Multiple sequence alignment - TraesCS5D01G549700

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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 TraesCS5D01G549700 chr5D 100.000 2404 0 0 1 2404 556579566 556577163 0.000000e+00 4440
1 TraesCS5D01G549700 chr2D 96.509 2406 63 13 1 2404 586830123 586832509 0.000000e+00 3958
2 TraesCS5D01G549700 chr3D 96.974 2214 64 3 193 2404 10934085 10931873 0.000000e+00 3714
3 TraesCS5D01G549700 chr3D 96.916 1978 57 4 193 2167 588695488 588697464 0.000000e+00 3312
4 TraesCS5D01G549700 chr3D 96.682 663 19 2 1718 2380 564469366 564468707 0.000000e+00 1099
5 TraesCS5D01G549700 chr6D 96.296 2214 66 7 193 2404 372614389 372612190 0.000000e+00 3620
6 TraesCS5D01G549700 chr1B 95.407 2221 88 8 193 2404 137870317 137872532 0.000000e+00 3524
7 TraesCS5D01G549700 chr5A 95.613 1778 64 9 193 1962 155591015 155592786 0.000000e+00 2839
8 TraesCS5D01G549700 chr5A 97.436 195 5 0 1 195 102197009 102196815 1.380000e-87 333
9 TraesCS5D01G549700 chr5A 97.436 195 5 0 1 195 517848712 517848906 1.380000e-87 333
10 TraesCS5D01G549700 chr1A 95.289 1486 69 1 919 2404 379647386 379648870 0.000000e+00 2355
11 TraesCS5D01G549700 chr7B 95.253 1243 55 2 481 1723 97120866 97119628 0.000000e+00 1965
12 TraesCS5D01G549700 chr7B 94.288 1243 58 5 481 1723 89870745 89869516 0.000000e+00 1890
13 TraesCS5D01G549700 chr7B 97.238 688 17 2 1718 2404 97118346 97117660 0.000000e+00 1164
14 TraesCS5D01G549700 chr7B 95.777 663 25 3 1718 2380 669055779 669055120 0.000000e+00 1066
15 TraesCS5D01G549700 chr7B 97.949 195 4 0 1 195 656270753 656270947 2.960000e-89 339
16 TraesCS5D01G549700 chr5B 96.717 396 11 2 193 586 652146191 652145796 0.000000e+00 658
17 TraesCS5D01G549700 chr5B 95.960 396 14 2 193 586 651940958 651940563 2.010000e-180 641
18 TraesCS5D01G549700 chr4D 96.220 291 9 2 193 481 500936366 500936076 2.160000e-130 475
19 TraesCS5D01G549700 chr3A 99.487 195 1 0 1 195 125406223 125406029 2.940000e-94 355
20 TraesCS5D01G549700 chr3A 98.974 195 2 0 1 195 237821776 237821582 1.370000e-92 350
21 TraesCS5D01G549700 chr3A 98.421 190 3 0 6 195 593146047 593146236 3.830000e-88 335
22 TraesCS5D01G549700 chr3A 97.436 195 5 0 1 195 45642788 45642982 1.380000e-87 333
23 TraesCS5D01G549700 chr6A 97.436 195 5 0 1 195 60060905 60060711 1.380000e-87 333
24 TraesCS5D01G549700 chr2A 97.436 195 2 1 1 195 698899060 698898869 1.780000e-86 329
25 TraesCS5D01G549700 chr2B 93.627 204 13 0 494 697 43958051 43958254 3.000000e-79 305


