00 0.00 0.00 2.24
221 225 4.902448 AGGCTAGATCCCCTACAAGTTTAG 59.098 45.833 0.00 0.00 0.00 1.85
453 457 6.042322 TGTTAGAACCCAGCACTTAAGAACTA 59.958 38.462 10.09 0.00 0.00 2.24
599 611 4.346730 ACAATGGACCATATATGCCCATG 58.653 43.478 25.69 21.97 38.66 3.66
600 612 4.680278 ACAATGGACCATATATGCCCAT 57.320 40.909 22.22 22.22 39.62 4.00
601 613 4.849235 TCTACAATGGACCATATATGCCCA 59.151 41.667 20.42 20.42 34.89 5.36
602 614 5.435686 TCTACAATGGACCATATATGCCC 57.564 43.478 7.59 10.59 0.00 5.36
603 615 8.023021 TCTATCTACAATGGACCATATATGCC 57.977 38.462 7.59 4.93 0.00 4.40
604 616 8.700051 ACTCTATCTACAATGGACCATATATGC 58.300 37.037 7.59 0.00 0.00 3.14
877 894 9.105844 AGTGATGATAAATATACCTGCCTACTT 57.894 33.333 0.00 0.00 0.00 2.24
944 961 4.076394 GGGTCAAGCAGTGGTTAATTGTA 58.924 43.478 7.35 0.00 0.00 2.41
976 993 1.662044 CAAACTTGTCAGGCAGCCC 59.338 57.895 8.22 0.00 0.00 5.19
1116 1133 2.285024 GGCAAAATGCTCCCAGCCA 61.285 57.895 2.00 0.00 44.28 4.75
1229 1246 1.135489 CGTCGTGCTGGTAGTACATGT 60.135 52.381 2.69 2.69 29.68 3.21
1304 1321 1.590525 GGTGTTGTCGTCGTGCAGA 60.591 57.895 0.00 0.00 0.00 4.26
1352 1369 2.753043 CCGCTGCTGCTCCCATTT 60.753 61.111 14.03 0.00 36.97 2.32
1425 1544 0.823769 TCCTCGTCATCCCCGATCTG 60.824 60.000 0.00 0.00 33.27 2.90
1426 1545 0.538516 CTCCTCGTCATCCCCGATCT 60.539 60.000 0.00 0.00 33.27 2.75
1427 1546 1.960612 CTCCTCGTCATCCCCGATC 59.039 63.158 0.00 0.00 33.27 3.69
1428 1547 2.203771 GCTCCTCGTCATCCCCGAT 61.204 63.158 0.00 0.00 33.27 4.18
1429 1548 2.833582 GCTCCTCGTCATCCCCGA 60.834 66.667 0.00 0.00 0.00 5.14
1430 1549 3.144120 CTGCTCCTCGTCATCCCCG 62.144 68.421 0.00 0.00 0.00 5.73
1431 1550 1.743321 CTCTGCTCCTCGTCATCCCC 61.743 65.000 0.00 0.00 0.00 4.81
1432 1551 1.739049 CTCTGCTCCTCGTCATCCC 59.261 63.158 0.00 0.00 0.00 3.85
1433 1552 1.067250 GCTCTGCTCCTCGTCATCC 59.933 63.158 0.00 0.00 0.00 3.51
1434 1553 1.299014 CGCTCTGCTCCTCGTCATC 60.299 63.158 0.00 0.00 0.00 2.92
1435 1554 2.780094 CCGCTCTGCTCCTCGTCAT 61.780 63.158 0.00 0.00 0.00 3.06
1436 1555 3.443925 CCGCTCTGCTCCTCGTCA 61.444 66.667 0.00 0.00 0.00 4.35
1437 1556 4.200283 CCCGCTCTGCTCCTCGTC 62.200 72.222 0.00 0.00 0.00 4.20
1440 1559 2.841988 ATCCCCGCTCTGCTCCTC 60.842 66.667 0.00 0.00 0.00 3.71
1441 1560 3.160047 CATCCCCGCTCTGCTCCT 61.160 66.667 0.00 0.00 0.00 3.69
1442 1561 3.157252 TCATCCCCGCTCTGCTCC 61.157 66.667 0.00 0.00 0.00 4.70
1485 1604 2.083774 CACCACCATAGCATGTTCGTT 58.916 47.619 0.00 0.00 0.00 3.85
1509 1628 2.235402 CCACCATAGTAGGGTTGTCGTT 59.765 50.000 3.10 0.00 36.19 3.85
1521 1640 0.980754 TCATCCGCCACCACCATAGT 60.981 55.000 0.00 0.00 0.00 2.12
1649 1768 2.662596 GCCACCATCACGAGGTCA 59.337 61.111 0.00 0.00 37.23 4.02
1688 1807 3.924507 GGCATGGTCATGTCACCC 58.075 61.111 10.31 0.98 42.66 4.61
2256 2388 2.258726 GCTTTTTGGCGACCGTCCT 61.259 57.895 0.00 0.00 0.00 3.85
2296 2429 4.120085 CCGAATTGCCGGGAGTAC 57.880 61.111 2.18 0.00 45.43 2.73
2343 2476 1.247567 CCCGCAGTTCAAATTCCAGT 58.752 50.000 0.00 0.00 0.00 4.00
2557 2691 3.701040 GGTAGGCCACATTTGATGATGTT 59.299 43.478 5.01 0.00 38.15 2.71
2610 2744 5.709966 AGAACACTTTTTCAAGAAAACGCT 58.290 33.333 7.44 0.00 39.70 5.07
2640 2774 3.821421 ATCTTCGTTCATGGTAGGTCC 57.179 47.619 0.00 0.00 0.00 4.46
2689 2823 2.783241 TTCAACGGACGCGGCCATAA 62.783 55.000 33.95 16.08 0.00 1.90


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

AutoCloner maintained by Alex Coulton.