Multiple sequence alignment - TraesCS5D01G084000

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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 TraesCS5D01G084000 chr5D 100.000 3901 0 0 1 3901 88141616 88145516 0.000000e+00 7204
1 TraesCS5D01G084000 chr1A 94.708 3137 135 15 1 3121 106531480 106534601 0.000000e+00 4844
2 TraesCS5D01G084000 chr1A 92.734 1968 103 12 1643 3593 433526031 433527975 0.000000e+00 2806
3 TraesCS5D01G084000 chr1A 91.752 1964 90 15 1643 3592 481216745 481218650 0.000000e+00 2663
4 TraesCS5D01G084000 chr1A 95.090 1609 55 10 1 1605 481215157 481216745 0.000000e+00 2512
5 TraesCS5D01G084000 chr1A 94.915 1357 44 9 1 1345 399895874 399894531 0.000000e+00 2100
6 TraesCS5D01G084000 chr1A 93.282 1429 75 8 1710 3121 399893488 399892064 0.000000e+00 2087
7 TraesCS5D01G084000 chr1A 88.751 1698 133 29 1883 3542 496853449 496851772 0.000000e+00 2025
8 TraesCS5D01G084000 chr1A 93.871 1191 47 10 77 1261 433524547 433525717 0.000000e+00 1772
9 TraesCS5D01G084000 chr1A 94.360 851 32 6 1 849 433734502 433735338 0.000000e+00 1291
10 TraesCS5D01G084000 chr1A 90.502 737 41 12 2863 3593 433738523 433739236 0.000000e+00 946
11 TraesCS5D01G084000 chr1A 93.269 312 20 1 3591 3901 399891832 399891521 3.550000e-125 459
12 TraesCS5D01G084000 chr1A 90.997 311 28 0 3591 3901 481218993 481219303 1.680000e-113 420
13 TraesCS5D01G084000 chr6A 94.692 2807 120 10 1 2792 161158445 161155653 0.000000e+00 4331
14 TraesCS5D01G084000 chr6A 93.642 1510 79 5 1000 2493 161412697 161411189 0.000000e+00 2241
15 TraesCS5D01G084000 chr6A 92.283 311 24 0 3591 3901 161147994 161147684 3.580000e-120 442
16 TraesCS5D01G084000 chr6A 90.997 311 28 0 3591 3901 161396121 161395811 1.680000e-113 420
17 TraesCS5D01G084000 chr1D 95.061 1802 62 12 1 1800 83125272 83127048 0.000000e+00 2809
18 TraesCS5D01G084000 chr1D 93.043 1811 80 20 1793 3593 83127368 83129142 0.000000e+00 2604
19 TraesCS5D01G084000 chr1D 93.938 1633 64 4 1119 2748 82303784 82305384 0.000000e+00 2435
20 TraesCS5D01G084000 chr1D 87.264 1484 108 42 2125 3573 400411456 400410019 0.000000e+00 1618
21 TraesCS5D01G084000 chr1D 94.828 522 19 3 1 520 380585789 380586304 0.000000e+00 808
22 TraesCS5D01G084000 chr1D 91.696 289 21 1 3613 3901 380586295 380586580 7.850000e-107 398
23 TraesCS5D01G084000 chr1B 92.619 1951 92 12 1643 3565 510208201 510210127 0.000000e+00 2758
