Multiple sequence alignment - TraesCS1D01G241100

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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 TraesCS1D01G241100 chr1D 100.000 2968 0 0 1 2968 331504734 331507701 0.000000e+00 5481.0
1 TraesCS1D01G241100 chr1A 93.924 1909 63 18 1 1884 428662723 428664603 0.000000e+00 2833.0
2 TraesCS1D01G241100 chr1A 90.403 521 42 8 1914 2433 428664602 428665115 0.000000e+00 678.0
3 TraesCS1D01G241100 chr1A 87.339 545 48 7 2422 2965 428665147 428665671 3.270000e-169 604.0
4 TraesCS1D01G241100 chr1B 92.335 1983 106 13 1011 2968 445877856 445879817 0.000000e+00 2778.0
5 TraesCS1D01G241100 chr1B 93.811 921 39 8 1 909 445876752 445877666 0.000000e+00 1369.0
6 TraesCS1D01G241100 chr2D 86.047 86 12 0 1579 1664 77170659 77170574 3.150000e-15 93.5
7 TraesCS1D01G241100 chr2B 84.043 94 12 2 1579 1672 119049476 119049386 1.470000e-13 87.9
8 TraesCS1D01G241100 chr2A 84.884 86 13 0 1579 1664 78183045 78182960 1.470000e-13 87.9
9 TraesCS1D01G241100 chr7A 81.081 111 16 4 1555 1664 547757616 547757510 1.900000e-12 84.2
10 TraesCS1D01G241100 chr7D 88.406 69 3 4 1555 1622 447908014 447908078 8.820000e-11 78.7
11 TraesCS1D01G241100 chr7B 87.879 66 3 4 1555 1619 465216986 465217047 4.100000e-09 73.1
12 TraesCS1D01G241100 chr6D 90.741 54 4 1 2188 2241 82472801 82472853 1.480000e-08 71.3


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 TraesCS1D01G241100 chr1D 331504734 331507701 2967 False 5481.000000 5481 100.000000 1 2968 1 chr1D.!!$F1 2967
1 TraesCS1D01G241100 chr1A 428662723 428665671 2948 False 1371.666667 2833 90.555333 1 2965 3 chr1A.!!$F1 2964
2 TraesCS1D01G241100 chr1B 445876752 445879817 3065 False 2073.500000 2778 93.073000 1 2968 2 chr1B.!!$F1 2967

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
370 374 3.246936 GGAAAACACGCGAAGAAGTAAGT 59.753 43.478 15.93 0.0 0.00 2.24 F
1035 1136 0.689080 TCAGTCAGAGCATCCCTCCC 60.689 60.000 0.00 0.0 41.74 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1878 0.617413 CTCTCTTGATGGCCACCACT 59.383 55.0 8.16 0.0 35.80 4.00 R
2435 2604 0.665835 TTTTGACGCGCCAATCAAGT 59.334 45.0 9.11 0.0 36.26 3.16 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
32 33 6.767456 CAGATATCTGAATAGCCTCTTGGTT 58.233 40.000 25.78 0.00 46.59 3.67
38 39 7.200434 TCTGAATAGCCTCTTGGTTAATCTT 57.800 36.000 0.00 0.00 32.34 2.40
