Multiple sequence alignment - TraesCS4D01G162500

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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 TraesCS4D01G162500 chr4D 100.000 2475 0 0 1 2475 248322903 248320429 0 4571
1 TraesCS4D01G162500 chr4D 93.969 514 29 2 1963 2474 248339942 248339429 0 776
2 TraesCS4D01G162500 chr5D 95.438 1973 79 7 1 1967 365120441 365118474 0 3134
3 TraesCS4D01G162500 chr5D 95.331 514 21 3 1963 2474 179405769 179405257 0 813
4 TraesCS4D01G162500 chr6D 95.390 1974 79 6 1 1963 31859057 31861029 0 3131
5 TraesCS4D01G162500 chr6D 94.358 514 27 2 1963 2474 124013469 124013982 0 787
6 TraesCS4D01G162500 chr1D 95.180 1971 83 10 1 1963 471280898 471282864 0 3103
7 TraesCS4D01G162500 chr1D 94.919 1968 88 9 1 1961 395974536 395976498 0 3070
8 TraesCS4D01G162500 chr1D 94.757 515 23 4 1963 2474 286436220 286435707 0 798
9 TraesCS4D01G162500 chr1D 94.358 514 25 3 1963 2474 212584858 212585369 0 785
10 TraesCS4D01G162500 chr1D 94.163 514 28 2 1963 2474 135670203 135669690 0 782
11 TraesCS4D01G162500 chr2D 95.074 1969 87 7 1 1963 476878767 476880731 0 3090
12 TraesCS4D01G162500 chr2D 95.074 1969 88 7 1 1963 588796860 588794895 0 3090
13 TraesCS4D01G162500 chr2D 95.023 1969 90 6 1 1963 16904391 16906357 0 3086
14 TraesCS4D01G162500 chr2D 94.163 514 28 2 1963 2474 130197268 130197781 0 782
15 TraesCS4D01G162500 chr2D 94.163 514 28 2 1963 2474 130208507 130209020 0 782
16 TraesCS4D01G162500 chr7D 94.881 1973 88 9 1 1966 384052922 384050956 0 3072
17 TraesCS4D01G162500 chr7D 94.820 1969 93 5 1 1963 464035252 464037217 0 3062
18 TraesCS4D01G162500 chr4A 94.553 514 26 2 1963 2474 632601358 632601871 0 793


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 TraesCS4D01G162500 chr4D 248320429 248322903 2474 True 4571 4571 100.000 1 2475 1 chr4D.!!$R1 2474
1 TraesCS4D01G162500 chr4D 248339429 248339942 513 True 776 776 93.969 1963 2474 1 chr4D.!!$R2 511
2 TraesCS4D01G162500 chr5D 365118474 365120441 1967 True 3134 3134 95.438 1 1967 1 chr5D.!!$R2 1966
3 TraesCS4D01G162500 chr5D 179405257 179405769 512 True 813 813 95.331 1963 2474 1 chr5D.!!$R1 511
4 TraesCS4D01G162500 chr6D 31859057 31861029 1972 False 3131 3131 95.390 1 1963 1 chr6D.!!$F1 1962
5 TraesCS4D01G162500 chr6D 124013469 124013982 513 False 787 787 94.358 1963 2474 1 chr6D.!!$F2 511
6 TraesCS4D01G162500 chr1D 471280898 471282864 1966 False 3103 3103 95.180 1 1963 1 chr1D.!!$F3 1962
7 TraesCS4D01G162500 chr1D 395974536 395976498 1962 False 3070 3070 94.919 1 1961 1 chr1D.!!$F2 1960