24 TraesCS5D01G084000 chr1B 94.743 837 32 6 1 835 510206495 510207321 0.000000e+00 1291
25 TraesCS5D01G084000 chr1B 96.658 778 21 3 829 1605 510207428 510208201 0.000000e+00 1288
26 TraesCS5D01G084000 chr1B 90.827 774 44 10 528 1301 537494008 537493262 0.000000e+00 1011
27 TraesCS5D01G084000 chr3B 86.384 2049 204 43 1109 3124 728776623 728778629 0.000000e+00 2169
28 TraesCS5D01G084000 chr4B 91.943 1539 79 16 2041 3570 451335689 451334187 0.000000e+00 2113
29 TraesCS5D01G084000 chr4B 91.813 1539 80 17 2041 3570 451242309 451240808 0.000000e+00 2102
30 TraesCS5D01G084000 chr4B 91.813 1539 80 18 2041 3570 451261759 451260258 0.000000e+00 2102
31 TraesCS5D01G084000 chr4B 91.813 1539 81 16 2041 3570 451311090 451309588 0.000000e+00 2102
32 TraesCS5D01G084000 chr4B 93.515 293 19 0 3609 3901 451309217 451308925 1.660000e-118 436
33 TraesCS5D01G084000 chr4B 93.515 293 19 0 3609 3901 451333816 451333524 1.660000e-118 436
34 TraesCS5D01G084000 chr4B 93.174 293 20 0 3609 3901 451240437 451240145 7.740000e-117 431
35 TraesCS5D01G084000 chr4B 93.174 293 20 0 3609 3901 451259888 451259596 7.740000e-117 431
36 TraesCS5D01G084000 chr3A 85.714 2051 200 49 1109 3124 686662407 686664399 0.000000e+00 2078
37 TraesCS5D01G084000 chr5A 81.818 319 47 9 763 1077 638601341 638601030 1.390000e-64 257


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 TraesCS5D01G084000 chr5D 88141616 88145516 3900 False 7204.000000 7204 100.000000 1 3901 1 chr5D.!!$F1 3900
1 TraesCS5D01G084000 chr1A 106531480 106534601 3121 False 4844.000000 4844 94.708000 1 3121 1 chr1A.!!$F1 3120
2 TraesCS5D01G084000 chr1A 433524547 433527975 3428 False 2289.000000 2806 93.302500 77 3593 2 chr1A.!!$F2 3516
3 TraesCS5D01G084000 chr1A 496851772 496853449 1677 True 2025.000000 2025 88.751000 1883 3542 1 chr1A.!!$R1 1659
4 TraesCS5D01G084000 chr1A 481215157 481219303 4146 False 1865.000000 2663 92.613000 1 3901 3 chr1A.!!$F4 3900
5 TraesCS5D01G084000 chr1A 399891521 399895874 4353 True 1548.666667 2100 93.822000 1 3901 3 chr1A.!!$R2 3900
6 TraesCS5D01G084000 chr1A 433734502 433739236 4734 False 1118.500000 1291 92.431000 1 3593 2 chr1A.!!$F3 3592
7 TraesCS5D01G084000 chr6A 161155653 161158445 2792 True 4331.000000 4331 94.692000 1 2792 1 chr6A.!!$R2 2791
8 TraesCS5D01G084000 chr6A 161411189 161412697 1508 True 2241.000000 2241 93.642000 1000 2493 1 chr6A.!!$R4 1493
9 TraesCS5D01G084000 chr1D 83125272 83129142 3870 False 2706.500000 2809 94.052000 1 3593 2 chr1D.!!$F2 3592
