Multiple sequence alignment - TraesCS5D01G101700

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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 TraesCS5D01G101700 chr5D 100.000 2549 0 0 1 2549 114515741 114518289 0.000000e+00 4708.0
1 TraesCS5D01G101700 chr5D 93.967 1989 73 14 575 2549 6910281 6908326 0.000000e+00 2964.0
2 TraesCS5D01G101700 chr5D 94.621 1729 76 12 574 2297 275163199 275161483 0.000000e+00 2662.0
3 TraesCS5D01G101700 chr5D 96.341 574 21 0 1 574 469975577 469976150 0.000000e+00 944.0
4 TraesCS5D01G101700 chr5D 95.101 347 16 1 567 913 357075975 357075630 1.720000e-151 545.0
5 TraesCS5D01G101700 chr7D 94.422 2008 80 12 567 2549 90563644 90561644 0.000000e+00 3059.0
6 TraesCS5D01G101700 chr7D 92.561 2003 96 18 575 2549 372082798 372084775 0.000000e+00 2824.0
7 TraesCS5D01G101700 chr7D 92.943 1913 91 20 658 2549 605599928 605601817 0.000000e+00 2745.0
8 TraesCS5D01G101700 chr7D 96.341 574 21 0 1 574 236034807 236035380 0.000000e+00 944.0
9 TraesCS5D01G101700 chr7D 96.341 574 21 0 1 574 390151537 390152110 0.000000e+00 944.0
10 TraesCS5D01G101700 chr7B 92.126 2032 99 29 575 2546 702337217 702339247 0.000000e+00 2809.0
11 TraesCS5D01G101700 chr7B 92.281 1995 113 29 575 2549 11744391 11746364 0.000000e+00 2793.0
12 TraesCS5D01G101700 chr7B 91.637 1997 114 21 575 2549 101862225 101864190 0.000000e+00 2713.0
13 TraesCS5D01G101700 chr1D 95.389 1670 62 9 895 2549 25464613 25466282 0.000000e+00 2643.0
14 TraesCS5D01G101700 chr1D 94.046 1730 83 14 575 2297 17040736 17039020 0.000000e+00 2606.0
15 TraesCS5D01G101700 chr3D 95.244 1661 70 6 898 2549 546486297 546487957 0.000000e+00 2621.0
16 TraesCS5D01G101700 chr3D 96.690 574 19 0 1 574 356717943 356717370 0.000000e+00 955.0
17 TraesCS5D01G101700 chr2B 94.050 1664 89 9 895 2549 485691135 485692797 0.000000e+00 2516.0
18 TraesCS5D01G101700 chr3A 91.586 1759 98 20 567 2302 683237681 683235950 0.000000e+00 2383.0
19 TraesCS5D01G101700 chr5A 92.277 1528 76 22 570 2089 357171117 357169624 0.000000e+00 2130.0
20 TraesCS5D01G101700 chr5A 95.283 318 13 1 578 893 553455274 553454957 1.050000e-138 503.0
21 TraesCS5D01G101700 chr6D 96.690 574 19 0 1 574 238875135 238875708 0.000000e+00 955.0
22 TraesCS5D01G101700 chr6D 96.684 573 19 0 2 574 33043793 33043221 0.000000e+00 953.0
23 TraesCS5D01G101700 chr6D 96.516 574 20 0 1 574 263258676 263259249 0.000000e+00 950.0
24 TraesCS5D01G101700 chr6D 96.341 574 21 0 1 574 121674155 121673582 0.000000e+00 944.0
25 TraesCS5D01G101700 chr6D 96.000 75 1 1 898 970 52521449 52521375 1.240000e-23 121.0
26 TraesCS5D01G101700 chr4D 96.516 574 19 1 1 574 231332927 231332355 0.000000e+00 948.0
27 TraesCS5D01G101700 chr2D 95.031 322 12 1 574 895 16065485 16065802 1.050000e-138 503.0
28 TraesCS5D01G101700 chr4B 92.647 340 22 2 574 913 251255860 251256196 1.060000e-133 486.0
29 TraesCS5D01G101700 chrUn 89.873 79 2 1 898 970 93726213 93726135 2.090000e-16 97.1


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 TraesCS5D01G101700 chr5D 114515741 114518289 2548 False 4708 4708 100.000 1 2549 1 chr5D.!!$F1 2548
1 TraesCS5D01G101700 chr5D 6908326 6910281 1955 True 2964 2964 93.967 575 2549 1 chr5D.!!$R1 1974
2 TraesCS5D01G101700 chr5D 275161483 275163199 1716 True 2662 2662 94.621 574 2297 1 chr5D.!!$R2 1723