8 TraesCS4D01G162500 chr1D 286435707 286436220 513 True 798 798 94.757 1963 2474 1 chr1D.!!$R2 511
9 TraesCS4D01G162500 chr1D 212584858 212585369 511 False 785 785 94.358 1963 2474 1 chr1D.!!$F1 511
10 TraesCS4D01G162500 chr1D 135669690 135670203 513 True 782 782 94.163 1963 2474 1 chr1D.!!$R1 511
11 TraesCS4D01G162500 chr2D 476878767 476880731 1964 False 3090 3090 95.074 1 1963 1 chr2D.!!$F4 1962
12 TraesCS4D01G162500 chr2D 588794895 588796860 1965 True 3090 3090 95.074 1 1963 1 chr2D.!!$R1 1962
13 TraesCS4D01G162500 chr2D 16904391 16906357 1966 False 3086 3086 95.023 1 1963 1 chr2D.!!$F1 1962
14 TraesCS4D01G162500 chr2D 130197268 130197781 513 False 782 782 94.163 1963 2474 1 chr2D.!!$F2 511
15 TraesCS4D01G162500 chr2D 130208507 130209020 513 False 782 782 94.163 1963 2474 1 chr2D.!!$F3 511
16 TraesCS4D01G162500 chr7D 384050956 384052922 1966 True 3072 3072 94.881 1 1966 1 chr7D.!!$R1 1965
17 TraesCS4D01G162500 chr7D 464035252 464037217 1965 False 3062 3062 94.820 1 1963 1 chr7D.!!$F1 1962
18 TraesCS4D01G162500 chr4A 632601358 632601871 513 False 793 793 94.553 1963 2474 1 chr4A.!!$F1 511

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
175 180 0.033109 CCCCTCCCAAATCCACTTCC 60.033 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 1990 1.129437 GCCTTGCTGACGATCTGAAAC 59.871 52.381 0.0 0.0 0.0 2.78 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
117 118 1.850345 GGGGAATGGATAAGGGTGACA 59.150 52.381 0.00 0.00 0.00 3.58
175 180 0.033109 CCCCTCCCAAATCCACTTCC 60.033 60.000 0.00 0.00 0.00 3.46
208 213 2.717390 CTCTATCCCGTCGATCTGGAT 58.283 52.381 15.04 15.04 41.75 3.41
251 256 2.926242 ACCGACCCCGTCCACATT 60.926 61.111 0.00 0.00 0.00 2.71
294 299 4.103749 AGCTTGTCGAGGAGCTCA 57.896 55.556 17.19 0.00 45.68 4.26
297 302 0.179140 GCTTGTCGAGGAGCTCAGAG 60.179 60.000 17.19 5.63 36.01 3.35
344 349 0.908198 GAGATCAAGTCCAGCACCCT 59.092 55.000 0.00 0.00 0.00 4.34
346 351 0.615331 GATCAAGTCCAGCACCCTCA 59.385 55.000 0.00 0.00 0.00 3.86
453 458 2.535485 CTAGGGCGCCATTGACACCA 62.535 60.000 30.85 2.36 0.00 4.17
480 485 1.080498 TCTCCTCTTGCCTTTCCCCTA 59.920 52.381 0.00 0.00 0.00 3.53
496 501 2.241430 CCCCTATTTCCCCTCTCGTTTT 59.759 50.000 0.00 0.00 0.00 2.43
513 518 7.373493 TCTCGTTTTCTCTCGTTAGGTATTTT 58.627 34.615 0.00 0.00 0.00 1.82
638 643 2.267324 GCCTGCCGCTCTTCTTCT 59.733 61.111 0.00 0.00 0.00 2.85
640 645 1.294780 CCTGCCGCTCTTCTTCTGT 59.705 57.895 0.00 0.00 0.00 3.41
672 677 1.692042 CTCCCTCTCCATGCCCACT 60.692 63.158 0.00 0.00 0.00 4.00
675 680 1.692042 CCTCTCCATGCCCACTCCT 60.692 63.158 0.00 0.00 0.00 3.69