10 TraesCS5D01G084000 chr1D 82303784 82305384 1600 False 2435.000000 2435 93.938000 1119 2748 1 chr1D.!!$F1 1629
11 TraesCS5D01G084000 chr1D 400410019 400411456 1437 True 1618.000000 1618 87.264000 2125 3573 1 chr1D.!!$R1 1448
12 TraesCS5D01G084000 chr1D 380585789 380586580 791 False 603.000000 808 93.262000 1 3901 2 chr1D.!!$F3 3900
13 TraesCS5D01G084000 chr1B 510206495 510210127 3632 False 1779.000000 2758 94.673333 1 3565 3 chr1B.!!$F1 3564
14 TraesCS5D01G084000 chr1B 537493262 537494008 746 True 1011.000000 1011 90.827000 528 1301 1 chr1B.!!$R1 773
15 TraesCS5D01G084000 chr3B 728776623 728778629 2006 False 2169.000000 2169 86.384000 1109 3124 1 chr3B.!!$F1 2015
16 TraesCS5D01G084000 chr4B 451333524 451335689 2165 True 1274.500000 2113 92.729000 2041 3901 2 chr4B.!!$R4 1860
17 TraesCS5D01G084000 chr4B 451308925 451311090 2165 True 1269.000000 2102 92.664000 2041 3901 2 chr4B.!!$R3 1860
18 TraesCS5D01G084000 chr4B 451240145 451242309 2164 True 1266.500000 2102 92.493500 2041 3901 2 chr4B.!!$R1 1860
19 TraesCS5D01G084000 chr4B 451259596 451261759 2163 True 1266.500000 2102 92.493500 2041 3901 2 chr4B.!!$R2 1860
20 TraesCS5D01G084000 chr3A 686662407 686664399 1992 False 2078.000000 2078 85.714000 1109 3124 1 chr3A.!!$F1 2015

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
845 974 1.282817 CCATTGATGCGCATTGGTTG 58.717 50.000 26.12 18.27 41.15 3.77 F
1968 4088 1.070758 GAAATCAGATCGGGGCTAGCA 59.929 52.381 18.24 0.00 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 4091 1.045350 TCTCTTCCCTGCCTCATCGG 61.045 60.0 0.00 0.0 0.00 4.18 R
3656 6728 0.988832 AGGACCGCTACCAAAATGGA 59.011 50.0 2.85 0.0 40.96 3.41 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
36 37 4.650734 TGTTCTTGCATCACCAGTGAATA 58.349 39.130 4.31 0.00 43.58 1.75
135 136 3.806625 GCCAATGCCACAATTGAGTAT 57.193 42.857 13.59 5.28 39.46 2.12
240 252 9.916397 GAAATAGTTCTGTAATTTACGGTCATG 57.084 33.333 13.70 0.00 36.45 3.07
241 253 9.661563 AAATAGTTCTGTAATTTACGGTCATGA 57.338 29.630 13.70 0.00 36.45 3.07
242 254 9.832445 AATAGTTCTGTAATTTACGGTCATGAT 57.168 29.630 13.70 0.00 36.45 2.45
301 313 3.095102 TCGTACAAATGTGAACCGTCA 57.905 42.857 0.00 0.00 0.00 4.35
453 468 5.425577 TTTTACTGCATGTTTCGTAGCAA 57.574 34.783 0.00 0.00 36.44 3.91
578 593 7.849804 TGCTAGACTAAAAGATCAATGGAAC 57.150 36.000 0.00 0.00 0.00 3.62
