Multiple sequence alignment - TraesCS4D01G051700

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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 TraesCS4D01G051700 chr4D 100.000 3314 0 0 1 3314 27543037 27546350 0.000000e+00 6120
1 TraesCS4D01G051700 chr3B 94.918 1948 93 6 1 1944 69462464 69460519 0.000000e+00 3044
2 TraesCS4D01G051700 chr3B 92.531 1995 129 18 1331 3314 69460842 69458857 0.000000e+00 2841
3 TraesCS4D01G051700 chr5D 94.710 1947 86 7 1 1943 151197444 151195511 0.000000e+00 3009
4 TraesCS4D01G051700 chr5D 91.282 1950 102 16 1 1943 546549776 546547888 0.000000e+00 2597
5 TraesCS4D01G051700 chr5D 94.171 995 53 4 1983 2972 546547525 546546531 0.000000e+00 1511
6 TraesCS4D01G051700 chr5D 93.688 1014 51 10 1983 2987 396224533 396223524 0.000000e+00 1506
7 TraesCS4D01G051700 chr5D 91.605 1084 72 16 1342 2418 151195817 151194746 0.000000e+00 1480
8 TraesCS4D01G051700 chr2B 94.559 1948 98 8 1 1943 690763502 690765446 0.000000e+00 3003
9 TraesCS4D01G051700 chr2B 92.154 2001 128 24 1331 3314 690765124 690767112 0.000000e+00 2798
10 TraesCS4D01G051700 chr5B 93.949 1950 111 7 1 1943 405541684 405539735 0.000000e+00 2940
11 TraesCS4D01G051700 chr5B 91.712 2003 136 26 1331 3314 405540059 405538068 0.000000e+00 2752
12 TraesCS4D01G051700 chr5B 90.538 1469 121 12 1 1465 391289231 391290685 0.000000e+00 1927
13 TraesCS4D01G051700 chr5B 90.545 1375 111 17 1943 3314 391291740 391293098 0.000000e+00 1801
14 TraesCS4D01G051700 chr7B 91.517 2004 134 33 1331 3314 165116684 165118671 0.000000e+00 2726
15 TraesCS4D01G051700 chr7B 94.390 1319 70 4 1 1315 165115022 165116340 0.000000e+00 2023
16 TraesCS4D01G051700 chr7D 92.549 1718 96 13 1 1709 24395885 24397579 0.000000e+00 2435
17 TraesCS4D01G051700 chr7D 90.818 1503 105 23 1483 2969 24397598 24399083 0.000000e+00 1980
18 TraesCS4D01G051700 chr7D 95.652 322 11 1 2993 3314 24399077 24399395 6.340000e-142 514
19 TraesCS4D01G051700 chr7D 93.137 102 4 3 1921 2020 24398001 24398101 2.660000e-31 147
20 TraesCS4D01G051700 chr4B 90.123 1377 121 11 9 1380 621554167 621555533 0.000000e+00 1775
21 TraesCS4D01G051700 chr5A 93.896 983 54 6 1983 2960 544478260 544479241 0.000000e+00 1478


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 TraesCS4D01G051700 chr4D 27543037 27546350 3313 False 6120.0 6120 100.0000 1 3314 1 chr4D.!!$F1 3313
1 TraesCS4D01G051700 chr3B 69458857 69462464 3607 True 2942.5 3044 93.7245 1 3314 2 chr3B.!!$R1 3313
2 TraesCS4D01G051700 chr5D 151194746 151197444 2698 True 2244.5 3009 93.1575 1 2418 2 chr5D.!!$R2 2417
3 TraesCS4D01G051700 chr5D 546546531 546549776 3245 True 2054.0 2597 92.7265 1 2972 2 chr5D.!!$R3 2971
4 TraesCS4D01G051700 chr5D 396223524 396224533 1009 True 1506.0 1506 93.6880 1983 2987 1 chr5D.!!$R1 1004