678 683 0.042581 TCTCCATGCCCACTCCTGTA 59.957 55.000 0.00 0.00 0.00 2.74
749 754 4.954970 CACCACTGTGCCCCGCTT 62.955 66.667 1.29 0.00 35.31 4.68
961 966 2.546494 GCTGCGTGTTGCTTCCTGT 61.546 57.895 0.00 0.00 46.63 4.00
973 978 1.939974 CTTCCTGTTGCTATGCGCTA 58.060 50.000 9.73 0.00 40.11 4.26
988 993 1.236628 CGCTACTCTACCGCTGGTAT 58.763 55.000 7.71 0.00 37.56 2.73
1014 1019 4.408821 GCCATGCCCTCGACACCA 62.409 66.667 0.00 0.00 0.00 4.17
1037 1042 0.770499 TGGACAAATGTGGCAGAGGA 59.230 50.000 0.00 0.00 32.51 3.71
1038 1043 1.271543 TGGACAAATGTGGCAGAGGAG 60.272 52.381 0.00 0.00 32.51 3.69
1053 1058 5.396884 GGCAGAGGAGTTGTTAATGGAGTAT 60.397 44.000 0.00 0.00 0.00 2.12
1074 1079 0.836400 AGAAGGAGGTGGCGGAGAAA 60.836 55.000 0.00 0.00 0.00 2.52
1084 1089 0.670854 GGCGGAGAAAGTGTGGAGAC 60.671 60.000 0.00 0.00 0.00 3.36
1246 1256 2.645838 ATCGATGGAGGGGTGATTTG 57.354 50.000 0.00 0.00 0.00 2.32
1269 1280 5.125417 TGCTTCAATAGGTGGAAAACATAGC 59.875 40.000 0.00 0.00 0.00 2.97
1383 1395 1.686587 CGTGATATCAGTACCTGCCCA 59.313 52.381 5.42 0.00 0.00 5.36
1590 1607 7.979115 TTTGTTTCCTAAGACAAATTGAACG 57.021 32.000 0.00 0.00 39.92 3.95
1628 1645 8.902806 TCGACTGATTTGCATAATTTAAGGAAT 58.097 29.630 0.00 0.00 0.00 3.01
1967 1989 4.998672 CGTCCATTAGGAGTAGAGACTAGG 59.001 50.000 0.00 0.00 46.92 3.02
1968 1990 5.318630 GTCCATTAGGAGTAGAGACTAGGG 58.681 50.000 0.00 0.00 46.92 3.53
2008 2030 7.592938 CAAGGCAAGTAACACTTTGATCATAA 58.407 34.615 0.00 0.00 36.03 1.90
2026 2048 9.184523 TGATCATAACCTTTATTACCCAGTTTG 57.815 33.333 0.00 0.00 0.00 2.93
2111 2134 5.422331 TGGGAAGTAGTTGATGAGGTAGAAG 59.578 44.000 0.00 0.00 0.00 2.85
2133 2157 6.436843 AGCTATGTCTTTAATTCAAACCCG 57.563 37.500 0.00 0.00 0.00 5.28
2148 2172 2.862850 ACCCGGGGAGTTACTTCTAT 57.137 50.000 27.92 0.00 0.00 1.98
2265 2290 9.174166 CTTAAGGTGGCTACTTTAATACACATT 57.826 33.333 16.08 3.34 37.61 2.71
2438 2463 2.483538 GGAAACTTTTGTGTGCAGCCAT 60.484 45.455 0.00 0.00 0.00 4.40
2474 2499 5.453339 GGCTCTGGCATAGTTGAGTATGTTA 60.453 44.000 1.64 0.00 40.87 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.597072 GAACAGGAGAAGACGACCGT 59.403 55.000 0.00 0.00 0.00 4.83
50 51 2.055042 AGCCCGGCTCTGTAGTGAG 61.055 63.158 5.94 0.00 30.62 3.51
117 118 4.720443 ATGGGGGCAGGGAAGGGT 62.720 66.667 0.00 0.00 0.00 4.34
175 180 1.582610 GATAGAGCGAGCGAGGAGGG 61.583 65.000 0.00 0.00 0.00 4.30
208 213 2.338620 CCGTGGCGTCTGACTTCA 59.661 61.111 6.21 1.31 0.00 3.02
313 318 0.108186 TTGATCTCGTTGGCGCAGAT 60.108 50.000 10.83 8.50 37.54 2.90
453 458 1.890552 AGGCAAGAGGAGATCATGGT 58.109 50.000 0.00 0.00 0.00 3.55