733 748 6.668541 ATTGAGTTATTCCACGACAATCTG 57.331 37.500 0.00 0.00 29.27 2.90
735 750 5.547465 TGAGTTATTCCACGACAATCTGTT 58.453 37.500 0.00 0.00 0.00 3.16
826 842 5.507985 CCTCGAATTGCCTATTTTTGGATCC 60.508 44.000 4.20 4.20 0.00 3.36
845 974 1.282817 CCATTGATGCGCATTGGTTG 58.717 50.000 26.12 18.27 41.15 3.77
846 975 1.404449 CCATTGATGCGCATTGGTTGT 60.404 47.619 26.12 0.00 41.15 3.32
847 976 2.159268 CCATTGATGCGCATTGGTTGTA 60.159 45.455 26.12 5.47 41.15 2.41
875 1892 6.722129 AGACACAATCCAGTCTTCTACTAACT 59.278 38.462 0.00 0.00 42.12 2.24
1051 2075 9.926158 ACATTACATCATTGCATTTCTTTACAA 57.074 25.926 0.00 0.00 0.00 2.41
1201 2225 3.200825 TGCCCTAAGATTTCTCCAAGAGG 59.799 47.826 0.00 0.00 0.00 3.69
1270 2294 3.520290 TCATGTACGGTGGATCAACTC 57.480 47.619 0.00 0.00 0.00 3.01
1368 3116 3.751175 TGCCGGTTTCTATGAACAAGAAG 59.249 43.478 1.90 0.00 34.59 2.85
1520 3272 6.719365 CCATATAGTGCAAGAAACAAGTAGC 58.281 40.000 0.00 0.00 0.00 3.58
1616 3407 1.671742 GACTCTCACCCTTTCGGCA 59.328 57.895 0.00 0.00 33.26 5.69
1738 3530 2.125552 TGTTCGATGCGCTGGGAG 60.126 61.111 9.73 0.00 0.00 4.30
1743 3536 4.166888 GATGCGCTGGGAGGCAGA 62.167 66.667 9.73 0.00 43.27 4.26
1939 4059 2.666508 CTGCGCTAGCTTTTAACGAGAA 59.333 45.455 13.93 0.00 45.42 2.87
1968 4088 1.070758 GAAATCAGATCGGGGCTAGCA 59.929 52.381 18.24 0.00 0.00 3.49
2051 4171 2.357034 GGCGAGGAAGCGACACAA 60.357 61.111 0.00 0.00 39.62 3.33
2202 4397 5.428253 ACAAGCGAAGGATTTCTATTGCTA 58.572 37.500 0.00 0.00 33.33 3.49
2301 4498 3.763360 TGGATTTGATGGAATTGCGAGTT 59.237 39.130 0.00 0.00 0.00 3.01
2358 4555 8.204836 AGTACTTAGGTCTATGCCTAACAATTG 58.795 37.037 3.24 3.24 43.84 2.32
2426 4624 0.969409 GCAAGGCTCAAGGGAAGCAT 60.969 55.000 0.00 0.00 0.00 3.79
2452 4652 6.097356 CGGTTCTGTAGTTCTTTGTATGCTA 58.903 40.000 0.00 0.00 0.00 3.49
2474 4674 2.126882 TGGTATCTTGGATGAGGGGTG 58.873 52.381 0.00 0.00 0.00 4.61
2476 4676 2.509964 GGTATCTTGGATGAGGGGTGTT 59.490 50.000 0.00 0.00 0.00 3.32
2668 4880 1.134037 TGGTTGTGTTCCTGGTGGTAC 60.134 52.381 0.00 0.00 34.67 3.34
2677 4889 1.479323 TCCTGGTGGTACGCATTCTAC 59.521 52.381 0.00 0.00 43.02 2.59
2947 5489 9.378551 CATTGTTGTAGAGTATAAAAGGTGCTA 57.621 33.333 0.00 0.00 0.00 3.49
3138 5718 4.510340 ACGCTATGTTTTTCTTCGTGTTCT 59.490 37.500 0.00 0.00 0.00 3.01
3346 5948 7.406553 TCGAATATGTGAACGATTTTGGAATC 58.593 34.615 0.00 0.00 38.62 2.52
3359 5961 6.798959 CGATTTTGGAATCTGTGAAGAGTTTC 59.201 38.462 0.00 0.00 39.61 2.78