5 TraesCS4D01G051700 chr2B 690763502 690767112 3610 False 2900.5 3003 93.3565 1 3314 2 chr2B.!!$F1 3313
6 TraesCS4D01G051700 chr5B 405538068 405541684 3616 True 2846.0 2940 92.8305 1 3314 2 chr5B.!!$R1 3313
7 TraesCS4D01G051700 chr5B 391289231 391293098 3867 False 1864.0 1927 90.5415 1 3314 2 chr5B.!!$F1 3313
8 TraesCS4D01G051700 chr7B 165115022 165118671 3649 False 2374.5 2726 92.9535 1 3314 2 chr7B.!!$F1 3313
9 TraesCS4D01G051700 chr7D 24395885 24399395 3510 False 1269.0 2435 93.0390 1 3314 4 chr7D.!!$F1 3313
10 TraesCS4D01G051700 chr4B 621554167 621555533 1366 False 1775.0 1775 90.1230 9 1380 1 chr4B.!!$F1 1371
11 TraesCS4D01G051700 chr5A 544478260 544479241 981 False 1478.0 1478 93.8960 1983 2960 1 chr5A.!!$F1 977

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
413 414 0.250901 GTTGTGTGGGATGCAGAGGT 60.251 55.000 0.0 0.0 0.0 3.85 F
1856 2544 1.203052 CCACAAACTTGCCTGCTATGG 59.797 52.381 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 3229 2.430465 ACAGTTGCTGCTATCAACCTG 58.570 47.619 0.00 0.0 43.45 4.00 R
2761 3800 0.174389 TTTGCGCAAAACAGAGGCAA 59.826 45.000 31.98 6.4 41.38 4.52 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
84 85 3.605749 CTGGCCACCGGTACCACAG 62.606 68.421 21.58 16.35 0.00 3.66
284 285 5.308825 AGTGATTTTCGATGAGTTGGAACT 58.691 37.500 0.00 0.00 43.16 3.01
337 338 6.254281 ACAAATGGGATGAAGTTCTTAACG 57.746 37.500 4.17 0.00 36.23 3.18
413 414 0.250901 GTTGTGTGGGATGCAGAGGT 60.251 55.000 0.00 0.00 0.00 3.85
536 537 4.018688 GGGGTCAGGTGGTAAGTTTTCTAT 60.019 45.833 0.00 0.00 0.00 1.98
639 640 3.129871 CACGGGCATTGACAACAAAAAT 58.870 40.909 0.00 0.00 39.54 1.82
700 701 5.412640 CATCTGTTATTTTGCATGCAAGGA 58.587 37.500 30.25 23.30 37.24 3.36
720 721 1.350351 AGCAGTGCAGAAGAATCACCT 59.650 47.619 19.20 0.00 0.00 4.00
1035 1037 2.958818 TCGGTAAGAGATGCACCCTAT 58.041 47.619 0.00 0.00 0.00 2.57
1363 1412 4.702131 ACCACTAGTTGCCTCATCATTTTC 59.298 41.667 0.00 0.00 0.00 2.29
1465 1554 5.452078 TGACAAGTCTAGCCCAAATTTTG 57.548 39.130 1.99 1.99 0.00 2.44
1601 1691 5.800296 TGCCTCAATTGTAGCTGTAAGTTA 58.200 37.500 18.62 0.00 35.30 2.24
1602 1692 6.414732 TGCCTCAATTGTAGCTGTAAGTTAT 58.585 36.000 18.62 0.00 30.48 1.89
1634 1725 5.441718 TTGAGGCAAGAATTACCTGATCT 57.558 39.130 0.00 0.00 43.46 2.75
1652 2042 5.907207 TGATCTAGTAGTTGCCTCATCAAC 58.093 41.667 0.00 0.00 44.88 3.18
1856 2544 1.203052 CCACAAACTTGCCTGCTATGG 59.797 52.381 0.00 0.00 0.00 2.74
2196 3229 1.305201 TTGTCTTGGACAAGAACGCC 58.695 50.000 15.66 5.13 45.88 5.68
2242 3275 7.097192 TCGTAGTTTATGGGAGCATCATTATC 58.903 38.462 0.00 0.00 36.25 1.75
2307 3340 0.400213 ATGTCCCGAGGCAGAACAAA 59.600 50.000 0.00 0.00 0.00 2.83
2508 3542 7.446625 AGTGATATTCCAAATATCAGGAAGCAC 59.553 37.037 18.15 18.99 46.25 4.40