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 TraesCS5D01G549700 chr5D 556577163 556579566 2403 True 4440.0 4440 100.0000 1 2404 1 chr5D.!!$R1 2403
1 TraesCS5D01G549700 chr2D 586830123 586832509 2386 False 3958.0 3958 96.5090 1 2404 1 chr2D.!!$F1 2403
2 TraesCS5D01G549700 chr3D 10931873 10934085 2212 True 3714.0 3714 96.9740 193 2404 1 chr3D.!!$R1 2211
3 TraesCS5D01G549700 chr3D 588695488 588697464 1976 False 3312.0 3312 96.9160 193 2167 1 chr3D.!!$F1 1974
4 TraesCS5D01G549700 chr3D 564468707 564469366 659 True 1099.0 1099 96.6820 1718 2380 1 chr3D.!!$R2 662
5 TraesCS5D01G549700 chr6D 372612190 372614389 2199 True 3620.0 3620 96.2960 193 2404 1 chr6D.!!$R1 2211
6 TraesCS5D01G549700 chr1B 137870317 137872532 2215 False 3524.0 3524 95.4070 193 2404 1 chr1B.!!$F1 2211
7 TraesCS5D01G549700 chr5A 155591015 155592786 1771 False 2839.0 2839 95.6130 193 1962 1 chr5A.!!$F1 1769
8 TraesCS5D01G549700 chr1A 379647386 379648870 1484 False 2355.0 2355 95.2890 919 2404 1 chr1A.!!$F1 1485
9 TraesCS5D01G549700 chr7B 89869516 89870745 1229 True 1890.0 1890 94.2880 481 1723 1 chr7B.!!$R1 1242
10 TraesCS5D01G549700 chr7B 97117660 97120866 3206 True 1564.5 1965 96.2455 481 2404 2 chr7B.!!$R3 1923
11 TraesCS5D01G549700 chr7B 669055120 669055779 659 True 1066.0 1066 95.7770 1718 2380 1 chr7B.!!$R2 662

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
28 29 0.112606 ACCTCTCTCACGTTCCCTGA 59.887 55.0 0.00 0.0 0.00 3.86 F
1046 1063 0.891373 TGGGAGCTCGTGAAGAAGAG 59.109 55.0 7.83 0.0 37.54 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1145 1162 1.295423 GCAAAGAGCTACGGACCCA 59.705 57.895 0.0 0.0 41.15 4.51 R
2017 3323 2.393271 AACACTCATCAGGTAGCAGC 57.607 50.000 0.0 0.0 0.00 5.25 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
28 29 0.112606 ACCTCTCTCACGTTCCCTGA 59.887 55.000 0.00 0.00 0.00 3.86
39 40 2.083774 CGTTCCCTGATTTTGCTGCTA 58.916 47.619 0.00 0.00 0.00 3.49
106 107 2.175284 AGTCCCTAGTCCCTAGTGCTAC 59.825 54.545 0.00 0.00 32.62 3.58
107 108 2.175284 GTCCCTAGTCCCTAGTGCTACT 59.825 54.545 0.00 0.00 32.62 2.57
108 109 3.393941 GTCCCTAGTCCCTAGTGCTACTA 59.606 52.174 0.00 0.00 32.62 1.82
109 110 3.651904 TCCCTAGTCCCTAGTGCTACTAG 59.348 52.174 13.35 13.35 45.93 2.57
110 111 3.395273 CCCTAGTCCCTAGTGCTACTAGT 59.605 52.174 16.87 0.00 45.12 2.57
111 112 4.505390 CCCTAGTCCCTAGTGCTACTAGTC 60.505 54.167 16.87 10.09 45.12 2.59
112 113 3.581265 AGTCCCTAGTGCTACTAGTCC 57.419 52.381 16.87 0.00 45.12 3.85