94 95 4.607293 TCTCCATTGTATCCGAATCTGG 57.393 45.455 0.00 0.00 0.00 3.86
183 184 5.200483 TCCCAACTCTGACAAAACAAAGAT 58.800 37.500 0.00 0.00 0.00 2.40
224 225 7.061905 CCGATACGACATCTAAATTAAAGCGAT 59.938 37.037 0.00 0.00 0.00 4.58
243 244 3.302740 CGATTGTTATCTTCTCTTGCGCC 60.303 47.826 4.18 0.00 0.00 6.53
321 325 7.402862 TGATATCTCTGGCAATCAATGATCAT 58.597 34.615 1.18 1.18 0.00 2.45
356 360 5.163733 TGACTAAAACTGAACCGGAAAACAC 60.164 40.000 9.46 0.00 0.00 3.32
370 374 3.246936 GGAAAACACGCGAAGAAGTAAGT 59.753 43.478 15.93 0.00 0.00 2.24
541 545 7.664758 AGAAGCAAAGCATCTTCTAAAATTGT 58.335 30.769 2.98 0.00 45.01 2.71
693 701 4.910195 TGGAGCACTGTTAGATGTCAAAT 58.090 39.130 0.00 0.00 0.00 2.32
757 766 3.719268 TTGCTAGAAGCTCCATTTCCA 57.281 42.857 0.00 0.00 42.97 3.53
760 769 4.406456 TGCTAGAAGCTCCATTTCCAAAA 58.594 39.130 0.00 0.00 42.97 2.44
901 914 7.088272 GCCGGTCAACTTTTGAGTAAAATAAT 58.912 34.615 1.90 0.00 41.01 1.28
981 994 4.174051 CCCCTCCCTATATATACATCCCCA 59.826 50.000 0.00 0.00 0.00 4.96
1035 1136 0.689080 TCAGTCAGAGCATCCCTCCC 60.689 60.000 0.00 0.00 41.74 4.30
1726 1827 4.767255 GTGAGGCTGGTCGGGCTG 62.767 72.222 10.68 0.00 42.23 4.85
1732 1833 3.058160 CTGGTCGGGCTGGCAAAG 61.058 66.667 0.00 0.00 0.00 2.77
1747 1848 5.803967 GCTGGCAAAGAATTCAAGATAACAG 59.196 40.000 8.44 7.96 0.00 3.16
1756 1857 3.543680 TCAAGATAACAGTAGCAGCCC 57.456 47.619 0.00 0.00 0.00 5.19
1774 1876 2.174592 CGCGTGCGTTATTGCCAA 59.825 55.556 6.00 0.00 34.35 4.52
1776 1878 0.999228 CGCGTGCGTTATTGCCAAAA 60.999 50.000 6.00 0.00 34.35 2.44
2066 2190 1.810755 GGACTCAAATTCCGTGTTCCC 59.189 52.381 0.00 0.00 0.00 3.97
2076 2200 6.510879 AATTCCGTGTTCCCTTTTCTAATC 57.489 37.500 0.00 0.00 0.00 1.75
2081 2205 4.326548 CGTGTTCCCTTTTCTAATCTCGAC 59.673 45.833 0.00 0.00 0.00 4.20
2104 2229 7.437267 CGACGGTACTAATAAGTTCCAAATGAT 59.563 37.037 0.00 0.00 41.92 2.45
2248 2373 4.537433 GCGAGCTCGGCCCTTGAT 62.537 66.667 35.10 0.00 40.23 2.57
2261 2386 4.016444 GGCCCTTGATTGTAGATCAAACA 58.984 43.478 0.00 0.00 39.62 2.83
2308 2433 2.640826 TGTGGAATTACGGGACTCCTTT 59.359 45.455 0.00 0.00 0.00 3.11
2343 2469 0.037734 TCGTGTGAGCTCTCCCTACA 59.962 55.000 16.19 7.53 0.00 2.74
2381 2507 2.124942 GGGCCGAGCTTCTTCTGG 60.125 66.667 0.00 0.00 0.00 3.86
2383 2509 1.296715 GGCCGAGCTTCTTCTGGAA 59.703 57.895 0.00 0.00 0.00 3.53