480 485 3.368531 CGAGAGAAAACGAGAGGGGAAAT 60.369 47.826 0.00 0.00 0.00 2.17
496 501 3.194116 ACGGCAAAATACCTAACGAGAGA 59.806 43.478 0.00 0.00 0.00 3.10
537 542 2.042741 CCCTGCAATGGCCATGGA 60.043 61.111 25.26 15.62 40.13 3.41
672 677 1.638388 CGACGCGGTGTAGTACAGGA 61.638 60.000 12.47 0.00 0.00 3.86
675 680 2.869646 CCGACGCGGTGTAGTACA 59.130 61.111 12.47 0.00 42.73 2.90
748 753 2.194597 GGCCAGGGTGTGTGTCAA 59.805 61.111 0.00 0.00 0.00 3.18
749 754 4.248842 CGGCCAGGGTGTGTGTCA 62.249 66.667 2.24 0.00 0.00 3.58
855 860 0.904865 AAGATGGCCACGACTGGAGA 60.905 55.000 8.16 0.00 40.55 3.71
904 909 2.673200 GGTGGAGGGCAGAGATGCA 61.673 63.158 2.29 0.00 36.33 3.96
973 978 0.747255 CAGCATACCAGCGGTAGAGT 59.253 55.000 11.98 0.00 41.83 3.24
1014 1019 1.152860 TGCCACATTTGTCCACGGT 60.153 52.632 0.00 0.00 0.00 4.83
1037 1042 7.365117 CCTCCTTCTCATACTCCATTAACAACT 60.365 40.741 0.00 0.00 0.00 3.16
1038 1043 6.763610 CCTCCTTCTCATACTCCATTAACAAC 59.236 42.308 0.00 0.00 0.00 3.32
1053 1058 1.984570 CTCCGCCACCTCCTTCTCA 60.985 63.158 0.00 0.00 0.00 3.27
1074 1079 2.920645 CGTCCTGCGTCTCCACACT 61.921 63.158 0.00 0.00 35.54 3.55
1091 1096 2.030562 GTGACACCACCCCAGACG 59.969 66.667 0.00 0.00 37.33 4.18
1100 1105 2.510411 CACAGCCAGGTGACACCA 59.490 61.111 26.30 0.00 41.95 4.17
1246 1256 5.125417 TGCTATGTTTTCCACCTATTGAAGC 59.875 40.000 0.00 0.00 0.00 3.86
1269 1280 9.369904 CCTTTCCTTGATAACAACCAATATTTG 57.630 33.333 0.00 0.00 32.27 2.32
1383 1395 5.147330 TCCTAATCAGACACGTCACAAAT 57.853 39.130 0.00 0.00 0.00 2.32
1590 1607 7.250569 TGCAAATCAGTCGATTCCTTTTATTC 58.749 34.615 0.00 0.00 41.12 1.75
1799 1816 2.687200 CCCACCCTGGTCCATCGA 60.687 66.667 0.00 0.00 35.17 3.59
1907 1928 1.131618 CGCGGTTTATTTTCGCTGGC 61.132 55.000 0.00 0.00 46.23 4.85
1963 1985 2.166459 TGCTGACGATCTGAAACCCTAG 59.834 50.000 0.00 0.00 0.00 3.02
1967 1989 1.734465 CCTTGCTGACGATCTGAAACC 59.266 52.381 0.00 0.00 0.00 3.27
1968 1990 1.129437 GCCTTGCTGACGATCTGAAAC 59.871 52.381 0.00 0.00 0.00 2.78
2008 2030 6.249951 TGCATACAAACTGGGTAATAAAGGT 58.750 36.000 0.00 0.00 0.00 3.50
2026 2048 9.076596 GTTTGAGGATTGAAAACTAATGCATAC 57.923 33.333 0.00 0.00 32.33 2.39
2111 2134 5.449999 CCCGGGTTTGAATTAAAGACATAGC 60.450 44.000 14.18 0.00 0.00 2.97
2133 2157 6.176014 AGCATAACATAGAAGTAACTCCCC 57.824 41.667 0.00 0.00 0.00 4.81
2163 2187 4.476862 CACGTCTACGAGCATAGCATATT 58.523 43.478 9.86 0.00 43.02 1.28
2265 2290 0.541764 GCCTCAACCAATCCACCCAA 60.542 55.000 0.00 0.00 0.00 4.12
2300 2325 1.174712 CCAAGTGCCCAGACAACCAG 61.175 60.000 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.