3 TraesCS5D01G101700 chr5D 469975577 469976150 573 False 944 944 96.341 1 574 1 chr5D.!!$F2 573
4 TraesCS5D01G101700 chr7D 90561644 90563644 2000 True 3059 3059 94.422 567 2549 1 chr7D.!!$R1 1982
5 TraesCS5D01G101700 chr7D 372082798 372084775 1977 False 2824 2824 92.561 575 2549 1 chr7D.!!$F2 1974
6 TraesCS5D01G101700 chr7D 605599928 605601817 1889 False 2745 2745 92.943 658 2549 1 chr7D.!!$F4 1891
7 TraesCS5D01G101700 chr7D 236034807 236035380 573 False 944 944 96.341 1 574 1 chr7D.!!$F1 573
8 TraesCS5D01G101700 chr7D 390151537 390152110 573 False 944 944 96.341 1 574 1 chr7D.!!$F3 573
9 TraesCS5D01G101700 chr7B 702337217 702339247 2030 False 2809 2809 92.126 575 2546 1 chr7B.!!$F3 1971
10 TraesCS5D01G101700 chr7B 11744391 11746364 1973 False 2793 2793 92.281 575 2549 1 chr7B.!!$F1 1974
11 TraesCS5D01G101700 chr7B 101862225 101864190 1965 False 2713 2713 91.637 575 2549 1 chr7B.!!$F2 1974
12 TraesCS5D01G101700 chr1D 25464613 25466282 1669 False 2643 2643 95.389 895 2549 1 chr1D.!!$F1 1654
13 TraesCS5D01G101700 chr1D 17039020 17040736 1716 True 2606 2606 94.046 575 2297 1 chr1D.!!$R1 1722
14 TraesCS5D01G101700 chr3D 546486297 546487957 1660 False 2621 2621 95.244 898 2549 1 chr3D.!!$F1 1651
15 TraesCS5D01G101700 chr3D 356717370 356717943 573 True 955 955 96.690 1 574 1 chr3D.!!$R1 573
16 TraesCS5D01G101700 chr2B 485691135 485692797 1662 False 2516 2516 94.050 895 2549 1 chr2B.!!$F1 1654
17 TraesCS5D01G101700 chr3A 683235950 683237681 1731 True 2383 2383 91.586 567 2302 1 chr3A.!!$R1 1735
18 TraesCS5D01G101700 chr5A 357169624 357171117 1493 True 2130 2130 92.277 570 2089 1 chr5A.!!$R1 1519
19 TraesCS5D01G101700 chr6D 238875135 238875708 573 False 955 955 96.690 1 574 1 chr6D.!!$F1 573
20 TraesCS5D01G101700 chr6D 33043221 33043793 572 True 953 953 96.684 2 574 1 chr6D.!!$R1 572
21 TraesCS5D01G101700 chr6D 263258676 263259249 573 False 950 950 96.516 1 574 1 chr6D.!!$F2 573
22 TraesCS5D01G101700 chr6D 121673582 121674155 573 True 944 944 96.341 1 574 1 chr6D.!!$R3 573
23 TraesCS5D01G101700 chr4D 231332355 231332927 572 True 948 948 96.516 1 574 1 chr4D.!!$R1 573

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
986 1161 0.391263 GCGACGTTGAGATCCCCTTT 60.391 55.0 7.08 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2578 4.492646 ACATTCCAACCCTCCAAATTTCT 58.507 39.13 0.0 0.0 0.0 2.52 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
144 145 8.915654 CAAGAGAATTAAACCATGTTTTAGCAC 58.084 33.333 0.00 0.00 0.00 4.40
330 331 6.507900 TCAGGATCGACAGAGAAATCATAAC 58.492 40.000 0.00 0.00 0.00 1.89
382 383 4.082026 AGCAAAAGCAGGGTCATATTTCAC 60.082 41.667 0.00 0.00 0.00 3.18
494 495 7.451731 TTCTTCATCCATAACATAACCCTCT 57.548 36.000 0.00 0.00 0.00 3.69
526 527 3.615155 GCAATTCATATCTAGGGGGAGC 58.385 50.000 0.00 0.00 0.00 4.70
726 727 1.164041 ACGTTTTGACTCGGCCCTTG 61.164 55.000 0.00 0.00 0.00 3.61
799 815 2.203480 GCTTGTGGGACCCAGCAA 60.203 61.111 15.52 18.90 32.34 3.91
888 921 4.778415 CGGTGACCACGGCGAGAG 62.778 72.222 16.62 3.65 0.00 3.20
889 922 3.371063 GGTGACCACGGCGAGAGA 61.371 66.667 16.62 0.00 0.00 3.10
890 923 2.179517 GTGACCACGGCGAGAGAG 59.820 66.667 16.62 0.00 0.00 3.20
891 924 2.033602 TGACCACGGCGAGAGAGA 59.966 61.111 16.62 0.00 0.00 3.10