2433 2602 3.248888 AGGATATTTCCCCCTAAGACCG 58.751 50.000 0.00 0.00 43.76 4.79
2435 2604 2.873053 TATTTCCCCCTAAGACCGGA 57.127 50.000 9.46 0.00 0.00 5.14
2479 2648 9.984190 AAGAAAAACGCCCTTACATTATTTAAA 57.016 25.926 0.00 0.00 0.00 1.52
2500 2669 3.520290 ATCGAGTGAATTCCGCACTTA 57.480 42.857 2.27 0.00 45.94 2.24
2598 2768 1.870580 CGCGTAAGGTTGACTGTTGGA 60.871 52.381 0.00 0.00 38.28 3.53
2618 2788 1.341976 ACCCACCCAATAGAACATGGC 60.342 52.381 0.00 0.00 35.28 4.40
2770 2940 8.200792 TCTTTAATATTTTGTGTTTGGCAGTGT 58.799 29.630 0.00 0.00 0.00 3.55
2816 2986 9.559958 CTTGTTTGACTAATTAGTATTTGCCTG 57.440 33.333 18.03 2.82 36.50 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.357579 ACCAAGAGGCTATTCAGATATCTG 57.642 41.667 24.32 24.32 41.24 2.90
63 64 8.430573 TCGGATACAATGGAGAAATTAGGATA 57.569 34.615 0.00 0.00 0.00 2.59
123 124 2.627945 TCTTATGTCACCAATGCGACC 58.372 47.619 0.00 0.00 0.00 4.79
183 184 2.979814 ATCGGTCACGGAATGATGAA 57.020 45.000 0.00 0.00 40.28 2.57
224 225 3.052455 TGGCGCAAGAGAAGATAACAA 57.948 42.857 10.83 0.00 43.02 2.83
321 325 7.865385 GGTTCAGTTTTAGTCATTGCATTAACA 59.135 33.333 0.00 0.00 0.00 2.41
356 360 4.555348 AGGAGATACTTACTTCTTCGCG 57.445 45.455 0.00 0.00 0.00 5.87
370 374 3.202906 GTGGCGTGCATTTTAGGAGATA 58.797 45.455 0.00 0.00 0.00 1.98
541 545 4.400529 TTGAAGAGATAACTATGCCGCA 57.599 40.909 0.00 0.00 0.00 5.69
640 644 9.551734 CTCAGTTCATTCAACCATGATAGAATA 57.448 33.333 0.00 0.00 35.28 1.75
723 731 6.660949 AGCTTCTAGCAATTAGTGAATGGTTT 59.339 34.615 1.09 0.00 45.56 3.27
757 766 1.607767 GGCAATGTCAACGCCCATTTT 60.608 47.619 4.82 0.00 40.07 1.82
760 769 3.287445 GGCAATGTCAACGCCCAT 58.713 55.556 4.82 0.00 40.07 4.00
922 935 5.067805 GGGTTGACATTTGAAAAGTCAGAGT 59.932 40.000 14.45 0.00 42.54 3.24
981 994 4.202609 ACAAGATTTGAGGATTCCTGGTGT 60.203 41.667 10.74 0.89 31.76 4.16
1035 1136 1.154035 GGTGCGAAATTGCGGAAGG 60.154 57.895 8.18 0.00 37.81 3.46
1723 1824 5.713025 TGTTATCTTGAATTCTTTGCCAGC 58.287 37.500 7.05 0.00 0.00 4.85
1724 1825 6.917533 ACTGTTATCTTGAATTCTTTGCCAG 58.082 36.000 7.05 6.76 0.00 4.85
1725 1826 6.899393 ACTGTTATCTTGAATTCTTTGCCA 57.101 33.333 7.05 0.00 0.00 4.92
1726 1827 6.969473 GCTACTGTTATCTTGAATTCTTTGCC 59.031 38.462 7.05 0.00 0.00 4.52
1727 1828 7.530010 TGCTACTGTTATCTTGAATTCTTTGC 58.470 34.615 7.05 0.00 0.00 3.68
1728 1829 7.695618 GCTGCTACTGTTATCTTGAATTCTTTG 59.304 37.037 7.05 0.00 0.00 2.77