3487 6214 7.802738 TGAGAACATTTTTCGAACACGATAAT 58.197 30.769 0.00 0.00 35.96 1.28
3488 6215 7.744276 TGAGAACATTTTTCGAACACGATAATG 59.256 33.333 17.54 17.54 40.27 1.90
3524 6251 7.340122 TGTGAACATTGTTTTAGAATCCACA 57.660 32.000 3.08 7.73 0.00 4.17
3646 6718 2.650322 GTGTGTCCCACTTTGGAGAAA 58.350 47.619 0.00 0.00 40.96 2.52
3656 6728 5.245977 CCCACTTTGGAGAAAAATACACCAT 59.754 40.000 0.00 0.00 40.96 3.55
3672 6744 1.005450 ACCATCCATTTTGGTAGCGGT 59.995 47.619 0.00 0.00 45.62 5.68
3705 6777 6.240894 TCATCTCAACAATTCTGTTTAGGCT 58.759 36.000 0.00 0.00 43.45 4.58
3712 6784 7.231317 TCAACAATTCTGTTTAGGCTTCATTCT 59.769 33.333 0.00 0.00 43.45 2.40
3718 6790 6.237901 TCTGTTTAGGCTTCATTCTGCTAAA 58.762 36.000 0.00 0.00 0.00 1.85
3799 6871 1.146774 TCCAACAGAGGGAATGCCAAA 59.853 47.619 0.00 0.00 35.15 3.28
3852 6924 2.679059 CGTGCCACTTGAGAGGATGAAT 60.679 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 8.426569 AAAATCAATATTATGGGTAGCAGCAT 57.573 30.769 0.00 0.00 0.00 3.79
135 136 7.914427 TTATTTTAGGAGAGACCATCTAGCA 57.086 36.000 0.00 0.00 38.84 3.49
196 197 8.774546 ACTATTTCTGACCAAGAGAGATATGA 57.225 34.615 0.00 0.00 35.91 2.15
234 245 5.192927 TGTTCTGGGTTTATCATCATGACC 58.807 41.667 0.00 0.00 0.00 4.02
283 295 9.997482 AATATAAATGACGGTTCACATTTGTAC 57.003 29.630 13.49 0.00 43.47 2.90
451 466 6.480524 TCCGTTTCATAAACAGATGTCTTG 57.519 37.500 3.68 0.00 41.44 3.02
453 468 5.643777 CCTTCCGTTTCATAAACAGATGTCT 59.356 40.000 3.68 0.00 41.44 3.41
630 645 9.941325 AATGTTGGTTGCAAAATTAATGATCTA 57.059 25.926 0.00 0.00 0.00 1.98
704 719 6.169800 TGTCGTGGAATAACTCAATTGATCA 58.830 36.000 8.96 0.00 0.00 2.92
705 720 6.662414 TGTCGTGGAATAACTCAATTGATC 57.338 37.500 8.96 2.96 0.00 2.92
733 748 2.095415 GCGGGACTTTATGGTCACAAAC 60.095 50.000 0.00 0.00 39.40 2.93
735 750 1.816074 GCGGGACTTTATGGTCACAA 58.184 50.000 0.00 0.00 39.40 3.33
845 974 6.518208 AGAAGACTGGATTGTGTCTACTAC 57.482 41.667 0.00 0.00 42.02 2.73
846 975 7.403671 AGTAGAAGACTGGATTGTGTCTACTA 58.596 38.462 8.33 0.00 42.02 1.82
847 976 6.249951 AGTAGAAGACTGGATTGTGTCTACT 58.750 40.000 4.94 4.94 42.02 2.57
1051 2075 5.321102 TGTATCACAACAGTGGGCTAATTT 58.679 37.500 0.00 0.00 34.04 1.82
1100 2124 8.345565 GCACCTTCAATTCTATAACATAGTTGG 58.654 37.037 0.00 0.00 0.00 3.77
1117 2141 6.303839 AGAAATTTAGTGTAGGCACCTTCAA 58.696 36.000 0.00 0.00 46.35 2.69
1201 2225 3.874392 AATTTTGCTCCTGGTATGCAC 57.126 42.857 10.21 0.00 36.37 4.57
1520 3272 2.091277 CACTAAGCTTTTGTCTCGCTCG 59.909 50.000 3.20 0.00 32.70 5.03