113 114 2.175284 AGTCCCTAGTGCTACTAGTCCC 59.825 54.545 16.87 0.00 45.12 4.46
114 115 2.175284 GTCCCTAGTGCTACTAGTCCCT 59.825 54.545 16.87 0.00 45.12 4.20
115 116 3.393941 GTCCCTAGTGCTACTAGTCCCTA 59.606 52.174 16.87 0.00 45.12 3.53
116 117 3.651904 TCCCTAGTGCTACTAGTCCCTAG 59.348 52.174 16.87 5.03 45.12 3.02
117 118 3.395273 CCCTAGTGCTACTAGTCCCTAGT 59.605 52.174 16.87 8.79 45.12 2.57
118 119 4.391155 CCTAGTGCTACTAGTCCCTAGTG 58.609 52.174 12.94 5.66 45.52 2.74
119 120 2.657143 AGTGCTACTAGTCCCTAGTGC 58.343 52.381 12.94 13.48 45.52 4.40
120 121 2.242708 AGTGCTACTAGTCCCTAGTGCT 59.757 50.000 12.94 4.70 45.52 4.40
121 122 3.458857 AGTGCTACTAGTCCCTAGTGCTA 59.541 47.826 12.94 4.90 45.52 3.49
296 298 7.704578 ACTGTAGAGATGTAGAACTAAAGCA 57.295 36.000 0.00 0.00 0.00 3.91
498 514 1.174712 GCACACAGGTCAACATGCCT 61.175 55.000 0.00 0.00 35.04 4.75
603 619 5.844396 GCCGTGAAGCAACGTTTATAATATC 59.156 40.000 0.00 0.00 42.01 1.63
665 681 8.831715 TCGCTAGCAAGATTTCAATCATAATA 57.168 30.769 16.45 0.00 37.89 0.98
964 980 1.950216 TGCTAGCTGTAGGATCTGACG 59.050 52.381 17.23 0.00 0.00 4.35
1016 1033 2.629051 GGAAATGACTACCGTTCCAGG 58.371 52.381 0.00 0.00 37.30 4.45
1046 1063 0.891373 TGGGAGCTCGTGAAGAAGAG 59.109 55.000 7.83 0.00 37.54 2.85
1083 1100 1.174712 AGCAGTTCGGCAACAGCAAT 61.175 50.000 15.37 0.00 45.21 3.56
1094 1111 1.067635 CAACAGCAATACCAAGGTGCC 60.068 52.381 1.07 0.00 39.13 5.01
1128 1145 2.228822 GCCCAACAACCTCTACAATGTG 59.771 50.000 0.00 0.00 0.00 3.21
1145 1162 3.838244 TGTGCACTCCTACAAGTTCTT 57.162 42.857 19.41 0.00 0.00 2.52
1358 1375 0.607620 AGCTCCAGCACAAGACTCTC 59.392 55.000 0.48 0.00 45.16 3.20
1699 1716 3.056821 TGCTCGTAGATGTTGCTACTTGT 60.057 43.478 0.00 0.00 38.83 3.16
1702 1719 3.437741 TCGTAGATGTTGCTACTTGTCGA 59.562 43.478 0.00 1.80 38.83 4.20
1981 3287 6.929606 AGTTTTTACTACTGCTTACACAGAGG 59.070 38.462 0.00 0.00 40.25 3.69
2017 3323 5.086058 ACTAAAACAGCGATTTTGTATGCG 58.914 37.500 10.23 0.00 33.80 4.73
2035 3341 0.174389 CGCTGCTACCTGATGAGTGT 59.826 55.000 0.00 0.00 0.00 3.55
2077 3383 4.496360 CTTGGCATGCATATGTTTGTTCA 58.504 39.130 21.36 0.00 36.65 3.18
2184 3491 5.001232 TGTACTTGAAGCTGTGGGTTAATC 58.999 41.667 0.00 0.00 32.93 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.693969 AGTGAATTTAGAGTAGCAGCAAAAT 57.306 32.000 0.00 0.00 0.00 1.82
39 40 7.987458 TCAGTCAAGTGAAAGTGAATTTAGAGT 59.013 33.333 0.00 0.00 0.00 3.24
78 79 0.614979 GGGACTAGGGACTGACAGCA 60.615 60.000 1.25 0.00 41.52 4.41
107 108 2.510382 AGAGCAGTAGCACTAGGGACTA 59.490 50.000 0.00 0.00 45.49 2.59