892 925 2.041115 TGACCACGGCGAGAGAGAG 61.041 63.158 16.62 0.00 0.00 3.20
893 926 1.745864 GACCACGGCGAGAGAGAGA 60.746 63.158 16.62 0.00 0.00 3.10
986 1161 0.391263 GCGACGTTGAGATCCCCTTT 60.391 55.000 7.08 0.00 0.00 3.11
1011 1186 1.110442 CGAGCTCCATGTCTTCCTCT 58.890 55.000 8.47 0.00 0.00 3.69
1079 1254 1.581954 CTGTCTTCGTCTGTCCGCT 59.418 57.895 0.00 0.00 0.00 5.52
1694 1894 7.684937 ACAAGAAGAAATGAGGAATTCAGAG 57.315 36.000 7.93 0.00 39.68 3.35
1711 1911 9.557338 GAATTCAGAGACTTTTGATCAATGAAG 57.443 33.333 18.22 16.88 30.86 3.02
1738 1940 1.274728 TCTCTGCTCTGCCTTTCTGTC 59.725 52.381 0.00 0.00 0.00 3.51
1947 2153 4.280677 TCCAGAGCCAAACAATTAAGGTTG 59.719 41.667 0.00 0.00 35.25 3.77
1950 2156 4.280929 AGAGCCAAACAATTAAGGTTGGAC 59.719 41.667 15.07 8.69 33.40 4.02
2050 2259 3.615224 AATGTCATGGAAAATGTGCCC 57.385 42.857 0.00 0.00 0.00 5.36
2337 2577 4.842574 AGTGGTTTTCCTTTGTTTTGCAT 58.157 34.783 0.00 0.00 41.38 3.96
2338 2578 5.983540 AGTGGTTTTCCTTTGTTTTGCATA 58.016 33.333 0.00 0.00 41.38 3.14
2358 2599 5.129320 GCATAGAAATTTGGAGGGTTGGAAT 59.871 40.000 0.00 0.00 0.00 3.01
2425 2666 3.344515 GCACTTGGTTTAGGGTTAGAGG 58.655 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.863126 GCTCATAAGAAACAAGCTGCTTTAAA 59.137 34.615 13.10 0.00 0.00 1.52
144 145 3.343941 TCCGTTCTCATTAAAGGGTGG 57.656 47.619 0.00 0.00 34.16 4.61
248 249 6.182627 TGGCTATGAATCTGAAACTGTTGAT 58.817 36.000 0.00 0.00 0.00 2.57
249 250 5.559770 TGGCTATGAATCTGAAACTGTTGA 58.440 37.500 0.00 0.00 0.00 3.18
330 331 6.210784 TCACCTATCTGTATTTCCGATAAGGG 59.789 42.308 0.00 0.00 41.52 3.95
426 427 9.379791 TGCTTGCAATGATAGATATGATCTTAG 57.620 33.333 0.00 0.00 40.76 2.18
494 495 1.340088 ATGAATTGCCTGTTGTGCCA 58.660 45.000 0.00 0.00 0.00 4.92
799 815 4.250305 ACACCCGCAACGGCTCTT 62.250 61.111 0.00 0.00 46.86 2.85
856 889 2.285773 ACCGCCATGCTCTCTGTCA 61.286 57.895 0.00 0.00 0.00 3.58
888 921 1.299541 CCGTGCTCTCTCTCTCTCTC 58.700 60.000 0.00 0.00 0.00 3.20
889 922 0.748005 GCCGTGCTCTCTCTCTCTCT 60.748 60.000 0.00 0.00 0.00 3.10
890 923 1.727467 GCCGTGCTCTCTCTCTCTC 59.273 63.158 0.00 0.00 0.00 3.20
891 924 2.112198 CGCCGTGCTCTCTCTCTCT 61.112 63.158 0.00 0.00 0.00 3.10
892 925 2.407210 CGCCGTGCTCTCTCTCTC 59.593 66.667 0.00 0.00 0.00 3.20
893 926 3.137459 CCGCCGTGCTCTCTCTCT 61.137 66.667 0.00 0.00 0.00 3.10
986 1161 2.685017 ACATGGAGCTCGGAGCCA 60.685 61.111 25.49 17.60 43.77 4.75
1584 1761 8.584157 TGACCAACATTTAAGCTATGTGAATTT 58.416 29.630 1.38 0.00 36.41 1.82
1671 1870 7.607223 AGTCTCTGAATTCCTCATTTCTTCTTG 59.393 37.037 2.27 0.00 32.14 3.02
1672 1871 7.688343 AGTCTCTGAATTCCTCATTTCTTCTT 58.312 34.615 2.27 0.00 32.14 2.52
1694 1894 4.620184 GCTGCACTTCATTGATCAAAAGTC 59.380 41.667 18.46 14.48 29.78 3.01
1746 1949 1.344114 GAATTTGGCCCAAGAGCAACA 59.656 47.619 0.00 0.00 0.00 3.33
1892 2098 8.203485 TCAATTAGCTTCCACAAAAAGTTTCAT 58.797 29.630 0.00 0.00 0.00 2.57
2337 2577 5.650283 ACATTCCAACCCTCCAAATTTCTA 58.350 37.500 0.00 0.00 0.00 2.10
2338 2578 4.492646 ACATTCCAACCCTCCAAATTTCT 58.507 39.130 0.00 0.00 0.00 2.52
2358 2599 4.795795 CAGTGCAAACATACGTTTTCAACA 59.204 37.500 0.00 0.00 42.82 3.33
2425 2666 5.337250 CCTTTAAATCCTAAACCAAGTGCCC 60.337 44.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.