1729 1830 7.148171 GGCTGCTACTGTTATCTTGAATTCTTT 60.148 37.037 7.05 0.00 0.00 2.52
1730 1831 6.317391 GGCTGCTACTGTTATCTTGAATTCTT 59.683 38.462 7.05 0.00 0.00 2.52
1731 1832 5.819901 GGCTGCTACTGTTATCTTGAATTCT 59.180 40.000 7.05 0.00 0.00 2.40
1732 1833 5.008118 GGGCTGCTACTGTTATCTTGAATTC 59.992 44.000 0.00 0.00 0.00 2.17
1756 1857 2.788172 TTTGGCAATAACGCACGCGG 62.788 55.000 16.70 0.00 44.69 6.46
1774 1876 1.425066 TCTCTTGATGGCCACCACTTT 59.575 47.619 8.16 0.00 35.80 2.66
1776 1878 0.617413 CTCTCTTGATGGCCACCACT 59.383 55.000 8.16 0.00 35.80 4.00
1808 1930 6.612247 TGAACAATTAAGCGAGACTGAAAA 57.388 33.333 0.00 0.00 0.00 2.29
2066 2190 9.941664 TTATTAGTACCGTCGAGATTAGAAAAG 57.058 33.333 0.00 0.00 0.00 2.27
2076 2200 5.490139 TGGAACTTATTAGTACCGTCGAG 57.510 43.478 0.00 0.00 33.17 4.04
2081 2205 8.765219 CAGATCATTTGGAACTTATTAGTACCG 58.235 37.037 0.00 0.00 33.17 4.02
2169 2294 9.887862 ATGATATTCAAGGGGTATTCTTTGAAT 57.112 29.630 15.53 15.53 32.46 2.57
2179 2304 4.660303 AGAGCACATGATATTCAAGGGGTA 59.340 41.667 0.00 0.00 28.70 3.69
2248 2373 7.623630 TCCTCATCTGATTGTTTGATCTACAA 58.376 34.615 13.76 13.76 39.58 2.41
2261 2386 5.723887 AGTTCCAGTAACTCCTCATCTGATT 59.276 40.000 0.00 0.00 45.64 2.57
2291 2416 2.026542 ACCCAAAGGAGTCCCGTAATTC 60.027 50.000 5.25 0.00 37.58 2.17
2308 2433 1.336440 CACGAATTTGCAGACAACCCA 59.664 47.619 0.00 0.00 34.87 4.51
2411 2537 3.651423 CGGTCTTAGGGGGAAATATCCTT 59.349 47.826 0.00 0.00 45.77 3.36
2433 2602 1.573829 TTGACGCGCCAATCAAGTCC 61.574 55.000 5.73 0.00 31.29 3.85
2435 2604 0.665835 TTTTGACGCGCCAATCAAGT 59.334 45.000 9.11 0.00 36.26 3.16
2479 2648 2.386661 AGTGCGGAATTCACTCGATT 57.613 45.000 7.93 0.00 40.47 3.34
2500 2669 1.453155 AGCCGCATCTTTCGAACATT 58.547 45.000 0.00 0.00 0.00 2.71
2529 2699 1.278238 CATTCCTCCAAGACGCGTAC 58.722 55.000 13.97 6.11 0.00 3.67
2586 2756 0.822121 GGGTGGGTCCAACAGTCAAC 60.822 60.000 7.40 0.00 38.11 3.18
2598 2768 1.341976 GCCATGTTCTATTGGGTGGGT 60.342 52.381 0.00 0.00 33.40 4.51
2693 2863 5.698832 TGAGTTTGTGACACTTTTGAACTG 58.301 37.500 7.20 0.00 0.00 3.16
2702 2872 8.150945 ACACTATAAGATTGAGTTTGTGACACT 58.849 33.333 7.20 0.00 0.00 3.55
2863 3033 9.034544 AGTTGAACTGCAAAATTGAAACTTATC 57.965 29.630 0.00 0.00 38.44 1.75


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

AutoCloner maintained by Alex Coulton.