2880 3921 3.218453 CACCAAGTATCAACCACACCAA 58.782 45.455 0.00 0.00 0.00 3.67
2912 3955 6.024552 TCTAAGTTGCCCAAAATGTCAATC 57.975 37.500 0.00 0.00 0.00 2.67
3014 4060 2.507339 TTTTGCTTCCTTCTTTGGCG 57.493 45.000 0.00 0.00 0.00 5.69
3059 4105 0.241749 CGCTGCATTGTGGTCAACAT 59.758 50.000 0.00 0.00 38.99 2.71
3064 4110 2.560542 TGCATTGTGGTCAACATAACCC 59.439 45.455 0.00 0.00 38.99 4.11
3286 4332 2.172717 AGGAGCACCAGTAGTTGTTTGT 59.827 45.455 2.07 0.00 38.94 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.482308 GCAAACTCAGGTTAGTCTTCAGTAAA 59.518 38.462 0.00 0.00 34.90 2.01
337 338 2.279741 TGCGATATCCTCTGTTTGCAC 58.720 47.619 0.00 0.00 0.00 4.57
413 414 1.511305 GCACACGCTGCCTCTAGTA 59.489 57.895 0.00 0.00 40.42 1.82
536 537 1.561643 CTCCCCTGAACTGCTACTGA 58.438 55.000 0.00 0.00 0.00 3.41
639 640 4.764823 ACTTCGGGTTTGCAATAGAATTCA 59.235 37.500 8.44 0.00 0.00 2.57
700 701 1.350351 AGGTGATTCTTCTGCACTGCT 59.650 47.619 1.98 0.00 33.25 4.24
720 721 6.774170 ACGGTACATACCTGTTATCTGTATCA 59.226 38.462 6.52 0.00 44.25 2.15
909 911 2.983907 TGACGAAACCACCACACTAA 57.016 45.000 0.00 0.00 0.00 2.24
910 912 3.478857 AATGACGAAACCACCACACTA 57.521 42.857 0.00 0.00 0.00 2.74
1035 1037 2.884639 GAGCAAGGGCAAAAAGACACTA 59.115 45.455 0.00 0.00 44.61 2.74
1230 1235 7.436933 CCAGCAGACTAAAAGAAGGAAAAATT 58.563 34.615 0.00 0.00 0.00 1.82
1384 1434 7.455891 AGATTTGAGGCAAGAATTTTTGGAAT 58.544 30.769 10.43 0.00 0.00 3.01
1465 1554 2.829120 AGGTTAAGTCTGTGGCTCTCTC 59.171 50.000 0.00 0.00 0.00 3.20
1652 2042 5.911752 AGATGATGAGGCAAGTACTTGTAG 58.088 41.667 30.90 11.61 42.31 2.74
1765 2156 9.968870 TGCAACGAATATAAAAAGGTTAAAACT 57.031 25.926 0.00 0.00 0.00 2.66
1768 2159 8.578151 AGGTGCAACGAATATAAAAAGGTTAAA 58.422 29.630 0.00 0.00 38.12 1.52
2196 3229 2.430465 ACAGTTGCTGCTATCAACCTG 58.570 47.619 0.00 0.00 43.45 4.00
2307 3340 7.175104 TGATATTGGGAAAAGTTGCTTACTCT 58.825 34.615 0.00 0.00 35.54 3.24
2508 3542 0.617413 AGACCCAGATGCTTGTGAGG 59.383 55.000 0.00 1.26 0.00 3.86
2511 3545 1.277273 TCTGAGACCCAGATGCTTGTG 59.723 52.381 0.00 0.00 46.38 3.33
2609 3645 8.991026 TCAAAAATAGCAAAATTCACTGAATGG 58.009 29.630 4.99 0.49 32.14 3.16
2761 3800 0.174389 TTTGCGCAAAACAGAGGCAA 59.826 45.000 31.98 6.40 41.38 4.52
2880 3921 6.478512 TTTGGGCAACTTAGAACTGATTTT 57.521 33.333 0.00 0.00 0.00 1.82
2998 4044 0.951558 GAACGCCAAAGAAGGAAGCA 59.048 50.000 0.00 0.00 0.00 3.91
3014 4060 0.668535 GAGGCAAGGTTGGTGTGAAC 59.331 55.000 0.00 0.00 0.00 3.18
3059 4105 6.607019 AGAACAAATGTAGTTTCTGGGGTTA 58.393 36.000 0.00 0.00 0.00 2.85
3064 4110 6.884280 AGGAAGAACAAATGTAGTTTCTGG 57.116 37.500 0.00 0.00 0.00 3.86
3262 4308 0.976641 CAACTACTGGTGCTCCTCCA 59.023 55.000 6.34 0.00 34.23 3.86
3286 4332 1.754803 CCAGCTCGTAGTGGGAATACA 59.245 52.381 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.