108 109 1.286553 AGAGCAGTAGCACTAGGGACT 59.713 52.381 0.00 0.00 45.49 3.85
109 110 1.770294 AGAGCAGTAGCACTAGGGAC 58.230 55.000 0.00 0.00 45.49 4.46
110 111 3.664551 TTAGAGCAGTAGCACTAGGGA 57.335 47.619 0.00 0.00 43.25 4.20
111 112 4.946478 ATTTAGAGCAGTAGCACTAGGG 57.054 45.455 0.00 0.00 43.25 3.53
112 113 5.751028 GTGAATTTAGAGCAGTAGCACTAGG 59.249 44.000 0.00 0.00 43.25 3.02
113 114 6.568869 AGTGAATTTAGAGCAGTAGCACTAG 58.431 40.000 0.00 0.00 43.25 2.57
114 115 6.531503 AGTGAATTTAGAGCAGTAGCACTA 57.468 37.500 0.00 0.00 45.49 2.74
115 116 5.413309 AGTGAATTTAGAGCAGTAGCACT 57.587 39.130 0.00 0.00 45.49 4.40
116 117 5.672321 GCAAGTGAATTTAGAGCAGTAGCAC 60.672 44.000 0.00 0.00 45.49 4.40
117 118 4.393062 GCAAGTGAATTTAGAGCAGTAGCA 59.607 41.667 0.00 0.00 45.49 3.49
118 119 4.393062 TGCAAGTGAATTTAGAGCAGTAGC 59.607 41.667 0.00 0.00 42.56 3.58
119 120 6.093219 ACATGCAAGTGAATTTAGAGCAGTAG 59.907 38.462 0.00 0.00 33.69 2.57
120 121 5.939883 ACATGCAAGTGAATTTAGAGCAGTA 59.060 36.000 0.00 0.00 33.69 2.74
121 122 4.763793 ACATGCAAGTGAATTTAGAGCAGT 59.236 37.500 0.00 0.00 33.69 4.40
296 298 9.174166 CCAACAACTTAAATAGCTAAGTACCAT 57.826 33.333 0.00 0.00 40.47 3.55
603 619 6.992063 ACTTCTTTGCATGGTAGAATACAG 57.008 37.500 0.00 0.00 45.43 2.74
964 980 4.693095 ACATCACCAAAACAACAACCAAAC 59.307 37.500 0.00 0.00 0.00 2.93
1083 1100 1.302192 GCTGAACGGCACCTTGGTA 60.302 57.895 0.40 0.00 0.00 3.25
1094 1111 1.600636 TTGGGCTCCTTGCTGAACG 60.601 57.895 0.00 0.00 42.39 3.95
1128 1145 2.224548 ACCCAAGAACTTGTAGGAGTGC 60.225 50.000 12.54 0.00 38.85 4.40
1145 1162 1.295423 GCAAAGAGCTACGGACCCA 59.705 57.895 0.00 0.00 41.15 4.51
1358 1375 2.787249 CGGAACTCCTTGCGCATG 59.213 61.111 12.75 14.64 34.23 4.06
1421 1438 4.641989 AGCATAAGGGCAATTCAAGTACAG 59.358 41.667 0.00 0.00 35.83 2.74
1464 1481 2.675317 GCAGAGACAAGCCGTGACTTAT 60.675 50.000 0.00 0.00 32.03 1.73
1699 1716 3.181475 GCTGTAGGAGGAATCAACATCGA 60.181 47.826 0.00 0.00 0.00 3.59
1702 1719 3.118112 CAGGCTGTAGGAGGAATCAACAT 60.118 47.826 6.28 0.00 0.00 2.71
1981 3287 6.532657 TCGCTGTTTTAGTAGTAGCAAATACC 59.467 38.462 0.00 0.00 34.67 2.73
2017 3323 2.393271 AACACTCATCAGGTAGCAGC 57.607 50.000 0.00 0.00 0.00 5.25
2035 3341 8.424918 TGCCAAGGTGAAATATTACAAAGAAAA 58.575 29.630 0.00 0.00 0.00 2.29
2077 3383 5.518848 TCATGTCATGCAAAGTTCAAACT 57.481 34.783 8.03 0.00 42.04 2.66
2184 3491 6.615088 CATCCAAGTAGAACAAAATCACCAG 58.385 40.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.