1623 3414 1.707427 AGTTCTCATGGTCCCTGCTTT 59.293 47.619 0.00 0.00 0.00 3.51
1738 3530 2.625790 ACGACCTTCATCTCTATCTGCC 59.374 50.000 0.00 0.00 0.00 4.85
1743 3536 4.272991 GTCACGTACGACCTTCATCTCTAT 59.727 45.833 24.41 0.00 0.00 1.98
1925 4045 6.289064 TCTTCTTCCTTTCTCGTTAAAAGCT 58.711 36.000 0.00 0.00 33.33 3.74
1929 4049 8.671384 TGATTTCTTCTTCCTTTCTCGTTAAA 57.329 30.769 0.00 0.00 0.00 1.52
1939 4059 4.384647 CCCCGATCTGATTTCTTCTTCCTT 60.385 45.833 0.00 0.00 0.00 3.36
1971 4091 1.045350 TCTCTTCCCTGCCTCATCGG 61.045 60.000 0.00 0.00 0.00 4.18
2051 4171 2.182825 GTACGTCGATTCGCATGTTCT 58.817 47.619 0.00 0.00 0.00 3.01
2202 4397 3.816994 AGCCAACGGTCTTTAAAGAACT 58.183 40.909 26.50 13.67 40.62 3.01
2301 4498 6.509418 GACACTAAAATATGTCAAAGGGCA 57.491 37.500 0.00 0.00 43.89 5.36
2426 4624 5.475719 CATACAAAGAACTACAGAACCGGA 58.524 41.667 9.46 0.00 0.00 5.14
2452 4652 3.139025 CACCCCTCATCCAAGATACCATT 59.861 47.826 0.00 0.00 0.00 3.16
2668 4880 8.138712 AGGATAGAAACTAAGAAGTAGAATGCG 58.861 37.037 0.00 0.00 33.75 4.73
2888 5425 4.336993 TGTGGGTTAATTTATCACCATCGC 59.663 41.667 0.00 0.00 31.50 4.58
2938 5480 7.179338 CCCATGTCTATACTCTATAGCACCTTT 59.821 40.741 0.00 0.00 38.39 3.11
3092 5672 7.740346 GCGTTGACCATAATTCTTTATACATCG 59.260 37.037 0.00 0.00 0.00 3.84
3346 5948 7.374272 TCACTGATTCTAGAAACTCTTCACAG 58.626 38.462 9.71 10.64 33.64 3.66
3457 6084 8.286800 TCGTGTTCGAAAAATGTTCTCATATTT 58.713 29.630 0.00 0.00 43.34 1.40
3487 6214 7.678947 ACAATGTTCACAAATTCCAAAAACA 57.321 28.000 0.00 0.00 0.00 2.83
3488 6215 8.962857 AAACAATGTTCACAAATTCCAAAAAC 57.037 26.923 0.00 0.00 0.00 2.43
3593 6665 4.829872 ACACGACCAACTGGGATATAAA 57.170 40.909 0.00 0.00 41.15 1.40
3656 6728 0.988832 AGGACCGCTACCAAAATGGA 59.011 50.000 2.85 0.00 40.96 3.41
3672 6744 8.762645 ACAGAATTGTTGAGATGAGTTATAGGA 58.237 33.333 0.00 0.00 32.28 2.94
3705 6777 3.374058 GCCTAGCGTTTTAGCAGAATGAA 59.626 43.478 0.00 0.00 39.69 2.57
3712 6784 2.394930 TGATGCCTAGCGTTTTAGCA 57.605 45.000 0.00 0.00 40.15 3.49
3718 6790 1.418334 AGGAGATGATGCCTAGCGTT 58.582 50.000 0.00 0.00 31.31 4.84
3799 6871 1.488390 GGACAATGCCACCATGGATT 58.512 50.000 21.47 4.45 40.96 3.01
3832 6904 2.479566 TTCATCCTCTCAAGTGGCAC 57.520 50.000 10.29 10.29 0.00 5.01
3881 6954 2.989422 GTGGCAAAATCACTAGCGTT 57.011 45.000 0.00 0.00 32.78 4.84


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

AutoCloner maintained by Alex Coulton.